Xyce™ Parallel Electronic Simulator Users' Guide, Version 6.5.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik V.; Mei, Ting

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to developmore » new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright © 2002-2016 Sandia Corporation. All rights reserved.« less

Formation of Electrostatic Potential Drops in the Auroral Zone

NASA Technical Reports Server (NTRS)

Schriver, D.; Ashour-Abdalla, M.; Richard, R. L.

2001-01-01

In order to examine the self-consistent formation of large-scale quasi-static parallel electric fields in the auroral zone on a micro/meso scale, a particle in cell simulation has been developed. The code resolves electron Debye length scales so that electron micro-processes are included and a variable grid scheme is used such that the overall length scale of the simulation is of the order of an Earth radii along the magnetic field. The simulation is electrostatic and includes the magnetic mirror force, as well as two types of plasmas, a cold dense ionospheric plasma and a warm tenuous magnetospheric plasma. In order to study the formation of parallel electric fields in the auroral zone, different magnetospheric ion and electron inflow boundary conditions are used to drive the system. It has been found that for conditions in the primary (upward) current region an upward directed quasi-static electric field can form across the system due to magnetic mirroring of the magnetospheric ions and electrons at different altitudes. For conditions in the return (downward) current region it is shown that a quasi-static parallel electric field in the opposite sense of that in the primary current region is formed, i.e., the parallel electric field is directed earthward. The conditions for how these different electric fields can be formed are discussed using satellite observations and numerical simulations.

Modelling and simulation of parallel triangular triple quantum dots (TTQD) by using SIMON 2.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathany, Maulana Yusuf, E-mail: myfathany@gmail.com; Fuada, Syifaul, E-mail: fsyifaul@gmail.com; Lawu, Braham Lawas, E-mail: bram-labs@rocketmail.com

2016-04-19

This research presents analysis of modeling on Parallel Triple Quantum Dots (TQD) by using SIMON (SIMulation Of Nano-structures). Single Electron Transistor (SET) is used as the basic concept of modeling. We design the structure of Parallel TQD by metal material with triangular geometry model, it is called by Triangular Triple Quantum Dots (TTQD). We simulate it with several scenarios using different parameters; such as different value of capacitance, various gate voltage, and different thermal condition.

Mirror force induced wave dispersion in Alfvén waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damiano, P. A.; Johnson, J. R.

2013-06-15

Recent hybrid MHD-kinetic electron simulations of global scale standing shear Alfvén waves along the Earth's closed dipolar magnetic field lines show that the upward parallel current region within these waves saturates and broadens perpendicular to the ambient magnetic field and that this broadening increases with the electron temperature. Using resistive MHD simulations, with a parallel Ohm's law derived from the linear Knight relation (which expresses the current-voltage relationship along an auroral field line), we explore the nature of this broadening in the context of the increased perpendicular Poynting flux resulting from the increased parallel electric field associated with mirror forcemore » effects. This increased Poynting flux facilitates wave energy dispersion across field lines which in-turn allows for electron acceleration to carry the field aligned current on adjacent field lines. This mirror force driven dispersion can dominate over that associated with electron inertial effects for global scale waves.« less

Theory and simulations of current drive via injection of an electron beam in the ACT-1 device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okuda, H.; Horton, R.; Ono, M.

1985-02-01

One- and two-dimensional particle simulations of beam-plasma interaction have been carried out in order to understand current drive experiments that use an electron beam injected into the ACT-1 device. Typically, the beam velocity along the magnetic field is V = 10/sup 9/ cm/sec while the thermal velocity of the background electrons is v/sub t/ = 10/sup 8//cm. The ratio of the beam density to the background density is about 10% so that a strong beam-plasma instability develops causing rapid diffusion of beam particles. For both one- and two- dimensional simulations, it is found that a significant amount of beam andmore » background electrons is accelerated considerably beyond the initial beam velocity when the beam density is more than a few percent of the background plasma density. In addition, electron distribution along the magnetic field has a smooth negative slope, f' (v/sub parallel/) < 0, for v/ sub parallel/ > 0 extending v/sub parallel/ = 1.5 V approx. 2 V, which is in sharp contrast to the predictions from quasilinear theory. An estimate of the mean-free path for beam electrons due to Coulomb collisions reveals that the beam electrons can propagate a much longer distance than is predicted from a quasilinear theory, due to the presence of a high energy tail. These simulation results agree well with the experimental observations from the ACT-1 device.« less

Xyce Parallel Electronic Simulator Users' Guide Version 6.7.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one tomore » develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

Nonlinear ELM simulations based on a nonideal peeling–ballooning model using the BOUT++ code

DOE PAGES

Xu, X. Q.; Dudson, B. D.; Snyder, P. B.; ...

2011-09-23

A minimum set of equations based on the peeling–ballooning (P–B) model with nonideal physics effects (diamagnetic drift, E × B drift, resistivity and anomalous electron viscosity) is found to simulate pedestal collapse when using the BOUT++ simulation code, developed in part from the original fluid edge code BOUT. Linear simulations of P–B modes find good agreement in growth rate and mode structure with ELITE calculations. The influence of the E × B drift, diamagnetic drift, resistivity, anomalous electron viscosity, ion viscosity and parallel thermal diffusivity on P–B modes is being studied; we find that (1) the diamagnetic drift and Emore » × B drift stabilize the P–B mode in a manner consistent with theoretical expectations; (2) resistivity destabilizes the P–B mode, leading to resistive P–B mode; (3) anomalous electron and parallel ion viscosities destabilize the P–B mode, leading to a viscous P–B mode; (4) perpendicular ion viscosity and parallel thermal diffusivity stabilize the P–B mode. With addition of the anomalous electron viscosity under the assumption that the anomalous kinematic electron viscosity is comparable to the anomalous electron perpendicular thermal diffusivity, or the Prandtl number is close to unity, it is found from nonlinear simulations using a realistic high Lundquist number that the pedestal collapse is limited to the edge region and the ELM size is about 5–10% of the pedestal stored energy. Furthermore, this is consistent with many observations of large ELMs. The estimated island size is consistent with the size of fast pedestal pressure collapse. In the stable α-zones of ideal P–B modes, nonlinear simulations of viscous ballooning modes or current-diffusive ballooning mode (CDBM) for ITER H-mode scenarios are presented.« less

A conservative scheme of drift kinetic electrons for gyrokinetic simulation of kinetic-MHD processes in toroidal plasmas

NASA Astrophysics Data System (ADS)

Bao, J.; Liu, D.; Lin, Z.

2017-10-01

A conservative scheme of drift kinetic electrons for gyrokinetic simulations of kinetic-magnetohydrodynamic processes in toroidal plasmas has been formulated and verified. Both vector potential and electron perturbed distribution function are decomposed into adiabatic part with analytic solution and non-adiabatic part solved numerically. The adiabatic parallel electric field is solved directly from the electron adiabatic response, resulting in a high degree of accuracy. The consistency between electrostatic potential and parallel vector potential is enforced by using the electron continuity equation. Since particles are only used to calculate the non-adiabatic response, which is used to calculate the non-adiabatic vector potential through Ohm's law, the conservative scheme minimizes the electron particle noise and mitigates the cancellation problem. Linear dispersion relations of the kinetic Alfvén wave and the collisionless tearing mode in cylindrical geometry have been verified in gyrokinetic toroidal code simulations, which show that the perpendicular grid size can be larger than the electron collisionless skin depth when the mode wavelength is longer than the electron skin depth.

Parallel Decomposition of the Fictitious Lagrangian Algorithm and its Accuracy for Molecular Dynamics Simulations of Semiconductors.

NASA Astrophysics Data System (ADS)

Yeh, Mei-Ling

We have performed a parallel decomposition of the fictitious Lagrangian method for molecular dynamics with tight-binding total energy expression into the hypercube computer. This is the first time in literature that the dynamical simulation of semiconducting systems containing more than 512 silicon atoms has become possible with the electrons treated as quantum particles. With the utilization of the Intel Paragon system, our timing analysis predicts that our code is expected to perform realistic simulations on very large systems consisting of thousands of atoms with time requirements of the order of tens of hours. Timing results and performance analysis of our parallel code are presented in terms of calculation time, communication time, and setup time. The accuracy of the fictitious Lagrangian method in molecular dynamics simulation is also investigated, especially the energy conservation of the total energy of ions. We find that the accuracy of the fictitious Lagrangian scheme in small silicon cluster and very large silicon system simulations is good for as long as the simulations proceed, even though we quench the electronic coordinates to the Born-Oppenheimer surface only in the beginning of the run. The kinetic energy of electrons does not increase as time goes on, and the energy conservation of the ionic subsystem remains very good. This means that, as far as the ionic subsystem is concerned, the electrons are on the average in the true quantum ground states. We also tie up some odds and ends regarding a few remaining questions about the fictitious Lagrangian method, such as the difference between the results obtained from the Gram-Schmidt and SHAKE method of orthonormalization, and differences between simulations where the electrons are quenched to the Born -Oppenheimer surface only once compared with periodic quenching.

Enhanced quasi-static particle-in-cell simulation of electron cloud instabilities in circular accelerators

NASA Astrophysics Data System (ADS)

Feng, Bing

Electron cloud instabilities have been observed in many circular accelerators around the world and raised concerns of future accelerators and possible upgrades. In this thesis, the electron cloud instabilities are studied with the quasi-static particle-in-cell (PIC) code QuickPIC. Modeling in three-dimensions the long timescale propagation of beam in electron clouds in circular accelerators requires faster and more efficient simulation codes. Thousands of processors are easily available for parallel computations. However, it is not straightforward to increase the effective speed of the simulation by running the same problem size on an increasingly number of processors because there is a limit to domain size in the decomposition of the two-dimensional part of the code. A pipelining algorithm applied on the fully parallelized particle-in-cell code QuickPIC is implemented to overcome this limit. The pipelining algorithm uses multiple groups of processors and optimizes the job allocation on the processors in parallel computing. With this novel algorithm, it is possible to use on the order of 102 processors, and to expand the scale and the speed of the simulation with QuickPIC by a similar factor. In addition to the efficiency improvement with the pipelining algorithm, the fidelity of QuickPIC is enhanced by adding two physics models, the beam space charge effect and the dispersion effect. Simulation of two specific circular machines is performed with the enhanced QuickPIC. First, the proposed upgrade to the Fermilab Main Injector is studied with an eye upon guiding the design of the upgrade and code validation. Moderate emittance growth is observed for the upgrade of increasing the bunch population by 5 times. But the simulation also shows that increasing the beam energy from 8GeV to 20GeV or above can effectively limit the emittance growth. Then the enhanced QuickPIC is used to simulate the electron cloud effect on electron beam in the Cornell Energy Recovery Linac (ERL) due to extremely small emittance and high peak currents anticipated in the machine. A tune shift is discovered from the simulation; however, emittance growth of the electron beam in electron cloud is not observed for ERL parameters.

Advanced PIC-MCC simulation for the investigation of step-ionization effect in intermediate-pressure capacitively coupled plasmas

NASA Astrophysics Data System (ADS)

Kim, Jin Seok; Hur, Min Young; Kim, Chang Ho; Kim, Ho Jun; Lee, Hae June

2018-03-01

A two-dimensional parallelized particle-in-cell simulation has been developed to simulate a capacitively coupled plasma reactor. The parallelization using graphics processing units is applied to resolve the heavy computational load. It is found that the step-ionization plays an important role in the intermediate gas pressure of a few Torr. Without the step-ionization, the average electron density decreases while the effective electron temperature increases with the increase of gas pressure at a fixed power. With the step-ionization, however, the average electron density increases while the effective electron temperature decreases with the increase of gas pressure. The cases with the step-ionization agree well with the tendency of experimental measurement. The electron energy distribution functions show that the population of electrons having intermediate energy from 4.2 to 12 eV is relaxed by the step-ionization. Also, it was observed that the power consumption by the electrons is increasing with the increase of gas pressure by the step-ionization process, while the power consumption by the ions decreases with the increase of gas pressure.

Nonlinear whistler waves

NASA Astrophysics Data System (ADS)

Vasko, I.; Agapitov, O. V.; Mozer, F.; Bonnell, J. W.; Krasnoselskikh, V.; Artemyev, A.; Drake, J. F.

2017-12-01

Chorus waves observed in the Earth inner magnetosphere sometimes exhibit significantly distorted (nonharmonic) parallel electric field waveform. In spectrograms these waveform features show up as overtones of chorus wave. In this work we show that the chorus wave parallel electric field is distorted due to finite temperature of electrons. The distortion of the parallel electric field is described analytically and reproduced in the numerical fluid simulations. Due to this effect the chorus energy is transferred to higher frequencies making possible efficient scattering of low ( a few keV) energy electrons.

The structure of the electron diffusion region during asymmetric anti-parallel magnetic reconnection

NASA Astrophysics Data System (ADS)

Swisdak, M.; Drake, J. F.; Price, L.; Burch, J. L.; Cassak, P.

2017-12-01

The structure of the electron diffusion region during asymmetric magnetic reconnection is ex- plored with high-resolution particle-in-cell simulations that focus on an magnetopause event ob- served by the Magnetospheric Multiscale Mission (MMS). A major surprise is the development of a standing, oblique whistler-like structure with regions of intense positive and negative dissipation. This structure arises from high-speed electrons that flow along the magnetosheath magnetic sepa- ratrices, converge in the dissipation region and jet across the x-line into the magnetosphere. The jet produces a region of negative charge and generates intense parallel electric fields that eject the electrons downstream along the magnetospheric separatrices. The ejected electrons produce the parallel velocity-space crescents documented by MMS.

Experimental verification of the role of electron pressure in fast magnetic reconnection with a guide field

DOE PAGES

Fox, W.; Sciortino, F.; v. Stechow, A.; ...

2017-03-21

We report detailed laboratory observations of the structure of a reconnection current sheet in a two-fluid plasma regime with a guide magnetic field. We observe and quantitatively analyze the quadrupolar electron pressure variation in the ion-diffusion region, as originally predicted by extended magnetohydrodynamics simulations. The projection of the electron pressure gradient parallel to the magnetic field contributes significantly to balancing the parallel electric field, and the resulting cross-field electron jets in the reconnection layer are diamagnetic in origin. Furthermore, these results demonstrate how parallel and perpendicular force balance are coupled in guide field reconnection and confirm basic theoretical models ofmore » the importance of electron pressure gradients for obtaining fast magnetic reconnection.« less

A description of electron heating with an electrostatic potential jump in a parallel, collisionless, fire hose shock

NASA Technical Reports Server (NTRS)

Ellison, Donald C.; Jones, Frank C.

1988-01-01

The electron heating required if protons scatter elastically in a parallel, collisionless shock is calculated. Near-elastic proton scattering off large amplitude background magnetic field fluctuations might be expected if the waves responsible for the shock dissipation are generated by the fire hose instability. The effects of an electrostatic potential jump in the shock layer are included by assuming that the energy lost by protons in traversing the potential jump is converted into electron thermal pressure. It is found that the electron temperature increase is a strong function of the potential jump. Comparison is made to the parallel shock plasma simulation of Quest (1987).

Magnitude of parallel pseudo potential in a magnetosonic shock wave

NASA Astrophysics Data System (ADS)

Ohsawa, Yukiharu

2018-05-01

The parallel pseudo potential F, which is the integral of the parallel electric field along the magnetic field, in a large-amplitude magnetosonic pulse (shock wave) is theoretically studied. Particle simulations revealed in the late 1990's that the product of the elementary charge and F can be much larger than the electron temperature in shock waves, i.e., the parallel electric field can be quite strong. However, no theory was presented for this unexpected result. This paper first revisits the small-amplitude theory for F and then investigates the parallel pseudo potential F in large-amplitude pulses based on the two-fluid model with finite thermal pressures. It is found that the magnitude of F in a shock wave is determined by the wave amplitude, the electron temperature, and the kinetic energy of an ion moving with the Alfvén speed. This theoretically obtained expression for F is nearly identical to the empirical relation for F discovered in the previous simulation work.

A derivation and scalable implementation of the synchronous parallel kinetic Monte Carlo method for simulating long-time dynamics

NASA Astrophysics Data System (ADS)

Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2017-10-01

Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.

Xyce Parallel Electronic Simulator Users Guide Version 6.2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows onemore » to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2014 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Xyce Parallel Electronic Simulator Users Guide Version 6.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows onemore » to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Dependence of synergy current driven by lower hybrid wave and electron cyclotron wave on the frequency and parallel refractive index of electron cyclotron wave for Tokamaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, J.; Chen, S. Y., E-mail: sychen531@163.com; Tang, C. J.

2014-01-15

The physical mechanism of the synergy current driven by lower hybrid wave (LHW) and electron cyclotron wave (ECW) in tokamaks is investigated using theoretical analysis and simulation methods in the present paper. Research shows that the synergy relationship between the two waves in velocity space strongly depends on the frequency ω and parallel refractive index N{sub //} of ECW. For a given spectrum of LHW, the parameter range of ECW, in which the synergy current exists, can be predicted by theoretical analysis, and these results are consistent with the simulation results. It is shown that the synergy effect is mainlymore » caused by the electrons accelerated by both ECW and LHW, and the acceleration of these electrons requires that there is overlap of the resonance regions of the two waves in velocity space.« less

Storm Time Evolution of Outer Radiation Belt Relativistic Electrons by a Nearly Continuous Distribution of Chorus

NASA Astrophysics Data System (ADS)

Yang, Chang; Xiao, Fuliang; He, Yihua; Liu, Si; Zhou, Qinghua; Guo, Mingyue; Zhao, Wanli

2018-03-01

During the 13-14 November 2012 storm, Van Allen Probe A simultaneously observed a 10 h period of enhanced chorus (including quasi-parallel and oblique propagation components) and relativistic electron fluxes over a broad range of L = 3-6 and magnetic local time = 2-10 within a complete orbit cycle. By adopting a Gaussian fit to the observed wave spectra, we obtain the wave parameters and calculate the bounce-averaged diffusion coefficients. We solve the Fokker-Planck diffusion equation to simulate flux evolutions of relativistic (1.8-4.2 MeV) electrons during two intervals when Probe A passed the location L = 4.3 along its orbit. The simulating results show that chorus with combined quasi-parallel and oblique components can produce a more pronounced flux enhancement in the pitch angle range ˜45°-80°, consistent well with the observation. The current results provide the first evidence on how relativistic electron fluxes vary under the drive of almost continuously distributed chorus with both quasi-parallel and oblique components within a complete orbit of Van Allen Probe.

Efficient, massively parallel eigenvalue computation

NASA Technical Reports Server (NTRS)

Huo, Yan; Schreiber, Robert

1993-01-01

In numerical simulations of disordered electronic systems, one of the most common approaches is to diagonalize random Hamiltonian matrices and to study the eigenvalues and eigenfunctions of a single electron in the presence of a random potential. An effort to implement a matrix diagonalization routine for real symmetric dense matrices on massively parallel SIMD computers, the Maspar MP-1 and MP-2 systems, is described. Results of numerical tests and timings are also presented.

Solar wind interaction with Venus and Mars in a parallel hybrid code

NASA Astrophysics Data System (ADS)

Jarvinen, Riku; Sandroos, Arto

2013-04-01

We discuss the development and applications of a new parallel hybrid simulation, where ions are treated as particles and electrons as a charge-neutralizing fluid, for the interaction between the solar wind and Venus and Mars. The new simulation code under construction is based on the algorithm of the sequential global planetary hybrid model developed at the Finnish Meteorological Institute (FMI) and on the Corsair parallel simulation platform also developed at the FMI. The FMI's sequential hybrid model has been used for studies of plasma interactions of several unmagnetized and weakly magnetized celestial bodies for more than a decade. Especially, the model has been used to interpret in situ particle and magnetic field observations from plasma environments of Mars, Venus and Titan. Further, Corsair is an open source MPI (Message Passing Interface) particle and mesh simulation platform, mainly aimed for simulations of diffusive shock acceleration in solar corona and interplanetary space, but which is now also being extended for global planetary hybrid simulations. In this presentation we discuss challenges and strategies of parallelizing a legacy simulation code as well as possible applications and prospects of a scalable parallel hybrid model for the solar wind interactions of Venus and Mars.

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Application of the stochastic parallel gradient descent algorithm for numerical simulation and analysis of the coherent summation of radiation from fibre amplifiers

NASA Astrophysics Data System (ADS)

Zhou, Pu; Wang, Xiaolin; Li, Xiao; Chen, Zilum; Xu, Xiaojun; Liu, Zejin

2009-10-01

Coherent summation of fibre laser beams, which can be scaled to a relatively large number of elements, is simulated by using the stochastic parallel gradient descent (SPGD) algorithm. The applicability of this algorithm for coherent summation is analysed and its optimisaton parameters and bandwidth limitations are studied.

An Optimization System with Parallel Processing for Reducing Common-Mode Current on Electronic Control Unit

NASA Astrophysics Data System (ADS)

Okazaki, Yuji; Uno, Takanori; Asai, Hideki

In this paper, we propose an optimization system with parallel processing for reducing electromagnetic interference (EMI) on electronic control unit (ECU). We adopt simulated annealing (SA), genetic algorithm (GA) and taboo search (TS) to seek optimal solutions, and a Spice-like circuit simulator to analyze common-mode current. Therefore, the proposed system can determine the adequate combinations of the parasitic inductance and capacitance values on printed circuit board (PCB) efficiently and practically, to reduce EMI caused by the common-mode current. Finally, we apply the proposed system to an example circuit to verify the validity and efficiency of the system.

Nongyrotropic Electrons in Guide Field Reconnection

NASA Technical Reports Server (NTRS)

Wendel, D. E.; Hesse, M.; Bessho, N.; Adrian, M. L.; Kuznetsova, M.

2016-01-01

We apply a scalar measure of nongyrotropy to the electron pressure tensor in a 2D particle-in-cell simulation of guide field reconnection and assess the corresponding electron distributions and the forces that account for the nongyrotropy. The scalar measure reveals that the nongyrotropy lies in bands that straddle the electron diffusion region and the separatrices, in the same regions where there are parallel electric fields. Analysis of electron distributions and fields shows that the nongyrotropy along the inflow and outflow separatrices emerges as a result of multiple populations of electrons influenced differently by large and small-scale parallel electric fields and by gradients in the electric field. The relevant parallel electric fields include large-scale potential ramps emanating from the x-line and sub-ion inertial scale bipolar electron holes. Gradients in the perpendicular electric field modify electrons differently depending on their phase, thus producing nongyrotropy. Magnetic flux violation occurs along portions of the separatrices that coincide with the parallel electric fields. An inductive electric field in the electron EB drift frame thus develops, which has the effect of enhancing nongyrotropies already produced by other mechanisms and under certain conditions producing their own nongyrotropy. Particle tracing of electrons from nongyrotropic populations along the inflows and outflows shows that the striated structure of nongyrotropy corresponds to electrons arriving from different source regions. We also show that the relevant parallel electric fields receive important contributions not only from the nongyrotropic portion of the electron pressure tensor but from electron spatial and temporal inertial terms as well.

Electron Cooling and Isotropization during Magnetotail Current Sheet Thinning: Implications for Parallel Electric Fields

NASA Astrophysics Data System (ADS)

Lu, San; Artemyev, A. V.; Angelopoulos, V.

2017-11-01

Magnetotail current sheet thinning is a distinctive feature of substorm growth phase, during which magnetic energy is stored in the magnetospheric lobes. Investigation of charged particle dynamics in such thinning current sheets is believed to be important for understanding the substorm energy storage and the current sheet destabilization responsible for substorm expansion phase onset. We use Time History of Events and Macroscale Interactions during Substorms (THEMIS) B and C observations in 2008 and 2009 at 18 - 25 RE to show that during magnetotail current sheet thinning, the electron temperature decreases (cooling), and the parallel temperature decreases faster than the perpendicular temperature, leading to a decrease of the initially strong electron temperature anisotropy (isotropization). This isotropization cannot be explained by pure adiabatic cooling or by pitch angle scattering. We use test particle simulations to explore the mechanism responsible for the cooling and isotropization. We find that during the thinning, a fast decrease of a parallel electric field (directed toward the Earth) can speed up the electron parallel cooling, causing it to exceed the rate of perpendicular cooling, and thus lead to isotropization, consistent with observation. If the parallel electric field is too small or does not change fast enough, the electron parallel cooling is slower than the perpendicular cooling, so the parallel electron anisotropy grows, contrary to observation. The same isotropization can also be accomplished by an increasing parallel electric field directed toward the equatorial plane. Our study reveals the existence of a large-scale parallel electric field, which plays an important role in magnetotail particle dynamics during the current sheet thinning process.

Free-electron laser simulations on the MPP

NASA Technical Reports Server (NTRS)

Vonlaven, Scott A.; Liebrock, Lorie M.

1987-01-01

Free electron lasers (FELs) are of interest because they provide high power, high efficiency, and broad tunability. FEL simulations can make efficient use of computers of the Massively Parallel Processor (MPP) class because most of the processing consists of applying a simple equation to a set of identical particles. A test version of the KMS Fusion FEL simulation, which resides mainly in the MPPs host computer and only partially in the MPP, has run successfully.

Parallel processing implementation for the coupled transport of photons and electrons using OpenMP

NASA Astrophysics Data System (ADS)

Doerner, Edgardo

2016-05-01

In this work the use of OpenMP to implement the parallel processing of the Monte Carlo (MC) simulation of the coupled transport for photons and electrons is presented. This implementation was carried out using a modified EGSnrc platform which enables the use of the Microsoft Visual Studio 2013 (VS2013) environment, together with the developing tools available in the Intel Parallel Studio XE 2015 (XE2015). The performance study of this new implementation was carried out in a desktop PC with a multi-core CPU, taking as a reference the performance of the original platform. The results were satisfactory, both in terms of scalability as parallelization efficiency.

ITG-TEM turbulence simulation with bounce-averaged kinetic electrons in tokamak geometry

NASA Astrophysics Data System (ADS)

Kwon, Jae-Min; Qi, Lei; Yi, S.; Hahm, T. S.

2017-06-01

We develop a novel numerical scheme to simulate electrostatic turbulence with kinetic electron responses in magnetically confined toroidal plasmas. Focusing on ion gyro-radius scale turbulences with slower frequencies than the time scales for electron parallel motions, we employ and adapt the bounce-averaged kinetic equation to model trapped electrons for nonlinear turbulence simulation with Coulomb collisions. Ions are modeled by employing the gyrokinetic equation. The newly developed scheme is implemented on a global δf particle in cell code gKPSP. By performing linear and nonlinear simulations, it is demonstrated that the new scheme can reproduce key physical properties of Ion Temperature Gradient (ITG) and Trapped Electron Mode (TEM) instabilities, and resulting turbulent transport. The overall computational cost of kinetic electrons using this novel scheme is limited to 200%-300% of the cost for simulations with adiabatic electrons. Therefore the new scheme allows us to perform kinetic simulations with trapped electrons very efficiently in magnetized plasmas.

Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure.

PubMed

Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei

2011-09-07

Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed.

New aspects of whistler waves driven by an electron beam studied by a 3-D electromagnetic code

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-Ichi; Buneman, Oscar; Neubert, Torsten

1994-01-01

We have restudied electron beam driven whistler waves with a 3-D electromagnetic particle code. The simulation results show electromagnetic whistler wave emissions and electrostatic beam modes like those observed in the Spacelab 2 electron beam experiment. It has been suggested in the past that the spatial bunching of beam electrons associated with the beam mode may directly generate whistler waves. However, the simulation results indicate several inconsistencies with this picture: (1) whistler waves continue to be generated even after the beam mode space charge modulation looses its coherence, (2) the parallel (to the background magnetic field) wavelength of the whistler wave is longer than that of the beam instability, and (3) the parallel phase velocity of the whistler wave is smaller than that of the beam mode. The complex structure of the whistler waves in the vicinity of the beam suggest that the transverse motion (gyration) of the beam and background electrons is also involved in the generation of whistler waves.

On the generation of double layers from ion- and electron-acoustic instabilities

NASA Astrophysics Data System (ADS)

Fu, Xiangrong; Cowee, Misa M.; Gary, S. Peter; Winske, Dan

2016-03-01

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric field structures traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs—electron acoustic DLs—generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e., the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. Linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric field structures that propagate at the electron thermal speed, suggesting another potential explanation for the observations.

Massive parallel 3D PIC simulation of negative ion extraction

NASA Astrophysics Data System (ADS)

Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu

2017-09-01

The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.

Kinetic Simulations of Particle Acceleration at Shocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caprioli, Damiano; Guo, Fan

2015-07-16

Collisionless shocks are mediated by collective electromagnetic interactions and are sources of non-thermal particles and emission. The full particle-in-cell approach and a hybrid approach are sketched, simulations of collisionless shocks are shown using a multicolor presentation. Results for SN 1006, a case involving ion acceleration and B field amplification where the shock is parallel, are shown. Electron acceleration takes place in planetary bow shocks and galaxy clusters. It is concluded that acceleration at shocks can be efficient: >15%; CRs amplify B field via streaming instability; ion DSA is efficient at parallel, strong shocks; ions are injected via reflection and shockmore » drift acceleration; and electron DSA is efficient at oblique shocks.« less

Spectral properties and associated plasma energization by magnetosonic waves in the Earth's magnetosphere: Particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Sun, Jicheng; Gao, Xinliang; Lu, Quanming; Chen, Lunjin; Liu, Xu; Wang, Xueyi; Tao, Xin; Wang, Shui

2017-05-01

In this paper, we perform a 1-D particle-in-cell (PIC) simulation model consisting of three species, cold electrons, cold ions, and energetic ion ring, to investigate spectral structures of magnetosonic waves excited by ring distribution protons in the Earth's magnetosphere, and dynamics of charged particles during the excitation of magnetosonic waves. As the wave normal angle decreases, the spectral range of excited magnetosonic waves becomes broader with upper frequency limit extending beyond the lower hybrid resonant frequency, and the discrete spectra tends to merge into a continuous one. This dependence on wave normal angle is consistent with the linear theory. The effects of magnetosonic waves on the background cold plasma populations also vary with wave normal angle. For exactly perpendicular magnetosonic waves (parallel wave number k|| = 0), there is no energization in the parallel direction for both background cold protons and electrons due to the negligible fluctuating electric field component in the parallel direction. In contrast, the perpendicular energization of background plasmas is rather significant, where cold protons follow unmagnetized motion while cold electrons follow drift motion due to wave electric fields. For magnetosonic waves with a finite k||, there exists a nonnegligible parallel fluctuating electric field, leading to a significant and rapid energization in the parallel direction for cold electrons. These cold electrons can also be efficiently energized in the perpendicular direction due to the interaction with the magnetosonic wave fields in the perpendicular direction. However, cold protons can be only heated in the perpendicular direction, which is likely caused by the higher-order resonances with magnetosonic waves. The potential impacts of magnetosonic waves on the energization of the background cold plasmas in the Earth's inner magnetosphere are also discussed in this paper.

Parallel Transport with Sheath and Collisional Effects in Global Electrostatic Turbulent Transport in FRCs

NASA Astrophysics Data System (ADS)

Bao, Jian; Lau, Calvin; Kuley, Animesh; Lin, Zhihong; Fulton, Daniel; Tajima, Toshiki; Tri Alpha Energy, Inc. Team

2017-10-01

Collisional and turbulent transport in a field reversed configuration (FRC) is studied in global particle simulation by using GTC (gyrokinetic toroidal code). The global FRC geometry is incorporated in GTC by using a field-aligned mesh in cylindrical coordinates, which enables global simulation coupling core and scrape-off layer (SOL) across the separatrix. Furthermore, fully kinetic ions are implemented in GTC to treat magnetic-null point in FRC core. Both global simulation coupling core and SOL regions and independent SOL region simulation have been carried out to study turbulence. In this work, the ``logical sheath boundary condition'' is implemented to study parallel transport in the SOL. This method helps to relax time and spatial steps without resolving electron plasma frequency and Debye length, which enables turbulent transports simulation with sheath effects. We will study collisional and turbulent SOL parallel transport with mirror geometry and sheath boundary condition in C2-W divertor.

Parallel 3D Finite Element Numerical Modelling of DC Electron Guns

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prudencio, E.; Candel, A.; Ge, L.

2008-02-04

In this paper we present Gun3P, a parallel 3D finite element application that the Advanced Computations Department at the Stanford Linear Accelerator Center is developing for the analysis of beam formation in DC guns and beam transport in klystrons. Gun3P is targeted specially to complex geometries that cannot be described by 2D models and cannot be easily handled by finite difference discretizations. Its parallel capability allows simulations with more accuracy and less processing time than packages currently available. We present simulation results for the L-band Sheet Beam Klystron DC gun, in which case Gun3P is able to reduce simulation timemore » from days to some hours.« less

2D imaging of helium ion velocity in the DIII-D divertor

NASA Astrophysics Data System (ADS)

Samuell, C. M.; Porter, G. D.; Meyer, W. H.; Rognlien, T. D.; Allen, S. L.; Briesemeister, A.; Mclean, A. G.; Zeng, L.; Jaervinen, A. E.; Howard, J.

2018-05-01

Two-dimensional imaging of parallel ion velocities is compared to fluid modeling simulations to understand the role of ions in determining divertor conditions and benchmark the UEDGE fluid modeling code. Pure helium discharges are used so that spectroscopic He+ measurements represent the main-ion population at small electron temperatures. Electron temperatures and densities in the divertor match simulated values to within about 20%-30%, establishing the experiment/model match as being at least as good as those normally obtained in the more regularly simulated deuterium plasmas. He+ brightness (HeII) comparison indicates that the degree of detachment is captured well by UEDGE, principally due to the inclusion of E ×B drifts. Tomographically inverted Coherence Imaging Spectroscopy measurements are used to determine the He+ parallel velocities which display excellent agreement between the model and the experiment near the divertor target where He+ is predicted to be the main-ion species and where electron-dominated physics dictates the parallel momentum balance. Upstream near the X-point where He+ is a minority species and ion-dominated physics plays a more important role, there is an underestimation of the flow velocity magnitude by a factor of 2-3. These results indicate that more effort is required to be able to correctly predict ion momentum in these challenging regimes.

Particle Acceleration, Magnetic Field Generation in Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-Ichi; Hardee, P.; Hededal, C. B.; Richardson, G.; Sol, H.; Preece, R.; Fishman, G. J.

2005-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient parallel magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. New simulations with an ambient perpendicular magnetic field show the strong interaction between the relativistic jet and the magnetic fields. The magnetic fields are piled up by the jet and the jet electrons are bent, which creates currents and displacement currents. At the nonlinear stage, the magnetic fields are reversed by the current and the reconnection may take place. Due to these dynamics the jet and ambient electron are strongly accelerated in both parallel and perpendicular directions.

Particle Acceleration, Magnetic Field Generation, and Emission in Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, Ken-IchiI.; Hededal, C.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G.

2004-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (m) code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient parallel magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. New simulations with an ambient perpendicular magnetic field show the strong interaction between the relativistic jet and the magnetic fields. The magnetic fields are piled up by the jet and the jet electrons are bent, which creates currents and displacement currents. At the nonlinear stage, the magnetic fields are reversed by the current and the reconnection may take place. Due to these dynamics the jet and ambient electron are strongly accelerated in both parallel and perpendicular directions.

THE MECHANISMS OF ELECTRON ACCELERATION DURING MULTIPLE X LINE MAGNETIC RECONNECTION WITH A GUIDE FIELD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Huanyu; Lu, Quanming; Huang, Can

2016-04-20

The interactions between magnetic islands are considered to play an important role in electron acceleration during magnetic reconnection. In this paper, two-dimensional particle-in-cell simulations are performed to study electron acceleration during multiple X line reconnection with a guide field. Because the electrons remain almost magnetized, we can analyze the contributions of the parallel electric field, Fermi, and betatron mechanisms to electron acceleration during the evolution of magnetic reconnection through comparison with a guide-center theory. The results show that with the magnetic reconnection proceeding, two magnetic islands are formed in the simulation domain. Next, the electrons are accelerated by both themore » parallel electric field in the vicinity of the X lines and the Fermi mechanism due to the contraction of the two magnetic islands. Then, the two magnetic islands begin to merge into one, and, in such a process, the electrons can be accelerated by both the parallel electric field and betatron mechanisms. During the betatron acceleration, the electrons are locally accelerated in the regions where the magnetic field is piled up by the high-speed flow from the X line. At last, when the coalescence of the two islands into one big island finishes, the electrons can be further accelerated by the Fermi mechanism because of the contraction of the big island. With the increase of the guide field, the contributions of the Fermi and betatron mechanisms to electron acceleration become less and less important. When the guide field is sufficiently large, the contributions of the Fermi and betatron mechanisms are almost negligible.« less

Particle-in-cell simulations of the critical ionization velocity effect in finite size clouds

NASA Technical Reports Server (NTRS)

Moghaddam-Taaheri, E.; Lu, G.; Goertz, C. K.; Nishikawa, K. - I.

1994-01-01

The critical ionization velocity (CIV) mechanism in a finite size cloud is studied with a series of electrostatic particle-in-cell simulations. It is observed that an initial seed ionization, produced by non-CIV mechanisms, generates a cross-field ion beam which excites a modified beam-plasma instability (MBPI) with frequency in the range of the lower hybrid frequency. The excited waves accelerate electrons along the magnetic field up to the ion drift energy that exceeds the ionization energy of the neutral atoms. The heated electrons in turn enhance the ion beam by electron-neutral impact ionization, which establishes a positive feedback loop in maintaining the CIV process. It is also found that the efficiency of the CIV mechanism depends on the finite size of the gas cloud in the following ways: (1) Along the ambient magnetic field the finite size of the cloud, L (sub parallel), restricts the growth of the fastest growing mode, with a wavelength lambda (sub m parallel), of the MBPI. The parallel electron heating at wave saturation scales approximately as (L (sub parallel)/lambda (sub m parallel)) (exp 1/2); (2) Momentum coupling between the cloud and the ambient plasma via the Alfven waves occurs as a result of the finite size of the cloud in the direction perpendicular to both the ambient magnetic field and the neutral drift. This reduces exponentially with time the relative drift between the ambient plasma and the neutrals. The timescale is inversely proportional to the Alfven velocity. (3) The transvers e charge separation field across the cloud was found to result in the modulation of the beam velocity which reduces the parallel heating of electrons and increases the transverse acceleration of electrons. (4) Some energetic electrons are lost from the cloud along the magnetic field at a rate characterized by the acoustic velocity, instead of the electron thermal velocity. The loss of energetic electrons from the cloud seems to be larger in the direction of plasma drift relative to the neutrals, where the loss rate is characterized by the neutral drift velocity. It is also shown that a factor of 4 increase in the ambient plasma density, increases the CIV ionization yield by almost 2 orders of magnitude at the end of a typical run. It is concluded that a larger ambient plasma density can result in a larger CIV yield because of (1) larger seed ion production by non-CIV mechanisms, (2) smaller Alfven velocity and hence weak momentum coupling, and (3) smaller ratio of the ion beam density to the ambient ion density, and therefore a weaker modulation of the beam velocity. The simulation results are used to interpret various chemical release experiments in space.

Study of Wave-Particle Interactions for Whistler Mode Waves at Oblique Angles by Utilizing the Gyroaveraging Method

NASA Astrophysics Data System (ADS)

Hsieh, Yi-Kai; Omura, Yoshiharu

2017-10-01

We investigate the properties of whistler mode wave-particle interactions at oblique wave normal angles to the background magnetic field. We find that electromagnetic energy of waves at frequencies below half the electron cyclotron frequency can flow nearly parallel to the ambient magnetic field. We thereby confirm that the gyroaveraging method, which averages the cyclotron motion to the gyrocenter and reduces the simulation from two-dimensional to one-dimensional, is valid for oblique wave-particle interaction. Multiple resonances appear for oblique propagation but not for parallel propagation. We calculate the possible range of resonances with the first-order resonance condition as a function of electron kinetic energy and equatorial pitch angle. To reveal the physical process and the efficiency of electron acceleration by multiple resonances, we assume a simple uniform wave model with constant amplitude and frequency in space and time. We perform test particle simulations with electrons starting at specific equatorial pitch angles and kinetic energies. The simulation results show that multiple resonances contribute to acceleration and pitch angle scattering of energetic electrons. Especially, we find that electrons with energies of a few hundred keV can be accelerated efficiently to a few MeV through the n = 0 Landau resonance.

Re-forming supercritical quasi-parallel shocks. I - One- and two-dimensional simulations

NASA Technical Reports Server (NTRS)

Thomas, V. A.; Winske, D.; Omidi, N.

1990-01-01

The process of reforming supercritical quasi-parallel shocks is investigated using one-dimensional and two-dimensional hybrid (particle ion, massless fluid electron) simulations both of shocks and of simpler two-stream interactions. It is found that the supercritical quasi-parallel shock is not steady. Instread of a well-defined shock ramp between upstream and downstream states that remains at a fixed position in the flow, the ramp periodically steepens, broadens, and then reforms upstream of its former position. It is concluded that the wave generation process is localized at the shock ramp and that the reformation process proceeds in the absence of upstream perturbations intersecting the shock.

Electron acceleration in a secondary magnetic island formed during magnetic reconnection with a guide field

NASA Astrophysics Data System (ADS)

Wang, Huanyu; Lu, Quanming; Huang, Can; Wang, Shui

2017-05-01

Secondary magnetic islands may be generated in the vicinity of an X line during magnetic reconnection. In this paper, by performing two-dimensional (2-D) particle-in-cell simulations, we investigate the role of a secondary magnetic island in electron acceleration during magnetic reconnection with a guide field. The electron motions are found to be adiabatic, and we analyze the contributions of the parallel electric field and Fermi and betatron mechanisms to electron acceleration in the secondary island during the evolution of magnetic reconnection. When the secondary island is formed, electrons are accelerated by the parallel electric field due to the existence of the reconnection electric field in the electron current sheet. Electrons can be accelerated by both the parallel electric field and Fermi mechanism when the secondary island begins to merge with the primary magnetic island, which is formed simultaneously with the appearance of X lines. With the increase in the guide field, the contributions of the Fermi mechanism to electron acceleration become less and less important. When the guide field is sufficiently large, the contribution of the Fermi mechanism is almost negligible.

Beyond 2D: Parallel Electric Fields and Dissipation in Guide Field Reconnectio

NASA Astrophysics Data System (ADS)

Wilder, F. D.; Ergun, R.; Ahmadi, N.; Goodrich, K.; Eriksson, S.; Shimoda, E.; Burch, J. L.; Phan, T.; Torbert, R. B.; Strangeway, R. J.; Giles, B. L.; Lindqvist, P. A.; Khotyaintsev, Y. V.

2017-12-01

In 2015, NASA launched the Magnetospheric Multiscale (MMS) mission to study phenomenon of magnetic reconnection down to the electron scale. Advantages of MMS include a 20s spin period and long axial booms, which together allow for measurement of 3-D electric fields with accuracy down to 1 mV/m. During the two dayside phases of the prime mission, MMS has observed multiple electron and ion diffusion region events at the Earth's subsolar and flank magnetopause, as well as in the magnetosheath, providing an option to study both symmetric and asymmetric reconnection at a variety of guide field strengths. We present a review of parallel electric fields observed by MMS during diffusion region events, and discuss their implications for simulations and laboratory observations of reconnection. We find that as the guide field increases, the dissipation in the diffusion region transitions from being due to currents and fields perpendicular to the background magnetic field, to being associated with parallel electric fields and currents. Additionally, the observed parallel electric fields are significantly larger than those predicted by simulations of reconnection under strong guide field conditions.

Simulation of electrostatic turbulence in the plasma sheet boundary layer with electron currents and bean-shaped ion beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nishikawa, K.; Frank, L.A.; Huang, C.Y.

Plasma data from ISEE 1 show the presence of electron currents as well as energetic ion beams in the plasma sheet boundary layer. Broadband electrostatic noise and low-frequency electromagnetic bursts are detected in the plasma sheet boundary layer, especially in the presence of strong ion flows, currents, and steep spacial gradients in the fluxes of few-keV electrons and ions. Particle simulations have been performed to investigate electrostatic turbulence driven by a cold electron beam and/or ion beams with a bean-shaped velocity distribution. The simulation results show that the counterstreaming ion beams as well as the counterstreaming of the cold electronmore » beam and the ion beam excite ion acoustic waves with the Doppler-shifted real frequency ..omega..approx. = +- k/sub parallel/(c/sub s/-V/sub i//sub //sub parallel/). However, the effect of the bean-shaped ion velocity distributions reduces the growth rates of ion acoustic instability. The simulation results also show that the slowing down of the ion beam is larger at the larger perpendicular velocity. The wave spectra of the electric fields at some points for simulations show turbulence generated by growing waves. The frequency of these spectra ranges from ..cap omega../sub i/ to ..omega../sub p//sub e/, which is in qualitative agreement with the satellite data. copyright American Geophysical Union 1988« less

Global gyrokinetic simulations of intrinsic rotation in ASDEX Upgrade Ohmic L-mode plasmas

NASA Astrophysics Data System (ADS)

Hornsby, W. A.; Angioni, C.; Lu, Z. X.; Fable, E.; Erofeev, I.; McDermott, R.; Medvedeva, A.; Lebschy, A.; Peeters, A. G.; The ASDEX Upgrade Team

2018-05-01

Non-linear, radially global, turbulence simulations of ASDEX Upgrade (AUG) plasmas are performed and the nonlinear generated intrinsic flow shows agreement with the intrinsic flow gradients measured in the core of Ohmic L-mode plasmas at nominal parameters. Simulations utilising the kinetic electron model show hollow intrinsic flow profiles as seen in a predominant number of experiments performed at similar plasma parameters. In addition, significantly larger flow gradients are seen than in a previous flux-tube analysis (Hornsby et al 2017 Nucl. Fusion 57 046008). Adiabatic electron model simulations can show a flow profile with opposing sign in the gradient with respect to a kinetic electron simulation, implying a reversal in the sign of the residual stress due to kinetic electrons. The shaping of the intrinsic flow is strongly determined by the density gradient profile. The sensitivity of the residual stress to variations in density profile curvature is calculated and seen to be significantly stronger than to neoclassical flows (Hornsby et al 2017 Nucl. Fusion 57 046008). This variation is strong enough on its own to explain the large variations in the intrinsic flow gradients seen in some AUG experiments. Analysis of the symmetry breaking properties of the turbulence shows that profile shearing is the dominant mechanism in producing a finite parallel wave-number, with turbulence gradient effects contributing a smaller portion of the parallel wave-vector.

Scaling of Electron Heating During Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, O.; Le, A.; Daughton, W. S.; Egedal, J.

2016-12-01

While magnetic reconnection plays a major role in accelerating and heating magnetospheric plasma, it remains poorly understood how the level of particle energization depends on the plasma conditions. Meanwhile, a recent survey of THEMIS magnetopause reconnection observations [Phan et al. GRL 2013] and a numerical study [Shay et al. PoP 2014] found empirically that the electron heating scales with the square of the upstream Alfven speed. Equivalently for weak guide fields, the fractional electron temperature increase is inversely proportional to the upstream electron beta (ratio of electron to magnetic pressure). We present models for symmetric reconnection with moderate [Ohia et al., GRL 2015] or zero guide field that predict the electron bulk heating. In the models, adiabatically trapped electrons gain energy from parallel electric fields in the inflowing region. For purely anti-parallel reconnection, meandering electrons receive additional energy from the reconnection electric field. The predicted scalings are in quantitative agreement with fluid and kinetic simulations, as well as spacecraft observations. Using kinetic simulations, we extend this work to explore how the layer dynamics and electron bulk heating vary as functions of the magnetic shear and plasma and magnetic pressure asymmetry across the reconnection layer. These results are pertinent to recent Magnetospheric Multiscale (MMS) Mission measurements of electron dynamics during dayside magnetopause reconnection.

On the generation of double layers from ion- and electron-acoustic instabilities

DOE PAGES

Fu, Xiangrong; Cowee, Misa M.; Gary, Stephen Peter; ...

2016-03-17

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric fields traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs – electron acoustic DLs – generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e.more » the hypothetical electron acoustic DLs cannot be formed in a way similar to ion acoustic DLs. We find that linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric fields that propagate at the electron thermal speed, suggesting another potential explanation for the observations.« less

Xyce Parallel Electronic Simulator Reference Guide Version 6.7.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TMmore » are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

A numerical analysis of plasma non-uniformity in the parallel plate VHF-CCP and the comparison among various model

NASA Astrophysics Data System (ADS)

Sawada, Ikuo

2012-10-01

We measured the radial distribution of electron density in a 200 mm parallel plate CCP and compared it with results from numerical simulations. The experiments were conducted with pure Ar gas with pressures ranging from 15 to 100 mTorr and 60 MHz applied at the top electrode with powers from 500 to 2000W. The measured electron profile is peaked in the center, and the relative non-uniformity is higher at 100 mTorr than at 15 mTorr. We compare the experimental results with simulations with both HPEM and Monte-Carlo/PIC codes. In HPEM simulations, we used either fluid or electron Monte-Carlo module, and the Poisson or the Electromagnetic solver. None of the models were able to duplicate the experimental results quantitatively. However, HPEM with the electron Monte-Carlo module and PIC qualitatively matched the experimental results. We will discuss the results from these models and how they illuminate the mechanism of enhanced electron central peak.[4pt] [1] T. Oshita, M. Matsukuma, S.Y. Kang, I. Sawada: The effect of non-uniform RF voltage in a CCP discharge, The 57^th JSAP Spring Meeting 2010[4pt] [2] I. Sawada, K. Matsuzaki, S.Y. Kang, T. Ohshita, M. Kawakami, S. Segawa: 1-st IC-PLANTS, 2008

Electron and ion heating by whistler turbulence: Three-dimensional particle-in-cell simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, R. Scott; Gary, S. Peter; Wang, Joseph

2014-12-17

Three-dimensional particle-in-cell simulations of decaying whistler turbulence are carried out on a collisionless, homogeneous, magnetized, electron-ion plasma model. In addition, the simulations use an initial ensemble of relatively long wavelength whistler modes with a broad range of initial propagation directions with an initial electron beta β e = 0.05. The computations follow the temporal evolution of the fluctuations as they cascade into broadband turbulent spectra at shorter wavelengths. Three simulations correspond to successively larger simulation boxes and successively longer wavelengths of the initial fluctuations. The computations confirm previous results showing electron heating is preferentially parallel to the background magnetic fieldmore » B o, and ion heating is preferentially perpendicular to B o. The new results here are that larger simulation boxes and longer initial whistler wavelengths yield weaker overall dissipation, consistent with linear dispersion theory predictions of decreased damping, stronger ion heating, consistent with a stronger ion Landau resonance, and weaker electron heating.« less

Neuromimetic Circuits with Synaptic Devices Based on Strongly Correlated Electron Systems

NASA Astrophysics Data System (ADS)

Ha, Sieu D.; Shi, Jian; Meroz, Yasmine; Mahadevan, L.; Ramanathan, Shriram

2014-12-01

Strongly correlated electron systems such as the rare-earth nickelates (R NiO3 , R denotes a rare-earth element) can exhibit synapselike continuous long-term potentiation and depression when gated with ionic liquids; exploiting the extreme sensitivity of coupled charge, spin, orbital, and lattice degrees of freedom to stoichiometry. We present experimental real-time, device-level classical conditioning and unlearning using nickelate-based synaptic devices in an electronic circuit compatible with both excitatory and inhibitory neurons. We establish a physical model for the device behavior based on electric-field-driven coupled ionic-electronic diffusion that can be utilized for design of more complex systems. We use the model to simulate a variety of associate and nonassociative learning mechanisms, as well as a feedforward recurrent network for storing memory. Our circuit intuitively parallels biological neural architectures, and it can be readily generalized to other forms of cellular learning and extinction. The simulation of neural function with electronic device analogs may provide insight into biological processes such as decision making, learning, and adaptation, while facilitating advanced parallel information processing in hardware.

A Metascalable Computing Framework for Large Spatiotemporal-Scale Atomistic Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nomura, K; Seymour, R; Wang, W

2009-02-17

A metascalable (or 'design once, scale on new architectures') parallel computing framework has been developed for large spatiotemporal-scale atomistic simulations of materials based on spatiotemporal data locality principles, which is expected to scale on emerging multipetaflops architectures. The framework consists of: (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms for high complexity problems; (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, while introducing multiple parallelization axes; and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these O(N) algorithms onto a multicore cluster based onmore » hybrid implementation combining message passing and critical section-free multithreading. The EDC-STEP-HCD framework exposes maximal concurrency and data locality, thereby achieving: (1) inter-node parallel efficiency well over 0.95 for 218 billion-atom molecular-dynamics and 1.68 trillion electronic-degrees-of-freedom quantum-mechanical simulations on 212,992 IBM BlueGene/L processors (superscalability); (2) high intra-node, multithreading parallel efficiency (nanoscalability); and (3) nearly perfect time/ensemble parallel efficiency (eon-scalability). The spatiotemporal scale covered by MD simulation on a sustained petaflops computer per day (i.e. petaflops {center_dot} day of computing) is estimated as NT = 2.14 (e.g. N = 2.14 million atoms for T = 1 microseconds).« less

The influence of the self-consistent mode structure on the Coriolis pinch effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peeters, A. G.; Camenen, Y.; Casson, F. J.

This paper discusses the effect of the mode structure on the Coriolis pinch effect [A. G. Peeters, C. Angioni, and D. Strintzi, Phys. Rev. Lett. 98, 265003 (2007)]. It is shown that the Coriolis drift effect can be compensated for by a finite parallel wave vector, resulting in a reduced momentum pinch velocity. Gyrokinetic simulations in full toroidal geometry reveal that parallel dynamics effectively removes the Coriolis pinch for the case of adiabatic electrons, while the compensation due to the parallel dynamics is incomplete for the case of kinetic electrons, resulting in a finite pinch velocity. The finite flux inmore » the case of kinetic electrons is interpreted to be related to the electron trapping, which prevents a strong asymmetry in the electrostatic potential with respect to the low field side position. The physics picture developed here leads to the discovery and explanation of two unexpected effects: First the pinch velocity scales with the trapped particle fraction (root of the inverse aspect ratio), and second there is no strong collisionality dependence. The latter is related to the role of the trapped electrons, which retain some symmetry in the eigenmode, but play no role in the perturbed parallel velocity.« less

Modeling of the energy resolution of a 1 meter and a 3 meter time of flight positron annihilation induced Auger electron spectrometers

NASA Astrophysics Data System (ADS)

Fairchild, A.; Chirayath, V.; Gladen, R.; McDonald, A.; Lim, Z.; Chrysler, M.; Koymen, A.; Weiss, A.

Simion 8.1®simulations were used to determine the energy resolution of a 1 meter long Time of Flight Positron annihilation induced Auger Electron Spectrometer (TOF-PAES). The spectrometer consists of: 1. a magnetic gradient section used to parallelize the electrons leaving the sample along the beam axis, 2. an electric field free time of flight tube and 3. a detection section with a set of ExB plates that deflect electrons exiting the TOF tube into a Micro-Channel Plate (MCP). Simulations of the time of flight distribution of electrons emitted according to a known secondary electron emission distribution, for various sample biases, were compared to experimental energy calibration peaks and found to be in excellent agreement. The TOF spectra at the highest sample bias was used to determine the timing resolution function describing the timing spread due to the electronics. Simulations were then performed to calculate the energy resolution at various electron energies in order to deconvolute the combined influence of the magnetic field parallelizer, the timing resolution, and the voltage gradient at the ExB plates. The energy resolution of the 1m TOF-PAES was compared to a newly constructed 3 meter long system. The results were used to optimize the geometry and the potentials of the ExB plates for obtaining the best energy resolution. This work was supported by NSF Grant NSF Grant No. DMR 1508719 and DMR 1338130.

Toward real-time Monte Carlo simulation using a commercial cloud computing infrastructure

NASA Astrophysics Data System (ADS)

Wang, Henry; Ma, Yunzhi; Pratx, Guillem; Xing, Lei

2011-09-01

Monte Carlo (MC) methods are the gold standard for modeling photon and electron transport in a heterogeneous medium; however, their computational cost prohibits their routine use in the clinic. Cloud computing, wherein computing resources are allocated on-demand from a third party, is a new approach for high performance computing and is implemented to perform ultra-fast MC calculation in radiation therapy. We deployed the EGS5 MC package in a commercial cloud environment. Launched from a single local computer with Internet access, a Python script allocates a remote virtual cluster. A handshaking protocol designates master and worker nodes. The EGS5 binaries and the simulation data are initially loaded onto the master node. The simulation is then distributed among independent worker nodes via the message passing interface, and the results aggregated on the local computer for display and data analysis. The described approach is evaluated for pencil beams and broad beams of high-energy electrons and photons. The output of cloud-based MC simulation is identical to that produced by single-threaded implementation. For 1 million electrons, a simulation that takes 2.58 h on a local computer can be executed in 3.3 min on the cloud with 100 nodes, a 47× speed-up. Simulation time scales inversely with the number of parallel nodes. The parallelization overhead is also negligible for large simulations. Cloud computing represents one of the most important recent advances in supercomputing technology and provides a promising platform for substantially improved MC simulation. In addition to the significant speed up, cloud computing builds a layer of abstraction for high performance parallel computing, which may change the way dose calculations are performed and radiation treatment plans are completed. This work was presented in part at the 2010 Annual Meeting of the American Association of Physicists in Medicine (AAPM), Philadelphia, PA.

Particle simulation of plasmas on the massively parallel processor

NASA Technical Reports Server (NTRS)

Gledhill, I. M. A.; Storey, L. R. O.

1987-01-01

Particle simulations, in which collective phenomena in plasmas are studied by following the self consistent motions of many discrete particles, involve several highly repetitive sets of calculations that are readily adaptable to SIMD parallel processing. A fully electromagnetic, relativistic plasma simulation for the massively parallel processor is described. The particle motions are followed in 2 1/2 dimensions on a 128 x 128 grid, with periodic boundary conditions. The two dimensional simulation space is mapped directly onto the processor network; a Fast Fourier Transform is used to solve the field equations. Particle data are stored according to an Eulerian scheme, i.e., the information associated with each particle is moved from one local memory to another as the particle moves across the spatial grid. The method is applied to the study of the nonlinear development of the whistler instability in a magnetospheric plasma model, with an anisotropic electron temperature. The wave distribution function is included as a new diagnostic to allow simulation results to be compared with satellite observations.

GPAW - massively parallel electronic structure calculations with Python-based software.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Enkovaara, J.; Romero, N.; Shende, S.

2011-01-01

Electronic structure calculations are a widely used tool in materials science and large consumer of supercomputing resources. Traditionally, the software packages for these kind of simulations have been implemented in compiled languages, where Fortran in its different versions has been the most popular choice. While dynamic, interpreted languages, such as Python, can increase the effciency of programmer, they cannot compete directly with the raw performance of compiled languages. However, by using an interpreted language together with a compiled language, it is possible to have most of the productivity enhancing features together with a good numerical performance. We have used thismore » approach in implementing an electronic structure simulation software GPAW using the combination of Python and C programming languages. While the chosen approach works well in standard workstations and Unix environments, massively parallel supercomputing systems can present some challenges in porting, debugging and profiling the software. In this paper we describe some details of the implementation and discuss the advantages and challenges of the combined Python/C approach. We show that despite the challenges it is possible to obtain good numerical performance and good parallel scalability with Python based software.« less

Enhanced electron mixing and heating in 3-D asymmetric reconnection at the Earth's magnetopause

DOE PAGES

Le, Ari Yitzchak; Daughton, William Scott; Chen, Li -Jen; ...

2017-03-01

Here, electron heating and mixing during asymmetric reconnection are studied with a 3-D kinetic simulation that matches plasma parameters from Magnetospheric Multiscale (MMS) spacecraft observations of a magnetopause diffusion region. The mixing and heating are strongly enhanced across the magnetospheric separatrix compared to a 2-D simulation. The transport of particles across the separatrix in 3-D is attributed to lower hybrid drift turbulence excited at the steep density gradient near the magnetopause. In the 3-D simulation (and not the 2-D simulation), the electron temperature parallel to the magnetic field within the mixing layer is significantly higher than its upstream value inmore » agreement with the MMS observations.« less

On the generation of double layers from ion- and electron-acoustic instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Xiangrong, E-mail: xrfu@lanl.gov; Cowee, Misa M.; Winske, Dan

2016-03-15

A plasma double layer (DL) is a nonlinear electrostatic structure that carries a uni-polar electric field parallel to the background magnetic field due to local charge separation. Past studies showed that DLs observed in space plasmas are mostly associated with the ion acoustic instability. Recent Van Allen Probes observations of parallel electric field structures traveling much faster than the ion acoustic speed have motivated a computational study to test the hypothesis that a new type of DLs—electron acoustic DLs—generated from the electron acoustic instability are responsible for these electric fields. Nonlinear particle-in-cell simulations yield negative results, i.e., the hypothetical electronmore » acoustic DLs cannot be formed in a way similar to ion acoustic DLs. Linear theory analysis and the simulations show that the frequencies of electron acoustic waves are too high for ions to respond and maintain charge separation required by DLs. However, our results do show that local density perturbations in a two-electron-component plasma can result in unipolar-like electric field structures that propagate at the electron thermal speed, suggesting another potential explanation for the observations.« less

Xyce Parallel Electronic Simulator Users' Guide Version 6.6.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows onemore » to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright c 2002-2016 Sandia Corporation. All rights reserved. Acknowledgements The BSIM Group at the University of California, Berkeley developed the BSIM3, BSIM4, BSIM6, BSIM-CMG and BSIM-SOI models. The BSIM3 is Copyright c 1999, Regents of the University of California. The BSIM4 is Copyright c 2006, Regents of the University of California. The BSIM6 is Copyright c 2015, Regents of the University of California. The BSIM-CMG is Copyright c 2012 and 2016, Regents of the University of California. The BSIM-SOI is Copyright c 1990, Regents of the University of California. All rights reserved. The Mextram model has been developed by NXP Semiconductors until 2007, Delft University of Technology from 2007 to 2014, and Auburn University since April 2015. Copyrights c of Mextram are with Delft University of Technology, NXP Semiconductors and Auburn University. The MIT VS Model Research Group developed the MIT Virtual Source (MVS) model. Copyright c 2013 Massachusetts Institute of Technology (MIT). The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

MMS observations and hybrid simulations of rippled and reforming quasi-parallel shocks

NASA Astrophysics Data System (ADS)

Gingell, I.; Schwartz, S. J.; Burgess, D.; Johlander, A.; Russell, C. T.; Burch, J. L.; Ergun, R.; Fuselier, S. A.; Gershman, D. J.; Giles, B. L.; Goodrich, K.; Khotyaintsev, Y. V.; Lavraud, B.; Lindqvist, P. A.; Strangeway, R. J.; Trattner, K. J.; Torbert, R. B.; Wilder, F. D.

2017-12-01

Surface ripples, i.e. deviations in the nominal local shock orientation, are expected to propagate in the ramp and overshoot of collisionless shocks. These ripples have typically been associated with observations and simulations of quasi-perpendicular shocks. We present observations of a crossing of Earth's marginally quasi-parallel (θBn ˜ 45°) bow shock by the MMS spacecraft on 2015-11-27 06:01:44 UTC, for which we identify signatures consistent with a propagating surface ripple. In order to demonstrate the differences between ripples at quasi-perpendicular and quasi-parallel shocks, we also present two-dimensional hybrid simulations over a range of shock normal angles θBn under the observed solar wind conditions. We show that in the quasi-parallel cases surface ripples are transient phenomena modulated by the cyclic reformation of the shock front. These ripples develop faster than an ion gyroperiod and only during the period of the reformation cycle when a newly developed shock ramp is unaffected by turbulence in the foot. We conclude that the change of properties of the surface ripple observed by MMS while crossing Earth's quasi-parallel bow shock are consistent with the influence of cyclic reformation on shock structure. Given that both surface ripples and cyclic reformation are expected to affect the acceleration of electrons within the shock, the interaction of these phenomena and any other sources of shock non-stationary are important for models of particle acceleration. We therefore discuss signatures of electron heating and acceleration in several rippled shocks observed by MMS.

Efficient electron open boundaries for simulating electrochemical cells

NASA Astrophysics Data System (ADS)

Zauchner, Mario G.; Horsfield, Andrew P.; Todorov, Tchavdar N.

2018-01-01

Nonequilibrium electrochemistry raises new challenges for atomistic simulation: we need to perform molecular dynamics for the nuclear degrees of freedom with an explicit description of the electrons, which in turn must be free to enter and leave the computational cell. Here we present a limiting form for electron open boundaries that we expect to apply when the magnitude of the electric current is determined by the drift and diffusion of ions in a solution and which is sufficiently computationally efficient to be used with molecular dynamics. We present tight-binding simulations of a parallel-plate capacitor with nothing, a dimer, or an atomic wire situated in the space between the plates. These simulations demonstrate that this scheme can be used to perform molecular dynamics simulations when there is an applied bias between two metal plates with, at most, weak electronic coupling between them. This simple system captures some of the essential features of an electrochemical cell, suggesting this approach might be suitable for simulations of electrochemical cells out of equilibrium.

Analysis of rapid increase in the plasma density during the ramp-up phase in a radio frequency negative ion source by large-scale particle simulation

NASA Astrophysics Data System (ADS)

Yasumoto, M.; Ohta, M.; Kawamura, Y.; Hatayama, A.

2014-02-01

Numerical simulations become useful for the developing RF-ICP (Radio Frequency Inductively Coupled Plasma) negative ion sources. We are developing and parallelizing a two-dimensional three velocity electromagnetic Particle-In-Cell code. The result shows rapid increase in the electron density during the density ramp-up phase. A radial electric field due to the space charge is produced with increase in the electron density and the electron transport in the radial direction is suppressed. As a result, electrons stay for a long period in the region where the inductive electric field is strong, and this leads efficient electron acceleration and a rapid increasing of the electron density.

Formalization, equivalence and generalization of basic resonance electrical circuits

NASA Astrophysics Data System (ADS)

Penev, Dimitar; Arnaudov, Dimitar; Hinov, Nikolay

2017-12-01

In the work are presented basic resonance circuits, which are used in resonance energy converters. The following resonant circuits are considered: serial, serial with parallel load parallel capacitor, parallel and parallel with serial loaded inductance. For the circuits under consideration, expressions are generated for the frequencies of own oscillations and for the equivalence of the active power emitted in the load. Mathematical expressions are graphically constructed and verified using computer simulations. The results obtained are used in the model based design of resonant energy converters with DC or AC output. This guaranteed the output indicators of power electronic devices.

Nonlinear damping of oblique whistler mode waves through Landau resonance

NASA Astrophysics Data System (ADS)

Hsieh, Y.; Omura, Y.

2017-12-01

Nonlinear trapping of electrons through Landau resonance is a characteristic dynamics in oblique whistler-mode wave particle interactions. The resonance velocity of the Landau resonance at quasi-parallel propagation becomes very close to the parallel group velocity of whistler-mode wave at frequency around 0.5 Ωe, causing a long distance of resonant interaction and strong acceleration of resonant electrons [1]. We demonstrate these effective accelerations for electrons with high equatorial pitch angle ( > 60°) by test particle simulations with parameters for the Earth's inner magnetosphere at L=5. In the simulations, we focus on slightly oblique whistler mode waves with wave normal angle < 20°. Analyzing the wave electric field E and the resonant current J, which is composed of electrons undergoing the Landau resonance, we find that the J·E is mainly positive, which denotes the damping of the wave. Furthermore, we confirm that this positive J•E is dominated by transverse component Jperp·Eperp rather than by longitudinal component Jpara·Eperp. The simulation results reveal that the Landau resonance contributes to the nonlinear damping at 0.5 Ωe for whistler mode waves. Reference [1] Hsieh, Y.-K., and Y. Omura (2017), Nonlinear dynamics of electrons interacting with oblique whistler mode chorus in the magnetosphere, J. Geophys. Res. Space Physics, 122, doi:10.1002/2016JA023255.

Xyce Parallel Electronic Simulator - Users' Guide Version 2.1.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, Scott A; Hoekstra, Robert J.; Russo, Thomas V.

This manual describes the use of theXyceParallel Electronic Simulator.Xycehasbeen designed as a SPICE-compatible, high-performance analog circuit simulator, andhas been written to support the simulation needs of the Sandia National Laboratorieselectrical designers. This development has focused on improving capability over thecurrent state-of-the-art in the following areas:%04Capability to solve extremely large circuit problems by supporting large-scale par-allel computing platforms (up to thousands of processors). Note that this includessupport for most popular parallel and serial computers.%04Improved performance for all numerical kernels (e.g., time integrator, nonlinearand linear solvers) through state-of-the-art algorithms and novel techniques.%04Device models which are specifically tailored to meet Sandia's needs, includingmanymore » radiation-aware devices.3 XyceTMUsers' Guide%04Object-oriented code design and implementation using modern coding practicesthat ensure that theXyceParallel Electronic Simulator will be maintainable andextensible far into the future.Xyceis a parallel code in the most general sense of the phrase - a message passingparallel implementation - which allows it to run efficiently on the widest possible numberof computing platforms. These include serial, shared-memory and distributed-memoryparallel as well as heterogeneous platforms. Careful attention has been paid to thespecific nature of circuit-simulation problems to ensure that optimal parallel efficiencyis achieved as the number of processors grows.The development ofXyceprovides a platform for computational research and de-velopment aimed specifically at the needs of the Laboratory. WithXyce, Sandia hasan %22in-house%22 capability with which both new electrical (e.g., device model develop-ment) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms)research and development can be performed. As a result,Xyceis a unique electricalsimulation capability, designed to meet the unique needs of the laboratory.4 XyceTMUsers' GuideAcknowledgementsThe authors would like to acknowledge the entire Sandia National Laboratories HPEMS(High Performance Electrical Modeling and Simulation) team, including Steve Wix, CarolynBogdan, Regina Schells, Ken Marx, Steve Brandon and Bill Ballard, for their support onthis project. We also appreciate very much the work of Jim Emery, Becky Arnold and MikeWilliamson for the help in reviewing this document.Lastly, a very special thanks to Hue Lai for typesetting this document with LATEX.TrademarksThe information herein is subject to change without notice.Copyrightc 2002-2003 Sandia Corporation. All rights reserved.XyceTMElectronic Simulator andXyceTMtrademarks of Sandia Corporation.Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence DesignSystems, Inc.Silicon Graphics, the Silicon Graphics logo and IRIX are registered trademarks of SiliconGraphics, Inc.Microsoft, Windows and Windows 2000 are registered trademark of Microsoft Corporation.Solaris and UltraSPARC are registered trademarks of Sun Microsystems Corporation.Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation.HP and Alpha are registered trademarks of Hewlett-Packard company.Amtec and TecPlot are trademarks of Amtec Engineering, Inc.Xyce's expression library is based on that inside Spice 3F5 developed by the EECS De-partment at the University of California.All other trademarks are property of their respective owners.ContactsBug Reportshttp://tvrusso.sandia.gov/bugzillaEmailxyce-support%40sandia.govWorld Wide Webhttp://www.cs.sandia.gov/xyce5 XyceTMUsers' GuideThis page is left intentionally blank6« less

Xyce parallel electronic simulator design.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thornquist, Heidi K.; Rankin, Eric Lamont; Mei, Ting

2010-09-01

This document is the Xyce Circuit Simulator developer guide. Xyce has been designed from the 'ground up' to be a SPICE-compatible, distributed memory parallel circuit simulator. While it is in many respects a research code, Xyce is intended to be a production simulator. As such, having software quality engineering (SQE) procedures in place to insure a high level of code quality and robustness are essential. Version control, issue tracking customer support, C++ style guildlines and the Xyce release process are all described. The Xyce Parallel Electronic Simulator has been under development at Sandia since 1999. Historically, Xyce has mostly beenmore » funded by ASC, the original focus of Xyce development has primarily been related to circuits for nuclear weapons. However, this has not been the only focus and it is expected that the project will diversify. Like many ASC projects, Xyce is a group development effort, which involves a number of researchers, engineers, scientists, mathmaticians and computer scientists. In addition to diversity of background, it is to be expected on long term projects for there to be a certain amount of staff turnover, as people move on to different projects. As a result, it is very important that the project maintain high software quality standards. The point of this document is to formally document a number of the software quality practices followed by the Xyce team in one place. Also, it is hoped that this document will be a good source of information for new developers.« less

Three axis electronic flight motion simulator real time control system design and implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Zhiyuan; Miao, Zhonghua, E-mail: zhonghua-miao@163.com; Wang, Xiaohua

2014-12-15

A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system.

Three axis electronic flight motion simulator real time control system design and implementation.

PubMed

Gao, Zhiyuan; Miao, Zhonghua; Wang, Xuyong; Wang, Xiaohua

2014-12-01

A three axis electronic flight motion simulator is reported in this paper including the modelling, the controller design as well as the hardware implementation. This flight motion simulator could be used for inertial navigation test and high precision inertial navigation system with good dynamic and static performances. A real time control system is designed, several control system implementation problems were solved including time unification with parallel port interrupt, high speed finding-zero method of rotary inductosyn, zero-crossing management with continuous rotary, etc. Tests were carried out to show the effectiveness of the proposed real time control system.

Tempest Neoclassical Simulation of Fusion Edge Plasmas

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Cohen, B. I.; Cohen, R. H.; Dorr, M.; Hittinger, J.; Kerbel, G. D.; Nevins, W. M.; Rognlien, T. D.

2006-04-01

We are developing a continuum gyrokinetic full-F code, TEMPEST, to simulate edge plasmas. The geometry is that of a fully diverted tokamak and so includes boundary conditions for both closed magnetic flux surfaces and open field lines. The code, presently 4-dimensional (2D2V), includes kinetic ions and electrons, a gyrokinetic Poisson solver for electric field, and the nonlinear Fokker-Planck collision operator. Here we present the simulation results of neoclassical transport with Boltzmann electrons. In a large aspect ratio circular geometry, excellent agreement is found for neoclassical equilibrium with parallel flows in the banana regime without a temperature gradient. In divertor geometry, it is found that the endloss of particles and energy induces pedestal-like density and temperature profiles inside the magnetic separatrix and parallel flow stronger than the neoclassical predictions in the SOL. The impact of the X-point divertor geometry on the self-consistent electric field and geo-acoustic oscillations will be reported. We will also discuss the status of extending TEMPEST into a 5-D code.

Magnetospheric Multiscale Observations of Large-Amplitude Parallel, Electrostatic Waves Associated with Magnetic Reconnection at the Magnetopause

NASA Technical Reports Server (NTRS)

Ergun, R. E.; Holmes, J. C.; Goodrich, K. A.; Wilder, F. D.; Stawarz, J. E.; Eriksson, S.; Newman, D. L.; Schwartz, S. J.; Goldman, M. V.; Sturner, A. P.;

Nonlinear Evolution of Counter-Propagating Whistler Mode Waves Excited by Anisotropic Electrons Within the Equatorial Source Region: 1-D PIC Simulations

NASA Astrophysics Data System (ADS)

Chen, Huayue; Gao, Xinliang; Lu, Quanming; Sun, Jicheng; Wang, Shui

2018-02-01

Nonlinear physical processes related to whistler mode waves are attracting more and more attention for their significant role in reshaping whistler mode spectra in the Earth's magnetosphere. Using a 1-D particle-in-cell simulation model, we have investigated the nonlinear evolution of parallel counter-propagating whistler mode waves excited by anisotropic electrons within the equatorial source region. In our simulations, after the linear phase of whistler mode instability, the strong electrostatic standing structures along the background magnetic field will be formed, resulting from the coupling between excited counter-propagating whistler mode waves. The wave numbers of electrostatic standing structures are about twice those of whistler mode waves generated by anisotropic hot electrons. Moreover, these electrostatic standing structures can further be coupled with either parallel or antiparallel propagating whistler mode waves to excite high-k modes in this plasma system. Compared with excited whistler mode waves, these high-k modes typically have 3 times wave number, same frequency, and about 2 orders of magnitude smaller amplitude. Our study may provide a fresh view on the evolution of whistler mode waves within their equatorial source regions in the Earth's magnetosphere.

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Kinetic Alfven turbulence: Electron and ion heating by particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Gary, S. P.; Hughes, R. S.; Wang, J.; Parashar, T. N.

2017-12-01

Three-dimensional particle-in-cell simulations of the forward cascade of decaying kinetic Alfvén turbulence have been carried out as an initial-value problem on a collisionless, homogeneous, magnetized, electron-ion plasma model with betae = betai =0.50 and mi/me=100 where subscripts e and i represent electrons and ions respectively. Initial anisotropic narrowband spectra of relatively long wavelength modes with approximately gyrotropic distributions in kperp undergo a forward cascade to broadband spectra of magnetic fluctuations at shorter wavelengths. Maximum electron and ion heating rates are computed as functions of the initial fluctuating magnetic field energy density eo on the range 0.05 < eo < 0.50. In contrast to dissipation by whistler turbulence, the maximum ion heating rate due to kinetic Alfvén turbulence is substantially greater than the maximum electron heating rate. Furthermore, ion heating as well as electron heating due to kinetic Alfvén turbulence scale approximately with eo. Finally, electron heating leads to anisotropies of the type T||e> Tperpe where the parallel and perpendicular symbols refer to directions parallel and perpendicular, respectively, to the background magnetic field, whereas the heated ions remain relatively isotropic. This implies that, for the range of eo values considered, the Landau wave-particle resonance is a likely heating mechanism for the electrons and may also contribute to ion heating.

Reversible electron heating vs. wave-particle interactions in quasi-perpendicular shocks

NASA Technical Reports Server (NTRS)

Veltri, P.; Mangeney, A.; Scudder, J. D.

1992-01-01

The energy necessary to explain the electron heating in quasi-perpendicular collisionless shocks can be derived either from the electron acceleration in the d.c. cross shock electric potential, or by the interactions between the electrons and the waves existing in the shock. A Monte Carlo simulation has been performed to study the electron distribution function evolution through the shock structure, with and without particle diffusion on waves. This simulation has allowed us to clarify the relative importance of the two possible energy sources; in particular it has been shown that the electron parallel temperature is determined by the d.c. electromagnetic field and not by any wave-particle-induced heating. Wave particle interactions are effective in smoothing out the large gradients in phase space produced by the 'reversible' motion of the electrons, thus producing a 'cooling' of the electrons.

Parallelization of a Monte Carlo particle transport simulation code

NASA Astrophysics Data System (ADS)

Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

2010-05-01

We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

Predicting mesoscale microstructural evolution in electron beam welding

DOE PAGES

Rodgers, Theron M.; Madison, Jonathan D.; Tikare, Veena; ...

2016-03-16

Using the kinetic Monte Carlo simulator, Stochastic Parallel PARticle Kinetic Simulator, from Sandia National Laboratories, a user routine has been developed to simulate mesoscale predictions of a grain structure near a moving heat source. Here, we demonstrate the use of this user routine to produce voxelized, synthetic, three-dimensional microstructures for electron-beam welding by comparing them with experimentally produced microstructures. When simulation input parameters are matched to experimental process parameters, qualitative and quantitative agreement for both grain size and grain morphology are achieved. The method is capable of simulating both single- and multipass welds. As a result, the simulations provide anmore » opportunity for not only accelerated design but also the integration of simulation and experiments in design such that simulations can receive parameter bounds from experiments and, in turn, provide predictions of a resultant microstructure.« less

Physics Computing '92: Proceedings of the 4th International Conference

NASA Astrophysics Data System (ADS)

de Groot, Robert A.; Nadrchal, Jaroslav

1993-04-01

The Table of Contents for the book is as follows: * Preface * INVITED PAPERS * Ab Initio Theoretical Approaches to the Structural, Electronic and Vibrational Properties of Small Clusters and Fullerenes: The State of the Art * Neural Multigrid Methods for Gauge Theories and Other Disordered Systems * Multicanonical Monte Carlo Simulations * On the Use of the Symbolic Language Maple in Physics and Chemistry: Several Examples * Nonequilibrium Phase Transitions in Catalysis and Population Models * Computer Algebra, Symmetry Analysis and Integrability of Nonlinear Evolution Equations * The Path-Integral Quantum Simulation of Hydrogen in Metals * Digital Optical Computing: A New Approach of Systolic Arrays Based on Coherence Modulation of Light and Integrated Optics Technology * Molecular Dynamics Simulations of Granular Materials * Numerical Implementation of a K.A.M. Algorithm * Quasi-Monte Carlo, Quasi-Random Numbers and Quasi-Error Estimates * What Can We Learn from QMC Simulations * Physics of Fluctuating Membranes * Plato, Apollonius, and Klein: Playing with Spheres * Steady States in Nonequilibrium Lattice Systems * CONVODE: A REDUCE Package for Differential Equations * Chaos in Coupled Rotators * Symplectic Numerical Methods for Hamiltonian Problems * Computer Simulations of Surfactant Self Assembly * High-dimensional and Very Large Cellular Automata for Immunological Shape Space * A Review of the Lattice Boltzmann Method * Electronic Structure of Solids in the Self-interaction Corrected Local-spin-density Approximation * Dedicated Computers for Lattice Gauge Theory Simulations * Physics Education: A Survey of Problems and Possible Solutions * Parallel Computing and Electronic-Structure Theory * High Precision Simulation Techniques for Lattice Field Theory * CONTRIBUTED PAPERS * Case Study of Microscale Hydrodynamics Using Molecular Dynamics and Lattice Gas Methods * Computer Modelling of the Structural and Electronic Properties of the Supported Metal Catalysis * Ordered Particle Simulations for Serial and MIMD Parallel Computers * "NOLP" -- Program Package for Laser Plasma Nonlinear Optics * Algorithms to Solve Nonlinear Least Square Problems * Distribution of Hydrogen Atoms in Pd-H Computed by Molecular Dynamics * A Ray Tracing of Optical System for Protein Crystallography Beamline at Storage Ring-SIBERIA-2 * Vibrational Properties of a Pseudobinary Linear Chain with Correlated Substitutional Disorder * Application of the Software Package Mathematica in Generalized Master Equation Method * Linelist: An Interactive Program for Analysing Beam-foil Spectra * GROMACS: A Parallel Computer for Molecular Dynamics Simulations * GROMACS Method of Virial Calculation Using a Single Sum * The Interactive Program for the Solution of the Laplace Equation with the Elimination of Singularities for Boundary Functions * Random-Number Generators: Testing Procedures and Comparison of RNG Algorithms * Micro-TOPIC: A Tokamak Plasma Impurities Code * Rotational Molecular Scattering Calculations * Orthonormal Polynomial Method for Calibrating of Cryogenic Temperature Sensors * Frame-based System Representing Basis of Physics * The Role of Massively Data-parallel Computers in Large Scale Molecular Dynamics Simulations * Short-range Molecular Dynamics on a Network of Processors and Workstations * An Algorithm for Higher-order Perturbation Theory in Radiative Transfer Computations * Hydrostochastics: The Master Equation Formulation of Fluid Dynamics * HPP Lattice Gas on Transputers and Networked Workstations * Study on the Hysteresis Cycle Simulation Using Modeling with Different Functions on Intervals * Refined Pruning Techniques for Feed-forward Neural Networks * Random Walk Simulation of the Motion of Transient Charges in Photoconductors * The Optical Hysteresis in Hydrogenated Amorphous Silicon * Diffusion Monte Carlo Analysis of Modern Interatomic Potentials for He * A Parallel Strategy for Molecular Dynamics Simulations of Polar Liquids on Transputer Arrays * Distribution of Ions Reflected on Rough Surfaces * The Study of Step Density Distribution During Molecular Beam Epitaxy Growth: Monte Carlo Computer Simulation * Towards a Formal Approach to the Construction of Large-scale Scientific Applications Software * Correlated Random Walk and Discrete Modelling of Propagation through Inhomogeneous Media * Teaching Plasma Physics Simulation * A Theoretical Determination of the Au-Ni Phase Diagram * Boson and Fermion Kinetics in One-dimensional Lattices * Computational Physics Course on the Technical University * Symbolic Computations in Simulation Code Development and Femtosecond-pulse Laser-plasma Interaction Studies * Computer Algebra and Integrated Computing Systems in Education of Physical Sciences * Coordinated System of Programs for Undergraduate Physics Instruction * Program Package MIRIAM and Atomic Physics of Extreme Systems * High Energy Physics Simulation on the T_Node * The Chapman-Kolmogorov Equation as Representation of Huygens' Principle and the Monolithic Self-consistent Numerical Modelling of Lasers * Authoring System for Simulation Developments * Molecular Dynamics Study of Ion Charge Effects in the Structure of Ionic Crystals * A Computational Physics Introductory Course * Computer Calculation of Substrate Temperature Field in MBE System * Multimagnetical Simulation of the Ising Model in Two and Three Dimensions * Failure of the CTRW Treatment of the Quasicoherent Excitation Transfer * Implementation of a Parallel Conjugate Gradient Method for Simulation of Elastic Light Scattering * Algorithms for Study of Thin Film Growth * Algorithms and Programs for Physics Teaching in Romanian Technical Universities * Multicanonical Simulation of 1st order Transitions: Interface Tension of the 2D 7-State Potts Model * Two Numerical Methods for the Calculation of Periodic Orbits in Hamiltonian Systems * Chaotic Behavior in a Probabilistic Cellular Automata? * Wave Optics Computing by a Networked-based Vector Wave Automaton * Tensor Manipulation Package in REDUCE * Propagation of Electromagnetic Pulses in Stratified Media * The Simple Molecular Dynamics Model for the Study of Thermalization of the Hot Nucleon Gas * Electron Spin Polarization in PdCo Alloys Calculated by KKR-CPA-LSD Method * Simulation Studies of Microscopic Droplet Spreading * A Vectorizable Algorithm for the Multicolor Successive Overrelaxation Method * Tetragonality of the CuAu I Lattice and Its Relation to Electronic Specific Heat and Spin Susceptibility * Computer Simulation of the Formation of Metallic Aggregates Produced by Chemical Reactions in Aqueous Solution * Scaling in Growth Models with Diffusion: A Monte Carlo Study * The Nucleus as the Mesoscopic System * Neural Network Computation as Dynamic System Simulation * First-principles Theory of Surface Segregation in Binary Alloys * Data Smooth Approximation Algorithm for Estimating the Temperature Dependence of the Ice Nucleation Rate * Genetic Algorithms in Optical Design * Application of 2D-FFT in the Study of Molecular Exchange Processes by NMR * Advanced Mobility Model for Electron Transport in P-Si Inversion Layers * Computer Simulation for Film Surfaces and its Fractal Dimension * Parallel Computation Techniques and the Structure of Catalyst Surfaces * Educational SW to Teach Digital Electronics and the Corresponding Text Book * Primitive Trinomials (Mod 2) Whose Degree is a Mersenne Exponent * Stochastic Modelisation and Parallel Computing * Remarks on the Hybrid Monte Carlo Algorithm for the ∫4 Model * An Experimental Computer Assisted Workbench for Physics Teaching * A Fully Implicit Code to Model Tokamak Plasma Edge Transport * EXPFIT: An Interactive Program for Automatic Beam-foil Decay Curve Analysis * Mapping Technique for Solving General, 1-D Hamiltonian Systems * Freeway Traffic, Cellular Automata, and Some (Self-Organizing) Criticality * Photonuclear Yield Analysis by Dynamic Programming * Incremental Representation of the Simply Connected Planar Curves * Self-convergence in Monte Carlo Methods * Adaptive Mesh Technique for Shock Wave Propagation * Simulation of Supersonic Coronal Streams and Their Interaction with the Solar Wind * The Nature of Chaos in Two Systems of Ordinary Nonlinear Differential Equations * Considerations of a Window-shopper * Interpretation of Data Obtained by RTP 4-Channel Pulsed Radar Reflectometer Using a Multi Layer Perceptron * Statistics of Lattice Bosons for Finite Systems * Fractal Based Image Compression with Affine Transformations * Algorithmic Studies on Simulation Codes for Heavy-ion Reactions * An Energy-Wise Computer Simulation of DNA-Ion-Water Interactions Explains the Abnormal Structure of Poly[d(A)]:Poly[d(T)] * Computer Simulation Study of Kosterlitz-Thouless-Like Transitions * Problem-oriented Software Package GUN-EBT for Computer Simulation of Beam Formation and Transport in Technological Electron-Optical Systems * Parallelization of a Boundary Value Solver and its Application in Nonlinear Dynamics * The Symbolic Classification of Real Four-dimensional Lie Algebras * Short, Singular Pulses Generation by a Dye Laser at Two Wavelengths Simultaneously * Quantum Monte Carlo Simulations of the Apex-Oxygen-Model * Approximation Procedures for the Axial Symmetric Static Einstein-Maxwell-Higgs Theory * Crystallization on a Sphere: Parallel Simulation on a Transputer Network * FAMULUS: A Software Product (also) for Physics Education * MathCAD vs. FAMULUS -- A Brief Comparison * First-principles Dynamics Used to Study Dissociative Chemisorption * A Computer Controlled System for Crystal Growth from Melt * A Time Resolved Spectroscopic Method for Short Pulsed Particle Emission * Green's Function Computation in Radiative Transfer Theory * Random Search Optimization Technique for One-criteria and Multi-criteria Problems * Hartley Transform Applications to Thermal Drift Elimination in Scanning Tunneling Microscopy * Algorithms of Measuring, Processing and Interpretation of Experimental Data Obtained with Scanning Tunneling Microscope * Time-dependent Atom-surface Interactions * Local and Global Minima on Molecular Potential Energy Surfaces: An Example of N3 Radical * Computation of Bifurcation Surfaces * Symbolic Computations in Quantum Mechanics: Energies in Next-to-solvable Systems * A Tool for RTP Reactor and Lamp Field Design * Modelling of Particle Spectra for the Analysis of Solid State Surface * List of Participants

Probing plasma wakefields using electron bunches generated from a laser wakefield accelerator

NASA Astrophysics Data System (ADS)

Zhang, C. J.; Wan, Y.; Guo, B.; Hua, J. F.; Pai, C.-H.; Li, F.; Zhang, J.; Ma, Y.; Wu, Y. P.; Xu, X. L.; Mori, W. B.; Chu, H.-H.; Wang, J.; Lu, W.; Joshi, C.

2018-04-01

We show experimental results of probing the electric field structure of plasma wakes by using femtosecond relativistic electron bunches generated from a laser wakefield accelerator. Snapshots of laser-driven linear wakes in plasmas with different densities and density gradients are captured. The spatiotemporal evolution of the wake in a plasma density up-ramp is recorded. Two parallel wakes driven by a laser with a main spot and sidelobes are identified in the experiment and reproduced in simulations. The capability of this new method for capturing the electron- and positron-driven wakes is also shown via 3D particle-in-cell simulations.

STEMsalabim: A high-performance computing cluster friendly code for scanning transmission electron microscopy image simulations of thin specimens.

PubMed

Oelerich, Jan Oliver; Duschek, Lennart; Belz, Jürgen; Beyer, Andreas; Baranovskii, Sergei D; Volz, Kerstin

2017-06-01

We present a new multislice code for the computer simulation of scanning transmission electron microscope (STEM) images based on the frozen lattice approximation. Unlike existing software packages, the code is optimized to perform well on highly parallelized computing clusters, combining distributed and shared memory architectures. This enables efficient calculation of large lateral scanning areas of the specimen within the frozen lattice approximation and fine-grained sweeps of parameter space. Copyright © 2017 Elsevier B.V. All rights reserved.

OSIRIS - an object-oriented parallel 3D PIC code for modeling laser and particle beam-plasma interaction

NASA Astrophysics Data System (ADS)

Hemker, Roy

1999-11-01

The advances in computational speed make it now possible to do full 3D PIC simulations of laser plasma and beam plasma interactions, but at the same time the increased complexity of these problems makes it necessary to apply modern approaches like object oriented programming to the development of simulation codes. We report here on our progress in developing an object oriented parallel 3D PIC code using Fortran 90. In its current state the code contains algorithms for 1D, 2D, and 3D simulations in cartesian coordinates and for 2D cylindrically-symmetric geometry. For all of these algorithms the code allows for a moving simulation window and arbitrary domain decomposition for any number of dimensions. Recent 3D simulation results on the propagation of intense laser and electron beams through plasmas will be presented.

Collisionless dissipation processes in quasi-parallel shocks. [in solar wind

NASA Technical Reports Server (NTRS)

Quest, K. B.; Forslund, D. W.; Brackbill, J. U.; Lee, K.

1983-01-01

The evolution of collisionless, quasi-parallel shocks (the angle between the shock normal and the upstream magnetic field being less than 45 deg) is examined using two dimensional particle simulations. Reflected ions upstream from the shock are observed with average guiding center velocity and gyrational energy which agree well with the prediction of simple specular reflection. Strong ion heating through the shock ramp is apparently caused by large amplitude whistler turbulence. A flux of suprathermal electrons is also the magnetic field direction. Much stronger ion heating occurs in the shock than electron heating. The relevance of this work to the earth's bow shock is discussed.

Electron scale magnetic reconnection in the turbulent magnetosheath: Kinetic PIC simulation study

NASA Astrophysics Data System (ADS)

Sharma, P.; Shay, M. A.; Drake, J. F.; Phan, T.; Haggerty, C. C.; TenBarge, J. M.; Cassak, P.; Swisdak, M.

2017-12-01

Recent MMS observations have revealed electron scale reconnection in the turbulent magnetosheath. Surprisingly, although one of the reconnection events is associated with a very strong guide field, the ions show no coupling to the reconnection dynamics. We first review the MMS observations. Then, using kinetic PIC simulations with similar plasma conditions, we study reconnection at electron scales and show that the reconnection exhibits whistler-like dynamics similar to the case of anti-parallel reconnection rather than the kinetic Alfven wave dynamics that is often associated with reconnection with a strong guide field. We study the factors controlling this behavior and discuss the implications for reconnection and turbulence at electron scales in both the magnetosheath and solar wind.

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE PAGES

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-10-25

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy.

PubMed

Pryor, Alan; Ophus, Colin; Miao, Jianwei

2017-01-01

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic , using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic .

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pryor, Alan; Ophus, Colin; Miao, Jianwei

Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. In this paper, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000 × for PRISM and 15 × for multislice are achieved relative to traditionalmore » multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic.« less

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

NASA Astrophysics Data System (ADS)

Andrade, Xavier; Strubbe, David; De Giovannini, Umberto; Larsen, Ask Hjorth; Oliveira, Micael J. T.; Alberdi-Rodriguez, Joseba; Varas, Alejandro; Theophilou, Iris; Helbig, Nicole; Verstraete, Matthieu J.; Stella, Lorenzo; Nogueira, Fernando; Aspuru-Guzik, Alán; Castro, Alberto; Marques, Miguel A. L.; Rubio, Angel

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schr\\"odinger equation for low-dimensionality systems.

The Relation between Reconnected Flux, the Parallel Electric Field, and the Reconnection Rate in a Three-Dimensional Kinetic Simulation of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Wendel, D. E.; Olson, D. K.; Hesse, M.; Karimabadi, H.; Daughton, W. S.

2013-12-01

We investigate the distribution of parallel electric fields and their relationship to the location and rate of magnetic reconnection of a large particle-in-cell simulation of 3D turbulent magnetic reconnection with open boundary conditions. The simulation's guide field geometry inhibits the formation of topological features such as separators and null points. Therefore, we derive the location of potential changes in magnetic connectivity by finding the field lines that experience a large relative change between their endpoints, i.e., the quasi-separatrix layer. We find a correspondence between the locus of changes in magnetic connectivity, or the quasi-separatrix layer, and the map of large gradients in the integrated parallel electric field (or quasi-potential). Furthermore, we compare the distribution of parallel electric fields along field lines with the reconnection rate. We find the reconnection rate is controlled by only the low-amplitude, zeroth and first-order trends in the parallel electric field, while the contribution from high amplitude parallel fluctuations, such as electron holes, is negligible. The results impact the determination of reconnection sites within models of 3D turbulent reconnection as well as the inference of reconnection rates from in situ spacecraft measurements. It is difficult through direct observation to isolate the locus of the reconnection parallel electric field amidst the large amplitude fluctuations. However, we demonstrate that a positive slope of the partial sum of the parallel electric field along the field line as a function of field line length indicates where reconnection is occurring along the field line.

Electron heating in quasi-perpendicular shocks - A Monte Carlo simulation

NASA Technical Reports Server (NTRS)

Veltri, Pierluigi; Mangeney, Andre; Scudder, Jack D.

1990-01-01

To study the problem of electron heating in quasi-perpendicular shocks, under the combined effects of 'reversible' motion, in the shock electric potential and magnetic field, and wave-particle interactions a diffusion equation was derived, in the drift (adiabatic) approximation and it was solved by using a Monte Carlo method. The results show that most of the observations can be explained within this framework. The simulation has also definitively shown that the electron parallel temperature is determined by the dc electromagnetic field and not by any wave particle induced heating. Wave-particle interactions are effective in smoothing out the large gradients in phase space produced by the 'reversible' motion of the electrons, thus producing a 'cooling' of the electrons. Some constraints on the wave-particle interaction process may be obtained from a detailed comparison between the simulation and observations. In particular, it appears that the adiabatic approximation must be violated in order to explain the observed evolution of the perpendicular temperature.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.

PubMed

Martins-Costa, Marilia T C; Ruiz-López, Manuel F

2017-04-15

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Simulation of self-generated magnetic fields in an inertial fusion hohlraum environment

DOE PAGES

Farmer, W. A.; Koning, J. M.; Strozzi, D. J.; ...

2017-05-09

Here, we present radiation-hydrodynamic simulations of self-generated magnetic field in a hohlraum, which show an increased temperature in large regions of the underdense fill. Non-parallel gradients in electron density and temperature in a laser-heated plasma give rise to a self-generated field by the “Biermann battery” mechanism. Here, HYDRA simulations of three hohlraum designs on the National Ignition Facility are reported, which use a partial magnetohydrodynamic (MHD) description that includes the self-generated source term, resistive dissipation, and advection of the field due to both the plasma flow and the Nernst term. Anisotropic electron heat conduction parallel and perpendicular to the fieldmore » is included, but not the Righi-Leduc heat flux. The field strength is too small to compete significantly with plasma pressure, but affects plasma conditions by reducing electron heat conduction perpendicular to the field. Significant reductions in heat flux can occur, especially for high Z plasma, at modest values of the Hall parameter, Ω eτ ei≲1, where Ω e = eB/m ec and τ ei is the electron-ion collision time. The inclusion of MHD in the simulations leads to 1 keV hotter electron temperatures in the laser entrance hole and high- Z wall blowoff, which reduces inverse-bremsstrahlung absorption of the laser beam. This improves propagation of the inner beams pointed at the hohlraum equator, resulting in a symmetry shift of the resulting capsule implosion towards a more prolate shape. The time of peak x-ray production in the capsule shifts later by only 70 ps (within experimental uncertainty), but a decomposition of the hotspot shape into Legendre moments indicates a shift of P 2/P 0 by ~20%. As a result, this indicates that MHD cannot explain why simulated x-ray drive exceeds measured levels, but may be partially responsible for failures to correctly model the symmetry.« less

Simulation of self-generated magnetic fields in an inertial fusion hohlraum environment

NASA Astrophysics Data System (ADS)

Farmer, W. A.; Koning, J. M.; Strozzi, D. J.; Hinkel, D. E.; Berzak Hopkins, L. F.; Jones, O. S.; Rosen, M. D.

2017-05-01

We present radiation-hydrodynamic simulations of self-generated magnetic field in a hohlraum, which show an increased temperature in large regions of the underdense fill. Non-parallel gradients in electron density and temperature in a laser-heated plasma give rise to a self-generated field by the "Biermann battery" mechanism. Here, HYDRA simulations of three hohlraum designs on the National Ignition Facility are reported, which use a partial magnetohydrodynamic (MHD) description that includes the self-generated source term, resistive dissipation, and advection of the field due to both the plasma flow and the Nernst term. Anisotropic electron heat conduction parallel and perpendicular to the field is included, but not the Righi-Leduc heat flux. The field strength is too small to compete significantly with plasma pressure, but affects plasma conditions by reducing electron heat conduction perpendicular to the field. Significant reductions in heat flux can occur, especially for high Z plasma, at modest values of the Hall parameter, Ωeτei≲1 , where Ωe=e B /mec and τei is the electron-ion collision time. The inclusion of MHD in the simulations leads to 1 keV hotter electron temperatures in the laser entrance hole and high-Z wall blowoff, which reduces inverse-bremsstrahlung absorption of the laser beam. This improves propagation of the inner beams pointed at the hohlraum equator, resulting in a symmetry shift of the resulting capsule implosion towards a more prolate shape. The time of peak x-ray production in the capsule shifts later by only 70 ps (within experimental uncertainty), but a decomposition of the hotspot shape into Legendre moments indicates a shift of P2/P0 by ˜20 % . This indicates that MHD cannot explain why simulated x-ray drive exceeds measured levels, but may be partially responsible for failures to correctly model the symmetry.

A DSMC Study of Low Pressure Argon Discharge

NASA Astrophysics Data System (ADS)

Hash, David; Meyyappan, M.

1997-10-01

Work toward a self-consistent plasma simulation using the DSMC method for examination of the flowfields of low-pressure high density plasma reactors is presented. Presently, DSMC simulations for these applications involve either treating the electrons as a fluid or imposing experimentally determined values for the electron number density profile. In either approach, the electrons themselves are not physically simulated. Self-consistent plasma DSMC simulations have been conducted for aerospace applications but at a severe computational cost due in part to the scalar architectures on which the codes were employed. The present work attempts to conduct such simulations at a more reasonable cost using a plasma version of the object-oriented parallel Cornell DSMC code, MONACO, on an IBM SP-2. Due the availability of experimental data, the GEC reference cell is chosen to conduct preliminary investigations. An argon discharge is examined thus affording a simple chemistry set with eight gas-phase reactions and five species: Ar, Ar^+, Ar^*, Ar_2, and e where Ar^* is a metastable.

Electron Heating and Acceleration in a Reconnecting Magnetotail

NASA Astrophysics Data System (ADS)

El-Alaoui, M.; Zhou, M.; Lapenta, G.; Berchem, J.; Richard, R. L.; Schriver, D.; Walker, R. J.

2017-12-01

Electron heating and acceleration in the magnetotail have been investigated intensively. A major site for this process is the reconnection region. However, where and how the electrons are accelerated in a realistic three-dimensional X-line geometry is not fully understood. In this study, we employed a three-dimensional implicit particle-in-cell (iPIC3D) simulation and large-scale kinetic (LSK) simulation to address these problems. We modeled a magnetotail reconnection event observed by THEMIS in an iPIC3D simulation with initial and boundary conditions given by a global magnetohydrodynamic (MHD) simulation of Earth's magnetosphere. The iPIC3D simulation system includes the region of fast outflow emanating from the reconnection site that drives dipolarization fronts. We found that current sheet electrons exhibit elongated (cigar-shaped) velocity distributions with a higher parallel temperature. Using LSK we then followed millions of test electrons using the electromagnetic fields from iPIC3D. We found that magnetotail reconnection can generate power law spectra around the near-Earth X-line. A significant number of electrons with energies higher than 50 keV are produced. We identified several acceleration mechanisms at different locations that were responsible for energizing these electrons: non-adiabatic cross-tail drift, betatron and Fermi acceleration. Relative contributions to the energy gain of these high energy electrons from the different mechanisms will be discussed.

Magnetospheric Multiscale observations of large-amplitude, parallel, electrostatic waves associated with magnetic reconnection at the magnetopause

NASA Astrophysics Data System (ADS)

Ergun, R. E.; Holmes, J. C.; Goodrich, K. A.; Wilder, F. D.; Stawarz, J. E.; Eriksson, S.; Newman, D. L.; Schwartz, S. J.; Goldman, M. V.; Sturner, A. P.; Malaspina, D. M.; Usanova, M. E.; Torbert, R. B.; Argall, M.; Lindqvist, P.-A.; Khotyaintsev, Y.; Burch, J. L.; Strangeway, R. J.; Russell, C. T.; Pollock, C. J.; Giles, B. L.; Dorelli, J. J. C.; Avanov, L.; Hesse, M.; Chen, L. J.; Lavraud, B.; Le Contel, O.; Retino, A.; Phan, T. D.; Eastwood, J. P.; Oieroset, M.; Drake, J.; Shay, M. A.; Cassak, P. A.; Nakamura, R.; Zhou, M.; Ashour-Abdalla, M.; André, M.

2016-06-01

We report observations from the Magnetospheric Multiscale satellites of large-amplitude, parallel, electrostatic waves associated with magnetic reconnection at the Earth's magnetopause. The observed waves have parallel electric fields (E||) with amplitudes on the order of 100 mV/m and display nonlinear characteristics that suggest a possible net E||. These waves are observed within the ion diffusion region and adjacent to (within several electron skin depths) the electron diffusion region. They are in or near the magnetosphere side current layer. Simulation results support that the strong electrostatic linear and nonlinear wave activities appear to be driven by a two stream instability, which is a consequence of mixing cold (<10 eV) plasma in the magnetosphere with warm (~100 eV) plasma from the magnetosheath on a freshly reconnected magnetic field line. The frequent observation of these waves suggests that cold plasma is often present near the magnetopause.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

NASA Astrophysics Data System (ADS)

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-01

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0…tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution time/parallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

A simulation study of interactions of space-shuttle generated electron beams with ambient plasma and neutral gas

NASA Technical Reports Server (NTRS)

Winglee, Robert M.

1991-01-01

The objective was to conduct large scale simulations of electron beams injected into space. The study of the active injection of electron beams from spacecraft is important, as it provides valuable insight into the plasma beam interactions and the development of current systems in the ionosphere. However, the beam injection itself is not simple, being constrained by the ability of the spacecraft to draw current from the ambient plasma. The generation of these return currents is dependent on several factors, including the density of the ambient plasma relative to the beam density, the presence of neutrals around the spacecraft, the configuration of the spacecraft, and the motion of the spacecraft through the plasma. Two dimensional (three velocity) particle simulations with collisional processes included are used to show how these different and often coupled processes can be used to enhance beam propagation from the spacecraft. To understand the radial expansion mechanism of an electron beam injected from a highly charged spacecraft, two dimensional particle-in-cell simulations were conducted for a high density electron beam injected parallel to magnetic fields from an isolated equipotential conductor into a cold background plasma. The simulations indicate that charge build-up at the beam stagnation point causes the beam to expand radially to the beam electron gyroradius.

A simulation study of interactions of Space-Shuttle generated electron beams with ambient plasma and neutral gas

NASA Technical Reports Server (NTRS)

1991-01-01

The object was to conduct large scale simulations of electron beams injected into space. The study of active injection of electron beams from spacecraft is important since it provides valuable insight into beam-plasma interactions and the development of current systems in the ionosphere. However, the beam injection itself is not simple, being constrained by the ability of the spacecraft to draw return current from the ambient plasma. The generation of these return currents is dependent on several factors, including the density of the ambient plasma relative to the beam density, the presence of neutrals around the spacecraft, the configuration of the spacecraft, and the motion of the spacecraft through the plasma. Two dimensional particle simulations with collisional processes included are used to show how these different and often coupled processes can be utilized to enhance beam propagation from the spacecraft. To understand the radical expansion of mechanism of an electron beam from a highly charged spacecraft, two dimensional particle in cell simulations were conducted for a high density electron beam injected parallel to magnetic fields from an isolated equipotential conductor into a cold background plasma. The simulations indicate that charge buildup at the beam stagnation point causes the beam to expand radially to the beam electron gyroradius.

Generation of Highly Oblique Lower Band Chorus Via Nonlinear Three-Wave Resonance

DOE PAGES

Fu, Xiangrong; Gary, Stephen Peter; Reeves, Geoffrey D.; ...

2017-09-05

Chorus in the inner magnetosphere has been observed frequently at geomagnetically active times, typically exhibiting a two-band structure with a quasi-parallel lower band and an upper band with a broad range of wave normal angles. But recent observations by Van Allen Probes confirm another type of lower band chorus, which has a large wave normal angle close to the resonance cone angle. It has been proposed that these waves could be generated by a low-energy beam-like electron component or by temperature anisotropy of keV electrons in the presence of a low-energy plateau-like electron component. This paper, however, presents an alternativemore » mechanism for generation of this highly oblique lower band chorus. Through a nonlinear three-wave resonance, a quasi-parallel lower band chorus wave can interact with a mildly oblique upper band chorus wave, producing a highly oblique quasi-electrostatic lower band chorus wave. This theoretical analysis is confirmed by 2-D electromagnetic particle-in-cell simulations. Furthermore, as the newly generated waves propagate away from the equator, their wave normal angle can further increase and they are able to scatter low-energy electrons to form a plateau-like structure in the parallel velocity distribution. As a result, the three-wave resonance mechanism may also explain the generation of quasi-parallel upper band chorus which has also been observed in the magnetosphere.« less

The effect of asymmetrical electrode form after negative bias illuminated stress in amorphous IGZO thin film transistors

NASA Astrophysics Data System (ADS)

Su, Wan-Ching; Chang, Ting-Chang; Liao, Po-Yung; Chen, Yu-Jia; Chen, Bo-Wei; Hsieh, Tien-Yu; Yang, Chung-I.; Huang, Yen-Yu; Chang, Hsi-Ming; Chiang, Shin-Chuan; Chang, Kuan-Chang; Tsai, Tsung-Ming

2017-03-01

This paper investigates the degradation behavior of InGaZnO thin film transistors (TFTs) under negative bias illumination stress (NBIS). TFT devices with two different source and drain layouts were exanimated: one having a parallel format electrode and the other with UI format electrode. UI means that source/drain electrodes shapes is defined as a forked-shaped structure. The I-V curve of the parallel electrode exhibited a symmetric degradation under forward and reverse sweeping in the saturation region after 1000 s NBIS. In contrast, the I-V curve of the UI electrode structure under similar conditions was asymmetric. The UI electrode structure also shows a stretch-out phenomenon in its C-V measurement. Finally, this work utilizes the ISE-Technology Computer Aided Design (ISE-TCAD) system simulations, which simulate the electron field and IV curves, to analyze the mechanisms dominating the parallel and UI device degradation behaviors.

Parallel 3-D numerical simulation of dielectric barrier discharge plasma actuators

NASA Astrophysics Data System (ADS)

Houba, Tomas

Dielectric barrier discharge plasma actuators have shown promise in a range of applications including flow control, sterilization and ozone generation. Developing numerical models of plasma actuators is of great importance, because a high-fidelity parallel numerical model allows new design configurations to be tested rapidly. Additionally, it provides a better understanding of the plasma actuator physics which is useful for further innovation. The physics of plasma actuators is studied numerically. A loosely coupled approach is utilized for the coupling of the plasma to the neutral fluid. The state of the art in numerical plasma modeling is advanced by the development of a parallel, three-dimensional, first-principles model with detailed air chemistry. The model incorporates 7 charged species and 18 reactions, along with a solution of the electron energy equation. To the author's knowledge, a parallel three-dimensional model of a gas discharge with a detailed air chemistry model and the solution of electron energy is unique. Three representative geometries are studied using the gas discharge model. The discharge of gas between two parallel electrodes is used to validate the air chemistry model developed for the gas discharge code. The gas discharge model is then applied to the discharge produced by placing a dc powered wire and grounded plate electrodes in a channel. Finally, a three-dimensional simulation of gas discharge produced by electrodes placed inside a riblet is carried out. The body force calculated with the gas discharge model is loosely coupled with a fluid model to predict the induced flow inside the riblet.

Joint Services Electronics Program

DTIC Science & Technology

1991-03-05

Parallel Computing Network and Program Professor Abhiram Ranade with M.T. Raghunath and Robert Boothe The goal of our research is to develop high...References/Publications [1] M. T. Raghunath and A. 0. Ranade. "A Simulation-Based Comparison of Interconnection Networks," Proceedings of the 2nd IEEE

Electron acceleration in the Solar corona - 3D PiC code simulations of guide field reconnection

NASA Astrophysics Data System (ADS)

Alejandro Munoz Sepulveda, Patricio

2017-04-01

The efficient electron acceleration in the solar corona detected by means of hard X-ray emission is still not well understood. Magnetic reconnection through current sheets is one of the proposed production mechanisms of non-thermal electrons in solar flares. Previous works in this direction were based mostly on test particle calculations or 2D fully-kinetic PiC simulations. We have now studied the consequences of self-generated current-aligned instabilities on the electron acceleration mechanisms by 3D magnetic reconnection. For this sake, we carried out 3D Particle-in-Cell (PiC) code numerical simulations of force free reconnecting current sheets, appropriate for the description of the solar coronal plasmas. We find an efficient electron energization, evidenced by the formation of a non-thermal power-law tail with a hard spectral index smaller than -2 in the electron energy distribution function. We discuss and compare the influence of the parallel electric field versus the curvature and gradient drifts in the guiding-center approximation on the overall acceleration, and their dependence on different plasma parameters.

PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

NASA Astrophysics Data System (ADS)

Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

2017-01-01

We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

Current structure and flow pattern on the electron separatrix in reconnection region

NASA Astrophysics Data System (ADS)

Guo, Ruilong; Pu, Zuyin; Wei, Yong

2017-12-01

Results from 2.5D Particle-in-cell (PIC) simulations of symmetric reconnection with negligible guide field reveal that the accessible boundary of the electrons accelerated in the magnetic reconnection region is displayed by enhanced electron nongyrotropy downstream from the X-line. The boundary, hereafter termed the electron separatrix, occurs at a few d e (electron inertial length) away from the exhaust side of the magnetic separatrix. On the inflow side of the electron separatrix, the current is mainly carried by parallel accelerated electrons, served as the inflow region patch of the Hall current. The out-of-plane current density enhances at the electron separatrix. The dominating current carriers are the electrons, nongyrotropic distribution functions of which contribute significantly to the perpendicular electron velocity by increasing the electron diamagnetic drift velocity. When crossing the separatrix region where the Hall electric field is enhanced, electron velocity orientation is changed dramatically, which could be a diagnostic indicator to detect the electron separatrix. In the exhaust region, ions are the main carriers for the out-of-plane current, while the parallel current is still mainly carried by electrons. The current density peak in the separatrix region implies that a thin current sheet is formed apart from the neutral line, which can evolve to the bifurcated current sheet.

Single flux quantum voltage amplifiers

NASA Astrophysics Data System (ADS)

Golomidov, Vladimir; Kaplunenko, Vsevolod; Khabipov, Marat; Koshelets, Valery; Kaplunenko, Olga

The novel elements of the Rapid Single Flux Quantum (RSFQ) logic family — a Quasi Digital Voltage Parallel and Series Amplifiers (QDVA) have been computer simulated, designed and experimentally investigated. The Parallel QDVA consists of six stages and provides multiplication of the input voltage with factor five. The output resistance of the QDVA is five times larger than the input so this amplifier seems to be a good matching stage between RSFQL and usual semiconductor electronics. The series QDVA provides a gain factor four and involves two doublers connected by transmission line. The proposed parallel QDVA can be integrated on the same chip with a SQUID sensor.

Observations of electron vortex magnetic holes and related wave-particle interactions in the turbulent magnetosheath

NASA Astrophysics Data System (ADS)

Huang, S.; Sahraoui, F.; Yuan, Z.; He, J.; Zhao, J.; Du, J.; Le Contel, O.; Wang, X.; Deng, X.; Fu, H.; Zhou, M.; Shi, Q.; Breuillard, H.; Pang, Y.; Yu, X.; Wang, D.

2017-12-01

Magnetic hole is characterized by a magnetic depression, a density peak, a total electron temperature increase (with a parallel temperature decrease but a perpendicular temperature increase), and strong currents carried by the electrons. The current has a dip in the core region of the magnetic hole and a peak in the outer region of the magnetic hole. There is an enhancement in the perpendicular electron fluxes at 90° pitch angles inside the magnetic hole, implying that the electrons are trapped within it. The variations of the electron velocity components Vem and Ven suggest that an electron vortex is formed by trapping electrons inside the magnetic hole in the circular cross-section. These observations demonstrate the existence of a new type of coherent structures behaving as an electron vortex magnetic hole in turbulent space plasmas as predicted by recent kinetic simulations. We perform a statistically study using high time solution data from the MMS mission. The magnetic holes with short duration (i.e., < 0.5 s) have their cross section smaller than the ion gyro-radius. Superposed epoch analysis of all events reveals that an increase in the electron density and total temperature, significantly increase (resp. decrease) the electron perpendicular (resp. parallel) temperature, and an electron vortex inside the holes. Electron fluxes at 90° pitch angles with selective energies increase in the KSMHs, are trapped inside KSMHs and form the electron vortex due to their collective motion. All these features are consistent with the electron vortex magnetic holes obtained in 2D and 3D particle-in-cell simulations, indicating that the observed the magnetic holes seem to be best explained as electron vortex magnetic holes. It is furthermore shown that the magnetic holes are likely to heat and accelerate the electrons. We also investigate the coupling between whistler waves and electron vortex magnetic holes. These whistler waves can be locally generated inside electron vortex magnetic holes by electron temperature anisotropic instability.

Non-inductive current generation in fusion plasmas with turbulence

NASA Astrophysics Data System (ADS)

Wang, Weixing; Ethier, S.; Startsev, E.; Chen, J.; Hahm, T. S.; Yoo, M. G.

2017-10-01

It is found that plasma turbulence may strongly influence non-inductive current generation. This may have radical impact on various aspects of tokamak physics. Our simulation study employs a global gyrokinetic model coupling self-consistent neoclassical and turbulent dynamics with focus on electron current. Distinct phases in electron current generation are illustrated in the initial value simulation. In the early phase before turbulence develops, the electron bootstrap current is established in a time scale of a few electron collision times, which closely agrees with the neoclassical prediction. The second phase follows when turbulence begins to saturate, during which turbulent fluctuations are found to strongly affect electron current. The profile structure, amplitude and phase space structure of electron current density are all significantly modified relative to the neoclassical bootstrap current by the presence of turbulence. Both electron parallel acceleration and parallel residual stress drive are shown to play important roles in turbulence-induced current generation. The current density profile is modified in a way that correlates with the fluctuation intensity gradient through its effect on k//-symmetry breaking in fluctuation spectrum. Turbulence is shown to deduct (enhance) plasma self-generated current in low (high) collisionality regime, and the reduction of total electron current relative to the neoclassical bootstrap current increases as collisionality decreases. The implication of this result to the fully non-inductive current operation in steady state burning plasma regime should be investigated. Finally, significant non-inductive current is observed in flat pressure region, which is a nonlocal effect and results from turbulence spreading induced current diffusion. Work supported by U.S. DOE Contract DE-AC02-09-CH11466.

Telescience - Concepts and contributions to the Extreme Ultraviolet Explorer mission

NASA Technical Reports Server (NTRS)

Marchant, Will; Dobson, Carl; Chakrabarti, Supriya; Malina, Roger F.

1987-01-01

It is shown how the contradictory goals of low-cost and fast data turnaround characterizing the Extreme Ultraviolet Explorer (EUVE) mission can be achieved via the early use of telescience style transparent tools and simulations. The use of transparent tools reduces the parallel development of capability while ensuring that valuable prelaunch experience is not lost in the operations phase. Efforts made to upgrade the 'EUVE electronics' simulator are described.

Monte Carlo study of electron relaxation in graphene with spin polarized, degenerate electron gas in presence of electron-electron scattering

NASA Astrophysics Data System (ADS)

Borowik, Piotr; Thobel, Jean-Luc; Adamowicz, Leszek

2017-12-01

The Monte Carlo simulation method is applied to study the relaxation of excited electrons in monolayer graphene. The presence of spin polarized background electrons population, with density corresponding to highly degenerate conditions is assumed. Formulas of electron-electron scattering rates, which properly account for electrons presence in two energetically degenerate, inequivalent valleys in this material are presented. The electron relaxation process can be divided into two phases: thermalization and cooling, which can be clearly distinguished when examining the standard deviation of electron energy distribution. The influence of the exchange effect in interactions between electrons with parallel spins is shown to be important only in transient conditions, especially during the thermalization phase.

Xyce Parallel Electronic Simulator Reference Guide Version 6.4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Mei, Ting; Russo, Thomas V.

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TMmore » are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)« less

Electron hole tracking PIC simulation

NASA Astrophysics Data System (ADS)

Zhou, Chuteng; Hutchinson, Ian

2016-10-01

An electron hole is a coherent BGK mode solitary wave. Electron holes are observed to travel at high velocities relative to bulk plasmas. The kinematics of a 1-D electron hole is studied using a novel Particle-In-Cell simulation code with fully kinetic ions. A hole tracking technique enables us to follow the trajectory of a fast-moving solitary hole and study quantitatively hole acceleration and coupling to ions. The electron hole signal is detected and the simulation domain moves by a carefully designed feedback control law to follow its propagation. This approach has the advantage that the length of the simulation domain can be significantly reduced to several times the hole width, which makes high resolution simulations tractable. We observe a transient at the initial stage of hole formation when the hole accelerates to several times the cold-ion sound speed. Artificially imposing slow ion speed changes on a fully formed hole causes its velocity to change even when the ion stream speed in the hole frame greatly exceeds the ion thermal speed, so there are no reflected ions. The behavior that we observe in numerical simulations agrees very well with our analytic theory of hole momentum conservation and energization effects we call ``jetting''. The work was partially supported by the NSF/DOE Basic Plasma Science Partnership under Grant DE-SC0010491. Computer simulations were carried out on the MIT PSFC parallel AMD Opteron/Infiniband cluster Loki.

Development of a 1.5D plasma transport code for coupling to full orbit runaway electron simulations

NASA Astrophysics Data System (ADS)

Lore, J. D.; Del Castillo-Negrete, D.; Baylor, L.; Carbajal, L.

2017-10-01

A 1.5D (1D radial transport + 2D equilibrium geometry) plasma transport code is being developed to simulate runaway electron generation, mitigation, and avoidance by coupling to the full-orbit kinetic electron transport code KORC. The 1.5D code solves the time-dependent 1D flux surface averaged transport equations with sources for plasma density, pressure, and poloidal magnetic flux, along with the Grad-Shafranov equilibrium equation for the 2D flux surface geometry. Disruption mitigation is simulated by introducing an impurity neutral gas `pellet', with impurity densities and electron cooling calculated from ionization, recombination, and line emission rate coefficients. Rapid cooling of the electrons increases the resistivity, inducing an electric field which can be used as an input to KORC. The runaway electron current is then included in the parallel Ohm's law in the transport equations. The 1.5D solver will act as a driver for coupled simulations to model effects such as timescales for thermal quench, runaway electron generation, and pellet impurity mixtures for runaway avoidance. Current progress on the code and details of the numerical algorithms will be presented. Work supported by the US DOE under DE-AC05-00OR22725.

Improved treatment of exact exchange in Quantum ESPRESSO

DOE PAGES

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre; ...

2017-01-18

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnes, Taylor A.; Kurth, Thorsten; Carrier, Pierre

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations ofmore » hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.« less

Symmetry Breaking by Parallel Flow Shear

NASA Astrophysics Data System (ADS)

Li, Jiacong; Diamond, Patrick

2015-11-01

Plasma rotation is important in reducing turbulent transport, suppressing MHD instabilities, and is beneficial to confinement. Intrinsic rotation without an external momentum input is of interest for its plausible application on ITER. k∥ spectrum asymmetry is required for residual Reynolds stress that drives the intrinsic rotation. Parallel flows are reported in linear devices without magnetic shear. In CSDX, parallel flows are mostly peaked in the core [Thakur et al., 2014]; more robust flows and reversed profiles are seen in PANTA [Oldenburger, et al. 2012]. A novel mechanism for symmetry breaking in momentum transport is proposed. Magnetic shear or mean flow profile are not required. A seed parallel flow shear (PFS) sets the sign of residual stress by selecting certain modes to grow faster. The resulted spectrum imbalance leads to a nonzero residual stress, which further drives a parallel flow with ∇n as the free energy source, adding to the shear until saturated by diffusion. Balanced flow gradient is set by Π∥Res /χϕ . Residual stress is calculated for ITG turbulence and collisional drift wave turbulence where electron-ion and electron-neutral collisions are discussed and compared. Numerical simulation is proposed for testing the effect of PFS.

A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shimojo, Fuyuki; Hattori, Shinnosuke; Department of Physics, Kumamoto University, Kumamoto 860-8555

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at themore » peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10{sup 6}-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.« less

On the interplay of morphology and electronic conductivity of rotationally spun carbon fiber mats

NASA Astrophysics Data System (ADS)

Opitz, Martin; Go, Dennis; Lott, Philipp; Müller, Sandra; Stollenwerk, Jochen; Kuehne, Alexander J. C.; Roling, Bernhard

2017-09-01

Carbon-based materials are used as electrode materials in a wide range of electrochemical applications, e.g., in batteries, supercapacitors, and fuel cells. For these applications, the electronic conductivity of the materials plays an important role. Currently, porous carbon materials with complex morphologies and hierarchical pore structures are in the focus of research. The complex morphologies influence the electronic transport and may lead to an anisotropic electronic conductivity. In this paper, we unravel the influence of the morphology of rotationally spun carbon fiber mats on their electronic conductivity. By combining experiments with finite-element simulations, we compare and evaluate different electrode setups for conductivity measurements. While the "bar-type method" with two parallel electrodes on the same face of the sample yields information about the intrinsic conductivity of the carbon fibers, the "parallel-plate method" with two electrodes on opposite faces gives information about the electronic transport orthogonal to the faces. Results obtained for the van-der-Pauw method suggest that this method is not well suited for understanding morphology-transport relations in these materials.

Implementation of highly parallel and large scale GW calculations within the OpenAtom software

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.

Evidence of a New Instability in Gyrokinetic Simulations of LAPD Plasmas

NASA Astrophysics Data System (ADS)

Terry, P. W.; Pueschel, M. J.; Rossi, G.; Jenko, F.; Told, D.; Carter, T. A.

2015-11-01

Recent experiments at the LArge Plasma Device (LAPD) have focused on structure formation driven by density and temperature gradients. A central difference relative to typical, tokamak-like plasmas stems from the linear geometry and absence of background magnetic shear. At sufficiently high β, strong excitation of parallel (compressional) magnetic fluctuations was observed. Here, linear and nonlinear simulations with the Gene code are used to demonstrate that these findings can be explained through the linear excitation of a Gradient-driven Drift Coupling mode (GDC). This recently-discovered instability, unlike other drift waves, relies on the grad-B drift due to parallel magnetic fluctuations in lieu of a parallel electron response, and can be driven by density or temperature gradients. The linear properties of the GDC for LAPD parameters are studied in detail, and the corresponding turbulence is investigated. It is found that, despite the very large collisionality in the experiment, many properties are recovered fairly well in the simulations. In addition to confirming the existence of the GDC, this opens up interesting questions regarding GDC activity in astrophysical and space plasmas. Supported by USDOE.

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

Generation of Rising-tone Chorus in a Two-dimensional Mirror Field by Using the General Curvilinear PIC Code

NASA Astrophysics Data System (ADS)

Ke, Y.; Gao, X.; Lu, Q.; Wang, X.; Wang, S.

2017-12-01

Recently, the generation of rising-tone chorus has been implemented with one-dimensional (1-D) particle-in-cell (PIC) simulations in an inhomogeneous background magnetic field, where both the propagation of waves and motion of electrons are simply forced to be parallel to the background magnetic field. We have developed a two-dimensional(2-D) general curvilinear PIC simulation code, and successfully reproduced rising-tone chorus waves excited from an anisotropic electron distribution in a 2-D mirror field. Our simulation results show that whistler waves are mainly generated around the magnetic equator, and continuously gain growth during their propagation toward higher-latitude regions. The rising-tone chorus waves are formed off the magnetic equator, which propagate quasi-parallel to the background magnetic field with the finite wave normal angle. Due to the propagating effect, the wave normal angle of chorus waves is increasing during their propagation toward higher-latitude regions along an enough curved field line. The chirping rate of chorus waves are found to be larger along a field line more close to the middle field line in the mirror field.

Generation of rising-tone chorus in a two-dimensional mirror field by using the general curvilinear PIC code

NASA Astrophysics Data System (ADS)

Ke, Yangguang; Gao, Xinliang; Lu, Quanming; Wang, Xueyi; Wang, Shui

2017-08-01

Recently, the generation of rising-tone chorus has been implemented with one-dimensional (1-D) particle-in-cell (PIC) simulations in an inhomogeneous background magnetic field, where both the propagation of waves and motion of electrons are simply forced to be parallel to the background magnetic field. In this paper, we have developed a two-dimensional (2-D) general curvilinear PIC simulation code and successfully reproduced rising-tone chorus waves excited from an anisotropic electron distribution in a 2-D mirror field. Our simulation results show that whistler waves are mainly generated around the magnetic equator and continuously gain growth during their propagation toward higher-latitude regions. The rising-tone chorus waves are observed off the magnetic equator, which propagate quasi-parallel to the background magnetic field with the wave normal angle smaller than 25°. Due to the propagating effect, the wave normal angle of chorus waves is increasing during their propagation toward higher-latitude regions along an enough curved field line. The chirping rate of chorus waves is found to be larger along a field line with a smaller curvature.

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f , (e.g. Verlet algorithm) is available to propagate the system from time ti (trajectory positions and velocities xi = (ri; vi)) to time ti+1 (xi+1) by xi+1 = fi(xi), the dynamics problem spanning an interval from t0 : : : tM can be transformed into a root finding problem, F(X) = [xi - f (x(i-1)]i=1;M = 0, for the trajectory variables. The root finding problem is solved using amore » variety of optimization techniques, including quasi-Newton and preconditioned quasi-Newton optimization schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed and the effectiveness of various approaches to solving the root finding problem are tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl+4H2O AIMD simulation at the MP2 level. The maximum speedup obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow TCP/IP networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl+4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. By using these algorithms we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 seconds per time step to 6.9 seconds per time step.« less

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

PubMed

Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

Finite element simulations of electrostatic dopant potentials in thin semiconductor specimens for electron holography.

PubMed

Somodi, P K; Twitchett-Harrison, A C; Midgley, P A; Kardynał, B E; Barnes, C H W; Dunin-Borkowski, R E

2013-11-01

Two-dimensional finite element simulations of electrostatic dopant potentials in parallel-sided semiconductor specimens that contain p-n junctions are used to assess the effect of the electrical state of the surface of a thin specimen on projected potentials measured using off-axis electron holography in the transmission electron microscope. For a specimen that is constrained to have an equipotential surface, the simulations show that the step in the projected potential across a p-n junction is always lower than would be predicted from the properties of the bulk device, but is relatively insensitive to the value of the surface state energy, especially for thicker specimens and higher dopant concentrations. The depletion width measured from the projected potential, however, has a complicated dependence on specimen thickness. The results of the simulations are of broader interest for understanding the influence of surfaces and interfaces on electrostatic potentials in nanoscale semiconductor devices. © 2013 Elsevier B.V. All rights reserved.

Analysis of Plane-Parallel Electron Beam Propagation in Different Media by Numerical Simulation Methods

NASA Astrophysics Data System (ADS)

Miloichikova, I. A.; Bespalov, V. I.; Krasnykh, A. A.; Stuchebrov, S. G.; Cherepennikov, Yu. M.; Dusaev, R. R.

2018-04-01

Simulation by the Monte Carlo method is widely used to calculate the character of ionizing radiation interaction with substance. A wide variety of programs based on the given method allows users to choose the most suitable package for solving computational problems. In turn, it is important to know exactly restrictions of numerical systems to avoid gross errors. Results of estimation of the feasibility of application of the program PCLab (Computer Laboratory, version 9.9) for numerical simulation of the electron energy distribution absorbed in beryllium, aluminum, gold, and water for industrial, research, and clinical beams are presented. The data obtained using programs ITS and Geant4 being the most popular software packages for solving the given problems and the program PCLab are presented in the graphic form. A comparison and an analysis of the results obtained demonstrate the feasibility of application of the program PCLab for simulation of the absorbed energy distribution and dose of electrons in various materials for energies in the range 1-20 MeV.

Three-dimensional Hybrid Simulation Study of Anisotropic Turbulence in the Proton Kinetic Regime

NASA Astrophysics Data System (ADS)

Vasquez, Bernard J.; Markovskii, Sergei A.; Chandran, Benjamin D. G.

2014-06-01

Three-dimensional numerical hybrid simulations with particle protons and quasi-neutralizing fluid electrons are conducted for a freely decaying turbulence that is anisotropic with respect to the background magnetic field. The turbulence evolution is determined by both the combined root-mean-square (rms) amplitude for fluctuating proton bulk velocity and magnetic field and by the ratio of perpendicular to parallel wavenumbers. This kind of relationship had been considered in the past with regard to interplanetary turbulence. The fluctuations nonlinearly evolve to a turbulent phase whose net wave vector anisotropy is usually more perpendicular than the initial one, irrespective of the initial ratio of perpendicular to parallel wavenumbers. Self-similar anisotropy evolution is found as a function of the rms amplitude and parallel wavenumber. Proton heating rates in the turbulent phase vary strongly with the rms amplitude but only weakly with the initial wave vector anisotropy. Even in the limit where wave vectors are confined to the plane perpendicular to the background magnetic field, the heating rate remains close to the corresponding case with finite parallel wave vector components. Simulation results obtained as a function of proton plasma to background magnetic pressure ratio β p in the range 0.1-0.5 show that the wave vector anisotropy also weakly depends on β p .

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov; Weare, Jonathan Q., E-mail: weare@uchicago.edu; Weare, John H., E-mail: jweare@ucsd.edu

2013-08-21

Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for themore » trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.« less

The formation of quasi-parallel shocks. [in space, solar and astrophysical plasmas

NASA Technical Reports Server (NTRS)

Cargill, Peter J.

1991-01-01

In a collisionless plasma, the coupling between a piston and the plasma must take place through either laminar or turbulent electromagnetic fields. Of the three types of coupling (laminar, Larmor and turbulent), shock formation in the parallel regime is dominated by the latter and in the quasi-parallel regime by a combination of all three, depending on the piston. In the quasi-perpendicular regime, there is usually a good separation between piston and shock. This is not true in the quasi-parallel and parallel regime. Hybrid numerical simulations for hot plasma pistons indicate that when the electrons are hot, a shock forms, but does not cleanly decouple from the piston. For hot ion pistons, no shock forms in the parallel limit: in the quasi-parallel case, a shock forms, but there is severe contamination from hot piston ions. These results suggest that the properties of solar and astrophysical shocks, such as particle acceleration, cannot be readily separated from their driving mechanism.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Farmer, W. A.; Koning, J. M.; Strozzi, D. J.

Here, we present radiation-hydrodynamic simulations of self-generated magnetic field in a hohlraum, which show an increased temperature in large regions of the underdense fill. Non-parallel gradients in electron density and temperature in a laser-heated plasma give rise to a self-generated field by the “Biermann battery” mechanism. Here, HYDRA simulations of three hohlraum designs on the National Ignition Facility are reported, which use a partial magnetohydrodynamic (MHD) description that includes the self-generated source term, resistive dissipation, and advection of the field due to both the plasma flow and the Nernst term. Anisotropic electron heat conduction parallel and perpendicular to the fieldmore » is included, but not the Righi-Leduc heat flux. The field strength is too small to compete significantly with plasma pressure, but affects plasma conditions by reducing electron heat conduction perpendicular to the field. Significant reductions in heat flux can occur, especially for high Z plasma, at modest values of the Hall parameter, Ω eτ ei≲1, where Ω e = eB/m ec and τ ei is the electron-ion collision time. The inclusion of MHD in the simulations leads to 1 keV hotter electron temperatures in the laser entrance hole and high- Z wall blowoff, which reduces inverse-bremsstrahlung absorption of the laser beam. This improves propagation of the inner beams pointed at the hohlraum equator, resulting in a symmetry shift of the resulting capsule implosion towards a more prolate shape. The time of peak x-ray production in the capsule shifts later by only 70 ps (within experimental uncertainty), but a decomposition of the hotspot shape into Legendre moments indicates a shift of P 2/P 0 by ~20%. As a result, this indicates that MHD cannot explain why simulated x-ray drive exceeds measured levels, but may be partially responsible for failures to correctly model the symmetry.« less

Evolving Nonthermal Electron Distributions in Simulations of Sgr A*

NASA Astrophysics Data System (ADS)

Chael, Andrew; Narayan, Ramesh

2018-01-01

The accretion flow around Sagittarius A* (Sgr A*), the black hole at the Galactic Center, produces strong variability from the radio to X-rays on timescales of minutes to hours. This rapid, powerful variability is thought to be powered by energetic particle acceleration by plasma processes like magnetic reconnection and shocks. These processes can accelerate particles into non-thermal distributions which do not quickly isothermal in the low densities found around hot accretion flows. Current state-of-the-art simulations of accretion flows around black holes assume either a single-temperature gas or, at best, a two-temperature gas with thermal ions and electrons. We present results from incorporating the self-consistent evolution of a non-thermal electron population in a GRRMHD simulation of Sgr A*. The electron distribution is evolved across space, time, and Lorentz factor in parallel with background thermal ion, electron, and radiation fluids. Energy injection into the non-thermal distribution is modeled with a sub-grid prescription based on results from particle-in-cell simulations of magnetic reconnection. The energy distribution of the non-thermal electrons shows strong variability, and the spectral shape traces the complex interplay between the local viscous heating rate, magnetic field strength, and fluid velocity. Results from these simulations will be used in interpreting forthcoming data from the Event Horizon Telescope that resolves Sgr A*'s sub-mm variability in both time and space.

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.

PubMed

Lemkul, Justin A; Roux, Benoît; van der Spoel, David; MacKerell, Alexander D

2015-07-15

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé-Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field. © 2015 Wiley Periodicals, Inc.

GAPD: a GPU-accelerated atom-based polychromatic diffraction simulation code.

PubMed

E, J C; Wang, L; Chen, S; Zhang, Y Y; Luo, S N

2018-03-01

GAPD, a graphics-processing-unit (GPU)-accelerated atom-based polychromatic diffraction simulation code for direct, kinematics-based, simulations of X-ray/electron diffraction of large-scale atomic systems with mono-/polychromatic beams and arbitrary plane detector geometries, is presented. This code implements GPU parallel computation via both real- and reciprocal-space decompositions. With GAPD, direct simulations are performed of the reciprocal lattice node of ultralarge systems (∼5 billion atoms) and diffraction patterns of single-crystal and polycrystalline configurations with mono- and polychromatic X-ray beams (including synchrotron undulator sources), and validation, benchmark and application cases are presented.

Nonadiabatic electron response in the Hasegawa-Wakatani equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoltzfus-Dueck, T.; Scott, B. D.; Krommes, J. A.

2013-08-15

Tokamak edge turbulence is strongly influenced by parallel electron physics, which relaxes density and potential fluctuations towards electron adiabatic response. Beginning with the paradigmatic Hasegawa-Wakatani equations (HWEs) for resistive tokamak edge turbulence, a unique decomposition of the electric potential (φ) into adiabatic (a) and nonadiabatic (b) portions is derived, based on the requirement that a neither drive nor respond to the parallel current j{sub ∥}. The form of the decomposition clarifies that, at perpendicular scales large relative to the sound radius, the electron adiabatic response controls the nonzonal φ, not the fluctuating density n. Simple energy balance arguments allow onemore » to rigorously bound the ratio of rms nonzonal nonadiabatic fluctuations (b(tilde sign)) relative to adiabatic ones (ã). The role of the vorticity nonlinearity in transferring energy between adiabatic and nonadiabatic fluctuations aids intuitive understanding of self-sustained turbulence in the HWEs. When the normalized parallel resistivity is weak, b(tilde sign) becomes effectively slaved, allowing the reduction to an approximate one-field model that remains valid for strong turbulence. In addition to guiding physical intuition, the one-field reduction should greatly ease further analytical manipulations. Direct numerical simulation of the 2D HWEs confirms the convergence of the asymptotic formula for b(tilde sign)« less

Massively parallel first-principles simulation of electron dynamics in materials

DOE PAGES

Draeger, Erik W.; Andrade, Xavier; Gunnels, John A.; ...

2017-08-01

Here we present a highly scalable, parallel implementation of first-principles electron dynamics coupled with molecular dynamics (MD). By using optimized kernels, network topology aware communication, and by fully distributing all terms in the time-dependent Kohn–Sham equation, we demonstrate unprecedented time to solution for disordered aluminum systems of 2000 atoms (22,000 electrons) and 5400 atoms (59,400 electrons), with wall clock time as low as 7.5 s per MD time step. Despite a significant amount of non-local communication required in every iteration, we achieved excellent strong scaling and sustained performance on the Sequoia Blue Gene/Q supercomputer at LLNL. We obtained up tomore » 59% of the theoretical sustained peak performance on 16,384 nodes and performance of 8.75 Petaflop/s (43% of theoretical peak) on the full 98,304 node machine (1,572,864 cores). Lastly, scalable explicit electron dynamics allows for the study of phenomena beyond the reach of standard first-principles MD, in particular, materials subject to strong or rapid perturbations, such as pulsed electromagnetic radiation, particle irradiation, or strong electric currents.« less

Nonlinear Electron Acoustic Waves in the Inner Magnetosphere

NASA Astrophysics Data System (ADS)

Dillard, C. S.; Vasko, I.; Mozer, F.; Agapitov, O. V.

2017-12-01

The Van Allen Probes observe intense broad-band electrostatic wave activity in the inner magnetosphere. The high-resolution electric field measurements show that these broad-band wave activity is made of large-amplitude electrostatic solitary waves propagating generally along the background magnetic field with velocities of a few thousands km/s. There are generally two types of the observed solitary waves. The solitary waves with the bipolar parallel electric field are interpreted as electron phase space holes, while the nature of solitary waves with asymmetric parallel electric field has remained puzzling. In the present work we show that asymmetric solitary waves propagate with velocities (1000-5000 km/s) and have spatial scales (100 m-1 km) similar to those for electron-acoustic waves existing due to two temperature electron population. Through the numerical fluid simulation we show that the spikes are produced from the initially harmonic electron-acoustic perturbation due to the nonlinear steepening. Through the analysis of the modified KdV equation we show that the steepening is arrested at some moment by the collisionless Landau dissipation and results in formation of the observed asymmetric spikes (shocklets).

Massively parallel first-principles simulation of electron dynamics in materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Draeger, Erik W.; Andrade, Xavier; Gunnels, John A.

Here we present a highly scalable, parallel implementation of first-principles electron dynamics coupled with molecular dynamics (MD). By using optimized kernels, network topology aware communication, and by fully distributing all terms in the time-dependent Kohn–Sham equation, we demonstrate unprecedented time to solution for disordered aluminum systems of 2000 atoms (22,000 electrons) and 5400 atoms (59,400 electrons), with wall clock time as low as 7.5 s per MD time step. Despite a significant amount of non-local communication required in every iteration, we achieved excellent strong scaling and sustained performance on the Sequoia Blue Gene/Q supercomputer at LLNL. We obtained up tomore » 59% of the theoretical sustained peak performance on 16,384 nodes and performance of 8.75 Petaflop/s (43% of theoretical peak) on the full 98,304 node machine (1,572,864 cores). Lastly, scalable explicit electron dynamics allows for the study of phenomena beyond the reach of standard first-principles MD, in particular, materials subject to strong or rapid perturbations, such as pulsed electromagnetic radiation, particle irradiation, or strong electric currents.« less

Massively Parallel Real-Time TDDFT Simulations of Electronic Stopping Processes

NASA Astrophysics Data System (ADS)

Yost, Dillon; Lee, Cheng-Wei; Draeger, Erik; Correa, Alfredo; Schleife, Andre; Kanai, Yosuke

Electronic stopping describes transfer of kinetic energy from fast-moving charged particles to electrons, producing massive electronic excitations in condensed matter. Understanding this phenomenon for ion irradiation has implications in modern technologies, ranging from nuclear reactors, to semiconductor devices for aerospace missions, to proton-based cancer therapy. Recent advances in high-performance computing allow us to achieve an accurate parameter-free description of these phenomena through numerical simulations. Here we discuss results from our recently-developed large-scale real-time TDDFT implementation for electronic stopping processes in important example materials such as metals, semiconductors, liquid water, and DNA. We will illustrate important insight into the physics underlying electronic stopping and we discuss current limitations of our approach both regarding physical and numerical approximations. This work is supported by the DOE through the INCITE awards and by the NSF. Part of this work was performed under the auspices of U.S. DOE by LLNL under Contract DE-AC52-07NA27344.

Monte Carlo calculations of electron beam quality conversion factors for several ion chamber types.

PubMed

Muir, B R; Rogers, D W O

2014-11-01

To provide a comprehensive investigation of electron beam reference dosimetry using Monte Carlo simulations of the response of 10 plane-parallel and 18 cylindrical ion chamber types. Specific emphasis is placed on the determination of the optimal shift of the chambers' effective point of measurement (EPOM) and beam quality conversion factors. The EGSnrc system is used for calculations of the absorbed dose to gas in ion chamber models and the absorbed dose to water as a function of depth in a water phantom on which cobalt-60 and several electron beam source models are incident. The optimal EPOM shifts of the ion chambers are determined by comparing calculations of R50 converted from I50 (calculated using ion chamber simulations in phantom) to R50 calculated using simulations of the absorbed dose to water vs depth in water. Beam quality conversion factors are determined as the calculated ratio of the absorbed dose to water to the absorbed dose to air in the ion chamber at the reference depth in a cobalt-60 beam to that in electron beams. For most plane-parallel chambers, the optimal EPOM shift is inside of the active cavity but different from the shift determined with water-equivalent scaling of the front window of the chamber. These optimal shifts for plane-parallel chambers also reduce the scatter of beam quality conversion factors, kQ, as a function of R50. The optimal shift of cylindrical chambers is found to be less than the 0.5 rcav recommended by current dosimetry protocols. In most cases, the values of the optimal shift are close to 0.3 rcav. Values of kecal are calculated and compared to those from the TG-51 protocol and differences are explained using accurate individual correction factors for a subset of ion chambers investigated. High-precision fits to beam quality conversion factors normalized to unity in a beam with R50 = 7.5 cm (kQ (')) are provided. These factors avoid the use of gradient correction factors as used in the TG-51 protocol although a chamber dependent optimal shift in the EPOM is required when using plane-parallel chambers while no shift is needed with cylindrical chambers. The sensitivity of these results to parameters used to model the ion chambers is discussed and the uncertainty related to the practical use of these results is evaluated. These results will prove useful as electron beam reference dosimetry protocols are being updated. The analysis of this work indicates that cylindrical ion chambers may be appropriate for use in low-energy electron beams but measurements are required to characterize their use in these beams.

Radiation transport in kinetic simulations and the influence of photoemission on electron current in self-sustaining discharges

DOE PAGES

Fierro, Andrew S.; Moore, Christopher Hudson; Scheiner, Brett; ...

2017-01-12

A kinetic description for electronic excitation of helium for principal quantum number nmore » $$\\leqslant $$ 4 has been included into a particle-in-cell (PIC) simulation utilizing direct simulation Monte Carlo (DSMC) for electron-neutral interactions. The excited electronic levels radiate state-dependent photons with wavelengths from the extreme ultraviolet (EUV) to visible regimes. Photon wavelengths are chosen according to a Voigt distribution accounting for the natural, pressure, and Doppler broadened linewidths. This method allows for reconstruction of the emission spectrum for a non-thermalized electron energy distribution function (EEDF) and investigation of high energy photon effects on surfaces, specifically photoemission. A parallel plate discharge with a fixed field (i.e. space charge neglected) is used to investigate the effects of including photoemission for a Townsend discharge. When operating at a voltage near the self-sustaining discharge threshold, it is observed that the electron current into the anode is higher when including photoemission from the cathode than without even when accounting for self-absorption from ground state atoms. As a result, the photocurrent has been observed to account for as much as 20% of the total current from the cathode under steady-state conditions.« less

A generalized plasma dispersion function for electron damping in tokamak plasmas

DOE PAGES

Berry, L. A.; Jaeger, E. F.; Phillips, C. K.; ...

2016-10-14

Radio frequency wave propagation in finite temperature, magnetized plasmas exhibits a wide range of physics phenomena. The plasma response is nonlocal in space and time, and numerous modes are possible with the potential for mode conversions and transformations. Additionally, diffraction effects are important due to finite wavelength and finite-size wave launchers. Multidimensional simulations are required to describe these phenomena, but even with this complexity, the fundamental plasma response is assumed to be the uniform plasma response with the assumption that the local plasma current for a Fourier mode can be described by the Stix conductivity. But, for plasmas with non-uniformmore » magnetic fields, the wave vector itself is nonlocal. When resolved into components perpendicular (k ) and parallel (k ||) to the magnetic field, locality of the parallel component can easily be violated when the wavelength is large. The impact of this inconsistency is that estimates of the wave damping can be incorrect (typically low) due to unresolved resonances. For the case of ion cyclotron damping, this issue has already been addressed by including the effect of parallel magnetic field gradients. In this case, a modified plasma response (Z function) allows resonance broadening even when k || = 0, and this improves the convergence and accuracy of wave simulations. In our paper, we extend this formalism to include electron damping and find improved convergence and accuracy for parameters where electron damping is dominant, such as high harmonic fast wave heating in the NSTX-U tokamak, and helicon wave launch for off-axis current drive in the DIII-D tokamak.« less

MITHRA 1.0: A full-wave simulation tool for free electron lasers

NASA Astrophysics Data System (ADS)

Fallahi, Arya; Yahaghi, Alireza; Kärtner, Franz X.

2018-07-01

Free Electron Lasers (FELs) are a solution for providing intense, coherent and bright radiation in the hard X-ray regime. Due to the low wall-plug efficiency of FEL facilities, it is crucial and additionally very useful to develop complete and accurate simulation tools for better optimizing a FEL interaction. The highly sophisticated dynamics involved in a FEL process was the main obstacle hindering the development of general simulation tools for this problem. We present a numerical algorithm based on finite difference time domain/Particle in cell (FDTD/PIC) in a Lorentz boosted coordinate system which is able to fulfill a full-wave simulation of a FEL process. The developed software offers a suitable tool for the analysis of FEL interactions without considering any of the usual approximations. A coordinate transformation to bunch rest frame makes the very different length scales of bunch size, optical wavelengths and the undulator period transform to values with the same order. Consequently, FDTD/PIC simulations in conjunction with efficient parallelization techniques make the full-wave simulation feasible using the available computational resources. Several examples of free electron lasers are analyzed using the developed software, the results are benchmarked based on standard FEL codes and discussed in detail.

Massively parallel and linear-scaling algorithm for second-order Møller-Plesset perturbation theory applied to the study of supramolecular wires

NASA Astrophysics Data System (ADS)

Kjærgaard, Thomas; Baudin, Pablo; Bykov, Dmytro; Eriksen, Janus Juul; Ettenhuber, Patrick; Kristensen, Kasper; Larkin, Jeff; Liakh, Dmitry; Pawłowski, Filip; Vose, Aaron; Wang, Yang Min; Jørgensen, Poul

2017-03-01

We present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide-Expand-Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide-Expand-Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalability of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the "resolution of the identity second-order Møller-Plesset perturbation theory" (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.

2-D Modeling of Nanoscale MOSFETs: Non-Equilibrium Green's Function Approach

NASA Technical Reports Server (NTRS)

Svizhenko, Alexei; Anantram, M. P.; Govindan, T. R.; Biegel, Bryan

2001-01-01

We have developed physical approximations and computer code capable of realistically simulating 2-D nanoscale transistors, using the non-equilibrium Green's function (NEGF) method. This is the most accurate full quantum model yet applied to 2-D device simulation. Open boundary conditions and oxide tunneling are treated on an equal footing. Electrons in the ellipsoids of the conduction band are treated within the anisotropic effective mass approximation. Electron-electron interaction is treated within Hartree approximation by solving NEGF and Poisson equations self-consistently. For the calculations presented here, parallelization is performed by distributing the solution of NEGF equations to various processors, energy wise. We present simulation of the "benchmark" MIT 25nm and 90nm MOSFETs and compare our results to those from the drift-diffusion simulator and the quantum-corrected results available. In the 25nm MOSFET, the channel length is less than ten times the electron wavelength, and the electron scattering time is comparable to its transit time. Our main results are: (1) Simulated drain subthreshold current characteristics are shown, where the potential profiles are calculated self-consistently by the corresponding simulation methods. The current predicted by our quantum simulation has smaller subthreshold slope of the Vg dependence which results in higher threshold voltage. (2) When gate oxide thickness is less than 2 nm, gate oxide leakage is a primary factor which determines off-current of a MOSFET (3) Using our 2-D NEGF simulator, we found several ways to drastically decrease oxide leakage current without compromising drive current. (4) Quantum mechanically calculated electron density is much smaller than the background doping density in the poly silicon gate region near oxide interface. This creates an additional effective gate voltage. Different ways to. include this effect approximately will be discussed.

Many-integrated core (MIC) technology for accelerating Monte Carlo simulation of radiation transport: A study based on the code DPM

NASA Astrophysics Data System (ADS)

Rodriguez, M.; Brualla, L.

2018-04-01

Monte Carlo simulation of radiation transport is computationally demanding to obtain reasonably low statistical uncertainties of the estimated quantities. Therefore, it can benefit in a large extent from high-performance computing. This work is aimed at assessing the performance of the first generation of the many-integrated core architecture (MIC) Xeon Phi coprocessor with respect to that of a CPU consisting of a double 12-core Xeon processor in Monte Carlo simulation of coupled electron-photonshowers. The comparison was made twofold, first, through a suite of basic tests including parallel versions of the random number generators Mersenne Twister and a modified implementation of RANECU. These tests were addressed to establish a baseline comparison between both devices. Secondly, through the p DPM code developed in this work. p DPM is a parallel version of the Dose Planning Method (DPM) program for fast Monte Carlo simulation of radiation transport in voxelized geometries. A variety of techniques addressed to obtain a large scalability on the Xeon Phi were implemented in p DPM. Maximum scalabilities of 84 . 2 × and 107 . 5 × were obtained in the Xeon Phi for simulations of electron and photon beams, respectively. Nevertheless, in none of the tests involving radiation transport the Xeon Phi performed better than the CPU. The disadvantage of the Xeon Phi with respect to the CPU owes to the low performance of the single core of the former. A single core of the Xeon Phi was more than 10 times less efficient than a single core of the CPU for all radiation transport simulations.

The theoretical simulation on electrostatic distribution of 1st proximity region in proximity focusing low-light-level image intensifier

NASA Astrophysics Data System (ADS)

Zhang, Liandong; Bai, Xiaofeng; Song, De; Fu, Shencheng; Li, Ye; Duanmu, Qingduo

2015-03-01

Low-light-level night vision technology is magnifying low light level signal large enough to be seen by naked eye, which uses the photons - photoelectron as information carrier. Until the micro-channel plate was invented, it has been possibility for the realization of high performance and miniaturization of low-light-level night vision device. The device is double-proximity focusing low-light-level image intensifier which places a micro-channel plate close to photocathode and phosphor screen. The advantages of proximity focusing low-light-level night vision are small size, light weight, small power consumption, no distortion, fast response speed, wide dynamic range and so on. It is placed parallel to each other for Micro-channel plate (both sides of it with metal electrode), the photocathode and the phosphor screen are placed parallel to each other. The voltage is applied between photocathode and the input of micro-channel plate when image intensifier works. The emission electron excited by photo on the photocathode move towards to micro-channel plate under the electric field in 1st proximity focusing region, and then it is multiplied through the micro-channel. The movement locus of emission electrons can be calculated and simulated when the distributions of electrostatic field equipotential lines are determined in the 1st proximity focusing region. Furthermore the resolution of image tube can be determined. However the distributions of electrostatic fields and equipotential lines are complex due to a lot of micro-channel existing in the micro channel plate. This paper simulates electrostatic distribution of 1st proximity region in double-proximity focusing low-light-level image intensifier with the finite element simulation analysis software Ansoft maxwell 3D. The electrostatic field distributions of 1st proximity region are compared when the micro-channel plates' pore size, spacing and inclination angle ranged. We believe that the electron beam movement trajectory in 1st proximity region will be better simulated when the electronic electrostatic fields are simulated.

Phase-space dynamics of runaway electrons in magnetic fields

DOE PAGES

Guo, Zehua; McDevitt, Christopher Joseph; Tang, Xian-Zhu

2017-02-16

Dynamics of runaway electrons in magnetic fields are governed by the competition of three dominant physics: parallel electric field acceleration, Coulomb collision, and synchrotron radiation. Examination of the energy and pitch-angle flows reveals that the presence of local vortex structure and global circulation is crucial to the saturation of primary runaway electrons. Models for the vortex structure, which has an O-point to X-point connection, and the bump of runaway electron distribution in energy space have been developed and compared against the simulation data. Lastly, identification of these velocity-space structures opens a new venue to re-examine the conventional understanding of runawaymore » electron dynamics in magnetic fields.« less

Particle-in-cell simulations of magnetically driven reconnection using laser-powered capacitor coils

NASA Astrophysics Data System (ADS)

Huang, Kai; Lu, Quanming; Gao, Lan; Ji, Hantao; Wang, Xueyi; Fan, Feibin

2018-05-01

In this paper, we propose an experimental scheme to fulfill magnetically driven reconnections. Here, two laser beams are focused on a capacitor-coil target and then strong currents are wired in two parallel circular coils. Magnetic reconnection occurs between the two magnetic bubbles created by the currents in the two parallel circular coils. A two-dimensional particle-in-cell simulation model in the cylindrical coordinate is used to investigate such a process, and the simulations are performed in the (r ,z ) plane. The results show that with the increase of the currents in the two coils, the associated magnetic bubbles expand and a current sheet is formed between the two bubbles. Magnetic reconnection occurs when the current sheet is sufficiently thin. A quadrupole structure of the magnetic field in the θ direction ( Bθ ) is generated in the diffusion region and a strong electron current along the r direction ( Je r ) is also formed due to the existence of the high-speed electron flow away from the X line in the center of the outflow region. Because the X line is a circle along the θ direction, the convergence of the plasma flow around r =0 will lead to the asymmetry of Je r and Bθ between the two outflow regions of magnetic reconnection.

Implementation of Multivariable Logic Functions in Parallel by Electrically Addressing a Molecule of Three Dopants in Silicon.

PubMed

Fresch, Barbara; Bocquel, Juanita; Hiluf, Dawit; Rogge, Sven; Levine, Raphael D; Remacle, Françoise

2017-07-05

To realize low-power, compact logic circuits, one can explore parallel operation on single nanoscale devices. An added incentive is to use multivalued (as distinct from Boolean) logic. Here, we theoretically demonstrate that the computation of all the possible outputs of a multivariate, multivalued logic function can be implemented in parallel by electrical addressing of a molecule made up of three interacting dopant atoms embedded in Si. The electronic states of the dopant molecule are addressed by pulsing a gate voltage. By simulating the time evolution of the non stationary electronic density built by the gate voltage, we show that one can implement a molecular decision tree that provides in parallel all the outputs for all the inputs of the multivariate, multivalued logic function. The outputs are encoded in the populations and in the bond orders of the dopant molecule, which can be measured using an STM tip. We show that the implementation of the molecular logic tree is equivalent to a spectral function decomposition. The function that is evaluated can be field-programmed by changing the time profile of the pulsed gate voltage. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation of therapeutic electron beam tracking through a non-uniform magnetic field using finite element method

PubMed Central

Tahmasebibirgani, Mohammad Javad; Maskani, Reza; Behrooz, Mohammad Ali; Zabihzadeh, Mansour; Shahbazian, Hojatollah; Fatahiasl, Jafar; Chegeni, Nahid

2017-01-01

Introduction In radiotherapy, megaelectron volt (MeV) electrons are employed for treatment of superficial cancers. Magnetic fields can be used for deflection and deformation of the electron flow. A magnetic field is composed of non-uniform permanent magnets. The primary electrons are not mono-energetic and completely parallel. Calculation of electron beam deflection requires using complex mathematical methods. In this study, a device was made to apply a magnetic field to an electron beam and the path of electrons was simulated in the magnetic field using finite element method. Methods A mini-applicator equipped with two neodymium permanent magnets was designed that enables tuning the distance between magnets. This device was placed in a standard applicator of Varian 2100 CD linear accelerator. The mini-applicator was simulated in CST Studio finite element software. Deflection angle and displacement of the electron beam was calculated after passing through the magnetic field. By determining a 2 to 5cm distance between two poles, various intensities of transverse magnetic field was created. The accelerator head was turned so that the deflected electrons became vertical to the water surface. To measure the displacement of the electron beam, EBT2 GafChromic films were employed. After being exposed, the films were scanned using HP G3010 reflection scanner and their optical density was extracted using programming in MATLAB environment. Displacement of the electron beam was compared with results of simulation after applying the magnetic field. Results Simulation results of the magnetic field showed good agreement with measured values. Maximum deflection angle for a 12 MeV beam was 32.9° and minimum deflection for 15 MeV was 12.1°. Measurement with the film showed precision of simulation in predicting the amount of displacement in the electron beam. Conclusion A magnetic mini-applicator was made and simulated using finite element method. Deflection angle and displacement of electron beam were calculated. With the method used in this study, a good prediction of the path of high-energy electrons was made before they entered the body. PMID:28607652

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

NASA Astrophysics Data System (ADS)

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

2018-04-01

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λDe, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρe and λDe, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τs, versus fast-ion charge are in agreement with unmagnetized slowing-down theory; with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. The implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.

On the parameter dependence of the whistler anisotropy instability

NASA Astrophysics Data System (ADS)

An, Xin; Yue, Chao; Bortnik, Jacob; Decyk, Viktor; Li, Wen; Thorne, Richard M.

2017-02-01

The evolution of the whistler anisotropy instability relevant to whistler-mode chorus waves in the Earth's inner magnetosphere is studied using kinetic simulations and is compared with satellite observations. The electron distribution is constrained by the whistler anisotropy instability to a marginal stability state and presents an upper bound of electron anisotropy, which agrees with satellite observations. The electron beta β∥e separates whistler waves into two groups: (i) quasi-parallel whistler waves for β∥e≳0.02 and (ii) oblique whistler waves close to the resonance cone for β∥e≲0.02. Landau damping is important in the saturation and relaxation stage of the oblique whistler wave growth. The saturated magnetic field energy of whistler waves roughly scales with the electron beta β∥e2, shown in both simulations and satellite observations. These results suggest the critical role of electron beta β∥e in determining the whistler wave properties in the inner magnetosphere.

Sheath energy transmission in a collisional plasma with collisionless sheath

DOE PAGES

Tang, Xian-Zhu; Guo, Zehua

2015-10-16

Sheath energy transmission governs the plasma energy exhaust onto a material surface. The ion channel is dominated by convection, but the electron channel has a significant thermal conduction component, which is dominated by the Knudsen layer effect in the presence of an absorbing wall. First-principle kinetic simulations also reveal a robustly supersonic sheath entry flow. The ion sheath energy transmission and the sheath potential are accurately predicted by a sheath model of truncated bi-Maxwellian electron distribution. The electron energy transmission is further enhanced by a parallel heat flux of the perpendicular degrees of freedom.

Calculation of heat sink around cracks formed under pulsed heat load

NASA Astrophysics Data System (ADS)

Lazareva, G. G.; Arakcheev, A. S.; Kandaurov, I. V.; Kasatov, A. A.; Kurkuchekov, V. V.; Maksimova, A. G.; Popov, V. A.; Shoshin, A. A.; Snytnikov, A. V.; Trunev, Yu A.; Vasilyev, A. A.; Vyacheslavov, L. N.

2017-10-01

The experimental and numerical simulations of the conditions causing the intensive erosion and expected to be realized infusion reactor were carried out. The influence of relevant pulsed heat loads to tungsten was simulated using a powerful electron beam source in BINP. The mechanical destruction, melting and splashing of the material were observed. The laboratory experiments are accompanied by computational ones. Computational experiment allowed to quantitatively describe the overheating near the cracks, caused by parallel to surface cracks.

Predictive design and interpretation of colliding pulse injected laser wakefield experiments

NASA Astrophysics Data System (ADS)

Cormier-Michel, Estelle; Ranjbar, Vahid H.; Cowan, Ben M.; Bruhwiler, David L.; Geddes, Cameron G. R.; Chen, Min; Ribera, Benjamin; Esarey, Eric; Schroeder, Carl B.; Leemans, Wim P.

2010-11-01

The use of colliding laser pulses to control the injection of plasma electrons into the plasma wake of a laser plasma accelerator is a promising approach to obtaining stable, tunable electron bunches with reduced emittance and energy spread. Colliding Pulse Injection (CPI) experiments are being performed by groups around the world. We will present recent particle-in-cell simulations, using the parallel VORPAL framework, of CPI for physical parameters relevant to ongoing experiments of the LOASIS program at LBNL. We evaluate the effect of laser and plasma tuning, on the trapped electron bunch and perform parameter scans in order to optimize the quality of the bunch. Impact of non-ideal effects such as imperfect laser modes and laser self focusing are also evaluated. Simulation data are validated against current experimental results, and are used to design future experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popovich, P.; Carter, T. A.; Friedman, B.

Numerical simulation of plasma turbulence in the Large Plasma Device (LAPD) [W. Gekelman, H. Pfister, Z. Lucky et al., Rev. Sci. Instrum. 62, 2875 (1991)] is presented. The model, implemented in the BOUndary Turbulence code [M. Umansky, X. Xu, B. Dudson et al., Contrib. Plasma Phys. 180, 887 (2009)], includes three-dimensional (3D) collisional fluid equations for plasma density, electron parallel momentum, and current continuity, and also includes the effects of ion-neutral collisions. In nonlinear simulations using measured LAPD density profiles but assuming constant temperature profile for simplicity, self-consistent evolution of instabilities and nonlinearly generated zonal flows results in a saturatedmore » turbulent state. Comparisons of these simulations with measurements in LAPD plasmas reveal good qualitative and reasonable quantitative agreement, in particular in frequency spectrum, spatial correlation, and amplitude probability distribution function of density fluctuations. For comparison with LAPD measurements, the plasma density profile in simulations is maintained either by direct azimuthal averaging on each time step, or by adding particle source/sink function. The inferred source/sink values are consistent with the estimated ionization source and parallel losses in LAPD. These simulations lay the groundwork for more a comprehensive effort to test fluid turbulence simulation against LAPD data.« less

Whistler turbulence heating of electrons and ions: Three-dimensional particle-in-cell simuations

DOE PAGES

Gary, S. Peter; Hughes, R. Scott; Wang, Joseph

2016-01-14

In this study, the decay of whistler turbulence in a collisionless, homogeneous, magnetized plasma is studied using three-dimensional particle-in-cell simulations. The simulations are initialized with a narrowband, relatively isotropic distribution of long wavelength whistler modes. A first ensemble of simulations at electron betamore » $${\\beta }_{{\\rm{e}}}$$ = 0.25 and ion-to-electron mass ratio $${m}_{{\\rm{i}}}$$/$${m}_{{\\rm{e}}}$$ = 400 is carried out on a domain cube of dimension $$L{\\omega }_{\\mathrm{pi}}$$/c = 5.12 where $${\\omega }_{\\mathrm{pi}}$$ is the ion plasma frequency. The simulations begin with a range of dimensionless fluctuating field energy densities, $${\\epsilon }_{{\\rm{o}}}$$, and follow the fluctuations as they cascade to broadband, anisotropic turbulence which dissipates at shorter wavelengths, heating both electrons and ions. The electron heating is stronger and preferentially parallel/antiparallel to the background magnetic field $${{\\boldsymbol{B}}}_{{\\rm{o}}};$$ the ion energy gain is weaker and is preferentially in directions perpendicular to $${{\\boldsymbol{B}}}_{{\\rm{o}}}$$. The important new results here are that, over 0.01 < $${\\epsilon }_{{\\rm{o}}}$$ < 0.25, the maximum rate of electron heating scales approximately as $${\\epsilon }_{{\\rm{o}}}$$, and the maximum rate of ion heating scales approximately as $${\\epsilon }_{{\\rm{o}}}^{1.5}$$. A second ensemble of simulations at $${\\epsilon }_{{\\rm{o}}}$$ = 0.10 and $${\\beta }_{{\\rm{e}}}$$ = 0.25 shows that, over 25 < $${m}_{{\\rm{i}}}$$/$${m}_{{\\rm{e}}}\\;$$< 1836, the ratio of the maximum ion heating rate to the maximum electron heating rate scales approximately as $${m}_{{\\rm{e}}}$$/$${m}_{{\\rm{i}}}$$.« less

Particle in cell/Monte Carlo collision analysis of the problem of identification of impurities in the gas by the plasma electron spectroscopy method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kusoglu Sarikaya, C.; Rafatov, I., E-mail: rafatov@metu.edu.tr; Kudryavtsev, A. A.

2016-06-15

The work deals with the Particle in Cell/Monte Carlo Collision (PIC/MCC) analysis of the problem of detection and identification of impurities in the nonlocal plasma of gas discharge using the Plasma Electron Spectroscopy (PLES) method. For this purpose, 1d3v PIC/MCC code for numerical simulation of glow discharge with nonlocal electron energy distribution function is developed. The elastic, excitation, and ionization collisions between electron-neutral pairs and isotropic scattering and charge exchange collisions between ion-neutral pairs and Penning ionizations are taken into account. Applicability of the numerical code is verified under the Radio-Frequency capacitively coupled discharge conditions. The efficiency of the codemore » is increased by its parallelization using Open Message Passing Interface. As a demonstration of the PLES method, parallel PIC/MCC code is applied to the direct current glow discharge in helium doped with a small amount of argon. Numerical results are consistent with the theoretical analysis of formation of nonlocal EEDF and existing experimental data.« less

Multipactor saturation in parallel-plate waveguides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sorolla, E.; Mattes, M.

2012-07-15

The saturation stage of a multipactor discharge is considered of interest, since it can guide towards a criterion to assess the multipactor onset. The electron cloud under multipactor regime within a parallel-plate waveguide is modeled by a thin continuous distribution of charge and the equations of motion are calculated taking into account the space charge effects. The saturation is identified by the interaction of the electron cloud with its image charge. The stability of the electron population growth is analyzed and two mechanisms of saturation to explain the steady-state multipactor for voltages near above the threshold onset are identified. Themore » impact energy in the collision against the metal plates decreases during the electron population growth due to the attraction of the electron sheet on the image through the initial plate. When this growth remains stable till the impact energy reaches the first cross-over point, the electron surface density tends to a constant value. When the stability is broken before reaching the first cross-over point the surface charge density oscillates chaotically bounded within a certain range. In this case, an expression to calculate the maximum electron surface charge density is found whose predictions agree with the simulations when the voltage is not too high.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wright, J. C.; Bonoli, P. T.; Schmidt, A. E.

Lower hybrid (LH) waves ({omega}{sub ci}<<{omega}<<{omega}{sub ce}, where {omega}{sub i,e}{identical_to}Z{sub i,e}eB/m{sub i,e}c) have the attractive property of damping strongly via electron Landau resonance on relatively fast tail electrons and consequently are well-suited to driving current. Established modeling techniques use Wentzel-Kramers-Brillouin (WKB) expansions with self-consistent non-Maxwellian distributions. Higher order WKB expansions have shown some effects on the parallel wave number evolution and consequently on the damping due to diffraction [G. Pereverzev, Nucl. Fusion 32, 1091 (1991)]. A massively parallel version of the TORIC full wave electromagnetic field solver valid in the LH range of frequencies has been developed [J. C. Wrightmore » et al., Comm. Comp. Phys. 4, 545 (2008)] and coupled to an electron Fokker-Planck solver CQL3D[R. W. Harvey and M. G. McCoy, in Proceedings of the IAEA Technical Committee Meeting, Montreal, 1992 (IAEA Institute of Physics Publishing, Vienna, 1993), USDOC/NTIS Document No. DE93002962, pp. 489-526] in order to self-consistently evolve nonthermal electron distributions characteristic of LH current drive (LHCD) experiments in devices such as Alcator C-Mod and ITER (B{sub 0}{approx_equal}5 T, n{sub e0}{approx_equal}1x10{sup 20} m{sup -3}). These simulations represent the first ever self-consistent simulations of LHCD utilizing both a full wave and Fokker-Planck calculation in toroidal geometry.« less

Computer simulation of the Farley-Buneman instability and anomalous electron heating in the auroral ionosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Machida, S.; Goertz, C.K.

1988-09-01

We study the nonlinear saturation of the Farley-Buneman instability in a collisional plasma by a 2 1/2 dimensional electrostatic particle simulation which includes inelastic and elastic collisions of electrons and elastic collision of ions with neutrals. In our simulation, a uniform convection electric field is applied externally so that the relative velocity between the electrons and ions is greater than the ion sound speed and destabilizes the instability. We find a nonlinear frequency shift from higher to lower frequencies and diffusion of the wave spectrum in two dimensional wave number space. We are especially interested in finding whether the saturatedmore » wave turbulence can account for the anomalous heating rates observed in the polar ionosphere by Schlegel and St.-Maurice (1981). We find that the dominant mechanism for electron heating is due to an enhanced effective electron collision frequency and hence enhanced resistive heating as suggested by Primdahl (1986) and Robinson (1986) and not due to the heating of electrons by the electric field of the waves parallel to the magnetic field. For the ionospheric conditions discussed by Schlegel and St.-Maurice (1981) we find an anomalous heating rate of about 4 x 10/sup -7/ W/m/sup 3/. copyright American Geophysical Union 1988« less

PIC simulations of wave-particle interactions with an initial electron velocity distribution from a kinetic ring current model

DOE PAGES

Yu, Yiqun; Delzanno, Gian Luca; Jordanova, Vania Koleva; ...

2017-07-15

Whistler wave-particle interactions play an important role in the Earth inner magnetospheric dynamics and have been the subject of numerous investigations. By running a global kinetic ring current model (RAM-SCB) in a storm event occurred on Oct 23–24 2002, we obtain the ring current electron distribution at a selected location at MLT of 9 and L of 6 where the electron distribution is composed of a warm population in the form of a partial ring in the velocity space (with energy around 15 keV) in addition to a cool population with a Maxwellian-like distribution. The warm population is likely frommore » the injected plasma sheet electrons during substorm injections that supply fresh source to the inner magnetosphere. These electron distributions are then used as input in an implicit particle-in-cell code (iPIC3D) to study whistler-wave generation and the subsequent wave-particle interactions. Here, we find that whistler waves are excited and propagate in the quasi-parallel direction along the background magnetic field. Several different wave modes are instantaneously generated with different growth rates and frequencies. The wave mode at the maximum growth rate has a frequency around 0.62ω ce, which corresponds to a parallel resonant energy of 2.5 keV. Linear theory analysis of wave growth is in excellent agreement with the simulation results. These waves grow initially due to the injected warm electrons and are later damped due to cyclotron absorption by electrons whose energy is close to the resonant energy and can effectively attenuate waves. The warm electron population overall experiences net energy loss and anisotropy drop while moving along the diffusion surfaces towards regions of lower phase space density, while the cool electron population undergoes heating when the waves grow, suggesting the cross-population interactions.« less

PIC simulations of wave-particle interactions with an initial electron velocity distribution from a kinetic ring current model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Yiqun; Delzanno, Gian Luca; Jordanova, Vania Koleva

Whistler wave-particle interactions play an important role in the Earth inner magnetospheric dynamics and have been the subject of numerous investigations. By running a global kinetic ring current model (RAM-SCB) in a storm event occurred on Oct 23–24 2002, we obtain the ring current electron distribution at a selected location at MLT of 9 and L of 6 where the electron distribution is composed of a warm population in the form of a partial ring in the velocity space (with energy around 15 keV) in addition to a cool population with a Maxwellian-like distribution. The warm population is likely frommore » the injected plasma sheet electrons during substorm injections that supply fresh source to the inner magnetosphere. These electron distributions are then used as input in an implicit particle-in-cell code (iPIC3D) to study whistler-wave generation and the subsequent wave-particle interactions. Here, we find that whistler waves are excited and propagate in the quasi-parallel direction along the background magnetic field. Several different wave modes are instantaneously generated with different growth rates and frequencies. The wave mode at the maximum growth rate has a frequency around 0.62ω ce, which corresponds to a parallel resonant energy of 2.5 keV. Linear theory analysis of wave growth is in excellent agreement with the simulation results. These waves grow initially due to the injected warm electrons and are later damped due to cyclotron absorption by electrons whose energy is close to the resonant energy and can effectively attenuate waves. The warm electron population overall experiences net energy loss and anisotropy drop while moving along the diffusion surfaces towards regions of lower phase space density, while the cool electron population undergoes heating when the waves grow, suggesting the cross-population interactions.« less

Monte Carlo study of the impact of a magnetic field on the dose distribution in MRI-guided HDR brachytherapy using Ir-192

NASA Astrophysics Data System (ADS)

Beld, E.; Seevinck, P. R.; Lagendijk, J. J. W.; Viergever, M. A.; Moerland, M. A.

2016-09-01

In the process of developing a robotic MRI-guided high-dose-rate (HDR) prostate brachytherapy treatment, the influence of the MRI scanner’s magnetic field on the dose distribution needs to be investigated. A magnetic field causes a deflection of electrons in the plane perpendicular to the magnetic field, and it leads to less lateral scattering along the direction parallel with the magnetic field. Monte Carlo simulations were carried out to determine the influence of the magnetic field on the electron behavior and on the total dose distribution around an Ir-192 source. Furthermore, the influence of air pockets being present near the source was studied. The Monte Carlo package Geant4 was utilized for the simulations. The simulated geometries consisted of a simplified point source inside a water phantom. Magnetic field strengths of 0 T, 1.5 T, 3 T, and 7 T were considered. The simulation results demonstrated that the dose distribution was nearly unaffected by the magnetic field for all investigated magnetic field strengths. Evidence was found that, from a dose perspective, the HDR prostate brachytherapy treatment using Ir-192 can be performed safely inside the MRI scanner. No need was found to account for the magnetic field during treatment planning. Nevertheless, the presence of air pockets in close vicinity to the source, particularly along the direction parallel with the magnetic field, appeared to be an important point for consideration.

Monte Carlo study of the impact of a magnetic field on the dose distribution in MRI-guided HDR brachytherapy using Ir-192.

PubMed

Beld, E; Seevinck, P R; Lagendijk, J J W; Viergever, M A; Moerland, M A

2016-09-21

In the process of developing a robotic MRI-guided high-dose-rate (HDR) prostate brachytherapy treatment, the influence of the MRI scanner's magnetic field on the dose distribution needs to be investigated. A magnetic field causes a deflection of electrons in the plane perpendicular to the magnetic field, and it leads to less lateral scattering along the direction parallel with the magnetic field. Monte Carlo simulations were carried out to determine the influence of the magnetic field on the electron behavior and on the total dose distribution around an Ir-192 source. Furthermore, the influence of air pockets being present near the source was studied. The Monte Carlo package Geant4 was utilized for the simulations. The simulated geometries consisted of a simplified point source inside a water phantom. Magnetic field strengths of 0 T, 1.5 T, 3 T, and 7 T were considered. The simulation results demonstrated that the dose distribution was nearly unaffected by the magnetic field for all investigated magnetic field strengths. Evidence was found that, from a dose perspective, the HDR prostate brachytherapy treatment using Ir-192 can be performed safely inside the MRI scanner. No need was found to account for the magnetic field during treatment planning. Nevertheless, the presence of air pockets in close vicinity to the source, particularly along the direction parallel with the magnetic field, appeared to be an important point for consideration.

A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations.

PubMed

Teoh, Chai Lean; Pham, Chi L L; Todorova, Nevena; Hung, Andrew; Lincoln, Craig N; Lees, Emma; Lam, Yuen Han; Binger, Katrina J; Thomson, Neil H; Radford, Sheena E; Smith, Trevor A; Müller, Shirley A; Engel, Andreas; Griffin, Michael D W; Yarovsky, Irene; Gooley, Paul R; Howlett, Geoffrey J

2011-02-04

The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops. Copyright © 2010 Elsevier Ltd. All rights reserved.

Solvent-assisted multistage nonequilibrium electron transfer in rigid supramolecular systems: Diabatic free energy surfaces and algorithms for numerical simulations

NASA Astrophysics Data System (ADS)

Feskov, Serguei V.; Ivanov, Anatoly I.

2018-03-01

An approach to the construction of diabatic free energy surfaces (FESs) for ultrafast electron transfer (ET) in a supramolecule with an arbitrary number of electron localization centers (redox sites) is developed, supposing that the reorganization energies for the charge transfers and shifts between all these centers are known. Dimensionality of the coordinate space required for the description of multistage ET in this supramolecular system is shown to be equal to N - 1, where N is the number of the molecular centers involved in the reaction. The proposed algorithm of FES construction employs metric properties of the coordinate space, namely, relation between the solvent reorganization energy and the distance between the two FES minima. In this space, the ET reaction coordinate zn n' associated with electron transfer between the nth and n'th centers is calculated through the projection to the direction, connecting the FES minima. The energy-gap reaction coordinates zn n' corresponding to different ET processes are not in general orthogonal so that ET between two molecular centers can create nonequilibrium distribution, not only along its own reaction coordinate but along other reaction coordinates too. This results in the influence of the preceding ET steps on the kinetics of the ensuing ET. It is important for the ensuing reaction to be ultrafast to proceed in parallel with relaxation along the ET reaction coordinates. Efficient algorithms for numerical simulation of multistage ET within the stochastic point-transition model are developed. The algorithms are based on the Brownian simulation technique with the recrossing-event detection procedure. The main advantages of the numerical method are (i) its computational complexity is linear with respect to the number of electronic states involved and (ii) calculations can be naturally parallelized up to the level of individual trajectories. The efficiency of the proposed approach is demonstrated for a model supramolecular system involving four redox centers.

Emergency Medicine Resident Physicians’ Perceptions of Electronic Documentation and Workflow

PubMed Central

Neri, P.M.; Redden, L.; Poole, S.; Pozner, C.N.; Horsky, J.; Raja, A.S.; Poon, E.; Schiff, G.

2015-01-01

Summary Objective To understand emergency department (ED) physicians’ use of electronic documentation in order to identify usability and workflow considerations for the design of future ED information system (EDIS) physician documentation modules. Methods We invited emergency medicine resident physicians to participate in a mixed methods study using task analysis and qualitative interviews. Participants completed a simulated, standardized patient encounter in a medical simulation center while documenting in the test environment of a currently used EDIS. We recorded the time on task, type and sequence of tasks performed by the participants (including tasks performed in parallel). We then conducted semi-structured interviews with each participant. We analyzed these qualitative data using the constant comparative method to generate themes. Results Eight resident physicians participated. The simulation session averaged 17 minutes and participants spent 11 minutes on average on tasks that included electronic documentation. Participants performed tasks in parallel, such as history taking and electronic documentation. Five of the 8 participants performed a similar workflow sequence during the first part of the session while the remaining three used different workflows. Three themes characterize electronic documentation: (1) physicians report that location and timing of documentation varies based on patient acuity and workload, (2) physicians report a need for features that support improved efficiency; and (3) physicians like viewing available patient data but struggle with integration of the EDIS with other information sources. Conclusion We confirmed that physicians spend much of their time on documentation (65%) during an ED patient visit. Further, we found that resident physicians did not all use the same workflow and approach even when presented with an identical standardized patient scenario. Future EHR design should consider these varied workflows while trying to optimize efficiency, such as improving integration of clinical data. These findings should be tested quantitatively in a larger, representative study. PMID:25848411

Massively parallel and linear-scaling algorithm for second-order Moller–Plesset perturbation theory applied to the study of supramolecular wires

DOE PAGES

Kjaergaard, Thomas; Baudin, Pablo; Bykov, Dmytro; ...

2016-11-16

Here, we present a scalable cross-platform hybrid MPI/OpenMP/OpenACC implementation of the Divide–Expand–Consolidate (DEC) formalism with portable performance on heterogeneous HPC architectures. The Divide–Expand–Consolidate formalism is designed to reduce the steep computational scaling of conventional many-body methods employed in electronic structure theory to linear scaling, while providing a simple mechanism for controlling the error introduced by this approximation. Our massively parallel implementation of this general scheme has three levels of parallelism, being a hybrid of the loosely coupled task-based parallelization approach and the conventional MPI +X programming model, where X is either OpenMP or OpenACC. We demonstrate strong and weak scalabilitymore » of this implementation on heterogeneous HPC systems, namely on the GPU-based Cray XK7 Titan supercomputer at the Oak Ridge National Laboratory. Using the “resolution of the identity second-order Moller–Plesset perturbation theory” (RI-MP2) as the physical model for simulating correlated electron motion, the linear-scaling DEC implementation is applied to 1-aza-adamantane-trione (AAT) supramolecular wires containing up to 40 monomers (2440 atoms, 6800 correlated electrons, 24 440 basis functions and 91 280 auxiliary functions). This represents the largest molecular system treated at the MP2 level of theory, demonstrating an efficient removal of the scaling wall pertinent to conventional quantum many-body methods.« less

CCMC Modeling of Magnetic Reconnection in Electron Diffusion Region Events

NASA Astrophysics Data System (ADS)

Marshall, A.; Reiff, P. H.; Daou, A.; Webster, J.; Sazykin, S. Y.; Kuznetsova, M.; Grocer, A.; Rastaetter, L.; Welling, D. T.; DeZeeuw, D.; Russell, C. T.

2017-12-01

We use the unprecedented spatial and temporal cadence of the Magnetospheric Multiscale Mission to study four electron diffusion events, and infer important physical properties of their respective magnetic reconnection processes. We couple these observations with numerical simulations using tools such as SWMF with RCM, and RECON-X, from the Coordinated Community Modeling Center, to provide, for a first time, a coherent temporal description of the magnetic reconnection process through tracing the coupling of IMF and closed Earth magnetic field lines, leading to the corresponding polar cap open field lines. We note that the reconnection geometry is far from slab-like: the IMF field lines drape over the magnetopause, lending to a stretching of the field lines. The stretched field lines become parallel to, and merge with the dayside separator. Surprisingly, the inner closed field lines also distort to become parallel to the separator. This parallel geometry allows a very sharp boundary between open and closed field lines. In three of the events, the MMS location was near the predicted separator location; in the fourth it was near the outflow region.

The effect of the earth's and stray magnetic fields on mobile mass spectrometer systems.

PubMed

Bell, Ryan J; Davey, Nicholas G; Martinsen, Morten; Short, R Timothy; Gill, Chris G; Krogh, Erik T

2015-02-01

Development of small, field-portable mass spectrometers has enabled a rapid growth of in-field measurements on mobile platforms. In such in-field measurements, unexpected signal variability has been observed by the authors in portable ion traps with internal electron ionization. The orientation of magnetic fields (such as the Earth's) relative to the ionization electron beam trajectory can significantly alter the electron flux into a quadrupole ion trap, resulting in significant changes in the instrumental sensitivity. Instrument simulations and experiments were performed relative to the earth's magnetic field to assess the importance of (1) nonpoint-source electron sources, (2) vertical versus horizontal electron beam orientation, and (3) secondary magnetic fields created by the instrument itself. Electron lens focus effects were explored by additional simulations, and were paralleled by experiments performed with a mass spectrometer mounted on a rotating platform. Additionally, magnetically permeable metals were used to shield (1) the entire instrument from the Earth's magnetic field, and (2) the electron beam from both the Earth's and instrument's magnetic fields. Both simulation and experimental results suggest the predominant influence on directionally dependent signal variability is the result of the summation of two magnetic vectors. As such, the most effective method for reducing this effect is the shielding of the electron beam from both magnetic vectors, thus improving electron beam alignment and removing any directional dependency. The improved ionizing electron beam alignment also allows for significant improvements in overall instrument sensitivity.

Modeling electron emission and surface effects from diamond cathodes

NASA Astrophysics Data System (ADS)

Dimitrov, D. A.; Smithe, D.; Cary, J. R.; Ben-Zvi, I.; Rao, T.; Smedley, J.; Wang, E.

2015-02-01

We developed modeling capabilities, within the Vorpal particle-in-cell code, for three-dimensional simulations of surface effects and electron emission from semiconductor photocathodes. They include calculation of emission probabilities using general, piece-wise continuous, space-time dependent surface potentials, effective mass, and band bending field effects. We applied these models, in combination with previously implemented capabilities for modeling charge generation and transport in diamond, to investigate the emission dependence on applied electric field in the range from approximately 2 MV/m to 17 MV/m along the [100] direction. The simulation results were compared to experimental data. For the considered parameter regime, conservation of transverse electron momentum (in the plane of the emission surface) allows direct emission from only two (parallel to [100]) of the six equivalent lowest conduction band valleys. When the electron affinity χ is the only parameter varied in the simulations, the value χ = 0.31 eV leads to overall qualitative agreement with the probability of emission deduced from experiments. Including band bending in the simulations improves the agreement with the experimental data, particularly at low applied fields, but not significantly. Using surface potentials with different profiles further allows us to investigate the emission as a function of potential barrier height, width, and vacuum level position. However, adding surface patches with different levels of hydrogenation, modeled with position-dependent electron affinity, leads to the closest agreement with the experimental data.

Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors

NASA Astrophysics Data System (ADS)

Ryu, Hoon; Jeong, Yosang; Kang, Ji-Hoon; Cho, Kyu Nam

2016-12-01

Modelling of multi-million atomic semiconductor structures is important as it not only predicts properties of physically realizable novel materials, but can accelerate advanced device designs. This work elaborates a new Technology-Computer-Aided-Design (TCAD) tool for nanoelectronics modelling, which uses a sp3d5s∗ tight-binding approach to describe multi-million atomic structures, and simulate electronic structures with high performance computing (HPC), including atomic effects such as alloy and dopant disorders. Being named as Quantum simulation tool for Advanced Nanoscale Devices (Q-AND), the tool shows nice scalability on traditional multi-core HPC clusters implying the strong capability of large-scale electronic structure simulations, particularly with remarkable performance enhancement on latest clusters of Intel Xeon PhiTM coprocessors. A review of the recent modelling study conducted to understand an experimental work of highly phosphorus-doped silicon nanowires, is presented to demonstrate the utility of Q-AND. Having been developed via Intel Parallel Computing Center project, Q-AND will be open to public to establish a sound framework of nanoelectronics modelling with advanced HPC clusters of a many-core base. With details of the development methodology and exemplary study of dopant electronics, this work will present a practical guideline for TCAD development to researchers in the field of computational nanoelectronics.

Alternative modeling methods for plasma-based Rf ion sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veitzer, Seth A., E-mail: veitzer@txcorp.com; Kundrapu, Madhusudhan, E-mail: madhusnk@txcorp.com; Stoltz, Peter H., E-mail: phstoltz@txcorp.com

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H{sup −} source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. Inmore » particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H{sup −} ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.« less

Alternative modeling methods for plasma-based Rf ion sources.

PubMed

Veitzer, Seth A; Kundrapu, Madhusudhan; Stoltz, Peter H; Beckwith, Kristian R C

2016-02-01

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H(-) source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. In particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H(-) ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.

Beam distribution reconstruction simulation for electron beam probe

NASA Astrophysics Data System (ADS)

Feng, Yong-Chun; Mao, Rui-Shi; Li, Peng; Kang, Xin-Cai; Yin, Yan; Liu, Tong; You, Yao-Yao; Chen, Yu-Cong; Zhao, Tie-Cheng; Xu, Zhi-Guo; Wang, Yan-Yu; Yuan, You-Jin

2017-07-01

An electron beam probe (EBP) is a detector which makes use of a low-intensity and low-energy electron beam to measure the transverse profile, bunch shape, beam neutralization and beam wake field of an intense beam with small dimensions. While it can be applied to many aspects, we limit our analysis to beam distribution reconstruction. This kind of detector is almost non-interceptive for all of the beam and does not disturb the machine environment. In this paper, we present the theoretical aspects behind this technique for beam distribution measurement and some simulation results of the detector involved. First, a method to obtain a parallel electron beam is introduced and a simulation code is developed. An EBP as a profile monitor for dense beams is then simulated using the fast scan method for various target beam profiles, including KV distribution, waterbag distribution, parabolic distribution, Gaussian distribution and halo distribution. Profile reconstruction from the deflected electron beam trajectory is implemented and compared with the actual profile, and the expected agreement is achieved. Furthermore, as well as fast scan, a slow scan, i.e. step-by-step scan, is considered, which lowers the requirement for hardware, i.e. Radio Frequency deflector. We calculate the three-dimensional electric field of a Gaussian distribution and simulate the electron motion in this field. In addition, a fast scan along the target beam direction and slow scan across the beam are also presented, and can provide a measurement of longitudinal distribution as well as transverse profile simultaneously. As an example, simulation results for the China Accelerator Driven Sub-critical System (CADS) and High Intensity Heavy Ion Accelerator Facility (HIAF) are given. Finally, a potential system design for an EBP is described.

MPI parallelization of Vlasov codes for the simulation of nonlinear laser-plasma interactions

NASA Astrophysics Data System (ADS)

Savchenko, V.; Won, K.; Afeyan, B.; Decyk, V.; Albrecht-Marc, M.; Ghizzo, A.; Bertrand, P.

2003-10-01

The simulation of optical mixing driven KEEN waves [1] and electron plasma waves [1] in laser-produced plasmas require nonlinear kinetic models and massive parallelization. We use Massage Passing Interface (MPI) libraries and Appleseed [2] to solve the Vlasov Poisson system of equations on an 8 node dual processor MAC G4 cluster. We use the semi-Lagrangian time splitting method [3]. It requires only row-column exchanges in the global data redistribution, minimizing the total number of communications between processors. Recurrent communication patterns for 2D FFTs involves global transposition. In the Vlasov-Maxwell case, we use splitting into two 1D spatial advections and a 2D momentum advection [4]. Discretized momentum advection equations have a double loop structure with the outer index being assigned to different processors. We adhere to a code structure with separate routines for calculations and data management for parallel computations. [1] B. Afeyan et al., IFSA 2003 Conference Proceedings, Monterey, CA [2] V. K. Decyk, Computers in Physics, 7, 418 (1993) [3] Sonnendrucker et al., JCP 149, 201 (1998) [4] Begue et al., JCP 151, 458 (1999)

Metascalable molecular dynamics simulation of nano-mechano-chemistry

NASA Astrophysics Data System (ADS)

Shimojo, F.; Kalia, R. K.; Nakano, A.; Nomura, K.; Vashishta, P.

2008-07-01

We have developed a metascalable (or 'design once, scale on new architectures') parallel application-development framework for first-principles based simulations of nano-mechano-chemical processes on emerging petaflops architectures based on spatiotemporal data locality principles. The framework consists of (1) an embedded divide-and-conquer (EDC) algorithmic framework based on spatial locality to design linear-scaling algorithms, (2) a space-time-ensemble parallel (STEP) approach based on temporal locality to predict long-time dynamics, and (3) a tunable hierarchical cellular decomposition (HCD) parallelization framework to map these scalable algorithms onto hardware. The EDC-STEP-HCD framework exposes and expresses maximal concurrency and data locality, thereby achieving parallel efficiency as high as 0.99 for 1.59-billion-atom reactive force field molecular dynamics (MD) and 17.7-million-atom (1.56 trillion electronic degrees of freedom) quantum mechanical (QM) MD in the framework of the density functional theory (DFT) on adaptive multigrids, in addition to 201-billion-atom nonreactive MD, on 196 608 IBM BlueGene/L processors. We have also used the framework for automated execution of adaptive hybrid DFT/MD simulation on a grid of six supercomputers in the US and Japan, in which the number of processors changed dynamically on demand and tasks were migrated according to unexpected faults. The paper presents the application of the framework to the study of nanoenergetic materials: (1) combustion of an Al/Fe2O3 thermite and (2) shock initiation and reactive nanojets at a void in an energetic crystal.

The computer-aided parallel external fixator for complex lower limb deformity correction.

PubMed

Wei, Mengting; Chen, Jianwen; Guo, Yue; Sun, Hao

2017-12-01

Since parameters of the parallel external fixator are difficult to measure and calculate in real applications, this study developed computer software that can help the doctor measure parameters using digital technology and generate an electronic prescription for deformity correction. According to Paley's deformity measurement method, we provided digital measurement techniques. In addition, we proposed an deformity correction algorithm to calculate the elongations of the six struts and developed a electronic prescription software. At the same time, a three-dimensional simulation of the parallel external fixator and deformed fragment was made using virtual reality modeling language technology. From 2013 to 2015, fifteen patients with complex lower limb deformity were treated with parallel external fixators and the self-developed computer software. All of the cases had unilateral limb deformity. The deformities were caused by old osteomyelitis in nine cases and traumatic sequelae in six cases. A doctor measured the related angulation, displacement and rotation on postoperative radiographs using the digital measurement techniques. Measurement data were input into the electronic prescription software to calculate the daily adjustment elongations of the struts. Daily strut adjustments were conducted according to the data calculated. The frame was removed when expected results were achieved. Patients lived independently during the adjustment. The mean follow-up was 15 months (range 10-22 months). The duration of frame fixation from the time of application to the time of removal averaged 8.4 months (range 2.5-13.1 months). All patients were satisfied with the corrected limb alignment. No cases of wound infections or complications occurred. Using the computer-aided parallel external fixator for the correction of lower limb deformities can achieve satisfactory outcomes. The correction process can be simplified and is precise and digitized, which will greatly improve the treatment in a clinical application.

HPC Insights, Fall 2011

DTIC Science & Technology

2011-01-01

Simulating Satellite Tracking Using Parallel Computing By Andrew Lindstrom ,University of Hawaii at Hilo — Mentors: Carl Holmberg, Maui High Performance...RDECOM) and his management team, RDECOM Deputy Director Gary Martin ; ARL Director John Miller; Communications- Electronics Research, Development...Saves Resources By Mike Knowles, ARL DSRC Site Lead, Lockheed Martin mode instead of full power down. The first phase of the EAS effort is an attempt

Joint Services Electronics Program

DTIC Science & Technology

1992-03-05

Packaging Considerations M. T. Raghunath (Professor Abhiram Ranade) A central issue in massively parallel computation is the design of the interconnection...programs on promising network architectures. Publications: [1] M. T. Raghunath and A. G. Ranade, A Simulation-Based Compari- son of Interconnection Networks...more difficult analog function approximation task. Network Design Issues for Fast Global Communication Professor A. Ranade with M.T. Raghunath A

Naval Surface Warfare Center Carderock Division, Technical Digest

DTIC Science & Technology

2001-12-01

Survivability Systems: An Overview Fred J. Fisch 139 Modeling and Simulation of Weapons Effects on Ships Robert R. Wunderlick 143 Intelligent Networks ...communications capability of forces afloat to support emerging network -centric warfare doc- trines. Stealth, for our next generation of warships...fully-inte- grated, fully- networked electronic countermeasures system, developed in parallel and in close coordination with sister systems. An

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Parallelization and automatic data distribution for nuclear reactor simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebrock, L.M.

1997-07-01

Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directlymore » affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.« less

A scalable parallel black oil simulator on distributed memory parallel computers

NASA Astrophysics Data System (ADS)

Wang, Kun; Liu, Hui; Chen, Zhangxin

2015-11-01

This paper presents our work on developing a parallel black oil simulator for distributed memory computers based on our in-house parallel platform. The parallel simulator is designed to overcome the performance issues of common simulators that are implemented for personal computers and workstations. The finite difference method is applied to discretize the black oil model. In addition, some advanced techniques are employed to strengthen the robustness and parallel scalability of the simulator, including an inexact Newton method, matrix decoupling methods, and algebraic multigrid methods. A new multi-stage preconditioner is proposed to accelerate the solution of linear systems from the Newton methods. Numerical experiments show that our simulator is scalable and efficient, and is capable of simulating extremely large-scale black oil problems with tens of millions of grid blocks using thousands of MPI processes on parallel computers.

Study of the effective point of measurement for ion chambers in electron beams by Monte Carlo simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, L. L. W.; Rogers, D. W. O.

In current dosimetry protocols for electron beams, for plane-parallel chambers, the effective point of measurement is at the front face of the cavity, and, for cylindrical chambers, it is at a point shifted 0.5r upstream from the cavity center. In this study, Monte Carlo simulations are employed to study the issue of effective point of measurement for both plane-parallel chambers and cylindrical thimble chambers in electron beams. It is found that there are two ways of determining the position of the effective point of measurement: One is to match the calculated depth-ionization curve obtained from a modeled chamber to amore » calculated depth-dose curve; the other is to match the electron fluence spectrum in the chamber cavity to that in the phantom. For plane-parallel chambers, the effective point of measurement determined by the first method is generally not at the front face of the chamber cavity, which is obtained by the second method, but shifted downstream toward the cavity center by an amount that could be larger than one-half a millimeter. This should not be ignored when measuring depth-dose curves in electron beams. For cylindrical chambers, these two methods also give different positions of the effective point of measurement: The first gives a shift of 0.5r, which is in agreement with measurements for high-energy beams and is the same as the value currently used in major dosimetry protocols; the latter gives a shift of 0.8r, which is closer to the value predicted by a theoretical calculation assuming no-scatter conditions. The results also show that the shift of 0.8r is more appropriate if the cylindrical chamber is to be considered as a Spencer-Attix cavity. In electron beams, since the water/air stopping-power ratio changes with depth in a water phantom, the difference of the two shifts (0.3r) will lead to an incorrect evaluation of the water/air stopping-power ratio at the point of measurement, thus resulting in a systematic error in determining the absorbed dose by cylindrical chambers. It is suggested that a shift of 0.8r be used for electron beam calibrations with cylindrical chambers and a shift of 0.4r-0.5r be used for depth-dose measurements.« less

Study of the effective point of measurement for ion chambers in electron beams by Monte Carlo simulation.

PubMed

Wang, L L W; Rogers, D W O

2009-06-01

In current dosimetry protocols for electron beams, for plane-parallel chambers, the effective point of measurement is at the front face of the cavity, and, for cylindrical chambers, it is at a point shifted 0.5r upstream from the cavity center. In this study, Monte Carlo simulations are employed to study the issue of effective point of measurement for both plane-parallel chambers and cylindrical thimble chambers in electron beams. It is found that there are two ways of determining the position of the effective point of measurement: One is to match the calculated depth-ionization curve obtained from a modeled chamber to a calculated depth-dose curve; the other is to match the electron fluence spectrum in the chamber cavity to that in the phantom. For plane-parallel chambers, the effective point of measurement determined by the first method is generally not at the front face of the chamber cavity, which is obtained by the second method, but shifted downstream toward the cavity center by an amount that could be larger than one-half a millimeter. This should not be ignored when measuring depth-dose curves in electron beams. For cylindrical chambers, these two methods also give different positions of the effective point of measurement: The first gives a shift of 0.5r, which is in agreement with measurements for high-energy beams and is the same as the value currently used in major dosimetry protocols; the latter gives a shift of 0.8r, which is closer to the value predicted by a theoretical calculation assuming no-scatter conditions. The results also show that the shift of 0.8r is more appropriate if the cylindrical chamber is to be considered as a Spencer-Attix cavity. In electron beams, since the water/air stopping-power ratio changes with depth in a water phantom, the difference of the two shifts (0.3r) will lead to an incorrect evaluation of the water/air stopping-power ratio at the point of measurement, thus resulting in a systematic error in determining the absorbed dose by cylindrical chambers. It is suggested that a shift of 0.8r be used for electron beam calibrations with cylindrical chambers and a shift of 0.4r-0.5r be used for depth-dose measurements.

A new hybrid code (CHIEF) implementing the inertial electron fluid equation without approximation

NASA Astrophysics Data System (ADS)

Muñoz, P. A.; Jain, N.; Kilian, P.; Büchner, J.

2018-03-01

We present a new hybrid algorithm implemented in the code CHIEF (Code Hybrid with Inertial Electron Fluid) for simulations of electron-ion plasmas. The algorithm treats the ions kinetically, modeled by the Particle-in-Cell (PiC) method, and electrons as an inertial fluid, modeled by electron fluid equations without any of the approximations used in most of the other hybrid codes with an inertial electron fluid. This kind of code is appropriate to model a large variety of quasineutral plasma phenomena where the electron inertia and/or ion kinetic effects are relevant. We present here the governing equations of the model, how these are discretized and implemented numerically, as well as six test problems to validate our numerical approach. Our chosen test problems, where the electron inertia and ion kinetic effects play the essential role, are: 0) Excitation of parallel eigenmodes to check numerical convergence and stability, 1) parallel (to a background magnetic field) propagating electromagnetic waves, 2) perpendicular propagating electrostatic waves (ion Bernstein modes), 3) ion beam right-hand instability (resonant and non-resonant), 4) ion Landau damping, 5) ion firehose instability, and 6) 2D oblique ion firehose instability. Our results reproduce successfully the predictions of linear and non-linear theory for all these problems, validating our code. All properties of this hybrid code make it ideal to study multi-scale phenomena between electron and ion scales such as collisionless shocks, magnetic reconnection and kinetic plasma turbulence in the dissipation range above the electron scales.

Application Note: Power Grid Modeling With Xyce.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sholander, Peter E.

This application note describes how to model steady-state power flows and transient events in electric power grids with the SPICE-compatible Xyce TM Parallel Electronic Simulator developed at Sandia National Labs. This application notes provides a brief tutorial on the basic devices (branches, bus shunts, transformers and generators) found in power grids. The focus is on the features supported and assumptions made by the Xyce models for power grid elements. It then provides a detailed explanation, including working Xyce netlists, for simulating some simple power grid examples such as the IEEE 14-bus test case.

The 3-D numerical simulation research of vacuum injector for linear induction accelerator

NASA Astrophysics Data System (ADS)

Liu, Dagang; Xie, Mengjun; Tang, Xinbing; Liao, Shuqing

2017-01-01

Simulation method for voltage in-feed and electron injection of vacuum injector is given, and verification of the simulated voltage and current is carried out. The numerical simulation for the magnetic field of solenoid is implemented, and a comparative analysis is conducted between the simulation results and experimental results. A semi-implicit difference algorithm is adopted to suppress the numerical noise, and a parallel acceleration algorithm is used for increasing the computation speed. The RMS emittance calculation method of the beam envelope equations is analyzed. In addition, the simulated results of RMS emittance are compared with the experimental data. Finally, influences of the ferromagnetic rings on the radial and axial magnetic fields of solenoid as well as the emittance of beam are studied.

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λ De, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρ e and λ De, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τ s, versus fast-ion charge are in agreement with unmagnetized slowing-down theory;more » with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. In conclusion, the implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.« less

Particle-in-cell studies of fast-ion slowing-down rates in cool tenuous magnetized plasma

DOE PAGES

Evans, Eugene S.; Cohen, Samuel A.; Welch, Dale R.

2018-04-05

We report on 3D-3V particle-in-cell simulations of fast-ion energy-loss rates in a cold, weakly-magnetized, weakly-coupled plasma where the electron gyroradius, ρe, is comparable to or less than the Debye length, λ De, and the fast-ion velocity exceeds the electron thermal velocity, a regime in which the electron response may be impeded. These simulations use explicit algorithms, spatially resolve ρ e and λ De, and temporally resolve the electron cyclotron and plasma frequencies. For mono-energetic dilute fast ions with isotropic velocity distributions, these scaling studies of the slowing-down time, τ s, versus fast-ion charge are in agreement with unmagnetized slowing-down theory;more » with an applied magnetic field, no consistent anisotropy between τs in the cross-field and field-parallel directions could be resolved. Scaling the fast-ion charge is confirmed as a viable way to reduce the required computational time for each simulation. In conclusion, the implications of these slowing down processes are described for one magnetic-confinement fusion concept, the small, advanced-fuel, field-reversed configuration device.« less

Investigations of Turbulent Transport Channels in Gyrokinetic Simulations

NASA Astrophysics Data System (ADS)

Dimits, A. M.; Candy, J.; Guttenfelder, W.; Holland, C.; Howard, N.; Nevins, W. M.; Wang, E.

2014-10-01

Magnetic-field stochasticity arises due to microtearing perturbations, which can be driven linearly or nonlinearly (in cases where they are linearly stable), even at very modest values of the plasma beta. The resulting magnetic-flutter contribution may or may not be a significant component of the overall electron (particle and thermal) transport. Investigations of the effect of ExB flow shear on electron-drift magnetic-flutter diffusion coefficient Dedr (r ,v||) using perturbed magnetic fields from simulations, using the GYRO code, of ITG turbulence show a significant effect for electrons with parallel velocities v|| surprisingly far from the resonant velocity. We further examine changes in the radial dependence of this diffusion coefficient vs. v|| and which resonant magnetic-field perturbations are important to the values and radial structure of Dedr. The resulting electron transport fluxes are compared with the simulation results. Improvements over in treating the ambipolar field in the relationship between the magnetic (or drift) diffusion coefficients and the transport have been made in these comparisons. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344, by GA under Contract DE-FG03-95ER54309, and by PPPL under Contract DE-AC02-09CH11466.

Cold Electrons as the Drivers of Parallel, Electrostatic Waves in Asymmetric Reconnection

NASA Astrophysics Data System (ADS)

Holmes, J.; Ergun, R.; Newman, D. L.; Wilder, F. D.; Schwartz, S. J.; Goodrich, K.; Eriksson, S.; Torbert, R. B.; Russell, C. T.; Lindqvist, P. A.; Giles, B. L.; Pollock, C. J.; Le Contel, O.; Strangeway, R. J.; Burch, J. L.

2016-12-01

The Magnetospheric MultiScale mission (MMS) has observed several instances of asymmetric reconnection at Earth's magnetopause, where plasma from the magnetosheath encounters that of the magnetosphere. On Earth's dayside, the magnetosphere is often made up of a two-component distribution of cold (<< 10 eV) and hot ( 1 keV) plasma, sometimes including the cold ion plume. Magnetosheath plasma is primarily warm ( 100 eV) post-shock solar wind. Where they meet, magnetopause reconnection alters the magnetic topology such that these two populations are left cohabiting a field line and rapidly mix. There have been several events observed by MMS where the Fast Plasma Instrument (FPI) clearly shows cold ions near the diffusion region impinging upon the warm magnetosheath population. In many of these, we also see patches of strong electrostatic waves parallel to the magnetic field - a smoking gun for rapid mixing via nonlinear processes. Cold ions alone are too slow to create the same waves; solving for roots of a simplified dispersion relation shows the electron population damps out the ion modes. From this, we infer the presence of cold electrons; in one notable case found by Wilder et al. 2016 (in review), they have been observed directly by FPI. Vlasov simulations of plasma mixing for a number of these events closely reproduce the observed electric field signatures. We conclude from numerical analysis and direct MMS observations that cold plasma mixing, including cold electrons, is the primary driver of parallel electrostatic waves observed near the electron diffusion region in asymmetric magnetic reconnection.

Advances in simulation of wave interactions with extended MHD phenomena

NASA Astrophysics Data System (ADS)

Batchelor, D.; Abla, G.; D'Azevedo, E.; Bateman, G.; Bernholdt, D. E.; Berry, L.; Bonoli, P.; Bramley, R.; Breslau, J.; Chance, M.; Chen, J.; Choi, M.; Elwasif, W.; Foley, S.; Fu, G.; Harvey, R.; Jaeger, E.; Jardin, S.; Jenkins, T.; Keyes, D.; Klasky, S.; Kruger, S.; Ku, L.; Lynch, V.; McCune, D.; Ramos, J.; Schissel, D.; Schnack, D.; Wright, J.

2009-07-01

The Integrated Plasma Simulator (IPS) provides a framework within which some of the most advanced, massively-parallel fusion modeling codes can be interoperated to provide a detailed picture of the multi-physics processes involved in fusion experiments. The presentation will cover four topics: 1) recent improvements to the IPS, 2) application of the IPS for very high resolution simulations of ITER scenarios, 3) studies of resistive and ideal MHD stability in tokamk discharges using IPS facilities, and 4) the application of RF power in the electron cyclotron range of frequencies to control slowly growing MHD modes in tokamaks and initial evaluations of optimized location for RF power deposition.

Parallelized direct execution simulation of message-passing parallel programs

NASA Technical Reports Server (NTRS)

Dickens, Phillip M.; Heidelberger, Philip; Nicol, David M.

1994-01-01

As massively parallel computers proliferate, there is growing interest in findings ways by which performance of massively parallel codes can be efficiently predicted. This problem arises in diverse contexts such as parallelizing computers, parallel performance monitoring, and parallel algorithm development. In this paper we describe one solution where one directly executes the application code, but uses a discrete-event simulator to model details of the presumed parallel machine such as operating system and communication network behavior. Because this approach is computationally expensive, we are interested in its own parallelization specifically the parallelization of the discrete-event simulator. We describe methods suitable for parallelized direct execution simulation of message-passing parallel programs, and report on the performance of such a system, Large Application Parallel Simulation Environment (LAPSE), we have built on the Intel Paragon. On all codes measured to date, LAPSE predicts performance well typically within 10 percent relative error. Depending on the nature of the application code, we have observed low slowdowns (relative to natively executing code) and high relative speedups using up to 64 processors.

Cyclic behavior at quasi-parallel collisionless shocks

NASA Technical Reports Server (NTRS)

Burgess, D.

1989-01-01

Large scale one-dimensional hybrid simulations with resistive electrons have been carried out of a quasi-parallel high-Mach-number collisionless shock. The shock initially appears stable, but then exhibits cyclic behavior. For the magnetic field, the cycle consists of a period when the transition from upstream to downstream is steep and well defined, followed by a period when the shock transition is extended and perturbed. This cyclic shock solution results from upstream perturbations caused by backstreaming gyrating ions convecting into the shock. The cyclic reformation of a sharp shock transition can allow ions, at one time upstream because of reflection or leakage, to contribute to the shock thermalization.

Wave Turning and Flow Angle in the E-Region Ionosphere

NASA Astrophysics Data System (ADS)

Young, M.; Oppenheim, M. M.; Dimant, Y. S.

2016-12-01

This work presents results of particle-in-cell (PIC) simulations of Farley-Buneman (FB) turbulence at various altitudes in the high-latitude E-region ionosphere. In that region, the FB instability regularly produces meter-scale plasma irregularities. VHF radars observe coherent echoes via Bragg scatter from wave fronts parallel or anti-parallel to the radar line of sight (LoS) but do not necessarily measure the mean direction of wave propagation. Haldoupis (1984) conducted a study of diffuse radar aurora and found that the spectral width of back-scattered power depends critically on the angle between the radar LoS and the true flow direction, called the flow angle. Knowledge of the flow angle will allow researchers to better interpret observations of coherent back-scatter. Experiments designed to observe meter-scale irregularities in the E-region ionosphere created by the FB instability typically assume that the predominant flow direction is the E×B direction. However, linear theory of Dimant and Oppenheim (2004) showed that FB waves should turn away from E×B and particle-in-cell simulations by Oppenheim and Dimant (2013) support the theory. The present study comprises a quantitative analysis of the dependence of back-scattered power, flow velocity, and spectral width as functions of the flow angle. It also demonstrates that the mean direction of meter-scale wave propagation may differ from the E×B direction by tens of degrees. The analysis includes 2-D and 3-D simulations at a range of altitudes in the auroral ionosphere. Comparison between 2-D and 3-D simulations illustrates the relative importance to the irregularity spectrum of a small but finite component in the direction parallel to B. Previous work has shown this small parallel component to be important to turbulent electron heating and nonlinear transport.

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Proton fire hose instabilities in the expanding solar wind: Role of oblique magnetic field

NASA Astrophysics Data System (ADS)

Hellinger, Petr

2016-04-01

The double adiabatic (CGL) approximation for the ideal (Parker) interplanetary magnetic field (IMF) predicts generation of the parallel particle temperature anisotropy (T∥ > T⊥) for a nearly radial magnetic field whereas for a strongly oblique IMF generation of the opposite temperature anisotropy is expected. The transition between the two behaviours is expected at around 45o, i.e. around 1 AU in the solar wind in the ecliptic plane. We investigate properties of a proton-electron plasma system in the solar wind using hybrid expanding box simulations starting with an oblique IMF. The simulated system becomes unstable with respect to the parallel and oblique fire hose instabilities and is forced to stay around the corresponding marginal stability. Rotation of the IMF reduces the time system stays near the marginal stability regions and for a strongly transverse IMF the system moves away from the regions unstable with respect to the fire hose instabilities.

A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor

NASA Technical Reports Server (NTRS)

Rao, Hariprasad Nannapaneni

1989-01-01

The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.

Parallel simulation today

NASA Technical Reports Server (NTRS)

Nicol, David; Fujimoto, Richard

1992-01-01

This paper surveys topics that presently define the state of the art in parallel simulation. Included in the tutorial are discussions on new protocols, mathematical performance analysis, time parallelism, hardware support for parallel simulation, load balancing algorithms, and dynamic memory management for optimistic synchronization.

Spatial dimensions of the electron diffusion region in anti-parallel magnetic reconnection

NASA Astrophysics Data System (ADS)

Nakamura, Takuma; Nakamura, Rumi; Haseagwa, Hiroshi

2016-03-01

Spatial dimensions of the detailed structures of the electron diffusion region in anti-parallel magnetic reconnection were analyzed based on two-dimensional fully kinetic particle-in-cell simulations. The electron diffusion region in this study is defined as the region where the positive reconnection electric field is sustained by the electron inertial and non-gyrotropic pressure components. Past kinetic studies demonstrated that the dimensions of the whole electron diffusion region and the inner non-gyrotropic region are scaled by the electron inertial length de and the width of the electron meandering motion, respectively. In this study, we successfully obtained more precise scalings of the dimensions of these two regions than the previous studies by performing simulations with sufficiently small grid spacing (1/16-1/8 de) and a sufficient number of particles (800 particles cell-1 on average) under different conditions changing the ion-to-electron mass ratio, the background density and the electron βe (temperature). The obtained scalings are adequately supported by some theories considering spatial variations of field and plasma parameters within the diffusion region. In the reconnection inflow direction, the dimensions of both regions are proportional to de based on the background density. Both dimensions also depend on βe based on the background values, but the dependence in the inner region ( ˜ 0.375th power) is larger than the whole region (0.125th power) reflecting the orbits of meandering and accelerated electrons within the inner region. In the outflow direction, almost only the non-gyrotropic component sustains the positive reconnection electric field. The dimension of this single-scale diffusion region is proportional to the ion-electron hybrid inertial length (dide)1/2 based on the background density and weakly depends on the background βe with the 0.25th power. These firm scalings allow us to predict observable dimensions in real space which are indeed in reasonable agreement with past in situ spacecraft observations in the Earth's magnetotail and have important implications for future observations with higher resolutions such as the NASA Magnetospheric Multiscale (MMS) mission.

Synchronization Of Parallel Discrete Event Simulations

NASA Technical Reports Server (NTRS)

Steinman, Jeffrey S.

1992-01-01

Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.

Evolving non-thermal electrons in simulations of black hole accretion

NASA Astrophysics Data System (ADS)

Chael, Andrew A.; Narayan, Ramesh; Saḑowski, Aleksander

2017-09-01

Current simulations of hot accretion flows around black holes assume either a single-temperature gas or, at best, a two-temperature gas with thermal ions and electrons. However, processes like magnetic reconnection and shocks can accelerate electrons into a non-thermal distribution, which will not quickly thermalize at the very low densities found in many systems. Such non-thermal electrons have been invoked to explain the infrared and X-ray spectra and strong variability of Sagittarius A* (Sgr A*), the black hole at the Galactic Center. We present a method for self-consistent evolution of a non-thermal electron population in the general relativistic magnetohydrodynamic code koral. The electron distribution is tracked across Lorentz factor space and is evolved in space and time, in parallel with thermal electrons, thermal ions and radiation. In this study, for simplicity, energy injection into the non-thermal distribution is taken as a fixed fraction of the local electron viscous heating rate. Numerical results are presented for a model with a low mass accretion rate similar to that of Sgr A*. We find that the presence of a non-thermal population of electrons has negligible effect on the overall dynamics of the system. Due to our simple uniform particle injection prescription, the radiative power in the non-thermal simulation is enhanced at large radii. The energy distribution of the non-thermal electrons shows a synchrotron cooling break, with the break Lorentz factor varying with location and time, reflecting the complex interplay between the local viscous heating rate, magnetic field strength and fluid velocity.

Beam quality corrections for parallel-plate ion chambers in electron reference dosimetry

NASA Astrophysics Data System (ADS)

Zink, K.; Wulff, J.

2012-04-01

Current dosimetry protocols (AAPM, IAEA, IPEM, DIN) recommend parallel-plate ionization chambers for dose measurements in clinical electron beams. This study presents detailed Monte Carlo simulations of beam quality correction factors for four different types of parallel-plate chambers: NACP-02, Markus, Advanced Markus and Roos. These chambers differ in constructive details which should have notable impact on the resulting perturbation corrections, hence on the beam quality corrections. The results reveal deviations to the recommended beam quality corrections given in the IAEA TRS-398 protocol in the range of 0%-2% depending on energy and chamber type. For well-guarded chambers, these deviations could be traced back to a non-unity and energy-dependent wall perturbation correction. In the case of the guardless Markus chamber, a nearly energy-independent beam quality correction is resulting as the effects of wall and cavity perturbation compensate each other. For this chamber, the deviations to the recommended values are the largest and may exceed 2%. From calculations of type-B uncertainties including effects due to uncertainties of the underlying cross-sectional data as well as uncertainties due to the chamber material composition and chamber geometry, the overall uncertainty of calculated beam quality correction factors was estimated to be <0.7%. Due to different chamber positioning recommendations given in the national and international dosimetry protocols, an additional uncertainty in the range of 0.2%-0.6% is present. According to the IAEA TRS-398 protocol, the uncertainty in clinical electron dosimetry using parallel-plate ion chambers is 1.7%. This study may help to reduce this uncertainty significantly.

3D PIC-MCC simulations of positive streamers in air gaps

NASA Astrophysics Data System (ADS)

Jiang, M.; Li, Y.; Wang, H.; Liu, C.

2017-10-01

Simulation of positive streamer evolution is important for understanding the microscopic physical process in discharges. Simulations described in this paper are done using a 3D Particle-In-Cell, Monte-Carlo-Collision code with photoionization. Three phases of a positive streamer evolution, identified as initiation, propagation, and branching are studied during simulations. A homogeneous electric field is applied between parallel-flat electrodes forming a millimeter air gap to make simulations and analysis more simple and general. Free electrons created by the photoionization process determine initiation, propagation, and branching of the streamers. Electron avalanches form a positive streamer tip, when the space charge of ions at the positive tip dominates the local electric field. The propagation of the positive tip toward a cathode is the result of combinations of the positive tip and secondary avalanches ahead of it. A curved feather-like channel is formed without obvious branches when the electric field between electrodes is 50 kV/cm. However, a channel is formed with obvious branches when the electric field increases up to 60 kV/cm. In contrast to the branches around a sharp needle electrode, branches near the flat anode are formed at a certain distance away from it. Simulated parameters of the streamer such as diameter, maximum electric field, propagation velocity, and electron density at the streamer tip are in a good agreement with those published earlier.

Demonstration of Anisotropic Fluid Closure Capturing the Kinetic Structure of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, Obioma

2012-10-01

Magnetic reconnection in collisionless plasmas plays an important role in space and laboratory plasmas. Allowing magnetic stress to be reduced by a rearrangement of magnetic line topology, this process is often accompanied by a large release of magnetic field energy, which can heat the plasma, drive large scale flows, or accelerate particles. Reconnection has been widely studied through fluid models and kinetic simulations. While two-fluid models often reproduce the fast reconnection that is observed in nature and seen in kinetic simulations, it is found that the structure surrounding the electron diffusion region and the electron current layer differ vastly between fluid models and kinetic simulations [1]. Recently, using an adiabatic solution of the Vlasov equation, a new fluid closure has been obtained for electrons that relate parallel and perpendicular pressures to the density and magnetic field [2]. Here we present the results of fluid simulation, developed using the HiFi framework [3], that implements new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations [4]. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding for reconnection in weakly collisional regimes.[4pt] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0pt] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0pt] [3] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011). [0pt] [4] Ohia O, et al., Phys. Rev. Lett. In Press (2012).

Fast simulation of the NICER instrument

NASA Astrophysics Data System (ADS)

Doty, John P.; Wampler-Doty, Matthew P.; Prigozhin, Gregory Y.; Okajima, Takashi; Arzoumanian, Zaven; Gendreau, Keith

2016-07-01

The NICER1 mission uses a complicated physical system to collect information from objects that are, by x-ray timing science standards, rather faint. To get the most out of the data we will need a rigorous understanding of all instrumental effects. We are in the process of constructing a very fast, high fidelity simulator that will help us to assess instrument performance, support simulation-based data reduction, and improve our estimates of measurement error. We will combine and extend existing optics, detector, and electronics simulations. We will employ the Compute Unified Device Architecture (CUDA2) to parallelize these calculations. The price of suitable CUDA-compatible multi-giga op cores is about $0.20/core, so this approach will be very cost-effective.

Dissipation and particle energization in moderate to low beta turbulent plasma via PIC simulations

NASA Astrophysics Data System (ADS)

Makwana, Kirit; Li, Hui; Guo, Fan; Li, Xiaocan

2017-05-01

We simulate decaying turbulence in electron-positron pair plasmas using a fully-kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma β (the ratio of thermal pressure to magnetic pressure). The energy decay rate is found to be similar in both cases. The perpendicular wave-number spectrum of magnetic energy shows a slope between {k}\\perp -1.3 and {k}\\perp -1.1, where the perpendicular (⊥) and parallel (∥) directions are defined with respect to the magnetic field. The particle kinetic energy distribution function shows the formation of a non-thermal feature in the case of lower plasma β, with a slope close to E-1. The correlation between thin turbulent current sheets and Ohmic heating by the dot product of electric field (E) and current density (J) is investigated. Heating by the parallel E∥ · J∥ term dominates the perpendicular E⊥ · J⊥ term. Regions of strong E∥ · J∥ are spatially well-correlated with regions of intense current sheets, which also appear correlated with regions of strong E∥ in the low β simulation, suggesting an important role of magnetic reconnection in the dissipation of low β plasma turbulence.

Modeling electron emission and surface effects from diamond cathodes

DOE PAGES

Dimitrov, D. A.; Smithe, D.; Cary, J. R.; ...

2015-02-05

We developed modeling capabilities, within the Vorpal particle-in-cell code, for three-dimensional (3D) simulations of surface effects and electron emission from semiconductor photocathodes. They include calculation of emission probabilities using general, piece-wise continuous, space-time dependent surface potentials, effective mass and band bending field effects. We applied these models, in combination with previously implemented capabilities for modeling charge generation and transport in diamond, to investigate the emission dependence on applied electric field in the range from approximately 2 MV/m to 17 MV/m along the [100] direction. The simulation results were compared to experimental data. For the considered parameter regime, conservation of transversemore » electron momentum (in the plane of the emission surface) allows direct emission from only two (parallel to [100]) of the six equivalent lowest conduction band valleys. When the electron affinity χ is the only parameter varied in the simulations, the value χ = 0.31 eV leads to overall qualitative agreement with the probability of emission deduced from experiments. Including band bending in the simulations improves the agreement with the experimental data, particularly at low applied fields, but not significantly. In this study, using surface potentials with different profiles further allows us to investigate the emission as a function of potential barrier height, width, and vacuum level position. However, adding surface patches with different levels of hydrogenation, modeled with position-dependent electron affinity, leads to the closest agreement with the experimental data.« less

A brightness exceeding simulated Langmuir limit

NASA Astrophysics Data System (ADS)

Nakasuji, Mamoru

2013-08-01

When an excitation of the first lens determines a beam is parallel beam, a brightness that is 100 times higher than Langmuir limit is measured experimentally, where Langmuir limits are estimated using a simulated axial cathode current density which is simulated based on a measured emission current. The measured brightness is comparable to Langmuir limit, when the lens excitation is such that an image position is slightly shorter than a lens position. Previously measured values of brightness for cathode apical radii of curvature 20, 60, 120, 240, and 480 μm were 8.7, 5.3, 3.3, 2.4, and 3.9 times higher than their corresponding Langmuir limits, respectively, in this experiment, the lens excitation was such that the lens and the image positions were 180 mm and 400 mm, respectively. From these measured brightness for three different lens excitation conditions, it is concluded that the brightness depends on the first lens excitation. For the electron gun operated in a space charge limited condition, some of the electrons emitted from the cathode are returned to the cathode without having crossed a virtual cathode. Therefore, method that assumes a Langmuir limit defining method using a Maxwellian distribution of electron velocities may need to be revised. For the condition in which the values of the exceeding the Langmuir limit are measured, the simulated trajectories of electrons that are emitted from the cathode do not cross the optical axis at the crossover, thus the law of sines may not be valid for high brightness electron beam systems.

Implementation of the DPM Monte Carlo code on a parallel architecture for treatment planning applications.

PubMed

Tyagi, Neelam; Bose, Abhijit; Chetty, Indrin J

2004-09-01

We have parallelized the Dose Planning Method (DPM), a Monte Carlo code optimized for radiotherapy class problems, on distributed-memory processor architectures using the Message Passing Interface (MPI). Parallelization has been investigated on a variety of parallel computing architectures at the University of Michigan-Center for Advanced Computing, with respect to efficiency and speedup as a function of the number of processors. We have integrated the parallel pseudo random number generator from the Scalable Parallel Pseudo-Random Number Generator (SPRNG) library to run with the parallel DPM. The Intel cluster consisting of 800 MHz Intel Pentium III processor shows an almost linear speedup up to 32 processors for simulating 1 x 10(8) or more particles. The speedup results are nearly linear on an Athlon cluster (up to 24 processors based on availability) which consists of 1.8 GHz+ Advanced Micro Devices (AMD) Athlon processors on increasing the problem size up to 8 x 10(8) histories. For a smaller number of histories (1 x 10(8)) the reduction of efficiency with the Athlon cluster (down to 83.9% with 24 processors) occurs because the processing time required to simulate 1 x 10(8) histories is less than the time associated with interprocessor communication. A similar trend was seen with the Opteron Cluster (consisting of 1400 MHz, 64-bit AMD Opteron processors) on increasing the problem size. Because of the 64-bit architecture Opteron processors are capable of storing and processing instructions at a faster rate and hence are faster as compared to the 32-bit Athlon processors. We have validated our implementation with an in-phantom dose calculation study using a parallel pencil monoenergetic electron beam of 20 MeV energy. The phantom consists of layers of water, lung, bone, aluminum, and titanium. The agreement in the central axis depth dose curves and profiles at different depths shows that the serial and parallel codes are equivalent in accuracy.

Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA.

PubMed

Kubař, Tomáš; Elstner, Marcus

2013-04-28

In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated DNA. It turns out that the mean-field approach, where the wave function of the hole is driven into a superposition of adiabatic states, leads to over-delocalization of the hole charge. This problem is avoided using a surface hopping scheme, resulting in a smaller rate of hole transfer. The method is highly efficient due to the on-the-fly computation of the coarse-grained DFT Hamiltonian for the nucleobases, which is coupled to the environment using a QM/MM approach. The computational efficiency and partial parallel character of the methodology make it possible to simulate electron transfer in systems of relevant biochemical size on a nanosecond time scale. Since standard non-polarizable force fields are applied in the molecular-mechanics part of the calculation, a simple scaling scheme was introduced into the electrostatic potential in order to simulate the effect of electronic polarization. It is shown that electronic polarization has an important effect on the features of charge transfer. The methodology is applied to two kinds of DNA sequences, illustrating the features of transfer along a flat energy landscape as well as over an energy barrier. The performance and relative merit of the mean-field scheme and the surface hopping for this application are discussed.

Two-dimensional Nonlinear Simulations of Temperature-anisotropy Instabilities with a Proton-alpha Drift

NASA Astrophysics Data System (ADS)

Markovskii, S. A.; Chandran, Benjamin D. G.; Vasquez, Bernard J.

2018-04-01

We present two-dimensional hybrid simulations of proton-cyclotron and mirror instabilities in a proton-alpha plasma with particle-in-cell ions and a neutralizing electron fluid. The instabilities are driven by the protons with temperature perpendicular to the background magnetic field larger than the parallel temperature. The alpha particles with initially isotropic temperature have a nonzero drift speed with respect to the protons. The minor ions are known to influence the relative effect of the proton-cyclotron and mirror instabilities. In this paper, we show that the mirror mode can dominate the power spectrum at the nonlinear stage even if its linear growth rate is significantly lower than that of the proton-cyclotron mode. The proton-cyclotron instability combined with the alpha-proton drift is a possible cause of the nonzero magnetic helicity observed in the solar wind for fluctuations propagating nearly parallel to the magnetic field. Our simulations generally confirm this concept but reveal a complex helicity spectrum that is not anticipated from the linear theory of the instability.

Modeling Plasma Turbulence and Flows in LAPD using BOUT++

NASA Astrophysics Data System (ADS)

Friedman, B.; Carter, T. A.; Schaffner, D.; Popovich, P.; Umansky, M. V.; Dudson, B.

2010-11-01

A Braginskii fluid model of plasma turbulence in the BOUT code has recently been applied to LAPD at UCLA [1]. While these initial simulations with a reduced model and periodic axial boundary conditions have shown good agreement with measurements (e.g. power spectrum, correlation lengths), these simulations have lacked physics essential for modeling self-consistent, quantitatively correct flows. In particular, the model did not contain parallel plasma flow induced by sheath boundary conditions, and the axisymmetric radial electric field was not consistent with experiment. This work addresses these issues by extending the simulation model in the BOUT++ code [2], a more advanced version of BOUT. Specifically, end-plate sheath boundary conditions are added, as well as equations to evolve electron temperature and parallel ion velocity. Finally, various techniques are used to attempt to match the experimental electric potential profile, including fixing an equilibrium profile, fixing the radial boundaries, and adding an angular momentum source. [4pt] [1] Popovich et al., http://arxiv.org/abs/1005.2418 (2010).[0pt] [2] Dudson et al., Computer Physics Communications 180 (2009).

The Acceleration of Thermal Protons and Minor Ions at a Quasi-Parallel Interplanetary Shock

NASA Astrophysics Data System (ADS)

Giacalone, J.; Lario, D.; Lepri, S. T.

2017-12-01

We compare the results from self-consistent hybrid simulations (kinetic ions, massless fluid electrons) and spacecraft observations of a strong, quasi-parallel interplanetary shock that crossed the Advanced Composition Explorer (ACE) on DOY 94, 2001. In our simulations, the un-shocked plasma-frame ion distributions are Maxwellian. Our simulations include protons and minor ions (alphas, 3He++, and C5+). The interplanetary shock crossed both the ACE and the Wind spacecraft, and was associated with significant increases in the flux of > 50 keV/nuc ions. Our simulation uses parameters (ion densities, magnetic field strength, Mach number, etc.) consistent with those observed. Acceleration of the ions by the shock, in a manner similar to that expected from diffusive shock acceleration theory, leads to a high-energy tail in the distribution of the post-shock plasma for all ions we considered. The simulated distributions are directly compared to those observed by ACE/SWICS, EPAM, and ULEIS, and Wind/STICS and 3DP, covering the energy range from below the thermal peak to the suprathermal tail. We conclude from our study that the solar wind is the most significant source of the high-energy ions for this event. Our results have important implications for the physics of the so-called `injection problem', which will be discussed.

Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

DTIC Science & Technology

2015-08-01

Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten and James P Larentzos Approved for...Massively Parallel Simulator ( LAMMPS ) Software by N Scott Weingarten Weapons and Materials Research Directorate, ARL James P Larentzos Engility...Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) Software 5a. CONTRACT NUMBER 5b

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-L.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2004-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The non-linear fluctuation amplitudes of densities, currents, electric, and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper at the comparable simulation time. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. Additionally, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by the Weibel instability scale proportional to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform: small-scale magnetic fields which contribute to the electron's (positron's) transverse deflection behind the jet head. This small scale magnetic field structure is appropriate to the generation of jitter radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a a uniform magnetic field. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2005-01-01

Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel, and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a three-dimensional relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. New simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. Furthermore, the nonlinear fluctuation amplitudes of densities, currents, and electric and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper at a comparable simulation time. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. In addition, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by tine Weibel instability scale proportionally to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform, small-scale magnetic fields, which contribute to the electron s (positron s) transverse deflection behind the jet head. This small- scale magnetic field structure is appropriate to the generation of "jitter" radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a uniform magnetic field. The jitter radiation resulting from small-scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Ion and electron dynamics generating the Hall current in the exhaust far downstream of the reconnection x-line

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujimoto, Keizo, E-mail: keizo.fujimoto@nao.ac.jp; Takamoto, Makoto

2016-01-15

We have investigated the ion and electron dynamics generating the Hall current in the reconnection exhaust far downstream of the x-line where the exhaust width is much larger than the ion gyro-radius. A large-scale particle-in-cell simulation shows that most ions are accelerated through the Speiser-type motion in the current sheet formed at the center of the exhaust. The transition layers formed at the exhaust boundary are not identified as slow mode shocks. (The layers satisfy mostly the Rankine-Hugoniot conditions for a slow mode shock, but the energy conversion hardly occurs there.) We find that the ion drift velocity is modifiedmore » around the layer due to a finite Larmor radius effect. As a result, the ions are accumulated in the downstream side of the layer, so that collimated ion jets are generated. The electrons experience two steps of acceleration in the exhaust. The first is a parallel acceleration due to the out-of-plane electric field E{sub y} which has a parallel component in most area of the exhaust. The second is a perpendicular acceleration due to E{sub y} at the center of the current sheet and the motion is converted to the parallel direction. Because of the second acceleration, the electron outflow velocity becomes almost uniform over the exhaust. The difference in the outflow profile between the ions and electrons results in the Hall current in large area of the exhaust. The present study demonstrates the importance of the kinetic treatments for collisionless magnetic reconnection even far downstream from the x-line.« less

Continuum Edge Gyrokinetic Theory and Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, X Q; Xiong, Z; Dorr, M R

The following results are presented from the development and application of TEMPEST, a fully nonlinear (full-f) five dimensional (3d2v) gyrokinetic continuum edge-plasma code. (1) As a test of the interaction of collisions and parallel streaming, TEMPEST is compared with published analytic and numerical results for endloss of particles confined by combined electrostatic and magnetic wells. Good agreement is found over a wide range of collisionality, confining potential, and mirror ratio; and the required velocity space resolution is modest. (2) In a large-aspect-ratio circular geometry, excellent agreement is found for a neoclassical equilibrium with parallel ion flow in the banana regimemore » with zero temperature gradient and radial electric field. (3) The four-dimensional (2d2v) version of the code produces the first self-consistent simulation results of collisionless damping of geodesic acoustic modes and zonal flow (Rosenbluth-Hinton residual) with Boltzmann electrons using a full-f code. The electric field is also found to agree with the standard neoclassical expression for steep density and ion temperature gradients in the banana regime. In divertor geometry, it is found that the endloss of particles and energy induces parallel flow stronger than the core neoclassical predictions in the SOL. (5) Our 5D gyrokinetic formulation yields a set of nonlinear electrostatic gyrokinetic equations that are for both neoclassical and turbulence simulations.« less

Protons and alpha particles in the expanding solar wind: Hybrid simulations

NASA Astrophysics Data System (ADS)

Hellinger, Petr; Trávníček, Pavel M.

2013-09-01

We present results of a two‒dimensional hybrid expanding box simulation of a plasma system with three ion populations, beam and core protons, and alpha particles (and fluid electrons), drifting with respect to each other. The expansion with a strictly radial magnetic field leads to a decrease of the ion perpendicular to parallel temperature ratios as well as to an increase of the ratio between the ion relative velocities and the local Alfvén velocity creating a free energy for many different instabilities. The system is most of the time marginally stable with respect to kinetic instabilities mainly due to the ion relative velocities; these instabilities determine the system evolution counteracting some effects of the expansion. Nonlinear evolution of these instabilities leads to large modifications of the ion velocity distribution functions. The beam protons and alpha particles are decelerated with respect to the core protons and all the populations are cooled in the parallel direction and heated in the perpendicular one. On the macroscopic level, the kinetic instabilities cause large departures of the system evolution from the double adiabatic prediction and lead to perpendicular heating and parallel cooling rates which are comparable to the heating rates estimated from the Helios observations.

Edge gyrokinetic theory and continuum simulations

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Xiong, Z.; Dorr, M. R.; Hittinger, J. A.; Bodi, K.; Candy, J.; Cohen, B. I.; Cohen, R. H.; Colella, P.; Kerbel, G. D.; Krasheninnikov, S.; Nevins, W. M.; Qin, H.; Rognlien, T. D.; Snyder, P. B.; Umansky, M. V.

2007-08-01

The following results are presented from the development and application of TEMPEST, a fully nonlinear (full-f) five-dimensional (3d2v) gyrokinetic continuum edge-plasma code. (1) As a test of the interaction of collisions and parallel streaming, TEMPEST is compared with published analytic and numerical results for endloss of particles confined by combined electrostatic and magnetic wells. Good agreement is found over a wide range of collisionality, confining potential and mirror ratio, and the required velocity space resolution is modest. (2) In a large-aspect-ratio circular geometry, excellent agreement is found for a neoclassical equilibrium with parallel ion flow in the banana regime with zero temperature gradient and radial electric field. (3) The four-dimensional (2d2v) version of the code produces the first self-consistent simulation results of collisionless damping of geodesic acoustic modes and zonal flow (Rosenbluth-Hinton residual) with Boltzmann electrons using a full-f code. The electric field is also found to agree with the standard neoclassical expression for steep density and ion temperature gradients in the plateau regime. In divertor geometry, it is found that the endloss of particles and energy induces parallel flow stronger than the core neoclassical predictions in the SOL.

Divide-and-conquer density functional theory on hierarchical real-space grids: Parallel implementation and applications

NASA Astrophysics Data System (ADS)

Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

2008-02-01

A linear-scaling algorithm based on a divide-and-conquer (DC) scheme has been designed to perform large-scale molecular-dynamics (MD) simulations, in which interatomic forces are computed quantum mechanically in the framework of the density functional theory (DFT). Electronic wave functions are represented on a real-space grid, which is augmented with a coarse multigrid to accelerate the convergence of iterative solutions and with adaptive fine grids around atoms to accurately calculate ionic pseudopotentials. Spatial decomposition is employed to implement the hierarchical-grid DC-DFT algorithm on massively parallel computers. The largest benchmark tests include 11.8×106 -atom ( 1.04×1012 electronic degrees of freedom) calculation on 131 072 IBM BlueGene/L processors. The DC-DFT algorithm has well-defined parameters to control the data locality, with which the solutions converge rapidly. Also, the total energy is well conserved during the MD simulation. We perform first-principles MD simulations based on the DC-DFT algorithm, in which large system sizes bring in excellent agreement with x-ray scattering measurements for the pair-distribution function of liquid Rb and allow the description of low-frequency vibrational modes of graphene. The band gap of a CdSe nanorod calculated by the DC-DFT algorithm agrees well with the available conventional DFT results. With the DC-DFT algorithm, the band gap is calculated for larger system sizes until the result reaches the asymptotic value.

Electron Scale Structures and Magnetic Reconnection Signatures in the Turbulent Magnetosheath

NASA Technical Reports Server (NTRS)

Yordanova, E.; Voros, Z.; Varsani, A.; Graham, D. B.; Norgren, C.; Khotyaintsev, Yu. V.; Vaivads, A.; Eriksson, E.; Nakamura, R.; Lindqvist, P.-A.;

Electron and ion distribution functions in magnetopause reconnection

NASA Astrophysics Data System (ADS)

Wang, S.; Chen, L. J.; Bessho, N.; Hesse, M.; Kistler, L. M.; Torbert, R. B.; Mouikis, C.; Pollock, C. J.

2015-12-01

We investigate electron and ion velocity distribution functions in dayside magnetopause reconnection events observed by the Cluster and MMS spacecraft. The goal is to build a spatial map of electron and ion distribution features to enable the indication of the spacecraft location in the reconnection structure, and to understand plasma energization processes. Distribution functions, together with electromagnetic field structures, plasma densities, and bulk velocities, are organized and compared with particle-in-cell simulation results to indicate the proximities to the reconnection X-line. Anisotropic features in the distributions of magnetospheric- and magnetosheath- origin electrons at different locations in the reconnection inflow and exhaust are identified. In particular, parallel electron heating is observed in both the magnetosheath and magnetosphere inflow regions. Possible effects of the guide field strength, waves, and upstream density and temperature asymmetries on the distribution features will be discussed.

Dynamics and Hall-edge-state mixing of localized electrons in a two-channel Mach-Zehnder interferometer

NASA Astrophysics Data System (ADS)

Bellentani, Laura; Beggi, Andrea; Bordone, Paolo; Bertoni, Andrea

2018-05-01

We present a numerical study of a multichannel electronic Mach-Zehnder interferometer, based on magnetically driven noninteracting edge states. The electron path is defined by a full-scale potential landscape on the two-dimensional electron gas at filling factor 2, assuming initially only the first Landau level as filled. We tailor the two beamsplitters with 50 % interchannel mixing and measure Aharonov-Bohm oscillations in the transmission probability of the second channel. We perform time-dependent simulations by solving the electron Schrödinger equation through a parallel implementation of the split-step Fourier method, and we describe the charge-carrier wave function as a Gaussian wave packet of edge states. We finally develop a simplified theoretical model to explain the features observed in the transmission probability, and we propose possible strategies to optimize gate performances.

Nonvolatile “AND,” “OR,” and “NOT” Boolean logic gates based on phase-change memory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Y.; Zhong, Y. P.; Deng, Y. F.

2013-12-21

Electronic devices or circuits that can implement both logic and memory functions are regarded as the building blocks for future massive parallel computing beyond von Neumann architecture. Here we proposed phase-change memory (PCM)-based nonvolatile logic gates capable of AND, OR, and NOT Boolean logic operations verified in SPICE simulations and circuit experiments. The logic operations are parallel computing and results can be stored directly in the states of the logic gates, facilitating the combination of computing and memory in the same circuit. These results are encouraging for ultralow-power and high-speed nonvolatile logic circuit design based on novel memory devices.

Beam dynamics in MABE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poukey, J.W.; Coleman, P.D.; Sanford, T.W.L.

1985-10-01

MABE is a multistage linear electron accelerator which accelerates up to nine beams in parallel. Nominal parameters per beam are 25 kA, final energy 7 MeV, and guide field 20 kG. We report recent progress via theory and simulation in understanding the beam dynamics in such a system. In particular, we emphasize our results on the radial oscillations and emittance growth for a beam passing through a series of accelerating gaps.

Large Amplitude Whistler Waves and Electron Acceleration in the Earth's Radiation Belts: A Review of STEREO and Wind Observations

NASA Technical Reports Server (NTRS)

Cattell, Cynthia; Breneman, A.; Goetz, K.; Kellogg, P.; Kersten, K.; Wygant, J.; Wilson, L. B., III; Looper, Mark D.; Blake, J. Bernard; Roth, I.

2012-01-01

One of the critical problems for understanding the dynamics of Earth's radiation belts is determining the physical processes that energize and scatter relativistic electrons. We review measurements from the Wind/Waves and STEREO S/Waves waveform capture instruments of large amplitude whistler-mode waves. These observations have provided strong evidence that large amplitude (100s mV/m) whistler-mode waves are common during magnetically active periods. The large amplitude whistlers have characteristics that are different from typical chorus. They are usually nondispersive and obliquely propagating, with a large longitudinal electric field and significant parallel electric field. We will also review comparisons of STEREO and Wind wave observations with SAMPEX observations of electron microbursts. Simulations show that the waves can result in energization by many MeV and/or scattering by large angles during a single wave packet encounter due to coherent, nonlinear processes including trapping. The experimental observations combined with simulations suggest that quasilinear theoretical models of electron energization and scattering via small-amplitude waves, with timescales of hours to days, may be inadequate for understanding radiation belt dynamics.

FDTD simulation of radar cross section reduction by a collisional inhomogeneous magnetized plasma

NASA Astrophysics Data System (ADS)

Foroutan, V.; Azarmanesh, M. N.; Foroutan, G.

2018-02-01

The recursive convolution finite difference time domain method is addressed in the scattered field formulation and employed to investigate the bistatic radar cross-section (RCS) of a square conductive plate covered by a collisional inhomogeneous magnetized plasma. The RCS is calculated for two different configurations of the magnetic field, i.e., parallel and perpendicular to the plate. The results of numerical simulations show that, for a perpendicularly applied magnetic field, the backscattered RCS is significantly reduced when the magnetic field intensity coincides with the value corresponding to the electron cyclotron resonance. By increasing the collision frequency, the resonant absorption is suppressed, but due to enhanced wave penetration and bending, the reduction in the bistatic RCS is improved. At very high collision frequencies, the external magnetic field has no significant impact on the bistatic RCS reduction. Application of a parallel magnetic field has an adverse effect near the electron cyclotron resonance and results in a large and asymmetric RCS profile. But, the problem is resolved by increasing the magnetic field and/or the collision frequency. By choosing proper values of the collision frequency and the magnetic field intensity, a perpendicular magnetic field can be effectively used to reduce the bistatic RCS of a conductive plate.

Investigation of electron-loss and photon scattering correction factors for FAC-IR-300 ionization chamber

NASA Astrophysics Data System (ADS)

Mohammadi, S. M.; Tavakoli-Anbaran, H.; Zeinali, H. Z.

2017-02-01

The parallel-plate free-air ionization chamber termed FAC-IR-300 was designed at the Atomic Energy Organization of Iran, AEOI. This chamber is used for low and medium X-ray dosimetry on the primary standard level. In order to evaluate the air-kerma, some correction factors such as electron-loss correction factor (ke) and photon scattering correction factor (ksc) are needed. ke factor corrects the charge loss from the collecting volume and ksc factor corrects the scattering of photons into collecting volume. In this work ke and ksc were estimated by Monte Carlo simulation. These correction factors are calculated for mono-energy photon. As a result of the simulation data, the ke and ksc values for FAC-IR-300 ionization chamber are 1.0704 and 0.9982, respectively.

3D measurements and simulations of ion and neutral velocity distribution functions in a magnetized plasma boundary

NASA Astrophysics Data System (ADS)

Thompson, Derek S.; Keniley, Shane; Curreli, Davide; Henriquez, Miguel F.; Caron, David D.; Jemiolo, Andrew J.; McLaughlin, Jacob W.; Dufor, Mikal T.; Neal, Luke A.; Scime, Earl E.; Siddiqui, M. Umair

2017-10-01

We present progress toward the first paired 3D laser induced fluorescence measurements of ion and neutral velocity distribution functions (I/NVDFs) in a magnetized plasma boundary. These measurements are performed in the presheath region of an absorbing boundary immersed in a background magnetic field that is obliquely incident to the boundary surface (ψ =74°). Parallel and perpendicular flow measurements demonstrate that cross-field ion flows occur and that ions within several gyro-radii of the surface are accelerated in the E-> × B-> direction. We present electrostatic probe measurements of electron temperature, plasma density, and electric potential in the same region. Ion, neutral and electron measurements are compared to Boltzmann simulations, allowing direct comparison between measured and theoretical distribution functions in the boundary region. NSF PHYS 1360278.

Relaxation of ferroelectric states in 2D distributions of quantum dots: EELS simulation

NASA Astrophysics Data System (ADS)

Cortés, C. M.; Meza-Montes, L.; Moctezuma, R. E.; Carrillo, J. L.

2016-06-01

The relaxation time of collective electronic states in a 2D distribution of quantum dots is investigated theoretically by simulating EELS experiments. From the numerical calculation of the probability of energy loss of an electron beam, traveling parallel to the distribution, it is possible to estimate the damping time of ferroelectric-like states. We generate this collective response of the distribution by introducing a mean field interaction among the quantum dots, and then, the model is extended incorporating effects of long-range correlations through a Bragg-Williams approximation. The behavior of the dielectric function, the energy loss function, and the relaxation time of ferroelectric-like states is then investigated as a function of the temperature of the distribution and the damping constant of the electronic states in the single quantum dots. The robustness of the trends and tendencies of our results indicate that this scheme of analysis can guide experimentalists to develop tailored quantum dots distributions for specific applications.

Gyrokinetic simulation of ITG modes in a three-mode coupling model

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Lee, W. W.

2004-11-01

A three-mode coupling model of ITG modes with adiabatic electrons is studied both analytically and numerically in 2-dimensional slab geometry using the gyrokinetic formalism. It can be shown analytically that the (quasilinear) saturation amplitude of the waves in the system should be enhanced by the inclusion of the parallel velocity nonlinearity in the governing gyrokinetic equation. The effect of this (frequently neglected) nonlinearity on the steady-state transport properties of the plasma is studied numerically using standard gyrokinetic particle simulation techniques. The balance [1] between various steady-state transport properties of the model (particle and heat flux, entropy production, and collisional dissipation) is examined. Effects resulting from the inclusion of nonadiabatic electrons in the model are also considered numerically, making use of the gyrokinetic split-weight scheme [2] in the simulations. [1] W. W. Lee and W. M. Tang, Phys. Fluids 31, 612 (1988). [2] I. Manuilskiy and W. W. Lee, Phys. Plasmas 7, 1381 (2000).

Electrostatic focal spot correction for x-ray tubes operating in strong magnetic fields.

PubMed

Lillaney, Prasheel; Shin, Mihye; Hinshaw, Waldo; Fahrig, Rebecca

2014-11-01

A close proximity hybrid x-ray/magnetic resonance (XMR) imaging system offers several critical advantages over current XMR system installations that have large separation distances (∼5 m) between the imaging fields of view. The two imaging systems can be placed in close proximity to each other if an x-ray tube can be designed to be immune to the magnetic fringe fields outside of the MR bore. One of the major obstacles to robust x-ray tube design is correcting for the effects of the MR fringe field on the x-ray tube focal spot. Any fringe field component orthogonal to the x-ray tube electric field leads to electron drift altering the path of the electron trajectories. The method proposed in this study to correct for the electron drift utilizes an external electric field in the direction of the drift. The electric field is created using two electrodes that are positioned adjacent to the cathode. These electrodes are biased with positive and negative potential differences relative to the cathode. The design of the focusing cup assembly is constrained primarily by the strength of the MR fringe field and high voltage standoff distances between the anode, cathode, and the bias electrodes. From these constraints, a focusing cup design suitable for the close proximity XMR system geometry is derived, and a finite element model of this focusing cup geometry is simulated to demonstrate efficacy. A Monte Carlo simulation is performed to determine any effects of the modified focusing cup design on the output x-ray energy spectrum. An orthogonal fringe field magnitude of 65 mT can be compensated for using bias voltages of +15 and -20 kV. These bias voltages are not sufficient to completely correct for larger orthogonal field magnitudes. Using active shielding coils in combination with the bias electrodes provides complete correction at an orthogonal field magnitude of 88.1 mT. Introducing small fields (<10 mT) parallel to the x-ray tube electric field in addition to the orthogonal field does not affect the electrostatic correction technique. However, rotation of the x-ray tube by 30° toward the MR bore increases the parallel magnetic field magnitude (∼72 mT). The presence of this larger parallel field along with the orthogonal field leads to incomplete correction. Monte Carlo simulations demonstrate that the mean energy of the x-ray spectrum is not noticeably affected by the electrostatic correction, but the output flux is reduced by 7.5%. The maximum orthogonal magnetic field magnitude that can be compensated for using the proposed design is 65 mT. Larger orthogonal field magnitudes cannot be completely compensated for because a pure electrostatic approach is limited by the dielectric strength of the vacuum inside the x-ray tube insert. The electrostatic approach also suffers from limitations when there are strong magnetic fields in both the orthogonal and parallel directions because the electrons prefer to stay aligned with the parallel magnetic field. These challenging field conditions can be addressed by using a hybrid correction approach that utilizes both active shielding coils and biasing electrodes.

Electrostatic focal spot correction for x-ray tubes operating in strong magnetic fields

PubMed Central

Lillaney, Prasheel; Shin, Mihye; Hinshaw, Waldo; Fahrig, Rebecca

2014-01-01

Purpose: A close proximity hybrid x-ray/magnetic resonance (XMR) imaging system offers several critical advantages over current XMR system installations that have large separation distances (∼5 m) between the imaging fields of view. The two imaging systems can be placed in close proximity to each other if an x-ray tube can be designed to be immune to the magnetic fringe fields outside of the MR bore. One of the major obstacles to robust x-ray tube design is correcting for the effects of the MR fringe field on the x-ray tube focal spot. Any fringe field component orthogonal to the x-ray tube electric field leads to electron drift altering the path of the electron trajectories. Methods: The method proposed in this study to correct for the electron drift utilizes an external electric field in the direction of the drift. The electric field is created using two electrodes that are positioned adjacent to the cathode. These electrodes are biased with positive and negative potential differences relative to the cathode. The design of the focusing cup assembly is constrained primarily by the strength of the MR fringe field and high voltage standoff distances between the anode, cathode, and the bias electrodes. From these constraints, a focusing cup design suitable for the close proximity XMR system geometry is derived, and a finite element model of this focusing cup geometry is simulated to demonstrate efficacy. A Monte Carlo simulation is performed to determine any effects of the modified focusing cup design on the output x-ray energy spectrum. Results: An orthogonal fringe field magnitude of 65 mT can be compensated for using bias voltages of +15 and −20 kV. These bias voltages are not sufficient to completely correct for larger orthogonal field magnitudes. Using active shielding coils in combination with the bias electrodes provides complete correction at an orthogonal field magnitude of 88.1 mT. Introducing small fields (<10 mT) parallel to the x-ray tube electric field in addition to the orthogonal field does not affect the electrostatic correction technique. However, rotation of the x-ray tube by 30° toward the MR bore increases the parallel magnetic field magnitude (∼72 mT). The presence of this larger parallel field along with the orthogonal field leads to incomplete correction. Monte Carlo simulations demonstrate that the mean energy of the x-ray spectrum is not noticeably affected by the electrostatic correction, but the output flux is reduced by 7.5%. Conclusions: The maximum orthogonal magnetic field magnitude that can be compensated for using the proposed design is 65 mT. Larger orthogonal field magnitudes cannot be completely compensated for because a pure electrostatic approach is limited by the dielectric strength of the vacuum inside the x-ray tube insert. The electrostatic approach also suffers from limitations when there are strong magnetic fields in both the orthogonal and parallel directions because the electrons prefer to stay aligned with the parallel magnetic field. These challenging field conditions can be addressed by using a hybrid correction approach that utilizes both active shielding coils and biasing electrodes. PMID:25370658

Monte Carlo simulations in X-ray imaging

NASA Astrophysics Data System (ADS)

Giersch, Jürgen; Durst, Jürgen

2008-06-01

Monte Carlo simulations have become crucial tools in many fields of X-ray imaging. They help to understand the influence of physical effects such as absorption, scattering and fluorescence of photons in different detector materials on image quality parameters. They allow studying new imaging concepts like photon counting, energy weighting or material reconstruction. Additionally, they can be applied to the fields of nuclear medicine to define virtual setups studying new geometries or image reconstruction algorithms. Furthermore, an implementation of the propagation physics of electrons and photons allows studying the behavior of (novel) X-ray generation concepts. This versatility of Monte Carlo simulations is illustrated with some examples done by the Monte Carlo simulation ROSI. An overview of the structure of ROSI is given as an example of a modern, well-proven, object-oriented, parallel computing Monte Carlo simulation for X-ray imaging.

The plasma-wall transition layers in the presence of collisions with a magnetic field parallel to the wall

NASA Astrophysics Data System (ADS)

Moritz, J.; Faudot, E.; Devaux, S.; Heuraux, S.

2018-01-01

The plasma-wall transition is studied by means of a particle-in-cell (PIC) simulation in the configuration of a parallel to the wall magnetic field (B), with collisions between charged particles vs. neutral atoms taken into account. The investigated system consists of a plasma bounded by two absorbing walls separated by 200 electron Debye lengths (λd). The strength of the magnetic field is chosen such as the ratio λ d / r l , with rl being the electron Larmor radius, is smaller or larger than unity. Collisions are modelled with a simple operator that reorients randomly ion or electron velocity, keeping constant the total kinetic energy of both the neutral atom (target) and the incident charged particle. The PIC simulations show that the plasma-wall transition consists in a quasi-neutral region (pre-sheath), from the center of the plasma towards the walls, where the electric potential or electric field profiles are well described by an ambipolar diffusion model, and in a second region at the vicinity of the walls, called the sheath, where the quasi-neutrality breaks down. In this peculiar geometry of B and for a certain range of the mean-free-path, the sheath is found to be composed of two charged layers: the positive one, close to the walls, and the negative one, towards the plasma and before the neutral pre-sheath. Depending on the amplitude of B, the spatial variation of the electric potential can be non-monotonic and presents a maximum within the sheath region. More generally, the sheath extent as well as the potential drop within the sheath and the pre-sheath is studied with respect to B, the mean-free-path, and the ion and electron temperatures.

Simulation Exploration through Immersive Parallel Planes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunhart-Lupo, Nicholas J; Bush, Brian W; Gruchalla, Kenny M

We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, eachmore » individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.« less

Simulation Exploration through Immersive Parallel Planes: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brunhart-Lupo, Nicholas; Bush, Brian W.; Gruchalla, Kenny

We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, eachmore » individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.« less

A path-level exact parallelization strategy for sequential simulation

NASA Astrophysics Data System (ADS)

Peredo, Oscar F.; Baeza, Daniel; Ortiz, Julián M.; Herrero, José R.

2018-01-01

Sequential Simulation is a well known method in geostatistical modelling. Following the Bayesian approach for simulation of conditionally dependent random events, Sequential Indicator Simulation (SIS) method draws simulated values for K categories (categorical case) or classes defined by K different thresholds (continuous case). Similarly, Sequential Gaussian Simulation (SGS) method draws simulated values from a multivariate Gaussian field. In this work, a path-level approach to parallelize SIS and SGS methods is presented. A first stage of re-arrangement of the simulation path is performed, followed by a second stage of parallel simulation for non-conflicting nodes. A key advantage of the proposed parallelization method is to generate identical realizations as with the original non-parallelized methods. Case studies are presented using two sequential simulation codes from GSLIB: SISIM and SGSIM. Execution time and speedup results are shown for large-scale domains, with many categories and maximum kriging neighbours in each case, achieving high speedup results in the best scenarios using 16 threads of execution in a single machine.

Electron Thermal Transport due to Magnetic Diffusion in the MST RFP

NASA Astrophysics Data System (ADS)

Reusch, J. A.; Anderson, J. K.; den Hartog, D. J.; Forest, C. B.; Kasten, C. P.; Schnack, D. D.; Stephens, H. D.

2011-10-01

Comparison of measurements made in the MST RFP to the results from extensive nonlinear resistive MHD simulations has provided two key observations. First, trapped particles reduce electron thermal diffusion; inclusion of this effect is required for quantitative agreement of simulation to measurement. Second, the structure and evolution of long-wavelength temperature fluctuations measured in MST shows remarkable qualitative similarity to fluctuations appearing in a finite-pressure simulation. These simulations were run at parameters matching those of 400 kA discharges in MST (S ~ 4 ×106). In a zero β simulation, the measured χe is compared to the thermal diffusion due to parallel losses along diffusing magnetic field lines, χst =v∥Dmag . Agreement is only found if the reduction in χst due to trapped particles is taken into account. In a second simulation, the pressure field was evolved self consistently assuming Ohmic heating and anisotropic thermal conduction. Fluctuations in the simulated temperature are very similar in character and time evolution to temperature fluctuations measured in MST. This includes m = 1 , n = 6 fluctuations that flatten the temperature profile as well as m = 1 , n = 5 fluctuations that generate hot island structures near the core shortly after sawtooth crashes. This work supported by the US DOE and NSF.

Plasma dynamics on current-carrying magnetic flux tubes

NASA Technical Reports Server (NTRS)

Swift, Daniel W.

1992-01-01

A 1D numerical simulation is used to investigate the evolution of a plasma in a current-carrying magnetic flux tube of variable cross section. A large potential difference, parallel to the magnetic field, is applied across the domain. The result is that density minimum tends to deepen, primarily in the cathode end, and the entire potential drop becomes concentrated across the region of density minimum. The evolution of the simulation shows some sensitivity to particle boundary conditions, but the simulations inevitably evolve into a final state with a nearly stationary double layer near the cathode end. The simulation results are at sufficient variance with observations that it appears unlikely that auroral electrons can be explained by a simple process of acceleration through a field-aligned potential drop.

Non-Thermal Spectra from Pulsar Magnetospheres in the Full Electromagnetic Cascade Scenario

NASA Astrophysics Data System (ADS)

Peng, Qi-Yong; Zhang, Li

2008-08-01

We simulated non-thermal emission from a pulsar magnetosphere within the framework of a full polar-cap cascade scenario by taking the acceleration gap into account, using the Monte Carlo method. For a given electric field parallel to open field lines located at some height above the surface of a neutron star, primary electrons were accelerated by parallel electric fields and lost their energies by curvature radiation; these photons were converted to electron-positron pairs, which emitted photons through subsequent quantum synchrotron radiation and inverse Compton scattering, leading to a cascade. In our calculations, the acceleration gap was assumed to be high above the stellar surface (about several stellar radii); the primary and secondary particles and photons emitted during the journey of those particles in the magnetosphere were traced using the Monte Carlo method. In such a scenario, we calculated the non-thermal photon spectra for different pulsar parameters and compared the model results for two normal pulsars and one millisecond pulsar with the observed data.

Theoretical analysis and Vsim simulation of a low-voltage high-efficiency 250 GHz gyrotron

NASA Astrophysics Data System (ADS)

An, Chenxiang; Zhang, Dian; Zhang, Jun; Zhong, Huihuang

2018-02-01

Low-voltage, high-frequency gyrotrons with hundreds of watts of power are useful in radar, magnetic resonance spectroscopy and plasma diagnostic applications. In this paper, a 10 kV, 478 W, 250 GHz gyrotron with an efficiency of nearly 40% and a pitch ratio of 1.5 was designed through linear and nonlinear numerical analyses and Vsim particle-in-cell (PIC) simulation. Vsim is a highly efficient parallel PIC code, but it has seldom been used to carry out electron beam wave interaction simulations of gyro-devices. The setting up of the parameters required for the Vsim simulations of the gyrotron is presented. The results of Vsim simulations agree well with that of nonlinear numerical calculation. The commercial software Vsim7.2 completed the 3D gyrotron simulation in 80 h using a 20 core, 2.2 GHz personal computer with 256 GBytes of memory.

A compositional reservoir simulator on distributed memory parallel computers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rame, M.; Delshad, M.

1995-12-31

This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. Amore » portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented.« less

Excited State Dynamics in Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Miyamoto, Yoshiyuki

2004-03-01

Carbon nanotube, one of the most promising materials for nano-technology, still suffers from its imperfection in crystalline structure that will make performance of nanotube behind theoretical limit. From the first-principles simulations, I propose efficient methods to overcome the imperfection. I show that photo-induced ion dynamics can (1) identify defects in nanotubes, (2) stabilize defected nanotubes, and (3) purify contaminated nanotubes. All of these methods can be alternative to conventional heat treatments and will be important techniques for realizing nanotube-devices. Ion dynamics under electronic excitation has been simulated with use of the computer code FPSEID (First-Principles Simulation tool for Electron Ion Dynamics) [1], which combines the time-dependent density functional method [2] to classical molecular dynamics. This very challenging approach is time-consuming but can automatically treat the level alternation of differently occupied states, and can observe initiation of non-adiabatic decay of excitation. The time-dependent Kohn-Sham equation has been solved by using the Suzuki-Trotter split operator method [3], which is a numerically stable method being suitable for plane wave basis, non-local pseudopotentials, and parallel computing. This work has been done in collaboration with Prof. Angel Rubio, Prof. David Tomanek, Dr. Savas Berber and Mina Yoon. Most of present calculations have been done by using the SX5 Vector-Parallel system in the NEC Fuchu-plant, and the Earth Simulator in Yokohama Japan. [1] O. Sugino and Y. Miyamoto, Phys. Rev. B59, 2579 (1999); ibid, B66 089901(E) (2001) [2] E. Runge and E. K. U. Gross, Phys. Rev. Lett. 52, 997 (1984). [3] M. Suzuki, J. Phys. Soc. Jpn. 61, L3015 (1992).

Particle-in-cell Simulations of Waves in a Plasma Described by Kappa Velocity Distribution as Observed in the Saturńs Magnetosphere

NASA Astrophysics Data System (ADS)

Alves, M. V.; Barbosa, M. V. G.; Simoes, F. J. L., Jr.

2016-12-01

Observations have shown that several regions in space plasmas exhibit non-Maxwellian distributions with high energy superthermal tails. Kappa velocity distribution functions can describe many of these regions and have been used since the 60's. They suit well to represent superthermal tails in solar wind as well as to obtain plasma parameters of plasma within planetary magnetospheres. A set of initial velocities following kappa distribution functions is used in KEMPO1 particle simulation code to analyze the normal modes of wave propagation. Initial conditions are determined using observed characteristics for Saturńs magnetosphere. Two electron species with different temperatures and densities and ions as a third species are used. Each electron population is described by a different kappa index. Particular attention is given to perpendicular propagation, Bernstein modes, and parallel propagation, Langmuir and electron-acoustic modes. The dispersion relation for the Bernstein modes is strongly influenced by the shape of the velocity distribution and consequently by the value of kappa index. Simulation results are compared with numerical solutions of the dispersion relation obtained in the literature and they are in good agreement.

On Multiple Hall-Like Electron Currents and Tripolar Guide Magnetic Field Perturbations During Kelvin-Helmholtz Waves

NASA Astrophysics Data System (ADS)

Sturner, Andrew P.; Eriksson, Stefan; Nakamura, Takuma; Gershman, Daniel J.; Plaschke, Ferdinand; Ergun, Robert E.; Wilder, Frederick D.; Giles, Barbara; Pollock, Craig; Paterson, William R.; Strangeway, Robert J.; Baumjohann, Wolfgang; Burch, James L.

2018-02-01

Two magnetopause current sheet crossings with tripolar guide magnetic field signatures were observed by multiple Magnetosphere Multiscale (MMS) spacecraft during Kelvin-Helmholtz wave activity. The two out-of-plane magnetic field depressions of the tripolar guide magnetic field are largely supported by the observed in-plane electron currents, which are reminiscent of two clockwise Hall current loop systems. A comparison with a three-dimensional kinetic simulation of Kelvin-Helmholtz waves and vortex-induced reconnection suggests that MMS likely encountered the two Hall magnetic field depressions on either side of a magnetic reconnection X-line. Moreover, MMS observed an out-of-plane current reversal and a corresponding in-plane magnetic field rotation at the center of one of the current sheets, suggesting the presence of two adjacent flux ropes. The region inside one of the ion-scale flux ropes was characterized by an observed decrease of the total magnetic field, a strong axial current, and significant enhancements of electron density and parallel electron temperature. The flux rope boundary was characterized by currents opposite this axial current, strong in-plane and converging electric fields, parallel electric fields, and weak electron-frame Joule dissipation. These return current region observations may reflect a need to support the axial current rather than representing local reconnection signatures in the absence of any exhausts.

Three-dimensional kinetic simulations of whistler turbulence in solar wind on parallel supercomputers

NASA Astrophysics Data System (ADS)

Chang, Ouliang

The objective of this dissertation is to study the physics of whistler turbulence evolution and its role in energy transport and dissipation in the solar wind plasmas through computational and theoretical investigations. This dissertation presents the first fully three-dimensional (3D) particle-in-cell (PIC) simulations of whistler turbulence forward cascade in a homogeneous, collisionless plasma with a uniform background magnetic field B o, and the first 3D PIC simulation of whistler turbulence with both forward and inverse cascades. Such computationally demanding research is made possible through the use of massively parallel, high performance electromagnetic PIC simulations on state-of-the-art supercomputers. Simulations are carried out to study characteristic properties of whistler turbulence under variable solar wind fluctuation amplitude (epsilon e) and electron beta (betae), relative contributions to energy dissipation and electron heating in whistler turbulence from the quasilinear scenario and the intermittency scenario, and whistler turbulence preferential cascading direction and wavevector anisotropy. The 3D simulations of whistler turbulence exhibit a forward cascade of fluctuations into broadband, anisotropic, turbulent spectrum at shorter wavelengths with wavevectors preferentially quasi-perpendicular to B o. The overall electron heating yields T ∥ > T⊥ for all epsilone and betae values, indicating the primary linear wave-particle interaction is Landau damping. But linear wave-particle interactions play a minor role in shaping the wavevector spectrum, whereas nonlinear wave-wave interactions are overall stronger and faster processes, and ultimately determine the wavevector anisotropy. Simulated magnetic energy spectra as function of wavenumber show a spectral break to steeper slopes, which scales as k⊥lambda e ≃ 1 independent of betae values, where lambdae is electron inertial length, qualitatively similar to solar wind observations. Specific spectral indices from simulated wavevector energy spectra do not match the frequency spectral indices from observations due to the inapplicability of Taylor's hypothesis. In contrast, the direct comparison of simulated frequency energy spectra and solar wind observations shows a closer similarity. Electron density fluctuations power spectra also exhibit a close similarity to solar wind observations and MHD predications, both qualitatively and quantitatively. Linear damping represents an intermediate fraction of the total dissipation of whistler turbulence over a wide range of betae and epsilone. The relative importance of linear damping by comparison to nonlinear dissipation increases with increasing beta e but decreases with increasing epsilone. Correlation coefficient calculations imply that the nonlinear dissipation processes in our simulation are primarily associated with dissipation in regions of intermittent current sheet structures. The simulation results suggest that whistler fluctuations could be the substantial constituent of solar wind turbulence at higher frequencies and short wavelengths, and support the magnetosonic-whistler interpretation of the quasilinear scenario. An even larger scale 3D whistler turbulence simulation exhibits both a forward cascade to shorter wavelengths with wavevectors preferentially k⊥ > k∥, and an inverse cascade to longer wavelengths with wavevectors k ≳ k⊥. The inverse cascade process is primarily driven by the nonlinear wave-wave interaction. It is shown that the energy inverse cascade rate is similar to the energy forward cascade rate at early times although the overall energy in the two cascades is very different. The presence of inverse cascade process does not affect qualitative conclusions established from the whistler turbulence forward cascade simulations.

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers

PubMed Central

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation. PMID:28239346

Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers.

PubMed

Chen, Weiliang; De Schutter, Erik

2017-01-01

Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of models and morphologies have exceeded the capacity of any serial implementation. This led to the development of parallel solutions that benefit from the boost in performance of modern supercomputers. In this paper, we describe an MPI-based, parallel operator-splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its application to real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecule density and mesh quality. In the best scenario, a parallel simulation with 2,000 processes runs more than 3,600 times faster than its serial SSA counterpart, and achieves more than 20-fold speedup relative to parallel simulation with 100 processes. In a more realistic scenario with dynamic calcium influx and data recording, the parallel simulation with 1,000 processes and no load balancing is still 500 times faster than the conventional serial SSA simulation.

Beam dynamics in MABE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poukey, J.W.; Coleman, P.D.; Sanford, T.W.L.

1985-01-01

MABE is a multistage linear electron accelerator which accelerates up to nine beams in parallel. Nominal parameters per beam are 25 kA, final energy 7 MeV, and guide field 20 kG. We report recent progress via theory and simulation in understanding the beam dynamics in such a system. In particular, we emphasize our results on the radial oscillations and emittance growth for a beam passing through a series of accelerating gaps. 12 refs., 8 figs.

Training Capabilities Test of Electronics Equipment Maintenance Trainer (EEMT): Findings and Conclusions.

DTIC Science & Technology

1984-07-01

primarily a stand-alone, equipment-specific trainer which uses both structured and free - play lessonware. Structured lessons provide instruction on various...topics in a typical interactive tutorial format. Free - play lessons present troubleshooting problems and students are allowed to observe and manipulate...the simulated equipment until a solution is reached. Free - play lessons closely parallel laboratory training problems. S3 4. O. .4 o• , e o . . o - o o

Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Shuangshuang; Chen, Yousu; Wu, Di

2015-12-09

Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Messagemore » Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.« less

Parallel tempering for the traveling salesman problem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Percus, Allon; Wang, Richard; Hyman, Jeffrey

We explore the potential of parallel tempering as a combinatorial optimization method, applying it to the traveling salesman problem. We compare simulation results of parallel tempering with a benchmark implementation of simulated annealing, and study how different choices of parameters affect the relative performance of the two methods. We find that a straightforward implementation of parallel tempering can outperform simulated annealing in several crucial respects. When parameters are chosen appropriately, both methods yield close approximation to the actual minimum distance for an instance with 200 nodes. However, parallel tempering yields more consistently accurate results when a series of independent simulationsmore » are performed. Our results suggest that parallel tempering might offer a simple but powerful alternative to simulated annealing for combinatorial optimization problems.« less

Study of multipactor suppression of microwave components using perforated waveguide technology for space applications

NASA Astrophysics Data System (ADS)

Ye, Ming; Li, Yun; He, Yongning; Daneshmand, Mojgan

2017-05-01

With the development of space technology, microwave components with increased power handling capability and reduced weight have been urgently required. In this work, the perforated waveguide technology is proposed to suppress the multipactor effect of high power microwave components. Meanwhile, this novel method has the advantage of reducing components' weight, which makes it to have great potential in space applications. The perforated part of the waveguide components can be seen as an electron absorber (namely, its total electron emission yield is zero) since most of the electrons impacting on this part will go out of the components. Based on thoroughly benchmarked numerical simulation procedures, we simulated an S band and an X band waveguide transformer to conceptually verify this idea. Both electron dynamic simulations and electrical loss simulations demonstrate that the perforation technology can improve the multipactor threshold at least ˜8 dB while maintaining the acceptable insertion loss level compared with its un-perforated components. We also found that the component with larger minimum gap is easier to achieve multipactor suppression. This effect is interpreted by a parallel plate waveguide model. What's more, to improve the multipactor threshold of the X band waveguide transformer with a minimum gap of ˜0.1 mm, we proposed a perforation structure with the slope edge and explained its mechanism. Future study will focus on further optimization of the perforation structure, size, and distribution to maximize the comprehensive performances of microwave components.

Secure Identifications of the Electron Diffusion Region with Spacecraft Observations

NASA Astrophysics Data System (ADS)

Scudder, J. D.; Karimabadi, H.; Daughton, W. S.

2009-12-01

The Electron Diffusion Region (EDR) plays a key role in the reconnection process and its detection in spacecraft data is one of the major goals of MMS. However, the observable and diagnostic properties of entry into the EDR of collisionless magnetic reconnection remain a matter of much debate. There are also even some theoretical disagreements as to how to define secondary and tertiary properties of the EDR, that may be the only properties that are practically observable. Here we start with first principles of what the EDR is in a general magnetic topology including anti-parallel and guide field regimes. We motivate the EDR as the site in the reconnection layer where magnetic flux is not preserved for the comoving electron observer. Observable diagnostics were then found based on kinetic theory that (i) can be measured in the data, and (ii) that also highlight the theoretically motivated EDR found in the PIC simulations. We compare and contrast our diagnostics with those used by others. We present results from PIC simulations of an RD, an EDR layer, and a fast shock to illustrate their degeneracy under evidence presented in the literature to support EDR “sightings”. Seven (7) properties are shared by these layers. Invariably one of these seven inspecific tests are invoked in the literature when “EDR’s” are identified. A particularly common inspecific test is any and all violations of the Ideal Electron MHD (IEMHD) condition: E+UexB=0, whether from parallel E field detection or perpendicular deviations from IEMHD=0. PIC simulations clearly show that all three current layers possess violations of the ideal electron MHD condition; this result implies that the common usage of violations of IEMHD=0 to define, identify or corroborate a current layer as the EDR are not theoretically appropriate. Our kinetic, observable diagnostics however do differentiate amongst this degenerate class of propagating current layers. For example, these observables clearly differentiate a freely propagating RD - Alfven wave from an EDR layer, although both degenerately would satisfy the Walen test performed with electron flow and magnetic variables. We also show that the first principles definition of the EDR only selects the EDR layers from amongst this degenerate set of current layers.

Dissipation and particle energization in moderate to low beta turbulent plasma via PIC simulations

DOE PAGES

Makwana, Kirit; Li, Hui; Guo, Fan; ...

2017-05-30

Here, we simulate decaying turbulence in electron-positron pair plasmas using a fully-kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma β (the ratio of thermal pressure to magnetic pressure). The energy decay rate is found to be similar in both cases. The perpendicular wave-number spectrum of magnetic energy shows a slope betweenmore » $${k}_{\\perp }^{-1.3}$$ and $${k}_{\\perp }^{-1.1}$$, where the perpendicular (⊥) and parallel (∥) directions are defined with respect to the magnetic field. The particle kinetic energy distribution function shows the formation of a non-thermal feature in the case of lower plasma β, with a slope close to E-1. The correlation between thin turbulent current sheets and Ohmic heating by the dot product of electric field (E) and current density (J) is investigated. By heating the parallel E∥ centerdot J∥ term dominates the perpendicular E⊥ centerdot J⊥ term. Regions of strong E∥ centerdot J∥ are spatially well-correlated with regions of intense current sheets, which also appear correlated with regions of strong E∥ in the low β simulation, suggesting an important role of magnetic reconnection in the dissipation of low β plasma turbulence.« less

Dissipation and particle energization in moderate to low beta turbulent plasma via PIC simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makwana, Kirit; Li, Hui; Guo, Fan

Here, we simulate decaying turbulence in electron-positron pair plasmas using a fully-kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma β (the ratio of thermal pressure to magnetic pressure). The energy decay rate is found to be similar in both cases. The perpendicular wave-number spectrum of magnetic energy shows a slope betweenmore » $${k}_{\\perp }^{-1.3}$$ and $${k}_{\\perp }^{-1.1}$$, where the perpendicular (⊥) and parallel (∥) directions are defined with respect to the magnetic field. The particle kinetic energy distribution function shows the formation of a non-thermal feature in the case of lower plasma β, with a slope close to E-1. The correlation between thin turbulent current sheets and Ohmic heating by the dot product of electric field (E) and current density (J) is investigated. By heating the parallel E∥ centerdot J∥ term dominates the perpendicular E⊥ centerdot J⊥ term. Regions of strong E∥ centerdot J∥ are spatially well-correlated with regions of intense current sheets, which also appear correlated with regions of strong E∥ in the low β simulation, suggesting an important role of magnetic reconnection in the dissipation of low β plasma turbulence.« less

Anisotropic electron temperature measurements without knowing the spectral transmissivity for a JT-60SA Thomson scattering diagnostic.

PubMed

Tojo, H; Hatae, T; Yatsuka, E; Itami, K

2012-10-01

This paper focuses on a method for measuring the electron temperature (T(e)) without knowing the transmissivity using Thomson scattering diagnostic with a double-pass scattering system. Application of this method for measuring the anisotropic T(e), i.e., the T(e) in the directions parallel (T(eparallel)) and perpendicular (T(eperpendicular)) to the magnetic field, is proposed. Simulations based on the designed parameters for a JT-60SA indicate the feasibility of the measurements except in certain T(e) ranges, e.g., T(eparallel) ~ 3.5T(eperpendicular) at 120° of the scattering angle.

Generation and evolution of anisotropic turbulence and related energy transfer in a multi-species solar wind

NASA Astrophysics Data System (ADS)

Maneva, Yana; Poedts, Stefaan

2017-04-01

The electromagnetic fluctuations in the solar wind represent a zoo of plasma waves with different properties, whose wavelengths range from largest fluid scales to the smallest dissipation scales. By nature the power spectrum of the magnetic fluctuations is anisotropic with different spectral slopes in parallel and perpendicular directions with respect to the background magnetic field. Furthermore, the magnetic field power spectra steepen as one moves from the inertial to the dissipation range and we observe multiple spectral breaks with different slopes in parallel and perpendicular direction at the ion scales and beyond. The turbulent dissipation of magnetic field fluctuations at the sub-ion scales is believed to go into local ion heating and acceleration, so that the spectral breaks are typically associated with particle energization. The gained energy can be in the form of anisotropic heating, formation of non-thermal features in the particle velocity distributions functions, and redistribution of the differential acceleration between the different ion populations. To study the relation between the evolution of the anisotropic turbulent spectra and the particle heating at the ion and sub-ion scales we perform a series of 2.5D hybrid simulations in a collisionless drifting proton-alpha plasma. We neglect the fast electron dynamics and treat the electrons as an isothermal fluid electrons, whereas the protons and a minor population of alpha particles are evolved in a fully kinetic manner. We start with a given wave spectrum and study the evolution of the magnetic field spectral slopes as a function of the parallel and perpendicular wave¬numbers. Simultaneously, we track the particle response and the energy exchange between the parallel and perpendicular scales. We observe anisotropic behavior of the turbulent power spectra with steeper slopes along the dominant energy-containing direction. This means that for parallel and quasi-parallel waves we have steeper spectral slope in parallel direction, whereas for highly oblique waves the dissipation occurs predominantly in perpendicular direction and the spectral slopes are steeper across the background magnetic field. The value of the spectral slopes depends on the angle of propagation, the spectral range, as well as the plasma properties. In general the dissipation is stronger at small scales and the corresponding spectral slopes there are steeper. For parallel and quasi-parallel propagation the prevailing energy cascade remains along the magnetic field, whereas for initially isotropic oblique turbulence the cascade develops mainly in perpendicular direction.

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

NASA Astrophysics Data System (ADS)

Adli, E.; Lindstrøm, C. A.; Allen, J.; Clarke, C. I.; Frederico, J.; Gessner, S. J.; Green, S. Z.; Hogan, M. J.; Litos, M. D.; O'Shea, B.; Yakimenko, V.; An, W.; Clayton, C. E.; Marsh, K. A.; Mori, W. B.; Joshi, C.; Vafaei-Najafabadi, N.; Corde, S.; Lu, W.

2016-10-01

We report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. The attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam-plasma interactions in general and plasma wakefield accelerator technology in particular.

Dielectric barrier structure with hollow electrodes and its recoil effect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Shuang; Chen, Qunzhi; Liu, Jiahui

2015-06-15

A dielectric barrier structure with hollow electrodes (HEDBS), in which gas flow oriented parallel to the electric field, was proposed. Results showed that with this structure, air can be effectively ignited, forming atmospheric low temperature plasma, and the proposed HEDBS could achieve much higher electron density (5 × 10{sup 15}/cm{sup 3}). It was also found that the flow condition, including outlet diameter and flow rate, played a key role in the evolution of electron density. Optical emission spectroscopy diagnostic results showed that the concentration of reactive species had the same variation trend as the electron density. The simulated distribution of discharge gasmore » flow indicated that the HEDBS had a strong recoil effect on discharge gas, and could efficiently promote generating electron density as well as reactive species.« less

Biofilm formation and control in a simulated spacecraft water system - Two-year results

NASA Technical Reports Server (NTRS)

Schultz, John R.; Taylor, Robert D.; Flanagan, David T.; Carr, Sandra E.; Bruce, Rebekah J.; Svoboda, Judy V.; Huls, M. H.; Sauer, Richard L.; Pierson, Duane L.

1991-01-01

The ability of iodine to maintain microbial water quality in a simulated spacecraft water system is being studied. An iodine level of about 2.0 mg/L is maintained by passing ultrapure influent water through an iodinated ion exchange resin. Six liters are withdrawn daily and the chemical and microbial quality of the water is monitored regularly. Stainless steel coupons used to monitor biofilm formation are being analyzed by culture methods, epifluorescence microscopy, and scanning electron microscopy. Results from the first two years of operation show a single episode of high bacterial colony counts in the iodinated system. This growth was apparently controlled by replacing the iodinated ion exchange resin. Scanning electron microscopy indicates that the iodine has limited but not completely eliminated the formation of biofilm during the first two years of operation. Significant microbial contamination has been present continuously in a parallel noniodinated system since the third week of operation.

Wave-Particle Interactions Involving Correlated Electron Bursts and Whistler Chorus in Earth's Radiation Belts

NASA Astrophysics Data System (ADS)

Echterling, N.; Schriver, D.; Roeder, J. L.; Fennell, J. F.

2017-12-01

During the recovery phase of substorm plasma injections, the Van Allen Probes commonly observe events of quasi-periodic energetic electron bursts correlating with simultaneously detected upper-band, whistler-mode chorus emissions. These electron bursts exhibit narrow ranges of pitch angles (75-80° and 100-105°) and energies (20-40 keV). Electron cyclotron harmonic (ECH) emissions are also commonly detected, but typically do not display correlation with the electron bursts. To examine sources of free energy and the generation of these wave emissions, an observed electron velocity distribution on January 13, 2013 is used as the starting condition for a particle in cell (PIC) simulation. Effects of temperature anisotropy (perpendicular temperature greater than parallel temperature), the presence of a loss cone and a cold electron population on the generation of whistler and ECH waves are examined to understand wave generation and nonlinear interactions with the particle population. These nonlinear interactions produce energy diffusion along with strong pitch angle scattering into the loss cone on the order of milliseconds, which is faster than a typical bounce period of seconds. To examine the quasi-periodic nature of the electron bursts, a loss-cone recycling technique is implemented to model the effects of the periodic emptying of the loss cone and electron injection on the growth of whistler and ECH waves. The results of the simulations are compared to the Van Allen Probe observations to determine electron acceleration, heating and transport in Earth's radiation belts due to wave-particle interactions.

Particle Acceleration and Magnetic Field Generation in Electron-Positron Relativistic Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Hardee, P.; Richardson, G.; Preece, R.; Sol, H.; Fishman, G. J.

2004-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic electron-positron jet front propagating into an ambient electron-positron plasma with and without initial magnetic fields. We find small differences in the results for no ambient and modest ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The non-linear fluctuation amplitudes of densities, currents, electric, and magnetic fields in the electron-positron shock are larger than those found in the electron-ion shock studied in a previous paper. This comes from the fact that both electrons and positrons contribute to generation of the Weibel instability. Additionally, we have performed simulations with different electron skin depths. We find that growth times scale inversely with the plasma frequency, and the sizes of structures created by the Weibel instability scale proportional to the electron skin depth. This is the expected result and indicates that the simulations have sufficient grid resolution. While some Fermi acceleration may occur at the jet front, the majority of electron and positron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying nonuniform, small-scale magnetic fields which contribute to the electron's (positron's) transverse deflection behind the jet head. This small scale magnetic field structure is appropriate to the generation of "jitter" radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation has different properties than synchrotron radiation calculated assuming a a uniform magnetic field. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Particle-in-cell simulation of multipactor discharge on a dielectric in a parallel-plate waveguide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakharov, A. S., E-mail: sakharov-as@mail.ru; Ivanov, V. A.; Konyzhev, M. E.

2016-06-15

An original 2D3V (two-dimensional in coordinate space and three-dimensional in velocity space) particle-in-cell code has been developed for simulation of multipactor discharge on a dielectric in a parallelplate metal waveguide with allowance for secondary electron emission (SEE) from the dielectric surface and waveguide walls, finite temperature of secondary electrons, electron space charge, and elastic and inelastic scattering of electrons from the dielectric and metal surfaces. The code allows one to simulate all stages of the multipactor discharge, from the onset of the electron avalanche to saturation. It is shown that the threshold for the excitation of a single-surface multipactor onmore » a dielectric placed in a low-profile waveguide with absorbing walls increases as compared to that in the case of an unbounded dielectric surface due to escape of electrons onto the waveguide walls. It is found that, depending on the microwave field amplitude and the SEE characteristics of the waveguide walls, the multipactor may operate in two modes. In the first mode, which takes place at relatively low microwave amplitudes, a single-surface multipactor develops only on the dielectric, the surface of which acquires a positively potential with respect to the waveguide walls. In the second mode, which occurs at sufficiently high microwave intensities, a single-surface multipactor on the dielectric and a two-surface multipactor between the waveguide walls operate simultaneously. In this case, both the dielectric surface and the interwall space acquire a negative potential. It is shown that electron scattering from the dielectric surface and waveguide walls results in the appearance of high-energy tails in the electron distribution function.« less

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Establishing a Novel Modeling Tool: A Python-Based Interface for a Neuromorphic Hardware System

PubMed Central

Brüderle, Daniel; Müller, Eric; Davison, Andrew; Muller, Eilif; Schemmel, Johannes; Meier, Karlheinz

2008-01-01

Neuromorphic hardware systems provide new possibilities for the neuroscience modeling community. Due to the intrinsic parallelism of the micro-electronic emulation of neural computation, such models are highly scalable without a loss of speed. However, the communities of software simulator users and neuromorphic engineering in neuroscience are rather disjoint. We present a software concept that provides the possibility to establish such hardware devices as valuable modeling tools. It is based on the integration of the hardware interface into a simulator-independent language which allows for unified experiment descriptions that can be run on various simulation platforms without modification, implying experiment portability and a huge simplification of the quantitative comparison of hardware and simulator results. We introduce an accelerated neuromorphic hardware device and describe the implementation of the proposed concept for this system. An example setup and results acquired by utilizing both the hardware system and a software simulator are demonstrated. PMID:19562085

Establishing a novel modeling tool: a python-based interface for a neuromorphic hardware system.

PubMed

Brüderle, Daniel; Müller, Eric; Davison, Andrew; Muller, Eilif; Schemmel, Johannes; Meier, Karlheinz

2009-01-01

Neuromorphic hardware systems provide new possibilities for the neuroscience modeling community. Due to the intrinsic parallelism of the micro-electronic emulation of neural computation, such models are highly scalable without a loss of speed. However, the communities of software simulator users and neuromorphic engineering in neuroscience are rather disjoint. We present a software concept that provides the possibility to establish such hardware devices as valuable modeling tools. It is based on the integration of the hardware interface into a simulator-independent language which allows for unified experiment descriptions that can be run on various simulation platforms without modification, implying experiment portability and a huge simplification of the quantitative comparison of hardware and simulator results. We introduce an accelerated neuromorphic hardware device and describe the implementation of the proposed concept for this system. An example setup and results acquired by utilizing both the hardware system and a software simulator are demonstrated.

Through the Eye of the Needle: The Separator and its Environs

NASA Astrophysics Data System (ADS)

Scudder, J. D.; Mozer, F. S.; Maynard, N. C.; Russell, C. T.

2001-05-01

The observed properties of the electromagnetic field and the plasma at and around a magnetic separator observed on May 29, 1996 with the ISTP GGS Polar satellite will be discussed. The electron pressure ridge will be illustrated astride the current layer, and the ion flow will be shown to impinge on the separator with MA ~= 0.1 and leave along the pressure ridge with MA ~= 1.1 33 traversals of rotational shear layers have been documented in this interval using the electron form of the Walen test. The electron fluid velocity is shown to have strong parallel Mach number enhancements along the separatrices, with peak parallel Alfven mach numbers of 4.5 that are probably limited by plasma time resolution (4.3s). These are similar in location to those in two fluid, hybrid, and particle - particle simulations of collisionless reconnection. The direct detection of the parallel electric field in the vicinity of the separator is shown in all cases to be limited by the so called Vasyliunas limit, $ E∥ <= O(1)√ {{{kTe}/{2m_ic2}}}| B|, that corresponds to the scale length of the pressure gradient being limited by the scale \\rho_s = \\beta_e^{1\\over2}{c\\over {\\omegapi}} seen to be important in the multi-species analysis of collisionless reconnection. In turn, the electron gas is shown at times not to drift at the E \\times B drift speed, but have substantial drifts perpendicular to B of a sense implied by the pressure divergences that cause the parallel electric field. Two techniques have been introduced to demonstrate the spectacular enhancement of the departures from cylindrical symmetry exhibited by the electrons as the separator null field region is traversed. Using totally separate arguments, the thermal electrons are shown to be clearly unmagnetized within the {c\\over{\\omegape}}$ scales about the separator, with the thermal gyroradius 10-30 times the scale length of B in this vicinity. At the moment level this demagnetization shows up as the loss of gyrotropy, or increase of ``agyrotropy''. In these regimes the thermal electrons can move onto different field lines and affect a loss of identity of field lines. Said differently, this agyrotropy requires the retention of the full tensorial electron pressure tensor to convey its effects in the multi-fluid treatments. Superposed epoch pictures of the spatial environment of the separator will be illustrated in different diagnostic "wavelengths" such as magnetic intensity, electron pressure, beta and gyroradius of electrons relative to scale lengths of B. In this way we provide the first in situ empirical definition of a site of collisionless magnetic reconnection and verify the demagnetization of electrons outlined by Vasyliunas 25 years ago as the likely mechanism for violation of the frozen flux theorem.

Spatial awareness comparisons between large-screen, integrated pictorial displays and conventional EFIS displays during simulated landing approaches

NASA Technical Reports Server (NTRS)

Parrish, Russell V.; Busquets, Anthony M.; Williams, Steven P.; Nold, Dean E.

1994-01-01

An extensive simulation study was performed to determine and compare the spatial awareness of commercial airline pilots on simulated landing approaches using conventional flight displays with their awareness using advanced pictorial 'pathway in the sky' displays. Sixteen commercial airline pilots repeatedly made simulated complex microwave landing system approaches to closely spaced parallel runways with an extremely short final segment. Scenarios involving conflicting traffic situation assessments and recoveries from flight path offset conditions were used to assess spatial awareness (own ship position relative the the desired flight route, the runway, and other traffic) with the various display formats. The situation assessment tools are presented, as well as the experimental designs and the results. The results demonstrate that the integrated pictorial displays substantially increase spatial awareness over conventional electronic flight information systems display formats.

Ef: Software for Nonrelativistic Beam Simulation by Particle-in-Cell Algorithm

NASA Astrophysics Data System (ADS)

Boytsov, A. Yu.; Bulychev, A. A.

2018-04-01

Understanding of particle dynamics is crucial in construction of electron guns, ion sources and other types of nonrelativistic beam devices. Apart from external guiding and focusing systems, a prominent role in evolution of such low-energy beams is played by particle-particle interaction. Numerical simulations taking into account these effects are typically accomplished by a well-known particle-in-cell method. In practice, for convenient work a simulation program should not only implement this method, but also support parallelization, provide integration with CAD systems and allow access to details of the simulation algorithm. To address the formulated requirements, development of a new open source code - Ef - has been started. It's current features and main functionality are presented. Comparison with several analytical models demonstrates good agreement between the numerical results and the theory. Further development plans are discussed.

The Influence of Shape on the Output Potential of ZnO Nanostructures: Sensitivity to Parallel versus Perpendicular Forces.

PubMed

Cardoso, José; Oliveira, Filipe F; Proenca, Mariana P; Ventura, João

2018-05-22

With the consistent shrinking of devices, micro-systems are, nowadays, widely used in areas such as biomedics, electronics, automobiles, and measurement devices. As devices shrunk, so too did their energy consumptions, opening the way for the use of nanogenerators (NGs) as power sources. In particular, to harvest energy from an object's motion (mechanical vibrations, torsional forces, or pressure), present NGs are mainly composed of piezoelectric materials in which, upon an applied compressive or strain force, an electrical field is produced that can be used to power a device. The focus of this work is to simulate the piezoelectric effect in different ZnO nanostructures to optimize the output potential generated by a nanodevice. In these simulations, cylindrical nanowires, nanomushrooms, and nanotrees were created, and the influence of the nanostructures' shape on the output potential was studied as a function of applied parallel and perpendicular forces. The obtained results demonstrated that the output potential is linearly proportional to the applied force and that perpendicular forces are more efficient in all structures. However, nanotrees were found to have an increased sensitivity to parallel applied forces, which resulted in a large enhancement of the output efficiency. These results could then open a new path to increase the efficiency of piezoelectric nanogenerators.

Parallel Signal Processing and System Simulation using aCe

NASA Technical Reports Server (NTRS)

Dorband, John E.; Aburdene, Maurice F.

2003-01-01

Recently, networked and cluster computation have become very popular for both signal processing and system simulation. A new language is ideally suited for parallel signal processing applications and system simulation since it allows the programmer to explicitly express the computations that can be performed concurrently. In addition, the new C based parallel language (ace C) for architecture-adaptive programming allows programmers to implement algorithms and system simulation applications on parallel architectures by providing them with the assurance that future parallel architectures will be able to run their applications with a minimum of modification. In this paper, we will focus on some fundamental features of ace C and present a signal processing application (FFT).

On the suitability of the connection machine for direct particle simulation

NASA Technical Reports Server (NTRS)

Dagum, Leonard

1990-01-01

The algorithmic structure was examined of the vectorizable Stanford particle simulation (SPS) method and the structure is reformulated in data parallel form. Some of the SPS algorithms can be directly translated to data parallel, but several of the vectorizable algorithms have no direct data parallel equivalent. This requires the development of new, strictly data parallel algorithms. In particular, a new sorting algorithm is developed to identify collision candidates in the simulation and a master/slave algorithm is developed to minimize communication cost in large table look up. Validation of the method is undertaken through test calculations for thermal relaxation of a gas, shock wave profiles, and shock reflection from a stationary wall. A qualitative measure is provided of the performance of the Connection Machine for direct particle simulation. The massively parallel architecture of the Connection Machine is found quite suitable for this type of calculation. However, there are difficulties in taking full advantage of this architecture because of lack of a broad based tradition of data parallel programming. An important outcome of this work has been new data parallel algorithms specifically of use for direct particle simulation but which also expand the data parallel diction.

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

Large-scale three-dimensional phase-field simulations for phase coarsening at ultrahigh volume fraction on high-performance architectures

NASA Astrophysics Data System (ADS)

Yan, Hui; Wang, K. G.; Jones, Jim E.

2016-06-01

A parallel algorithm for large-scale three-dimensional phase-field simulations of phase coarsening is developed and implemented on high-performance architectures. From the large-scale simulations, a new kinetics in phase coarsening in the region of ultrahigh volume fraction is found. The parallel implementation is capable of harnessing the greater computer power available from high-performance architectures. The parallelized code enables increase in three-dimensional simulation system size up to a 5123 grid cube. Through the parallelized code, practical runtime can be achieved for three-dimensional large-scale simulations, and the statistical significance of the results from these high resolution parallel simulations are greatly improved over those obtainable from serial simulations. A detailed performance analysis on speed-up and scalability is presented, showing good scalability which improves with increasing problem size. In addition, a model for prediction of runtime is developed, which shows a good agreement with actual run time from numerical tests.

Energetic Electrons in Dipolarization Events: Spatial Properties and Anisotropy

NASA Technical Reports Server (NTRS)

Birn, J.; Runov, A.; Hesse, M.

2014-01-01

Using the electromagnetic fields of an MHD simulation of magnetotail reconnection, flow bursts, and dipolarization, we further investigate the acceleration of electrons to suprathermal energies. Particular emphasis is on spatial properties and anisotropies as functions of energy and time. The simulation results are compared with Time History of Events and Macroscale Interactions during Substorms observations. The test particle approach successfully reproduces several observed injection features and puts them into a context of spatial maps of the injection region(s): a dominance of perpendicular anisotropies farther down the tail and closer to the equatorial plane, an increasing importance of parallel anisotropy closer to Earth and at higher latitudes, a drop in energy fluxes at energies below approximately 10 keV, coinciding with the plasma density drop, together with increases at higher energy, a triple peak structure of flux increases near 0 deg, 90 deg, and 180 deg, and a tendency of flux increases to extend to higher energy closer to Earth and at lower latitudes. We identified the plasma sheet boundary layers and adjacent lobes as a main source region for both increased and decreased energetic electron fluxes, related to the different effects of adiabatic acceleration at high and low energies. The simulated anisotropies tend to exceed the observed ones, particularly for perpendicular fluxes at high energies. The most plausible reason is that the MHD simulation lacks the effects of anisotropy-driven microinstabilities and waves, which would reduce anisotropies.

Impact of Shock Front Rippling and Self-reformation on the Electron Dynamics at Low-Mach-number Shocks

NASA Astrophysics Data System (ADS)

Yang, Zhongwei; Lu, Quanming; Liu, Ying D.; Wang, Rui

2018-04-01

Electron dynamics at low-Mach-number collisionless shocks are investigated by using two-dimensional electromagnetic particle-in-cell simulations with various shock normal angles. We found: (1) The reflected ions and incident electrons at the shock front provide an effective mechanism for the quasi-electrostatic wave generation due to the charge-separation. A fraction of incident electrons can be effectively trapped and accelerated at the leading edge of the shock foot. (2) At quasi-perpendicular shocks, the electron trapping and reflection is nonuniform due to the shock rippling along the shock surface and is more likely to take place at some locations accompanied by intense reflected ion-beams. The electron trapping process has a periodical evolution over time due to the shock front self-reformation, which is controlled by ion dynamics. Thus, this is a cross-scale coupling phenomenon. (3) At quasi-parallel shocks, reflected ions can travel far back upstream. Consequently, quasi-electrostatic waves can be excited in the shock transition and the foreshock region. The electron trajectory analysis shows these waves can trap electrons at the foot region and reflect a fraction of them far back upstream. Simulation runs in this paper indicate that the micro-turbulence at the shock foot can provide a possible scenario for producing the reflected electron beam, which is a basic condition for the type II radio burst emission at low-Mach-number interplanetary shocks driven by Coronal Mass Ejections (CMEs).

Xyce Parallel Electronic Simulator Reference Guide Version 6.6.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keiter, Eric R.; Aadithya, Karthik Venkatraman; Mei, Ting

This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . The information herein is subject to change without notice. Copyright c 2002-2016 Sandia Corporation. All rights reserved. Acknowledgements The BSIM Group at the University ofmore » California, Berkeley developed the BSIM3, BSIM4, BSIM6, BSIM-CMG and BSIM-SOI models. The BSIM3 is Copyright c 1999, Regents of the University of California. The BSIM4 is Copyright c 2006, Regents of the University of California. The BSIM6 is Copyright c 2015, Regents of the University of California. The BSIM-CMG is Copyright c 2012 and 2016, Regents of the University of California. The BSIM-SOI is Copyright c 1990, Regents of the University of California. All rights reserved. The Mextram model has been developed by NXP Semiconductors until 2007, Delft University of Technology from 2007 to 2014, and Auburn University since April 2015. Copyrights c of Mextram are with Delft University of Technology, NXP Semiconductors and Auburn University. The MIT VS Model Research Group developed the MIT Virtual Source (MVS) model. Copyright c 2013 Massachusetts Institute of Technology (MIT). The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla« less

Electron heating in the exhaust of magnetic reconnection with negligible guide field

NASA Astrophysics Data System (ADS)

Wang, Shan; Chen, Li-Jen; Bessho, Naoki; Kistler, Lynn M.; Shuster, Jason R.; Guo, Ruilong

2016-03-01

Electron heating in the magnetic reconnection exhaust is investigated with particle-in-cell simulations, space observations, and theoretical analysis. Spatial variations of the electron temperature (Te) and associated velocity distribution functions (VDFs) are examined and understood in terms of particle energization and randomization processes that vary with exhaust locations. Inside the electron diffusion region (EDR), the electron temperature parallel to the magnetic field (Te∥) exhibits a local minimum and the perpendicular temperature (Te⊥) shows a maximum at the current sheet midplane. In the intermediate exhaust downstream from the EDR and far from the magnetic field pileup region, Te⊥/Te∥ is close to unity and Te is approximately uniform, but the VDFs are structured: close to the midplane, VDFs are quasi-isotropic, whereas farther away from the midplane, VDFs exhibit field-aligned beams directed toward the midplane. In the far exhaust, Te generally increases toward the midplane and the pileup region, and the corresponding VDFs show counter-streaming beams. A distinct population with low v∥ and high v⊥ is prominent in the VDFs around the midplane. Test particle results show that the magnetic curvature near the midplane produces pitch angle scattering to generate quasi-isotropic distributions in the intermediate exhaust. In the far exhaust, electrons with initial high v∥ (v⊥) are accelerated mainly through curvature (gradient-B) drift opposite to the electric field, without significant pitch angle scattering. The VDF structures predicted by simulations are observed in magnetotail reconnection measurements, indicating that the energization mechanisms captured in the reported simulations are applicable to magnetotail reconnection with negligible guide field.

Intrinsic uncoupling of mitochondrial proton pumps. 2. Modeling studies.

PubMed

Pietrobon, D; Zoratti, M; Azzone, G F; Caplan, S R

1986-02-25

The thermodynamic and kinetic properties associated with intrinsic uncoupling in a six-state model of a redox proton pump have been studied by computing the flow-force relations for different degrees of coupling. Analysis of these relations shows the regulatory influence of the thermodynamic forces on the extent and relative contributions of redox slip and proton slip. Inhibition has been introduced into the model in two different ways, corresponding to possible modes of action of experimental inhibitors. Experiments relating the rate of electron transfer to delta microH at static head upon progressive inhibition of the pumps have been simulated considering (1) the limiting case that the nonzero rate of electron transfer at static head is only due to intrinsic uncoupling (no leaks) and (2) the experimentally observed case that about 30% of the nonzero rate of electron transfer at static head is due to a constant proton leakage conductance in parallel with the pumps, the rest being due to intrinsic uncoupling. The same simulations have been performed for experiments in which the rate of electron transfer is varied by varying the substrate concentration rather than by using an inhibitor. The corresponding experimental results obtained by measuring delta microH and the rate of electron transfer at different succinate concentrations in rat liver mitochondria are presented. Comparison between simulated behavior and experimental results leads to the general conclusion that the typical relationship between rate of electron transfer and delta microH found in mitochondria at static head could certainly be a manifestation of some degree of intrinsic uncoupling in the redox proton pumps.(ABSTRACT TRUNCATED AT 250 WORDS)

Self-consistent electrostatic simulations of reforming double layers in the downward current region of the aurora

NASA Astrophysics Data System (ADS)

Gunell, H.; Andersson, L.; De Keyser, J.; Mann, I.

2015-10-01

The plasma on a magnetic field line in the downward current region of the aurora is simulated using a Vlasov model. It is found that an electric field parallel to the magnetic fields is supported by a double layer moving toward higher altitude. The double layer accelerates electrons upward, and these electrons give rise to plasma waves and electron phase-space holes through beam-plasma interaction. The double layer is disrupted when reaching altitudes of 1-2 Earth radii where the Langmuir condition no longer can be satisfied due to the diminishing density of electrons coming up from the ionosphere. During the disruption the potential drop is in part carried by the electron holes. The disruption creates favourable conditions for double layer formation near the ionosphere and double layers form anew in that region. The process repeats itself with a period of approximately 1 min. This period is determined by how far the double layer can reach before being disrupted: a higher disruption altitude corresponds to a longer repetition period. The disruption altitude is, in turn, found to increase with ionospheric density and to decrease with total voltage. The current displays oscillations around a mean value. The period of the oscillations is the same as the recurrence period of the double layer formations. The oscillation amplitude increases with increasing voltage, whereas the mean value of the current is independent of voltage in the 100 to 800 V range covered by our simulations. Instead, the mean value of the current is determined by the electron density at the ionospheric boundary.

Suppressing correlations in massively parallel simulations of lattice models

NASA Astrophysics Data System (ADS)

Kelling, Jeffrey; Ódor, Géza; Gemming, Sibylle

2017-11-01

For lattice Monte Carlo simulations parallelization is crucial to make studies of large systems and long simulation time feasible, while sequential simulations remain the gold-standard for correlation-free dynamics. Here, various domain decomposition schemes are compared, concluding with one which delivers virtually correlation-free simulations on GPUs. Extensive simulations of the octahedron model for 2 + 1 dimensional Kardar-Parisi-Zhang surface growth, which is very sensitive to correlation in the site-selection dynamics, were performed to show self-consistency of the parallel runs and agreement with the sequential algorithm. We present a GPU implementation providing a speedup of about 30 × over a parallel CPU implementation on a single socket and at least 180 × with respect to the sequential reference.

SPEEDES - A multiple-synchronization environment for parallel discrete-event simulation

NASA Technical Reports Server (NTRS)

Steinman, Jeff S.

1992-01-01

Synchronous Parallel Environment for Emulation and Discrete-Event Simulation (SPEEDES) is a unified parallel simulation environment. It supports multiple-synchronization protocols without requiring users to recompile their code. When a SPEEDES simulation runs on one node, all the extra parallel overhead is removed automatically at run time. When the same executable runs in parallel, the user preselects the synchronization algorithm from a list of options. SPEEDES currently runs on UNIX networks and on the California Institute of Technology/Jet Propulsion Laboratory Mark III Hypercube. SPEEDES also supports interactive simulations. Featured in the SPEEDES environment is a new parallel synchronization approach called Breathing Time Buckets. This algorithm uses some of the conservative techniques found in Time Bucket synchronization, along with the optimism that characterizes the Time Warp approach. A mathematical model derived from first principles predicts the performance of Breathing Time Buckets. Along with the Breathing Time Buckets algorithm, this paper discusses the rules for processing events in SPEEDES, describes the implementation of various other synchronization protocols supported by SPEEDES, describes some new ones for the future, discusses interactive simulations, and then gives some performance results.

Calculation of secondary-electron escape currents from inclined-spacecraft surfaces in a magnetic field

NASA Technical Reports Server (NTRS)

Laframboise, J. G.

1985-01-01

In low Earth orbit, the geomagnetic field B(vector) is strong enough that secondary electrons emitted from spacecraft surfaces have an average gyroradius much smaller than typical dimensions of large spacecraft. This implies that escape of secondaries will be strongly inhibited on surfaces which are nearly parallel to B(vector), even if a repelling electric field exists outside them. This effect is likely to make an important contribution to the current balance and hence the equilibrium potential of such surfaces, making high voltage charging of them more likely. Numerically calculated escaping secondary electron fluxes are presented for these conditions. For use in numerical spacecraft charging simulations, an analytic curve fit to these results is given which is accurate to within 3% of the emitted current.

Potential Role of the Mirror and Ion Bernstein Instabilities on the Pickup Ion Dynamics in the Outer Heliosheath: Linear Theory and Hybrid Simulations

NASA Astrophysics Data System (ADS)

Min, K.; Liu, K.; Gary, S. P.

2017-12-01

The main challenge of the secondary ENA mechanism, a theory put forth to explain the IBEX ENA ribbon, is maintaining the stability of the pickup ion velocity distribution before the pickup ions in the outer heliosheath go through two consecutive charge exchanges. The Alfvén/ion-cyclotron instability, which has its maximum growth at propagation parallel to Bo, the background magnetic field, is believed to be the main agent leading to rapid isotropization of the pickup ions. However, recent studies found that this instability can be suppressed when parallel temperatures of the background plasma and the pickup ion ring distribution are comparable, allowing the pickup ion distribution to remain stable for a long period. This paper demonstrates that a pickup ion ring distribution can also drive the mirror and ion Bernstein instabilities which lead to growing modes at propagation oblique to Bo. For idealized proton-electron plasmas where relatively cool background electron and proton populations are represented by isotropic Maxwellian distributions and tenuous (1%) pickup protons are represented by a Maxwellian-ring distribution (assuming a 90˚ pickup angle), linear Vlasov theory predicts unstable mirror and ion Bernstein modes with growth rates comparable to or exceeding that of the Alfvén-cyclotron instability. According to quasilinear theory, interactions with these obliquely-propagating modes can lead to substantial pitch angle scattering of the ring protons. Two-dimensional hybrid (kinetic ions and massless fluid electrons) simulations are carried out to examine the nonlinear consequences of the mirror and Bernstein instabilities. The preliminary simulation results are presented. The study suggests a scenario that the oblique mirror and ion Bernstein modes can be an active agent of the pickup ion isotropization when the condition is such that the Alfvén-cyclotron instability is suppressed.

Influence of equilibrium shear flow in the parallel magnetic direction on edge localized mode crash

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Y.; Xiong, Y. Y.; Chen, S. Y., E-mail: sychen531@163.com

2016-04-15

The influence of the parallel shear flow on the evolution of peeling-ballooning (P-B) modes is studied with the BOUT++ four-field code in this paper. The parallel shear flow has different effects in linear simulation and nonlinear simulation. In the linear simulations, the growth rate of edge localized mode (ELM) can be increased by Kelvin-Helmholtz term, which can be caused by the parallel shear flow. In the nonlinear simulations, the results accord with the linear simulations in the linear phase. However, the ELM size is reduced by the parallel shear flow in the beginning of the turbulence phase, which is recognizedmore » as the P-B filaments' structure. Then during the turbulence phase, the ELM size is decreased by the shear flow.« less

Magnetic shielding investigation for a 6 MV in-line linac within the parallel configuration of a linac-MR system.

PubMed

Santos, D M; St Aubin, J; Fallone, B G; Steciw, S

2012-02-01

In our current linac-magnetic resonance (MR) design, a 6 MV in-line linac is placed along the central axis of the MR's magnet where the MR's fringe magnetic fields are parallel to the overall electron trajectories in the linac waveguide. Our previous study of this configuration comprising a linac-MR SAD of 100 cm and a 0.5 T superconducting (open, split) MR imager. It showed the presence of longitudinal magnetic fields of 0.011 T at the electron gun, which caused a reduction in target current to 84% of nominal. In this study, passive and active magnetic shielding was investigated to recover the linac output losses caused by magnetic deflections of electron trajectories in the linac within a parallel linac-MR configuration. Magnetic materials and complex shield structures were used in a 3D finite element method (FEM) magnetic field model, which emulated the fringe magnetic fields of the MR imagers. The effects of passive magnetic shielding was studied by surrounding the electron gun and its casing with a series of capped steel cylinders of various inner lengths (26.5-306.5 mm) and thicknesses (0.75-15 mm) in the presence of the fringe magnetic fields from a commercial MR imager. In addition, the effects of a shield of fixed length (146.5 mm) with varying thicknesses were studied against a series of larger homogeneous magnetic fields (0-0.2 T). The effects of active magnetic shielding were studied by adding current loops around the electron gun and its casing. The loop currents, separation, and location were optimized to minimize the 0.011 T longitudinal magnetic fields in the electron gun. The magnetic field solutions from the FEM model were added to a validated linac simulation, consisting of a 3D electron gun (using OPERA-3d/scala) and 3D waveguide (using comsol Multiphysics and PARMELA) simulations. PARMELA's target current and output phase-space were analyzed to study the linac's output performance within the magnetic shields. The FEM model above agreed within 1.5% with the manufacturer supplied fringe magnetic field isoline data. When passive magnetic shields are used, the target current is recoverable to greater than 99% of nominal for shield thicknesses greater than 0.75 mm. The optimized active shield which resulted in 100% target current recovery consists of two thin current rings 110 mm in diameter with 625 and 430 A-turns in each ring. With the length of the passive shield kept constant, the thickness of the shield had to be increased to achieve the same target current within the increased longitudinal magnetic fields. A ≥99% original target current is recovered with passive shield thicknesses >0.75 mm. An active shield consisting of two current rings of diameter of 110 mm with 625 and 430 A-turns fully recovers the loss that would have been caused by the magnetic fields. The minimal passive or active shielding requirements to essentially fully recover the current output of the linac in our parallel-configured linac-MR system have been determined and are easily achieved for practical implementation of the system.

TU-AB-BRC-07: Efficiency of An IAEA Phase-Space Source for a Low Energy X-Ray Tube Using Egs++

DOE Office of Scientific and Technical Information (OSTI.GOV)

Watson, PGF; Renaud, MA; Seuntjens, J

Purpose: To extend the capability of the EGSnrc C++ class library (egs++) to write and read IAEA phase-space files as a particle source, and to assess the relative efficiency gain in dose calculation using an IAEA phase-space source for modelling a miniature low energy x-ray source. Methods: We created a new ausgab object to score particles exiting a user-defined geometry and write them to an IAEA phase-space file. A new particle source was created to read from IAEA phase-space data. With these tools, a phase-space file was generated for particles exiting a miniature 50 kVp x-ray tube (The INTRABEAM System,more » Carl Zeiss). The phase-space source was validated by comparing calculated PDDs with a full electron source simulation of the INTRABEAM. The dose calculation efficiency gain of the phase-space source was determined relative to the full simulation. The efficiency gain as a function of i) depth in water, and ii) job parallelization was investigated. Results: The phase-space and electron source PDDs were found to agree to 0.5% RMS, comparable to statistical uncertainties. The use of a phase-space source for the INTRABEAM led to a relative efficiency gain of greater than 20 over the full electron source simulation, with an increase of up to a factor of 196. The efficiency gain was found to decrease with depth in water, due to the influence of scattering. Job parallelization (across 2 to 256 cores) was not found to have any detrimental effect on efficiency gain. Conclusion: A set of tools has been developed for writing and reading IAEA phase-space files, which can be used with any egs++ user code. For simulation of a low energy x-ray tube, the use of a phase-space source was found to increase the relative dose calculation efficiency by factor of up to 196. The authors acknowledge partial support by the CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council (Grant No. 432290).« less

The linearly scaling 3D fragment method for large scale electronic structure calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-07-28

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Zhengji; Meza, Juan; Lee, Byounghak

2009-06-26

The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

Particle Acceleration, Magnetic Field Generation, and Emission in Relativistic Pair Jets

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Ramirez-Ruiz, E.; Hardee, P.; Hededal, C.; Mizuno, Y.

2005-01-01

Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created by relativistic pair jets are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet propagating through an ambient plasma with and without initial magnetic fields. The growth rates of the Weibel instability depends on the distribution of pair jets. Simulations show that the Weibel instability created in the collisionless shock accelerates particles perpendicular and parallel to the jet propagation direction. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron's transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Study on acceleration processes of the radiation belt electrons through interaction with sub-packet chorus waves in parallel propagation

NASA Astrophysics Data System (ADS)

Hiraga, R.; Omura, Y.

2017-12-01

By recent observations, chorus waves include fine structures such as amplitude fluctuations (i.e. sub-packet structure), and it has not been verified in detail yet how energetic electrons are efficiently accelerated under the wave features. In this study, we firstly focus on the acceleration process of a single electron: how it experiences the efficient energy increase by interaction with sub-packet chorus waves in parallel propagation along the Earth's magnetic field. In order to reproduce the chorus waves as seen by the latest observations by Van Allen Probes (Foster et al. 2017), the wave model amplitude in our simulation is structured such that when the wave amplitude nonlinearly grows to reach the optimum amplitude, it starts decreasing until crossing the threshold. Once it crosses the threshold, the wave dissipates and a new wave rises to repeat the nonlinear growth and damping in the same manner. The multiple occurrence of this growth-damping cycle forms a saw tooth-like amplitude variation called sub-packet. This amplitude variation also affects the wave frequency behavior which is derived by the chorus wave equations as a function of the wave amplitude (Omura et al. 2009). It is also reasonable to assume that when a wave packet diminishes and the next wave rises, it has a random phase independent of the previous wave. This randomness (discontinuity) in phase variation is included in the simulation. Through interaction with such waves, dynamics of energetic electrons were tracked. As a result, some electrons underwent an efficient acceleration process defined as successive entrapping, in which an electron successfully continues to surf the trapping potential generated by consecutive wave packets. When successive entrapping occurs, an electron trapped and de-trapped (escape the trapping potential) by a single wave packet falls into another trapping potential generated by the next wave sub-packet and continuously accelerated. The occurrence of successive entrapping is influenced by some factors such as the magnitude of wave amplitude or inhomogeneity of the Earth's dipole magnetic field. In addition, an energy range of electrons is also a major factor. In this way, it has been examined in detail how and under which conditions electrons are efficiently accelerated in the formation process of the radiation belts.

Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells.

PubMed

Wagler, Patrick F; Tangen, Uwe; Maeke, Thomas; McCaskill, John S

2012-07-01

The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Hybrid simulations of radial transport driven by the Rayleigh-Taylor instability

NASA Astrophysics Data System (ADS)

Delamere, P. A.; Stauffer, B. H.; Ma, X.

2017-12-01

Plasma transport in the rapidly rotating giant magnetospheres is thought to involve a centrifugally-driven flux tube interchange instability, similar to the Rayleigh-Taylor (RT) instability. In three dimensions, the convective flow patterns associated with the RT instability can produce strong guide field reconnection, allowing plasma mass to move radially outward while conserving magnetic flux (Ma et al., 2016). We present a set of hybrid (kinetic ion / fluid electron) plasma simulations of the RT instability using high plasma beta conditions appropriate for Jupiter's inner and middle magnetosphere. A density gradient, combined with a centrifugal force, provide appropriate RT onset conditions. Pressure balance is achieved by initializing two ion populations: one with fixed temperature, but varying density, and the other with fixed density, but a temperature gradient that offsets the density gradient from the first population and the centrifugal force (effective gravity). We first analyze two-dimensional results for the plane perpendicular to the magnetic field by comparing growth rates as a function of wave vector following Huba et al. (1998). Prescribed perpendicular wave modes are seeded with an initial velocity perturbation. We then extend the model to three dimensions, introducing a stabilizing parallel wave vector. Boundary conditions in the parallel direction prohibit motion of the magnetic field line footprints to model the eigenmodes of the magnetodisc's resonant cavity. We again compare growth rates based on perpendicular wave number, but also on the parallel extent of the resonant cavity, which fixes the size of the largest parallel wavelength. Finally, we search for evidence of strong guide field magnetic reconnection within the domain by identifying areas with large parallel electric fields or changes in magnetic field topology.

Random number generators for large-scale parallel Monte Carlo simulations on FPGA

NASA Astrophysics Data System (ADS)

Lin, Y.; Wang, F.; Liu, B.

2018-05-01

Through parallelization, field programmable gate array (FPGA) can achieve unprecedented speeds in large-scale parallel Monte Carlo (LPMC) simulations. FPGA presents both new constraints and new opportunities for the implementations of random number generators (RNGs), which are key elements of any Monte Carlo (MC) simulation system. Using empirical and application based tests, this study evaluates all of the four RNGs used in previous FPGA based MC studies and newly proposed FPGA implementations for two well-known high-quality RNGs that are suitable for LPMC studies on FPGA. One of the newly proposed FPGA implementations: a parallel version of additive lagged Fibonacci generator (Parallel ALFG) is found to be the best among the evaluated RNGs in fulfilling the needs of LPMC simulations on FPGA.

A sweep algorithm for massively parallel simulation of circuit-switched networks

NASA Technical Reports Server (NTRS)

Gaujal, Bruno; Greenberg, Albert G.; Nicol, David M.

1992-01-01

A new massively parallel algorithm is presented for simulating large asymmetric circuit-switched networks, controlled by a randomized-routing policy that includes trunk-reservation. A single instruction multiple data (SIMD) implementation is described, and corresponding experiments on a 16384 processor MasPar parallel computer are reported. A multiple instruction multiple data (MIMD) implementation is also described, and corresponding experiments on an Intel IPSC/860 parallel computer, using 16 processors, are reported. By exploiting parallelism, our algorithm increases the possible execution rate of such complex simulations by as much as an order of magnitude.

A parallel orbital-updating based plane-wave basis method for electronic structure calculations

NASA Astrophysics Data System (ADS)

Pan, Yan; Dai, Xiaoying; de Gironcoli, Stefano; Gong, Xin-Gao; Rignanese, Gian-Marco; Zhou, Aihui

2017-11-01

Motivated by the recently proposed parallel orbital-updating approach in real space method [1], we propose a parallel orbital-updating based plane-wave basis method for electronic structure calculations, for solving the corresponding eigenvalue problems. In addition, we propose two new modified parallel orbital-updating methods. Compared to the traditional plane-wave methods, our methods allow for two-level parallelization, which is particularly interesting for large scale parallelization. Numerical experiments show that these new methods are more reliable and efficient for large scale calculations on modern supercomputers.

Plasma non-uniformity in a symmetric radiofrequency capacitively-coupled reactor with dielectric side-wall: a two dimensional particle-in-cell/Monte Carlo collision simulation

NASA Astrophysics Data System (ADS)

Liu, Yue; Booth, Jean-Paul; Chabert, Pascal

2018-02-01

A Cartesian-coordinate two-dimensional electrostatic particle-in-cell/Monte Carlo collision (PIC/MCC) plasma simulation code is presented, including a new treatment of charge balance at dielectric boundaries. It is used to simulate an Ar plasma in a symmetric radiofrequency capacitively-coupled parallel-plate reactor with a thick (3.5 cm) dielectric side-wall. The reactor size (12 cm electrode width, 2.5 cm electrode spacing) and frequency (15 MHz) are such that electromagnetic effects can be ignored. The dielectric side-wall effectively shields the plasma from the enhanced electric field at the powered-grounded electrode junction, which has previously been shown to produce locally enhanced plasma density (Dalvie et al 1993 Appl. Phys. Lett. 62 3207-9 Overzet and Hopkins 1993 Appl. Phys. Lett. 63 2484-6 Boeuf and Pitchford 1995 Phys. Rev. E 51 1376-90). Nevertheless, enhanced electron heating is observed in a region adjacent to the dielectric boundary, leading to maxima in ionization rate, plasma density and ion flux to the electrodes in this region, and not at the reactor centre as would otherwise be expected. The axially-integrated electron power deposition peaks closer to the dielectric edge than the electron density. The electron heating components are derived from the PIC/MCC simulations and show that this enhanced electron heating results from increased Ohmic heating in the axial direction as the electron density decreases towards the side-wall. We investigated the validity of different analytical formulas to estimate the Ohmic heating by comparing them to the PIC results. The widespread assumption that a time-averaged momentum transfer frequency, v m , can be used to estimate the momentum change can cause large errors, since it neglects both phase and amplitude information. Furthermore, the classical relationship between the total electron current and the electric field must be used with caution, particularly close to the dielectric edge where the (neglected) pressure gradient term becomes significant.

Streamer properties and associated x-rays in perturbed air

NASA Astrophysics Data System (ADS)

Köhn, C.; Chanrion, O.; Babich, L. P.; Neubert, T.

2018-01-01

Streamers are ionization waves in electric discharges. One of the key ingredients of streamer propagation is an ambient gas that serves as a source of free electrons. Here, we explore the dependence of streamer dynamics on different spatial distributions of ambient air molecules. We vary the spatial profile of air parallel and perpendicular to the ambient electric field. We consider local sinusoidal perturbations of 5%-100%, as induced from discharge shock waves. We use a cylindrically symmetric particle-in-cell code to simulate the evolution of bidirectional streamers and compare the electron density, electric field, streamer velocity and electron energy of streamers in uniform air and in perturbed air. In all considered cases, the motion is driven along in decreasing air density and damped along increasing air density. Perturbations of at most 5%-10% change the velocity differences by up to approximately 40%. Perturbations perpendicular to the electric field additionally squeeze or branch streamers. Air variations can thus partly explain the difference of velocities and morphologies of streamer discharges. In cases with large perturbations, electrons gain energies of up to 30 keV compared to 100 eV in uniformly distributed air. For such perturbations parallel to the ambient electric field, we see the spontaneous initiation of a negative streamer; for perpendicular perturbations, x-rays with energies of up to 20 keV are emitted within 0.17 ns.

High-altitude closed magnetic loops at Mars observed by MAVEN

NASA Astrophysics Data System (ADS)

Xu, Shaosui; Mitchell, David; Luhmann, Janet; Ma, Yingjuan; Fang, Xiaohua; Harada, Yuki; Hara, Takuya; Brain, David; Webber, Tristan; Mazelle, Christian; DiBraccio, Gina A.

2017-10-01

With electron and magnetic field data obtained by the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft, we have identified closed magnetic field lines, with both footpoints embedded in the dayside ionosphere, extending up to 6200 km altitude (2.8 $R_m$) into the Martian tail. This topology is deduced from photoelectrons produced in the dayside ionosphere being observed in both parallel and anti-parallel directions along the magnetic field line. At perpendicular pitch angles, cases with either solar wind electrons or photoelectrons have been found, indicative of different formation mechanisms of these closed loops. These large closed loops are predicted by MHD simulations. The case with field-aligned photoelectrons mixed with perpendicular solar wind electrons is likely to be associated with reconnection, while the case with photoelectrons in all directions are probably due to closed field lines being pulled back down tail. We have developed an automated algorithm for distinguishing photoelectrons from solar wind electrons in pitch angle resolved energy spectra. This allows us to systematically analyze the MAVEN database and map the spatial distribution and occurrence rate of these closed magnetic loops, ranging from a few percent to a few tens percent outside of the optical shadow and less than one percent within the wake. These observations can be used to investigate the general magnetic topology in the tail, which is relevant to ion escape, reconnection, and flux ropes.

Parallelization of sequential Gaussian, indicator and direct simulation algorithms

NASA Astrophysics Data System (ADS)

Nunes, Ruben; Almeida, José A.

2010-08-01

Improving the performance and robustness of algorithms on new high-performance parallel computing architectures is a key issue in efficiently performing 2D and 3D studies with large amount of data. In geostatistics, sequential simulation algorithms are good candidates for parallelization. When compared with other computational applications in geosciences (such as fluid flow simulators), sequential simulation software is not extremely computationally intensive, but parallelization can make it more efficient and creates alternatives for its integration in inverse modelling approaches. This paper describes the implementation and benchmarking of a parallel version of the three classic sequential simulation algorithms: direct sequential simulation (DSS), sequential indicator simulation (SIS) and sequential Gaussian simulation (SGS). For this purpose, the source used was GSLIB, but the entire code was extensively modified to take into account the parallelization approach and was also rewritten in the C programming language. The paper also explains in detail the parallelization strategy and the main modifications. Regarding the integration of secondary information, the DSS algorithm is able to perform simple kriging with local means, kriging with an external drift and collocated cokriging with both local and global correlations. SIS includes a local correction of probabilities. Finally, a brief comparison is presented of simulation results using one, two and four processors. All performance tests were carried out on 2D soil data samples. The source code is completely open source and easy to read. It should be noted that the code is only fully compatible with Microsoft Visual C and should be adapted for other systems/compilers.

Simulated potential for enhanced performance of mechanically stacked hybrid III–V/Si tandem photovoltaic modules using DC–DC converters

DOE PAGES

MacAlpine, Sara; Bobela, David C.; Kurtz, Sarah; ...

2017-10-01

This work examines a tandem module design with GaInP2 mechanically stacked on top of crystalline Si, using a detailed photovoltaic (PV) system model to simulate four-terminal (4T) unconstrained and two-terminal voltage-matched (2T VM) parallel architectures. Module-level power electronics is proposed for the 2T VM module design to enhance its performance over the breadth of temperatures experienced by a typical PV installation. Annual, hourly simulations of various scenarios indicate that this design can reduce annual energy losses to ~0.5% relative to the 4T module configuration. Consideration is given to both performance and practical design for building or ground mount installations, emphasizingmore » compatibility with existing standard Si modules.« less

Simulated potential for enhanced performance of mechanically stacked hybrid III–V/Si tandem photovoltaic modules using DC–DC converters

DOE Office of Scientific and Technical Information (OSTI.GOV)

MacAlpine, Sara; Bobela, David C.; Kurtz, Sarah

This work examines a tandem module design with GaInP2 mechanically stacked on top of crystalline Si, using a detailed photovoltaic (PV) system model to simulate four-terminal (4T) unconstrained and two-terminal voltage-matched (2T VM) parallel architectures. Module-level power electronics is proposed for the 2T VM module design to enhance its performance over the breadth of temperatures experienced by a typical PV installation. Annual, hourly simulations of various scenarios indicate that this design can reduce annual energy losses to ~0.5% relative to the 4T module configuration. Consideration is given to both performance and practical design for building or ground mount installations, emphasizingmore » compatibility with existing standard Si modules.« less

Simulated potential for enhanced performance of mechanically stacked hybrid III-V/Si tandem photovoltaic modules using DC-DC converters

NASA Astrophysics Data System (ADS)

MacAlpine, Sara; Bobela, David C.; Kurtz, Sarah; Lumb, Matthew P.; Schmieder, Kenneth J.; Moore, James E.; Walters, Robert J.; Alberi, Kirstin

2017-10-01

This work examines a tandem module design with GaInP2 mechanically stacked on top of crystalline Si, using a detailed photovoltaic (PV) system model to simulate four-terminal (4T) unconstrained and two-terminal voltage-matched (2T VM) parallel architectures. Module-level power electronics is proposed for the 2T VM module design to enhance its performance over the breadth of temperatures experienced by a typical PV installation. Annual, hourly simulations of various scenarios indicate that this design can reduce annual energy losses to ˜0.5% relative to the 4T module configuration. Consideration is given to both performance and practical design for building or ground mount installations, emphasizing compatibility with existing standard Si modules.

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

DOE PAGES

Adli, Erik; Lindstrom, C. A.; Allen, J.; ...

2016-10-12

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

Long-range attraction of an ultrarelativistic electron beam by a column of neutral plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adli, Erik; Lindstrom, C. A.; Allen, J.

Here, we report on the experimental observation of the attraction of a beam of ultrarelativistic electrons towards a column of neutral plasma. In experiments performed at the FACET test facility at SLAC we observe that an electron beam moving parallel to a neutral plasma column, at an initial distance of many plasma column radii, is attracted into the column. Once the beam enters the plasma it drives a plasma wake similar to that of an electron beam entering the plasma column head-on. A simple analytical model is developed in order to capture the essential physics of the attractive force. Themore » attraction is further studied by 3D particle-in-cell numerical simulations. The results are an important step towards better understanding of particle beam–plasma interactions in general and plasma wakefield accelerator technology in particular.« less

Relation of Parallel Discrete Event Simulation algorithms with physical models

NASA Astrophysics Data System (ADS)

Shchur, L. N.; Shchur, L. V.

2015-09-01

We extend concept of local simulation times in parallel discrete event simulation (PDES) in order to take into account architecture of the current hardware and software in high-performance computing. We shortly review previous research on the mapping of PDES on physical problems, and emphasise how physical results may help to predict parallel algorithms behaviour.

Parallel Simulation of Subsonic Fluid Dynamics on a Cluster of Workstations.

DTIC Science & Technology

1994-11-01

inside wind musical instruments. Typical simulations achieve $80\\%$ parallel efficiency (speedup/processors) using 20 HP-Apollo workstations. Detailed...TERMS AI, MIT, Artificial Intelligence, Distributed Computing, Workstation Cluster, Network, Fluid Dynamics, Musical Instruments 17. SECURITY...for example, the flow of air inside wind musical instruments. Typical simulations achieve 80% parallel efficiency (speedup/processors) using 20 HP

PIC simulation of a thermal anisotropy-driven Weibel instability in a circular rarefaction wave

NASA Astrophysics Data System (ADS)

Dieckmann, M. E.; Sarri, G.; Murphy, G. C.; Bret, A.; Romagnani, L.; Kourakis, I.; Borghesi, M.; Ynnerman, A.; O'C Drury, L.

2012-02-01

The expansion of an initially unmagnetized planar rarefaction wave has recently been shown to trigger a thermal anisotropy-driven Weibel instability (TAWI), which can generate magnetic fields from noise levels. It is examined here whether the TAWI can also grow in a curved rarefaction wave. The expansion of an initially unmagnetized circular plasma cloud, which consists of protons and hot electrons, into a vacuum is modelled for this purpose with a two-dimensional particle-in-cell (PIC) simulation. It is shown that the momentum transfer from the electrons to the radially accelerating protons can indeed trigger a TAWI. Radial current channels form and the aperiodic growth of a magnetowave is observed, which has a magnetic field that is oriented orthogonal to the simulation plane. The induced electric field implies that the electron density gradient is no longer parallel to the electric field. Evidence is presented here that this electric field modification triggers a second magnetic instability, which results in a rotational low-frequency magnetowave. The relevance of the TAWI is discussed for the growth of small-scale magnetic fields in astrophysical environments, which are needed to explain the electromagnetic emissions by astrophysical jets. It is outlined how this instability could be examined experimentally.

Dislocation mediated alignment during metal nanoparticle coalescence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lange, A. P.; Samanta, A.; Majidi, H.

2016-09-13

Dislocation mediated alignment processes during gold nanoparticle coalescence were studied at low and high temperatures using molecular dynamics simulations and transmission electron microscopy. Particles underwent rigid body rotations immediately following attachment in both low temperature (500 K) simulated coalescence events and low temperature (~315 K) transmission electron microscopy beam heating experiments. In many low temperature simulations, some degree of misorientation between particles remained after rigid body rotations, which was accommodated by grain boundary dislocation nodes. These dislocations were either sessile and remained at the interface for the duration of the simulation or dissociated and cross-slipped through the adjacent particles, leadingmore » to improved co-alignment. Minimal rigid body rotations were observed during or immediately following attachment in high temperature (1100 K) simulations, which is attributed to enhanced diffusion at the particles' interface. However, rotation was eventually induced by {111} slip on planes parallel to the neck groove. These deformation modes led to the formation of single and multi-fold twins whose structures depended on the initial orientation of the particles. The driving force for {111} slip is attributed to high surface stresses near the intersection of low energy {111} facets in the neck region. The details of this twinning process were examined in detail using simulated trajectories, and the results reveal possible mechanisms for the nucleation and propagation of Shockley partials on consecutive planes. Deformation twinning was also observed in-situ using transmission electron microscopy, which resulted in the co-alignment of a set of the particles' {111} planes across their grain boundary and an increase in their dihedral angle. As a result, this constitutes the first detailed experimental observation of deformation twinning during nanoparticle coalescence, validating simulation results presented here and elsewhere.« less

Nonlinear Electrostatic Steepening of Whistler Waves: The Guiding Factors and Dynamics in Inhomogeneous Systems

NASA Astrophysics Data System (ADS)

Agapitov, O.; Drake, J. F.; Vasko, I.; Mozer, F. S.; Artemyev, A.; Krasnoselskikh, V.; Angelopoulos, V.; Wygant, J.; Reeves, G. D.

2018-03-01

Whistler mode chorus waves are particularly important in outer radiation belt dynamics due to their key role in controlling the acceleration and scattering of electrons over a very wide energy range. The efficiency of wave-particle resonant interactions is defined by whistler wave properties which have been described by the approximation of plane linear waves propagating through the cold plasma of the inner magnetosphere. However, recent observations of extremely high-amplitude whistlers suggest the importance of nonlinear wave-particle interactions for the dynamics of the outer radiation belt. Oblique chorus waves observed in the inner magnetosphere often exhibit drastically nonsinusoidal (with significant power in the higher harmonics) waveforms of the parallel electric field, presumably due to the feedback from hot resonant electrons. We have considered the nature and properties of such nonlinear whistler waves observed by the Van Allen Probes and Time History of Events and Macroscale Interactions define during Substorms in the inner magnetosphere, and we show that the significant enhancement of the wave electrostatic component can result from whistler wave coupling with the beam-driven electrostatic mode through the resonant interaction with hot electron beams. Being modulated by a whistler wave, the electron beam generates a driven electrostatic mode significantly enhancing the parallel electric field of the initial whistler wave. We confirm this mechanism using a self-consistent particle-in-cell simulation. The nonlinear electrostatic component manifests properties of the beam-driven electron acoustic mode and can be responsible for effective electron acceleration in the inhomogeneous magnetic field.

Data parallel sorting for particle simulation

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1992-01-01

Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O (N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimun performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analyzed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.

A Computational Framework for Efficient Low Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Verma, Abhishek Kumar; Venkattraman, Ayyaswamy

2016-10-01

Over the past years, scientific computing has emerged as an essential tool for the investigation and prediction of low temperature plasmas (LTP) applications which includes electronics, nanomaterial synthesis, metamaterials etc. To further explore the LTP behavior with greater fidelity, we present a computational toolbox developed to perform LTP simulations. This framework will allow us to enhance our understanding of multiscale plasma phenomenon using high performance computing tools mainly based on OpenFOAM FVM distribution. Although aimed at microplasma simulations, the modular framework is able to perform multiscale, multiphysics simulations of physical systems comprises of LTP. Some salient introductory features are capability to perform parallel, 3D simulations of LTP applications on unstructured meshes. Performance of the solver is tested based on numerical results assessing accuracy and efficiency of benchmarks for problems in microdischarge devices. Numerical simulation of microplasma reactor at atmospheric pressure with hemispherical dielectric coated electrodes will be discussed and hence, provide an overview of applicability and future scope of this framework.

X-Ray Spectroscopic Laboratory Experiments in Support of the X-Ray Astronomy Program

NASA Technical Reports Server (NTRS)

Kahn, Steven M.

1997-01-01

Our program is to perform a series of laboratory investigations designed to resolved significant atomic physics uncertainties that limit the interpretation of cosmic X-ray spectra. Specific goals include a quantitative characterization of Fe L-shell spectra; the development of new techniques to simulate Maxwellian plasmas using an Electron Beam Ion Trap (EBIT); and the measurement of dielectronic recombination rates for photoionized gas. New atomic calculations have also been carried out in parallel with the laboratory investigations.

The microlasertron: An efficient switched-power source of mm wavelength radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palmer, R.B.

1986-12-01

An extension of W. Willis' ''Switched Power Linac'' is studied. Pulsed laser light falls on a photocathode wire, or wires, within a simple resonant structure. The resulting pulsed electron current between the wire and the structure wall drives the resonant field, and rf energy is extracted in the mm to cm wavelength range. Various geometries are presented, including one consisting of a simple array of parallel wires over a plane conductor. Results from a one-dimensional simulation are presented.

New Expression for Collisionless Magnetic Reconnection Rate

NASA Technical Reports Server (NTRS)

Klimas, Alexander J.

2014-01-01

For 2D, symmetric, anti-parallel, collisionless magnetic reconnection, a new expression for the reconnection rate in the electron diffusion region is introduced. It is shown that this expression can be derived in just a few simple steps from a physically intuitive starting point; the derivation is given in its entirety and the validity of each step is confirmed. The predictions of this expression are compared to the results of several long-duration, open-boundary PIC reconnection simulations to demonstrate excellent agreement.

On the p(dis) correction factor for cylindrical chambers.

PubMed

Andreo, Pedro

2010-03-07

The authors of a recent paper (Wang and Rogers 2009 Phys. Med. Biol. 54 1609) have used the Monte Carlo method to simulate the 'classical' experiment made more than 30 years ago by Johansson et al (1978 National and International Standardization of Radiation Dosimetry (Atlanta 1977) vol 2 (Vienna: IAEA) pp 243-70) on the displacement (or replacement) perturbation correction factor p(dis) for cylindrical chambers in 60Co and high-energy photon beams. They conclude that an 'unreasonable normalization at dmax' of the ionization chambers response led to incorrect results, and for the IAEA TRS-398 Code of Practice, which uses ratios of those results, 'the difference in the correction factors can lead to a beam calibration deviation of more than 0.5% for Farmer-like chambers'. The present work critically examines and questions some of the claims and generalized conclusions of the paper. It is demonstrated that for real, commercial Farmer-like chambers, the possible deviations in absorbed dose would be much smaller (typically 0.13%) than those stated by Wang and Rogers, making the impact of their proposed values negligible on practical high-energy photon dosimetry. Differences of the order of 0.4% would only appear at the upper extreme of the energies potentially available for clinical use (around 25 MV) and, because lower energies are more frequently used, the number of radiotherapy photon beams for which the deviations would be larger than say 0.2% is extremely small. This work also raises concerns on the proposed value of pdis for Farmer chambers at the reference quality of 60Co in relation to their impact on electron beam dosimetry, both for direct dose determination using these chambers and for the cross-calibration of plane-parallel chambers. The proposed increase of about 1% in p(dis) (compared with TRS-398) would lower the kQ factors and therefore Dw in electron beams by the same amount. This would yield a severe discrepancy with the current good agreement between electron dosimetry based on an electron cross-calibrated plane-parallel chamber (against a Farmer) or on a directly 60Co calibrated plane-parallel chamber, which is not likely to be in error by 1%. It is suggested that the influence of the 60Co source spectrum used in the simulations may not be negligible for calculations aimed at an uncertainty level of 0.1%.

LETTER TO THE EDITOR: On the pdis correction factor for cylindrical chambers

NASA Astrophysics Data System (ADS)

Andreo, Pedro

2010-03-01

The authors of a recent paper (Wang and Rogers 2009 Phys. Med. Biol. 54 1609) have used the Monte Carlo method to simulate the 'classical' experiment made more than 30 years ago by Johansson et al (1978 National and International Standardization of Radiation Dosimetry (Atlanta 1977) vol 2 (Vienna: IAEA) pp 243-70) on the displacement (or replacement) perturbation correction factor pdis for cylindrical chambers in 60Co and high-energy photon beams. They conclude that an 'unreasonable normalization at dmax' of the ionization chambers response led to incorrect results, and for the IAEA TRS-398 Code of Practice, which uses ratios of those results, 'the difference in the correction factors can lead to a beam calibration deviation of more than 0.5% for Farmer-like chambers'. The present work critically examines and questions some of the claims and generalized conclusions of the paper. It is demonstrated that for real, commercial Farmer-like chambers, the possible deviations in absorbed dose would be much smaller (typically 0.13%) than those stated by Wang and Rogers, making the impact of their proposed values negligible on practical high-energy photon dosimetry. Differences of the order of 0.4% would only appear at the upper extreme of the energies potentially available for clinical use (around 25 MV) and, because lower energies are more frequently used, the number of radiotherapy photon beams for which the deviations would be larger than say 0.2% is extremely small. This work also raises concerns on the proposed value of pdis for Farmer chambers at the reference quality of 60Co in relation to their impact on electron beam dosimetry, both for direct dose determination using these chambers and for the cross-calibration of plane-parallel chambers. The proposed increase of about 1% in pdis (compared with TRS-398) would lower the kQ factors and therefore Dw in electron beams by the same amount. This would yield a severe discrepancy with the current good agreement between electron dosimetry based on an electron cross-calibrated plane-parallel chamber (against a Farmer) or on a directly 60Co calibrated plane-parallel chamber, which is not likely to be in error by 1%. It is suggested that the influence of the 60Co source spectrum used in the simulations may not be negligible for calculations aimed at an uncertainty level of 0.1%.

Design and implementation of the modified signed digit multiplication routine on a ternary optical computer.

PubMed

Xu, Qun; Wang, Xianchao; Xu, Chao

2017-06-01

Multiplication with traditional electronic computers is faced with a low calculating accuracy and a long computation time delay. To overcome these problems, the modified signed digit (MSD) multiplication routine is established based on the MSD system and the carry-free adder. Also, its parallel algorithm and optimization techniques are studied in detail. With the help of a ternary optical computer's characteristics, the structured data processor is designed especially for the multiplication routine. Several ternary optical operators are constructed to perform M transformations and summations in parallel, which has accelerated the iterative process of multiplication. In particular, the routine allocates data bits of the ternary optical processor based on digits of multiplication input, so the accuracy of the calculation results can always satisfy the users. Finally, the routine is verified by simulation experiments, and the results are in full compliance with the expectations. Compared with an electronic computer, the MSD multiplication routine is not only good at dealing with large-value data and high-precision arithmetic, but also maintains lower power consumption and fewer calculating delays.

A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

DOE PAGES

Engelmann, Christian; Naughton, III, Thomas J.

2016-03-22

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matchingmore » algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.« less

A Systems Approach to Scalable Transportation Network Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S

2006-01-01

Emerging needs in transportation network modeling and simulation are raising new challenges with respect to scal-ability of network size and vehicular traffic intensity, speed of simulation for simulation-based optimization, and fidel-ity of vehicular behavior for accurate capture of event phe-nomena. Parallel execution is warranted to sustain the re-quired detail, size and speed. However, few parallel simulators exist for such applications, partly due to the challenges underlying their development. Moreover, many simulators are based on time-stepped models, which can be computationally inefficient for the purposes of modeling evacuation traffic. Here an approach is presented to de-signing a simulator with memory andmore » speed efficiency as the goals from the outset, and, specifically, scalability via parallel execution. The design makes use of discrete event modeling techniques as well as parallel simulation meth-ods. Our simulator, called SCATTER, is being developed, incorporating such design considerations. Preliminary per-formance results are presented on benchmark road net-works, showing scalability to one million vehicles simu-lated on one processor.« less

ANNarchy: a code generation approach to neural simulations on parallel hardware

PubMed Central

Vitay, Julien; Dinkelbach, Helge Ü.; Hamker, Fred H.

2015-01-01

Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957

ExoCross: Spectra from molecular line lists

NASA Astrophysics Data System (ADS)

Yurchenko, Sergei N.; Al-Refaie, Ahmed; Tennyson, Jonathan

2018-03-01

ExoCross generates spectra and thermodynamic properties from molecular line lists in ExoMol, HITRAN, or several other formats. The code is parallelized and also shows a high degree of vectorization; it works with line profiles such as Doppler, Lorentzian and Voigt and supports several broadening schemes. ExoCross is also capable of working with the recently proposed method of super-lines. It supports calculations of lifetimes, cooling functions, specific heats and other properties. ExoCross converts between different formats, such as HITRAN, ExoMol and Phoenix, and simulates non-LTE spectra using a simple two-temperature approach. Different electronic, vibronic or vibrational bands can be simulated separately using an efficient filtering scheme based on the quantum numbers.

A fast sorting algorithm for a hypersonic rarefied flow particle simulation on the connection machine

NASA Technical Reports Server (NTRS)

Dagum, Leonardo

1989-01-01

The data parallel implementation of a particle simulation for hypersonic rarefied flow described by Dagum associates a single parallel data element with each particle in the simulation. The simulated space is divided into discrete regions called cells containing a variable and constantly changing number of particles. The implementation requires a global sort of the parallel data elements so as to arrange them in an order that allows immediate access to the information associated with cells in the simulation. Described here is a very fast algorithm for performing the necessary ranking of the parallel data elements. The performance of the new algorithm is compared with that of the microcoded instruction for ranking on the Connection Machine.

Design of a high-speed digital processing element for parallel simulation

NASA Technical Reports Server (NTRS)

Milner, E. J.; Cwynar, D. S.

1983-01-01

A prototype of a custom designed computer to be used as a processing element in a multiprocessor based jet engine simulator is described. The purpose of the custom design was to give the computer the speed and versatility required to simulate a jet engine in real time. Real time simulations are needed for closed loop testing of digital electronic engine controls. The prototype computer has a microcycle time of 133 nanoseconds. This speed was achieved by: prefetching the next instruction while the current one is executing, transporting data using high speed data busses, and using state of the art components such as a very large scale integration (VLSI) multiplier. Included are discussions of processing element requirements, design philosophy, the architecture of the custom designed processing element, the comprehensive instruction set, the diagnostic support software, and the development status of the custom design.

Symplectic molecular dynamics simulations on specially designed parallel computers.

PubMed

Borstnik, Urban; Janezic, Dusanka

2005-01-01

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Parallel discrete-event simulation of FCFS stochastic queueing networks

NASA Technical Reports Server (NTRS)

Nicol, David M.

1988-01-01

Physical systems are inherently parallel. Intuition suggests that simulations of these systems may be amenable to parallel execution. The parallel execution of a discrete-event simulation requires careful synchronization of processes in order to ensure the execution's correctness; this synchronization can degrade performance. Largely negative results were recently reported in a study which used a well-known synchronization method on queueing network simulations. Discussed here is a synchronization method (appointments), which has proven itself to be effective on simulations of FCFS queueing networks. The key concept behind appointments is the provision of lookahead. Lookahead is a prediction on a processor's future behavior, based on an analysis of the processor's simulation state. It is shown how lookahead can be computed for FCFS queueing network simulations, give performance data that demonstrates the method's effectiveness under moderate to heavy loads, and discuss performance tradeoffs between the quality of lookahead, and the cost of computing lookahead.

Nonlinear Delta-f Simulations of Collective Effects in Intense Charged Particle Beams

NASA Astrophysics Data System (ADS)

Qin, Hong

2002-11-01

A nonlinear delta-f particle simulation method based on the Vlasov-Maxwell equations has been recently developed to study collective processes in high-intensity beams, where space-charge and magnetic self-field effects play a critical role in determining the nonlinear beam dynamics. Implemented in the Beam Equilibrium, Stability and Transport (BEST) code, the nonlinear delta-f method provides a low-noise and self-consistent tool for simulating collective interactions and nonlinear dynamics of high-intensity beams in modern and next- generation accelerators and storage rings, such as the Spallation Neutron Source, and heavy ion fusion drivers. Simulation results for the electron-proton two-stream instability in the Proton Storage Ring (PSR) experiment at Los Alamos National Laboratory agree well with experimental observations. Large-scale parallel simulations have also been carried out for the ion-electron two-stream instability in the very high-intensity heavy ion beams envisioned for heavy ion fusion applications. In both cases, the simulation results indicate that the dominant two-stream instability has a dipole-mode (hose-like) structure and can be stabilized by a modest axial momentum spread of the beam particles of less than 0.25collective processes in high-intensity beams, such as anisotropy-driven instabilities, collective eigenmode excitations for perturbations about stable beam equilibria, and the Darwin model for fully electromagnetic perturbations will also be discussed.

Interplay between protons and electrons in a firehose-unstable plasma: Particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Bourdin, Philippe-A.; Maneva, Yana

2017-04-01

Kinetic plasma instabilities originating from unstable, non-Maxwellian shapes of the velocity distribution functions serve as internal degrees of freedom in plasma dynamics, and play an important role near solar current sheets and in solar wind plasmas. In the presence of strong temperature anisotropy (different thermal spreads in the velocity space with respect to the mean magnetic field), plasmas are unstable either to the firehose mode or to the mirror mode in the case of predominant parallel and perpendicular temperatures, respectively. The growth rates of these instabilities and their thresholds depend on plasma properties, such as the temperature anisotropy and the plasma beta. The physics of the temperature anisotropy-driven instabilities becomes even more diverse for various shapes of velocity distribution functions and the particle species of interest. Recent studies based on a linear instability analysis show an interplay in the firehose instability between protons and electrons when the both types of particle species are prone to unstable velocity distribution functions and their instability thresholds. In this work we perform for the first time 3D nonlinear PIC (particle-in-cell) numerical simulations to test for the linear-theory prediction of the simultaneous proton-electron firehose instability. The simulation setup allows us not only to evaluate the growth rate of each firehose instability, but also to track its nonlinear evolution and the related wave-particle interactions such as the pitch-angle scattering or saturation effects. The specialty of our simulation is that the magnetic and electric fields have a low numerical noise level by setting a sufficiently large number of super-particles into the simulation box and enhancing the statistical significance of the velocity distribution functions. We use the iPIC3D code with fully periodic boundaries under various conditions of the electron-to-proton mass ratio, which gives insight into the instability interplay at the intermediate electron-proton and on the scaling of our results towards more realistic particle settings.

Heat loads on poloidal and toroidal edges of castellated plasma-facing components in COMPASS

NASA Astrophysics Data System (ADS)

Dejarnac, R.; Corre, Y.; Vondracek, P.; Gaspar, J.; Gauthier, E.; Gunn, J. P.; Komm, M.; Gardarein, J.-L.; Horacek, J.; Hron, M.; Matejicek, J.; Pitts, R. A.; Panek, R.

2018-06-01

Dedicated experiments have been performed in the COMPASS tokamak to thoroughly study the power deposition processes occurring on poloidal and toroidal edges of castellated plasma-facing components in tokamaks during steady-state L-mode conditions. Surface temperatures measured by a high resolution infra-red camera are compared with reconstructed synthetic data from a 2D thermal model using heat flux profiles derived from both the optical approximation and 2D particle-in-cell (PIC) simulations. In the case of poloidal leading edges, when the contribution from local radiation is taken into account, the parallel heat flux deduced from unperturbed, upstream measurements is fully consistent with the observed temperature increase at the leading edges of various heights, respecting power balance assuming simple projection of the parallel flux density. Smoothing of the heat flux deposition profile due to finite ion Larmor radius predicted by the PIC simulations is found to be weak and the power deposition on misaligned poloidal edges is better described by the optical approximation. This is consistent with an electron-dominated regime associated with a non-ambipolar parallel current flow. In the case of toroidal gap edges, the different contributions of the total incoming flux along the gap have been observed experimentally for the first time. They confirm the results of recent numerical studies performed for ITER showing that in specific cases the heat deposition does not necessarily follow the optical approximation. Indeed, ions can spiral onto the magnetically shadowed toroidal edge. Particle-in-cell simulations emphasize again the role played by local non-ambipolarity in the deposition pattern.

Progress in Unsteady Turbopump Flow Simulations

NASA Technical Reports Server (NTRS)

Kiris, Cetin C.; Chan, William; Kwak, Dochan; Williams, Robert

2002-01-01

This viewgraph presentation discusses unsteady flow simulations for a turbopump intended for a reusable launch vehicle (RLV). The simulation process makes use of computational grids and parallel processing. The architecture of the parallel computers used is discussed, as is the scripting of turbopump simulations.

A hybrid parallel framework for the cellular Potts model simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Yi; He, Kejing; Dong, Shoubin

2009-01-01

The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approachmore » achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).« less

Acceleration of charged particles by crossed cyclotron waves, Resonant Moments Method

NASA Astrophysics Data System (ADS)

Ponomarjov, M.; Carati, D.

A mechanism for enhanced acceleration of charged particles in crossing radio frequency or micro waves propagating at different angles with respect to an external magnetic field is investigated. This mechanism consists in introducing low amplitude secondary waves in order to improve the parallel momentum transfer from the high amplitude primary wave to charged particles. The use of two parallel counter-propagating waves has recently been considered (Gell and Nakach, 1999) and numerical tests (Louies et al, 2001) have shown that the two-wave scheme may lead to higher averaged parallel velocity. On the other hand, it has been concluded that it may be more effective to accelerate electrons when the waves propagate obliquely to the external magnetic field (Karimabadi and Angelopoulos 1989, Cohen et al 1991). The idea considered here is similar although no constraint is imposed on the refraction indices of the primary and the secondary waves. The theoretical analysis of the acceleration mechanism is based on the Resonance Moments Method (RMM) in which moments of the velocity distribution are computed by using an averages over the resonant layers (RL)i only instead of a complete phase-space average. The quantities obtained using this approach, referred to as Resonant Moments (RM), suggest the existence of optimal angles of propagation for the primary and secondary waves as long as the maximization of the parallel flux of charged particles is considered. The fraction of charged particles that are close to the resonance conditions, that correspond to the RL, becomes then as important as the time these particles remain resonant. The secondary wave tends to maintain a pseudo-equilibrium velocity distribution by continuously re-filling the RL. Our suggestions are confirmed by direct numerical simulations for a populations of 105 relativistic electrons. The secondary wave yields a clear increase (up to one order of magnitude) of the average parallel velocity of the particles. It is a quite promising result since the amplitude of the secondary wave is ten times lower the one of the first wave. Qualitative results give one of the enhanced acceleration mechanisms of the charged particles (including relativistic electrons in planetary magnetospheres) by the crossed cyclotron waves in ambient magnetic field.

Parallel discrete event simulation: A shared memory approach

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.

1987-01-01

With traditional event list techniques, evaluating a detailed discrete event simulation model can often require hours or even days of computation time. Parallel simulation mimics the interacting servers and queues of a real system by assigning each simulated entity to a processor. By eliminating the event list and maintaining only sufficient synchronization to insure causality, parallel simulation can potentially provide speedups that are linear in the number of processors. A set of shared memory experiments is presented using the Chandy-Misra distributed simulation algorithm to simulate networks of queues. Parameters include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential simulation of most queueing network models.

Excitation of Plasma Waves in Aurora by Electron Beams

NASA Technical Reports Server (NTRS)

daSilva, C. E.; Vinas, A. F.; deAssis, A. S.; deAzevedo, C. A.

1996-01-01

In this paper, we study numerically the excitation of plasma waves by electron beams, in the auroral region above 2000 km of altitude. We have solved the fully kinetic dispersion relation, using numerical method and found the real frequency and the growth rate of the plasma wave modes. We have examined the instability properties of low-frequency waves such as the Electromagnetic Ion Cyclotron (EMIC) wave as well as Lower-Hybrid (LH) wave in the range of high-frequency. In all cases, the source of free energy are electron beams propagating parallel to the geomagnetic field. We present some features of the growth rate modes, when the cold plasma parameters are changed, such as background electrons and ions species (H(+) and O(+)) temperature, density or the electron beam density and/or drift velocity. These results can be used in a test-particle simulation code, to investigate the ion acceleration and their implication in the auroral acceleration processes, by wave-particle interaction.

Ion temperature effects on magnetotail Alfvén wave propagation and electron energization: ION TEMPERATURE EFFECTS ON ALFVÉN WAVES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damiano, P. A.; Johnson, J. R.; Chaston, C. C.

2015-07-01

A new 2-D self-consistent hybrid gyrofluid-kinetic electron model in dipolar coordinates is presented and used to simulate dispersive-scale Alfvén wave pulse propagation from the equator to the ionosphere along an L = 10 magnetic field line. The model is an extension of the hybrid MHD-kinetic electron model that incorporates ion Larmor radius corrections via the kinetic fluid model of Cheng and Johnson (1999). It is found that consideration of a realistic ion to electron temperature ratio decreases the propagation time of the wave from the plasma sheet to the ionosphere by several seconds relative to a ρi=0 case (which alsomore » implies shorter timing for a substorm onset signal) and leads to significant dispersion of wave energy perpendicular to the ambient magnetic field. Additionally, ion temperature effects reduce the parallel current and electron energization all along the field line for the same magnitude perpendicular electric field perturbation.« less

SciDAC Center for Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Zhihong

2013-12-18

During the first year of the SciDAC gyrokinetic particle simulation (GPS) project, the GPS team (Zhihong Lin, Liu Chen, Yasutaro Nishimura, and Igor Holod) at the University of California, Irvine (UCI) studied the tokamak electron transport driven by electron temperature gradient (ETG) turbulence, and by trapped electron mode (TEM) turbulence and ion temperature gradient (ITG) turbulence with kinetic electron effects, extended our studies of ITG turbulence spreading to core-edge coupling. We have developed and optimized an elliptic solver using finite element method (FEM), which enables the implementation of advanced kinetic electron models (split-weight scheme and hybrid model) in the SciDACmore » GPS production code GTC. The GTC code has been ported and optimized on both scalar and vector parallel computer architectures, and is being transformed into objected-oriented style to facilitate collaborative code development. During this period, the UCI team members presented 11 invited talks at major national and international conferences, published 22 papers in peer-reviewed journals and 10 papers in conference proceedings. The UCI hosted the annual SciDAC Workshop on Plasma Turbulence sponsored by the GPS Center, 2005-2007. The workshop was attended by about fifties US and foreign researchers and financially sponsored several gradual students from MIT, Princeton University, Germany, Switzerland, and Finland. A new SciDAC postdoc, Igor Holod, has arrived at UCI to initiate global particle simulation of magnetohydrodynamics turbulence driven by energetic particle modes. The PI, Z. Lin, has been promoted to the Associate Professor with tenure at UCI.« less

Particle in cell simulation of instabilities in space and astrophysical plasmas

NASA Astrophysics Data System (ADS)

Tonge, John William

Several plasma instabilities relevant to space physics are investigated using the parallel PIC plasma simulation code P3arsec. This thesis addresses electrostatic micro-instabilities relevant to ion ring distributions, proceeds to electromagnetic micro-instabilities pertinent to streaming plasmas, and then to the stability of a plasma held in the field of a current rod. The physical relevance of each of these instabilities is discussed, a phenomenological description is given, and analytic and simulation results are presented and compared. Instability of a magnetized plasma with a portion of the ions in a velocity ring distribution around the magnetic field is investigated using simulation and analytic theory. The physics of this distribution is relevant to solar flares, x-ray emission by comets, and pulsars. Physical parameters, including the mass ratio, are near those of a solar flare in the simulation. The simulation and analytic results show agreement in the linear regime. In the nonlinear stage the simulation shows highly accelerated electrons in agreement with the observed spectrum of x-rays emitted by solar flares. A mildly relativistic streaming electron positron plasma with no ambient magnetic field is known to be unstable to electrostatic (two-stream/beam instability) and purely electromagnetic (Weibel) modes. This instability is relevant to highly energetic interstellar phenomena, including pulsars, supernova remnants, and the early universe. It is also important for experiments in which relativistic beams penetrate a background plasma, as in fast ignitor scenarios. Cold analytic theory is presented and compared to simulations. There is good agreement in the regime where cold theory applies. The simulation and theory shows that to properly characterize the instability, directions parallel and perpendicular to propagation of the beams must be considered. A residual magnetic field is observed which may be of astro-physical significance. The stability of a plasma in the magnetic field of a current rod is investigated for various temperature and density profiles. Such a plasma obeys similar physics to a plasma in a dipole magnetic field, while the current rod is much easier to analyze theoretically and realize in simulations. The stability properties of a plasma confined in a dipole field are important for understanding a variety of space phenomena and the Levitated Dipole eXperiment (LDX). Simple energy principle calculations and simulations with a variety of temperature and density profiles show that the plasma is stable to interchange for pressure profiles ∝ r-10/3. The simulations also show that the density profile will be stationary as long as density ∝ r -2 even though the temperature profile may not be stable.

Linear and nonlinear interactions of an electron beam with oblique whistler and electrostatic waves in the magnetosphere

NASA Astrophysics Data System (ADS)

Zhang, Y. L.; Matsumoto, H.; Omura, Y.

1993-12-01

Both linear and nonlinear interactions between oblique whistler, electrostatic, quasi-upper hybrid mode waves and an electron beam are studied by linear analyses and electromagnetic particle simulations. In addition to a background cold plasma, we assumed a hot electron beam drifting along a static magnetic field. Growth rates of the oblique whistler, oblique electrostatic, and quasi-upper hybrid instabilities were first calculated. We found that there are four kinds of unstable mode waves for parallel and oblique propagations. They are the electromagnetic whistler mode wave (WW1), the electrostatic whistler mode wave (WW2), the electrostatic mode wave (ESW), and the quasi-upper hybrid mode wave (UHW). A possible mechanism is proposed to explain the satellite observations of whistler mode chorus and accompanied electrostatic waves, whose amplitudes are sometimes modulated at the chorus frequency.

Wakefield Simulation of CLIC PETS Structure Using Parallel 3D Finite Element Time-Domain Solver T3P

DOE Office of Scientific and Technical Information (OSTI.GOV)

Candel, A.; Kabel, A.; Lee, L.

In recent years, SLAC's Advanced Computations Department (ACD) has developed the parallel 3D Finite Element electromagnetic time-domain code T3P. Higher-order Finite Element methods on conformal unstructured meshes and massively parallel processing allow unprecedented simulation accuracy for wakefield computations and simulations of transient effects in realistic accelerator structures. Applications include simulation of wakefield damping in the Compact Linear Collider (CLIC) power extraction and transfer structure (PETS).

A Generalized Electron Heat Flow Relation and its Connection to the Thermal Force and the Solar Wind Parallel Electric Field

NASA Astrophysics Data System (ADS)

Scudder, J. D.

2017-12-01

Enroute to a new formulation of the heat law for the solar wind plasma the role of the invariably neglected, but omnipresent, thermal force for the multi-fluid physics of the corona and solar wind expansion will be discussed. This force (a) controls the size of the collisional ion electron energy exchange, favoring the thermal vs supra thermal electrons; (b) occurs whenever heat flux occurs; (c) remains after the electron and ion fluids come to a no slip, zero parallel current, equilibrium; (d) enhances the equilibrium parallel electric field; but (e) has a size that is theoretically independent of the electron collision frequency - allowing its importance to persist far up into the corona where collisions are invariably ignored in first approximation. The constituent parts of the thermal force allow the derivation of a new generalized electron heat flow relation that will be presented. It depends on the separate field aligned divergences of electron and ion pressures and the gradients of the ion gravitational potential and parallel flow energies and is based upon a multi-component electron distribution function. The new terms in this heat law explicitly incorporate the astrophysical context of gradients, acceleration and external forces that make demands on the parallel electric field and quasi-neutrality; essentially all of these effects are missing in traditional formulations.

Hall-Effect Thruster Simulations with 2-D Electron Transport and Hydrodynamic Ions

NASA Technical Reports Server (NTRS)

Mikellides, Ioannis G.; Katz, Ira; Hofer, Richard H.; Goebel, Dan M.

2009-01-01

A computational approach that has been used extensively in the last two decades for Hall thruster simulations is to solve a diffusion equation and energy conservation law for the electrons in a direction that is perpendicular to the magnetic field, and use discrete-particle methods for the heavy species. This "hybrid" approach has allowed for the capture of bulk plasma phenomena inside these thrusters within reasonable computational times. Regions of the thruster with complex magnetic field arrangements (such as those near eroded walls and magnets) and/or reduced Hall parameter (such as those near the anode and the cathode plume) challenge the validity of the quasi-one-dimensional assumption for the electrons. This paper reports on the development of a computer code that solves numerically the 2-D axisymmetric vector form of Ohm's law, with no assumptions regarding the rate of electron transport in the parallel and perpendicular directions. The numerical challenges related to the large disparity of the transport coefficients in the two directions are met by solving the equations in a computational mesh that is aligned with the magnetic field. The fully-2D approach allows for a large physical domain that extends more than five times the thruster channel length in the axial direction, and encompasses the cathode boundary. Ions are treated as an isothermal, cold (relative to the electrons) fluid, accounting for charge-exchange and multiple-ionization collisions in the momentum equations. A first series of simulations of two Hall thrusters, namely the BPT-4000 and a 6-kW laboratory thruster, quantifies the significance of ion diffusion in the anode region and the importance of the extended physical domain on studies related to the impact of the transport coefficients on the electron flow field.

Total fluid pressure imbalance in the scrape-off layer of tokamak plasmas

NASA Astrophysics Data System (ADS)

Churchill, R. M.; Canik, J. M.; Chang, C. S.; Hager, R.; Leonard, A. W.; Maingi, R.; Nazikian, R.; Stotler, D. P.

2017-04-01

Simulations using the fully kinetic neoclassical code XGCa (X-point included guiding- center axisymmetric) were undertaken to explore the impact of kinetic effects on scrape-off layer (SOL) physics in DIII-D H-mode plasmas. XGCa is a total-f, gyrokinetic code which self-consistently calculates the axisymmetric electrostatic potential and plasma dynamics, and includes modules for Monte Carlo neutral transport. Previously presented XGCa results showed several noteworthy features, including large variations of ion density and pressure along field lines in the SOL, experimentally relevant levels of SOL parallel ion flow (Mach number  ˜ 0.5), skewed ion distributions near the sheath entrance leading to subsonic flow there, and elevated sheath potentials (Churchill 2016 Nucl. Mater. Energy 1-6). In this paper, we explore in detail the question of pressure balance in the SOL, as it was observed in the simulation that there was a large deviation from a simple total pressure balance (the sum of ion and electron static pressure plus ion inertia). It will be shown that both the contributions from the ion viscosity (driven by ion temperature anisotropy) and neutral source terms can be substantial, and should be retained in the parallel momentum equation in the SOL, but still falls short of accounting for the observed fluid pressure imbalance in the XGCa simulation results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Churchill, Randy M.; Canik, John M.; Chang, C. S.

Simulations using the fully kinetic neoclassical code XGCa (X-point included guiding-center axisymmetric) were undertaken to explore the impact of kinetic effects on scrape-off layer (SOL) physics in DIII-D H-mode plasmas. XGCa is a total-f, gyrokinetic code which self-consistently calculates the axisymmetric electrostatic potential and plasma dynamics, and includes modules for Monte Carlo neutral transport. Previously presented XGCa results showed several noteworthy features, including large variations of ion density and pressure along field lines in the SOL, experimentally relevant levels of SOL parallel ion flow (Mach number similar to 0.5), skewed ion distributions near the sheath entrance leading to subsonic flowmore » there, and elevated sheath potentials (Churchill 2016 Nucl. Mater. Energy 1-6). In this paper, we explore in detail the question of pressure balance in the SOL, as it was observed in the simulation that there was a large deviation from a simple total pressure balance (the sum of ion and electron static pressure plus ion inertia). It will be shown that both the contributions from the ion viscosity (driven by ion temperature anisotropy) and neutral source terms can be substantial, and should be retained in the parallel momentum equation in the SOL, but still falls short of accounting for the observed fluid pressure imbalance in the XGCa simulation results.« less

A hybrid algorithm for parallel molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mangiardi, Chris M.; Meyer, R.

2017-10-01

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

AMITIS: A 3D GPU-Based Hybrid-PIC Model for Space and Plasma Physics

NASA Astrophysics Data System (ADS)

Fatemi, Shahab; Poppe, Andrew R.; Delory, Gregory T.; Farrell, William M.

2017-05-01

We have developed, for the first time, an advanced modeling infrastructure in space simulations (AMITIS) with an embedded three-dimensional self-consistent grid-based hybrid model of plasma (kinetic ions and fluid electrons) that runs entirely on graphics processing units (GPUs). The model uses NVIDIA GPUs and their associated parallel computing platform, CUDA, developed for general purpose processing on GPUs. The model uses a single CPU-GPU pair, where the CPU transfers data between the system and GPU memory, executes CUDA kernels, and writes simulation outputs on the disk. All computations, including moving particles, calculating macroscopic properties of particles on a grid, and solving hybrid model equations are processed on a single GPU. We explain various computing kernels within AMITIS and compare their performance with an already existing well-tested hybrid model of plasma that runs in parallel using multi-CPU platforms. We show that AMITIS runs ∼10 times faster than the parallel CPU-based hybrid model. We also introduce an implicit solver for computation of Faraday’s Equation, resulting in an explicit-implicit scheme for the hybrid model equation. We show that the proposed scheme is stable and accurate. We examine the AMITIS energy conservation and show that the energy is conserved with an error < 0.2% after 500,000 timesteps, even when a very low number of particles per cell is used.

A parallel simulated annealing algorithm for standard cell placement on a hypercube computer

NASA Technical Reports Server (NTRS)

Jones, Mark Howard

1987-01-01

A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.

Methods of parallel computation applied on granular simulations

NASA Astrophysics Data System (ADS)

Martins, Gustavo H. B.; Atman, Allbens P. F.

2017-06-01

Every year, parallel computing has becoming cheaper and more accessible. As consequence, applications were spreading over all research areas. Granular materials is a promising area for parallel computing. To prove this statement we study the impact of parallel computing in simulations of the BNE (Brazil Nut Effect). This property is due the remarkable arising of an intruder confined to a granular media when vertically shaken against gravity. By means of DEM (Discrete Element Methods) simulations, we study the code performance testing different methods to improve clock time. A comparison between serial and parallel algorithms, using OpenMP® is also shown. The best improvement was obtained by optimizing the function that find contacts using Verlet's cells.

Turbomachinery CFD on parallel computers

NASA Technical Reports Server (NTRS)

Blech, Richard A.; Milner, Edward J.; Quealy, Angela; Townsend, Scott E.

1992-01-01

The role of multistage turbomachinery simulation in the development of propulsion system models is discussed. Particularly, the need for simulations with higher fidelity and faster turnaround time is highlighted. It is shown how such fast simulations can be used in engineering-oriented environments. The use of parallel processing to achieve the required turnaround times is discussed. Current work by several researchers in this area is summarized. Parallel turbomachinery CFD research at the NASA Lewis Research Center is then highlighted. These efforts are focused on implementing the average-passage turbomachinery model on MIMD, distributed memory parallel computers. Performance results are given for inviscid, single blade row and viscous, multistage applications on several parallel computers, including networked workstations.

Massively parallel multicanonical simulations

NASA Astrophysics Data System (ADS)

Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard

2018-03-01

Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.

Collaborative Research: Simulation of Beam-Electron Cloud Interactions in Circular Accelerators Using Plasma Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Katsouleas, Thomas; Decyk, Viktor

Final Report for grant DE-FG02-06ER54888, "Simulation of Beam-Electron Cloud Interactions in Circular Accelerators Using Plasma Models" Viktor K. Decyk, University of California, Los Angeles Los Angeles, CA 90095-1547 The primary goal of this collaborative proposal was to modify the code QuickPIC and apply it to study the long-time stability of beam propagation in low density electron clouds present in circular accelerators. The UCLA contribution to this collaborative proposal was in supporting the development of the pipelining scheme for the QuickPIC code, which extended the parallel scaling of this code by two orders of magnitude. The USC work was as describedmore » here the PhD research for Ms. Bing Feng, lead author in reference 2 below, who performed the research at USC under the guidance of the PI Tom Katsouleas and the collaboration of Dr. Decyk The QuickPIC code [1] is a multi-scale Particle-in-Cell (PIC) code. The outer 3D code contains a beam which propagates through a long region of plasma and evolves slowly. The plasma response to this beam is modeled by slices of a 2D plasma code. This plasma response then is fed back to the beam code, and the process repeats. The pipelining is based on the observation that once the beam has passed a 2D slice, its response can be fed back to the beam immediately without waiting for the beam to pass all the other slices. Thus independent blocks of 2D slices from different time steps can be running simultaneously. The major difficulty was when particles at the edges needed to communicate with other blocks. Two versions of the pipelining scheme were developed, for the the full quasi-static code and the other for the basic quasi-static code used by this e-cloud proposal. Details of the pipelining scheme were published in [2]. The new version of QuickPIC was able to run with more than 1,000 processors, and was successfully applied in modeling e-clouds by our collaborators in this proposal [3-8]. Jean-Luc Vay at Lawrence Berkeley National Lab later implemented a similar basic quasistatic scheme including pipelining in the code WARP [9] and found good to very good quantitative agreement between the two codes in modeling e-clouds. References [1] C. Huang, V. K. Decyk, C. Ren, M. Zhou, W. Lu, W. B. Mori, J. H. Cooley, T. M. Antonsen, Jr., and T. Katsouleas, "QUICKPIC: A highly efficient particle-in-cell code for modeling wakefield acceleration in plasmas," J. Computational Phys. 217, 658 (2006). [2] B. Feng, C. Huang, V. K. Decyk, W. B. Mori, P. Muggli, and T. Katsouleas, "Enhancing parallel quasi-static particle-in-cell simulations with a pipelining algorithm," J. Computational Phys, 228, 5430 (2009). [3] C. Huang, V. K. Decyk, M. Zhou, W. Lu, W. B. Mori, J. H. Cooley, T. M. Antonsen, Jr., and B. Feng, T. Katsouleas, J. Vieira, and L. O. Silva, "QUICKPIC: A highly efficient fully parallelized PIC code for plasma-based acceleration," Proc. of the SciDAC 2006 Conf., Denver, Colorado, June, 2006 [Journal of Physics: Conference Series, W. M. Tang, Editor, vol. 46, Institute of Physics, Bristol and Philadelphia, 2006], p. 190. [4] B. Feng, C. Huang, V. Decyk, W. B. Mori, T. Katsouleas, P. Muggli, "Enhancing Plasma Wakefield and E-cloud Simulation Performance Using a Pipelining Algorithm," Proc. 12th Workshop on Advanced Accelerator Concepts, Lake Geneva, WI, July, 2006, p. 201 [AIP Conf. Proceedings, vol. 877, Melville, NY, 2006]. [5] B. Feng, P. Muggli, T. Katsouleas, V. Decyk, C. Huang, and W. Mori, "Long Time Electron Cloud Instability Simulation Using QuickPIC with Pipelining Algorithm," Proc. of the 2007 Particle Accelerator Conference, Albuquerque, NM, June, 2007, p. 3615. [6] B. Feng, C. Huang, V. Decyk, W. B. Mori, G. H. Hoffstaetter, P. Muggli, T. Katsouleas, "Simulation of Electron Cloud Effects on Electron Beam at ERL with Pipelined QuickPIC," Proc. 13th Workshop on Advanced Accelerator Concepts, Santa Cruz, CA, July-August, 2008, p. 340 [AIP Conf. Proceedings, vol. 1086, Melville, NY, 2008]. [7] B. Feng, C. Huang, V. K. Decyk, W. B. Mori, P. Muggli, and T. Katsouleas, "Enhancing parallel quasi-static particle-in-cell simulations with a pipelining algorithm," J. Computational Phys, 228, 5430 (2009). [8] C. Huang, W. An, V. K. Decyk, W. Lu, W. B. Mori, F. S. Tsung, M. Tzoufras, S. Morshed, T. Antonsen, B. Feng, T. Katsouleas, R., A. Fonseca, S. F. Martins, J. Vieira, L. O. Silva, E. Esarey, C. G. R. Geddes, W. P. Leemans, E. Cormier-Michel, J.-L. Vay, D. L. Bruhwiler, B. Cowan, J. R. Cary, and K. Paul, "Recent results and future challenges for large scale particleion- cell simulations of plasma-based accelerator concepts," Proc. of the SciDAC 2009 Conf., San Diego, CA, June, 2009 [Journal of Physics: Conference Series, vol. 180, Institute of Physics, Bristol and Philadelphia, 2009], p. 012005. [9] J.-L. Vay, C. M. Celata, M. A. Furman, G. Penn, M. Venturini, D. P. Grote, and K. G. Sonnad, ?Update on Electron-Cloud Simulations Using the Package WARP-POSINST.? Proc. of the 2009 Particle Accelerator Conference PAC09, Vancouver, Canada, June, 2009, paper FR5RFP078.« less

Forced Reconnection in the Near Magnetotail: Onset and Energy Conversion in PIC and MHD Simulations

NASA Technical Reports Server (NTRS)

Birn, J.; Hesse, Michael

2014-01-01

Using two-dimensional particle-in-cell (PIC) together with magnetohydrodynamic (MHD) Q1 simulations of magnetotail dynamics, we investigate the evolution toward onset of reconnection and the subsequent energy transfer and conversion. In either case, reconnection onset is preceded by a driven phase, during which magnetic flux is added to the tail at the high-latitude boundaries, followed by a relaxation phase, during which the configuration continues to respond to the driving. The boundary deformation leads to the formation of thin embedded current sheets, which are bifurcated in the near tail, converging to a single sheet farther out in the MHD simulations. The thin current sheets in the PIC simulation are carried by electrons and are associated with a strong perpendicular electrostatic field, which may provide a connection to parallel potentials and auroral arcs and an ionospheric signal even prior to the onset of reconnection. The PIC simulation very well satisfies integral entropy conservation (intrinsic to ideal MHD) during this phase, supporting ideal ballooning stability. Eventually, the current intensification leads to the onset of reconnection, the formation and ejection of a plasmoid, and a collapse of the inner tail. The earthward flow shows the characteristics of a dipolarization front: enhancement of Bz, associated with a thin vertical electron current sheet in the PIC simulation. Both MHD and PIC simulations show a dominance of energy conversion from incoming Poynting flux to outgoing enthalpy flux, resulting in heating of the inner tail. Localized Joule dissipation plays only a minor role.

Ion Larmor radius effects near a reconnection X line at the magnetopause: THEMIS observations and simulation comparison

NASA Astrophysics Data System (ADS)

Phan, T. D.; Shay, M. A.; Haggerty, C. C.; Gosling, J. T.; Eastwood, J. P.; Fujimoto, M.; Malakit, K.; Mozer, F. S.; Cassak, P. A.; Oieroset, M.; Angelopoulos, V.

2016-09-01

We report a Time History of Events and Macroscale Interactions during Substorms (THEMIS-D) spacecraft crossing of a magnetopause reconnection exhaust ~9 ion skin depths (di) downstream of an X line. The crossing was characterized by ion jetting at speeds substantially below the predicted reconnection outflow speed. In the magnetospheric inflow region THEMIS detected (a) penetration of magnetosheath ions and the resulting flows perpendicular to the reconnection plane, (b) ion outflow extending into the magnetosphere, and (c) enhanced electron parallel temperature. Comparison with a simulation suggests that these signatures are associated with the gyration of magnetosheath ions onto magnetospheric field lines due to the shift of the flow stagnation point toward the low-density magnetosphere. Our observations indicate that these effects, ~2-3 di in width, extend at least 9 di downstream of the X line. The detection of these signatures could indicate large-scale proximity of the X line but do not imply that the spacecraft was upstream of the electron diffusion region.

Acoustic simulation in architecture with parallel algorithm

NASA Astrophysics Data System (ADS)

Li, Xiaohong; Zhang, Xinrong; Li, Dan

2004-03-01

In allusion to complexity of architecture environment and Real-time simulation of architecture acoustics, a parallel radiosity algorithm was developed. The distribution of sound energy in scene is solved with this method. And then the impulse response between sources and receivers at frequency segment, which are calculated with multi-process, are combined into whole frequency response. The numerical experiment shows that parallel arithmetic can improve the acoustic simulating efficiency of complex scene.

Surface Modification Engineered Assembly of Novel Quantum Dot Architectures for Advanced Applications

DTIC Science & Technology

2008-02-09

Campbell, S. Ogata, and F. Shimojo, “ Multimillion atom simulations of nanosystems on parallel computers,” in Proceedings of the International...nanomesas: multimillion -atom molecular dynamics simulations on parallel computers,” J. Appl. Phys. 94, 6762 (2003). 21. P. Vashishta, R. K. Kalia...and A. Nakano, “ Multimillion atom molecular dynamics simulations of nanoparticles on parallel computers,” Journal of Nanoparticle Research 5, 119-135

Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media.

PubMed

Malektaji, Siavash; Lima, Ivan T; Escobar I, Mauricio R; Sherif, Sherif S

2017-10-01

An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT, or to design OCT systems with improved performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Next Generation Extended Lagrangian Quantum-based Molecular Dynamics

NASA Astrophysics Data System (ADS)

Negre, Christian

2017-06-01

A new framework for extended Lagrangian first-principles molecular dynamics simulations is presented, which overcomes shortcomings of regular, direct Born-Oppenheimer molecular dynamics, while maintaining important advantages of the unified extended Lagrangian formulation of density functional theory pioneered by Car and Parrinello three decades ago. The new framework allows, for the first time, energy conserving, linear-scaling Born-Oppenheimer molecular dynamics simulations, which is necessary to study larger and more realistic systems over longer simulation times than previously possible. Expensive, self-consinstent-field optimizations are avoided and normal integration time steps of regular, direct Born-Oppenheimer molecular dynamics can be used. Linear scaling electronic structure theory is presented using a graph-based approach that is ideal for parallel calculations on hybrid computer platforms. For the first time, quantum based Born-Oppenheimer molecular dynamics simulation is becoming a practically feasible approach in simulations of +100,000 atoms-representing a competitive alternative to classical polarizable force field methods. In collaboration with: Anders Niklasson, Los Alamos National Laboratory.

Parallel processing for nonlinear dynamics simulations of structures including rotating bladed-disk assemblies

NASA Technical Reports Server (NTRS)

Hsieh, Shang-Hsien

1993-01-01

The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.

On the Measurement of Electron Temperature by Single Langmuir Probes in High Recycling Divertors

NASA Astrophysics Data System (ADS)

Pitts, Richard; Horacek, Jan; Loarte, Alberto

2000-10-01

Under high recycling and detached conditions, divertor Langmuir probes often yield a significantly higher value of Te than expected. The influence of plasma turbulence and the effect of fast electrons/plasma collisionality are two reasons why this might occur. We concentrate on these two candidates, with particular reference to observations on the TCV tokamak. A systematic study of the effects of noise on simulated probe characteristics at low T_e, shows that the asymmetric, exponential nature of the characteristic favours electron collection such that fluctuations in Vf alone actually tend to reduce the derived Te from that which would otherwise be found. We have also studied the effects of correlated density and potential fluctuations, finding no effect on the fitted T_e. The sheath potential fall energetically filters electrons such that at high densities, the probe measured Te may be characteristic of hotter, more distant zones in the plasma. We use model parallel field profiles of Te and ne generated from B2-Eirene simulations of TCV discharges as input to the analytic theory of Wesson [1] to show how a divertor plate measurement of Te in TCV can exceed the expected value by factors of up to 6 as detachment is approached. [1] J. A. Wesson, Plasma Phys. and Contr. Fusion 37 (1995) 1459

Testing cosmic ray acceleration with radio relics: a high-resolution study using MHD and tracers

NASA Astrophysics Data System (ADS)

Wittor, D.; Vazza, F.; Brüggen, M.

2017-02-01

Weak shocks in the intracluster medium may accelerate cosmic-ray protons and cosmic-ray electrons differently depending on the angle between the upstream magnetic field and the shock normal. In this work, we investigate how shock obliquity affects the production of cosmic rays in high-resolution simulations of galaxy clusters. For this purpose, we performed a magnetohydrodynamical simulation of a galaxy cluster using the mesh refinement code ENZO. We use Lagrangian tracers to follow the properties of the thermal gas, the cosmic rays and the magnetic fields over time. We tested a number of different acceleration scenarios by varying the obliquity-dependent acceleration efficiencies of protons and electrons, and by examining the resulting hadronic γ-ray and radio emission. We find that the radio emission does not change significantly if only quasi-perpendicular shocks are able to accelerate cosmic-ray electrons. Our analysis suggests that radio-emitting electrons found in relics have been typically shocked many times before z = 0. On the other hand, the hadronic γ-ray emission from clusters is found to decrease significantly if only quasi-parallel shocks are allowed to accelerate cosmic ray protons. This might reduce the tension with the low upper limits on γ-ray emission from clusters set by the Fermi satellite.

Particle Acceleration and Radiation associated with Magnetic Field Generation from Relativistic Collisionless Shocks

NASA Technical Reports Server (NTRS)

Nishikawa, K.; Hardee, P. E.; Richardson, G. A.; Preece, R. D.; Sol, H.; Fishman, G. J.

2003-01-01

Shock acceleration is an ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, two-streaming instability, and the Weibel instability) created in the shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating through an ambient plasma with and without initial magnetic fields. We find only small differences in the results between no ambient and weak ambient magnetic fields. Simulations show that the Weibel instability created in the collisionless shock front accelerates particles perpendicular and parallel to the jet propagation direction. While some Fermi acceleration may occur at the jet front, the majority of electron acceleration takes place behind the jet front and cannot be characterized as Fermi acceleration. The simulation results show that this instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields, which contribute to the electron s transverse deflection behind the jet head. The "jitter" radiation from deflected electrons has different properties than synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets, and supernova remnants.

Cavity-photon contribution to the effective interaction of electrons in parallel quantum dots

NASA Astrophysics Data System (ADS)

Gudmundsson, Vidar; Sitek, Anna; Abdullah, Nzar Rauf; Tang, Chi-Shung; Manolescu, Andrei

2016-05-01

A single cavity photon mode is expected to modify the Coulomb interaction of an electron system in the cavity. Here we investigate this phenomena in a parallel double quantum dot system. We explore properties of the closed system and the system after it has been opened up for electron transport. We show how results for both cases support the idea that the effective electron-electron interaction becomes more repulsive in the presence of a cavity photon field. This can be understood in terms of the cavity photons dressing the polarization terms in the effective mutual electron interaction leading to nontrivial delocalization or polarization of the charge in the double parallel dot potential. In addition, we find that the effective repulsion of the electrons can be reduced by quadrupolar collective oscillations excited by an external classical dipole electric field.

A gyrokinetic one-dimensional scrape-off layer model of an edge-localized mode heat pulse

DOE PAGES

Shi, E. L.; Hakim, A. H.; Hammett, G. W.

2015-02-03

An electrostatic gyrokinetic-based model is applied to simulate parallel plasma transport in the scrape-off layer to a divertor plate. We focus on a test problem that has been studied previously, using parameters chosen to model a heat pulse driven by an edge-localized mode in JET. Previous work has used direct particle-in-cellequations with full dynamics, or Vlasov or fluid equations with only parallel dynamics. With the use of the gyrokinetic quasineutrality equation and logical sheathboundary conditions, spatial and temporal resolution requirements are no longer set by the electron Debye length and plasma frequency, respectively. Finally, this test problem also helps illustratemore » some of the physics contained in the Hamiltonian form of the gyrokineticequations and some of the numerical challenges in developing an edge gyrokinetic code.« less

High-performance parallel processors based on star-coupled wavelength division multiplexing optical interconnects

DOEpatents

Deri, Robert J.; DeGroot, Anthony J.; Haigh, Ronald E.

2002-01-01

As the performance of individual elements within parallel processing systems increases, increased communication capability between distributed processor and memory elements is required. There is great interest in using fiber optics to improve interconnect communication beyond that attainable using electronic technology. Several groups have considered WDM, star-coupled optical interconnects. The invention uses a fiber optic transceiver to provide low latency, high bandwidth channels for such interconnects using a robust multimode fiber technology. Instruction-level simulation is used to quantify the bandwidth, latency, and concurrency required for such interconnects to scale to 256 nodes, each operating at 1 GFLOPS performance. Performance scales have been shown to .apprxeq.100 GFLOPS for scientific application kernels using a small number of wavelengths (8 to 32), only one wavelength received per node, and achievable optoelectronic bandwidth and latency.

Crashworthiness simulations with DYNA3D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schauer, D.A.; Hoover, C.G.; Kay, G.J.

1996-04-01

Current progress in parallel algorithm research and applications in vehicle crash simulation is described for the explicit, finite element algorithms in DYNA3D. Problem partitioning methods and parallel algorithms for contact at material interfaces are the two challenging algorithm research problems that are addressed. Two prototype parallel contact algorithms have been developed for treating the cases of local and arbitrary contact. Demonstration problems for local contact are crashworthiness simulations with 222 locally defined contact surfaces and a vehicle/barrier collision modeled with arbitrary contact. A simulation of crash tests conducted for a vehicle impacting a U-channel small sign post embedded in soilmore » has been run on both the serial and parallel versions of DYNA3D. A significant reduction in computational time has been observed when running these problems on the parallel version. However, to achieve maximum efficiency, complex problems must be appropriately partitioned, especially when contact dominates the computation.« less

pWeb: A High-Performance, Parallel-Computing Framework for Web-Browser-Based Medical Simulation.

PubMed

Halic, Tansel; Ahn, Woojin; De, Suvranu

2014-01-01

This work presents a pWeb - a new language and compiler for parallelization of client-side compute intensive web applications such as surgical simulations. The recently introduced HTML5 standard has enabled creating unprecedented applications on the web. Low performance of the web browser, however, remains the bottleneck of computationally intensive applications including visualization of complex scenes, real time physical simulations and image processing compared to native ones. The new proposed language is built upon web workers for multithreaded programming in HTML5. The language provides fundamental functionalities of parallel programming languages as well as the fork/join parallel model which is not supported by web workers. The language compiler automatically generates an equivalent parallel script that complies with the HTML5 standard. A case study on realistic rendering for surgical simulations demonstrates enhanced performance with a compact set of instructions.

n-body simulations using message passing parallel computers.

NASA Astrophysics Data System (ADS)

Grama, A. Y.; Kumar, V.; Sameh, A.

The authors present new parallel formulations of the Barnes-Hut method for n-body simulations on message passing computers. These parallel formulations partition the domain efficiently incurring minimal communication overhead. This is in contrast to existing schemes that are based on sorting a large number of keys or on the use of global data structures. The new formulations are augmented by alternate communication strategies which serve to minimize communication overhead. The impact of these communication strategies is experimentally studied. The authors report on experimental results obtained from an astrophysical simulation on an nCUBE2 parallel computer.

A conservative approach to parallelizing the Sharks World simulation

NASA Technical Reports Server (NTRS)

Nicol, David M.; Riffe, Scott E.

1990-01-01

Parallelizing a benchmark problem for parallel simulation, the Sharks World, is described. The described solution is conservative, in the sense that no state information is saved, and no 'rollbacks' occur. The used approach illustrates both the principal advantage and principal disadvantage of conservative parallel simulation. The advantage is that by exploiting lookahead an approach was found that dramatically improves the serial execution time, and also achieves excellent speedups. The disadvantage is that if the model rules are changed in such a way that the lookahead is destroyed, it is difficult to modify the solution to accommodate the changes.

Understanding the impact of insulating and conducting endplate boundary conditions on turbulence in CSDX through nonlocal simulations

DOE PAGES

Vaezi, P.; Holland, C.; Thakur, S. C.; ...

2017-04-01

The Controlled Shear Decorrelation Experiment (CSDX) linear plasma device provides a unique platform for investigating the underlying physics of self-regulating drift-wave turbulence/zonal flow dynamics. A minimal model of 3D drift-reduced nonlocal cold ion fluid equations which evolves density, vorticity, and electron temperature fluctuations, with proper sheath boundary conditions, is used to simulate dynamics of the turbulence in CSDX and its response to changes in parallel boundary conditions. These simulations are then carried out using the BOUndary Turbulence (BOUT++) framework and use equilibrium electron density and temperature profiles taken from experimental measurements. The results show that density gradient-driven drift-waves are themore » dominant instability in CSDX. However, the choice of insulating or conducting endplate boundary conditions affects the linear growth rates and energy balance of the system due to the absence or addition of Kelvin-Helmholtz modes generated by the sheath-driven equilibrium E × B shear and sheath-driven temperature gradient instability. Moreover, nonlinear simulation results show that the boundary conditions impact the turbulence structure and zonal flow formation, resulting in less broadband (more quasi-coherent) turbulence and weaker zonal flow in conducting boundary condition case. These results are qualitatively consistent with earlier experimental observations.« less

AC losses in horizontally parallel HTS tapes for possible wireless power transfer applications

NASA Astrophysics Data System (ADS)

Shen, Boyang; Geng, Jianzhao; Zhang, Xiuchang; Fu, Lin; Li, Chao; Zhang, Heng; Dong, Qihuan; Ma, Jun; Gawith, James; Coombs, T. A.

2017-12-01

This paper presents the concept of using horizontally parallel HTS tapes with AC loss study, and the investigation on possible wireless power transfer (WPT) applications. An example of three parallel HTS tapes was proposed, whose AC loss study was carried out both from experiment using electrical method; and simulation using 2D H-formulation on the FEM platform of COMSOL Multiphysics. The electromagnetic induction around the three parallel tapes was monitored using COMSOL simulation. The electromagnetic induction and AC losses generated by a conventional three turn coil was simulated as well, and then compared to the case of three parallel tapes with the same AC transport current. The analysis demonstrates that HTS parallel tapes could be potentially used into wireless power transfer systems, which could have lower total AC losses than conventional HTS coils.

Slow dynamics in glasses: A comparison between theory and experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Phillips, J. C.

Minimalist theories of complex systems are broadly of two kinds: mean field and axiomatic. So far, all theories of complex properties absent from simple systems and intrinsic to glasses are axiomatic. Stretched Exponential Relaxation (SER) is the prototypical complex temporal property of glasses, discovered by Kohlrausch 150 years ago, and now observed almost universally in microscopically homogeneous, complex nonequilibrium materials, including luminescent electronic Coulomb glasses. A critical comparison of alternative axiomatic theories with both numerical simulations and experiments strongly favors channeled dynamical trap models over static percolative or energy landscape models. The topics discussed cover those reported since the author'smore » review article in 1996, with an emphasis on parallels between channel bifurcation in electronic and molecular relaxation.« less

An in situ Comparison of Electron Acceleration at Collisionless Shocks under Differing Upstream Magnetic Field Orientations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masters, A.; Dougherty, M. K.; Sulaiman, A. H.

A leading explanation for the origin of Galactic cosmic rays is acceleration at high-Mach number shock waves in the collisionless plasma surrounding young supernova remnants. Evidence for this is provided by multi-wavelength non-thermal emission thought to be associated with ultrarelativistic electrons at these shocks. However, the dependence of the electron acceleration process on the orientation of the upstream magnetic field with respect to the local normal to the shock front (quasi-parallel/quasi-perpendicular) is debated. Cassini spacecraft observations at Saturn’s bow shock have revealed examples of electron acceleration under quasi-perpendicular conditions, and the first in situ evidence of electron acceleration at amore » quasi-parallel shock. Here we use Cassini data to make the first comparison between energy spectra of locally accelerated electrons under these differing upstream magnetic field regimes. We present data taken during a quasi-perpendicular shock crossing on 2008 March 8 and during a quasi-parallel shock crossing on 2007 February 3, highlighting that both were associated with electron acceleration to at least MeV energies. The magnetic signature of the quasi-perpendicular crossing has a relatively sharp upstream–downstream transition, and energetic electrons were detected close to the transition and immediately downstream. The magnetic transition at the quasi-parallel crossing is less clear, energetic electrons were encountered upstream and downstream, and the electron energy spectrum is harder above ∼100 keV. We discuss whether the acceleration is consistent with diffusive shock acceleration theory in each case, and suggest that the quasi-parallel spectral break is due to an energy-dependent interaction between the electrons and short, large-amplitude magnetic structures.« less

Effects of Shock and Turbulence Properties on Electron Acceleration

NASA Astrophysics Data System (ADS)

Qin, G.; Kong, F.-J.; Zhang, L.-H.

2018-06-01

Using test particle simulations, we study electron acceleration at collisionless shocks with a two-component model turbulent magnetic field with slab component including dissipation range. We investigate the importance of the shock-normal angle θ Bn, magnetic turbulence level {(b/{B}0)}2, and shock thickness on the acceleration efficiency of electrons. It is shown that at perpendicular shocks the electron acceleration efficiency is enhanced with the decrease of {(b/{B}0)}2, and at {(b/{B}0)}2=0.01 the acceleration becomes significant due to a strong drift electric field with long time particles staying near the shock front for shock drift acceleration (SDA). In addition, at parallel shocks the electron acceleration efficiency is increasing with the increase of {(b/{B}0)}2, and at {(b/{B}0)}2=10.0 the acceleration is very strong due to sufficient pitch-angle scattering for first-order Fermi acceleration, as well as due to the large local component of the magnetic field perpendicular to the shock-normal angle for SDA. On the other hand, the high perpendicular shock acceleration with {(b/{B}0)}2=0.01 is stronger than the high parallel shock acceleration with {(b/{B}0)}2=10.0, the reason might be the assumption that SDA is more efficient than first-order Fermi acceleration. Furthermore, for oblique shocks, the acceleration efficiency is small no matter whether the turbulence level is low or high. Moreover, for the effect of shock thickness on electron acceleration at perpendicular shocks, we show that there exists the bendover thickness, L diff,b. The acceleration efficiency does not noticeably change if the shock thickness is much smaller than L diff,b. However, if the shock thickness is much larger than L diff,b, the acceleration efficiency starts to drop abruptly.

DL_MG: A Parallel Multigrid Poisson and Poisson-Boltzmann Solver for Electronic Structure Calculations in Vacuum and Solution.

PubMed

Womack, James C; Anton, Lucian; Dziedzic, Jacek; Hasnip, Phil J; Probert, Matt I J; Skylaris, Chris-Kriton

2018-03-13

The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with nonlinear dependencies, and diverse boundary conditions. The analytic solutions generally used to solve the Poisson equation in vacuum (or with homogeneous permittivity) are not applicable in these circumstances, and numerical methods must be used. In this work, we present DL_MG, a flexible, scalable, and accurate solver library, developed specifically to tackle the challenges of solving the Poisson equation in modern large-scale electronic structure calculations on parallel computers. Our solver is based on the multigrid approach and uses an iterative high-order defect correction method to improve the accuracy of solutions. Using two chemically relevant model systems, we tested the accuracy and computational performance of DL_MG when solving the generalized Poisson and Poisson-Boltzmann equations, demonstrating excellent agreement with analytic solutions and efficient scaling to ∼10 9 unknowns and 100s of CPU cores. We also applied DL_MG in actual large-scale electronic structure calculations, using the ONETEP linear-scaling electronic structure package to study a 2615 atom protein-ligand complex with routinely available computational resources. In these calculations, the overall execution time with DL_MG was not significantly greater than the time required for calculations using a conventional FFT-based solver.

Measurement of large parallel and perpendicular electric fields on electron spatial scales in the terrestrial bow shock.

PubMed

Bale, S D; Mozer, F S

2007-05-18

Large parallel (

Effect of parallel electric fields on the ponderomotive stabilization of MHD instabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litwin, C.; Hershkowitz, N.

The contribution of the wave electric field component E/sub parallel/, parallel to the magnetic field, to the ponderomotive stabilization of curvature driven instabilities is evaluated and compared to the transverse component contribution. For the experimental density range, in which the stability is primarily determined by the m = 1 magnetosonic wave, this contribution is found to be the dominant and stabilizing when the electron temperature is neglected. For sufficiently high electron temperatures the dominant fast wave is found to be axially evanescent. In the same limit, E/sub parallel/ becomes radially oscillating. It is concluded that the increased electron temperature nearmore » the plasma surface reduces the magnitude of ponderomotive effects.« less

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04531j

PubMed Central

Lagardère, Louis; Jolly, Luc-Henri; Lipparini, Filippo; Aviat, Félix; Stamm, Benjamin; Jing, Zhifeng F.; Harger, Matthew; Torabifard, Hedieh; Cisneros, G. Andrés; Schnieders, Michael J.; Gresh, Nohad; Maday, Yvon; Ren, Pengyu Y.; Ponder, Jay W.

2017-01-01

We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) encompassing distributed multipoles electrostatics. Tinker-HP is an evolution of the popular Tinker package code that conserves its simplicity of use and its reference double precision implementation for CPUs. Grounded on interdisciplinary efforts with applied mathematics, Tinker-HP allows for long polarizable MD simulations on large systems up to millions of atoms. We detail in the paper the newly developed extension of massively parallel 3D spatial decomposition to point dipole polarizable models as well as their coupling to efficient Krylov iterative and non-iterative polarization solvers. The design of the code allows the use of various computer systems ranging from laboratory workstations to modern petascale supercomputers with thousands of cores. Tinker-HP proposes therefore the first high-performance scalable CPU computing environment for the development of next generation point dipole PFFs and for production simulations. Strategies linking Tinker-HP to Quantum Mechanics (QM) in the framework of multiscale polarizable self-consistent QM/MD simulations are also provided. The possibilities, performances and scalability of the software are demonstrated via benchmarks calculations using the polarizable AMOEBA force field on systems ranging from large water boxes of increasing size and ionic liquids to (very) large biosystems encompassing several proteins as well as the complete satellite tobacco mosaic virus and ribosome structures. For small systems, Tinker-HP appears to be competitive with the Tinker-OpenMM GPU implementation of Tinker. As the system size grows, Tinker-HP remains operational thanks to its access to distributed memory and takes advantage of its new algorithmic enabling for stable long timescale polarizable simulations. Overall, a several thousand-fold acceleration over a single-core computation is observed for the largest systems. The extension of the present CPU implementation of Tinker-HP to other computational platforms is discussed. PMID:29732110

Accelerated Electron-Beam Formation with a High Capture Coefficient in a Parallel Coupled Accelerating Structure

NASA Astrophysics Data System (ADS)

Chernousov, Yu. D.; Shebolaev, I. V.; Ikryanov, I. M.

2018-01-01

An electron beam with a high (close to 100%) coefficient of electron capture into the regime of acceleration has been obtained in a linear electron accelerator based on a parallel coupled slow-wave structure, electron gun with microwave-controlled injection current, and permanent-magnet beam-focusing system. The high capture coefficient was due to the properties of the accelerating structure, beam-focusing system, and electron-injection system. Main characteristics of the proposed systems are presented.

A Wigner Monte Carlo approach to density functional theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sellier, J.M., E-mail: jeanmichel.sellier@gmail.com; Dimov, I.

2014-08-01

In order to simulate quantum N-body systems, stationary and time-dependent density functional theories rely on the capacity of calculating the single-electron wave-functions of a system from which one obtains the total electron density (Kohn–Sham systems). In this paper, we introduce the use of the Wigner Monte Carlo method in ab-initio calculations. This approach allows time-dependent simulations of chemical systems in the presence of reflective and absorbing boundary conditions. It also enables an intuitive comprehension of chemical systems in terms of the Wigner formalism based on the concept of phase-space. Finally, being based on a Monte Carlo method, it scales verymore » well on parallel machines paving the way towards the time-dependent simulation of very complex molecules. A validation is performed by studying the electron distribution of three different systems, a Lithium atom, a Boron atom and a hydrogenic molecule. For the sake of simplicity, we start from initial conditions not too far from equilibrium and show that the systems reach a stationary regime, as expected (despite no restriction is imposed in the choice of the initial conditions). We also show a good agreement with the standard density functional theory for the hydrogenic molecule. These results demonstrate that the combination of the Wigner Monte Carlo method and Kohn–Sham systems provides a reliable computational tool which could, eventually, be applied to more sophisticated problems.« less

Drift turbulence, particle transport, and anomalous dissipation at the reconnecting magnetopause

NASA Astrophysics Data System (ADS)

Le, A.; Daughton, W.; Ohia, O.; Chen, L.-J.; Liu, Y.-H.; Wang, S.; Nystrom, W. D.; Bird, R.

2018-06-01

Using fully kinetic 3D simulations, the reconnection dynamics of asymmetric current sheets are examined at the Earth's magnetopause. The plasma parameters are selected to model MMS magnetopause diffusion region crossings with guide fields of 0.1, 0.4, and 1 of the reconnecting magnetosheath field. In each case, strong drift-wave fluctuations are observed in the lower-hybrid frequency range at the steep density gradient across the magnetospheric separatrix. These fluctuations give rise to cross-field electron particle transport. In addition, this turbulent mixing leads to significantly enhanced electron parallel heating in comparison to 2D simulations. We study three different methods of quantifying the anomalous dissipation produced by the drift fluctuations, based on spatial averaging, temporal averaging, and temporal averaging followed by integrating along magnetic field lines. A comparison of different methods reveals complications in identifying and measuring the anomalous dissipation. Nevertheless, the anomalous dissipation from short wavelength drift fluctuations appears weak for each case, and the reconnection rates observed in 3D are nearly the same as in 2D models. The 3D simulations feature a number of interesting new features that are consistent with recent MMS observations, including cold beams of magnetosheath electrons that penetrate into the hotter magnetospheric inflow, the related observation of decreasing temperature in regions of increasing total density, and an effective turbulent diffusion coefficient that agrees with predictions from quasi-linear theory.

On efficiency of fire simulation realization: parallelization with greater number of computational meshes

NASA Astrophysics Data System (ADS)

Valasek, Lukas; Glasa, Jan

2017-12-01

Current fire simulation systems are capable to utilize advantages of high-performance computer (HPC) platforms available and to model fires efficiently in parallel. In this paper, efficiency of a corridor fire simulation on a HPC computer cluster is discussed. The parallel MPI version of Fire Dynamics Simulator is used for testing efficiency of selected strategies of allocation of computational resources of the cluster using a greater number of computational cores. Simulation results indicate that if the number of cores used is not equal to a multiple of the total number of cluster node cores there are allocation strategies which provide more efficient calculations.

Development of a parallel FE simulator for modeling the whole trans-scale failure process of rock from meso- to engineering-scale

NASA Astrophysics Data System (ADS)

Li, Gen; Tang, Chun-An; Liang, Zheng-Zhao

2017-01-01

Multi-scale high-resolution modeling of rock failure process is a powerful means in modern rock mechanics studies to reveal the complex failure mechanism and to evaluate engineering risks. However, multi-scale continuous modeling of rock, from deformation, damage to failure, has raised high requirements on the design, implementation scheme and computation capacity of the numerical software system. This study is aimed at developing the parallel finite element procedure, a parallel rock failure process analysis (RFPA) simulator that is capable of modeling the whole trans-scale failure process of rock. Based on the statistical meso-damage mechanical method, the RFPA simulator is able to construct heterogeneous rock models with multiple mechanical properties, deal with and represent the trans-scale propagation of cracks, in which the stress and strain fields are solved for the damage evolution analysis of representative volume element by the parallel finite element method (FEM) solver. This paper describes the theoretical basis of the approach and provides the details of the parallel implementation on a Windows - Linux interactive platform. A numerical model is built to test the parallel performance of FEM solver. Numerical simulations are then carried out on a laboratory-scale uniaxial compression test, and field-scale net fracture spacing and engineering-scale rock slope examples, respectively. The simulation results indicate that relatively high speedup and computation efficiency can be achieved by the parallel FEM solver with a reasonable boot process. In laboratory-scale simulation, the well-known physical phenomena, such as the macroscopic fracture pattern and stress-strain responses, can be reproduced. In field-scale simulation, the formation process of net fracture spacing from initiation, propagation to saturation can be revealed completely. In engineering-scale simulation, the whole progressive failure process of the rock slope can be well modeled. It is shown that the parallel FE simulator developed in this study is an efficient tool for modeling the whole trans-scale failure process of rock from meso- to engineering-scale.

Computational Particle Dynamic Simulations on Multicore Processors (CPDMu) Final Report Phase I

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schmalz, Mark S

2011-07-24

Statement of Problem - Department of Energy has many legacy codes for simulation of computational particle dynamics and computational fluid dynamics applications that are designed to run on sequential processors and are not easily parallelized. Emerging high-performance computing architectures employ massively parallel multicore architectures (e.g., graphics processing units) to increase throughput. Parallelization of legacy simulation codes is a high priority, to achieve compatibility, efficiency, accuracy, and extensibility. General Statement of Solution - A legacy simulation application designed for implementation on mainly-sequential processors has been represented as a graph G. Mathematical transformations, applied to G, produce a graph representation {und G}more » for a high-performance architecture. Key computational and data movement kernels of the application were analyzed/optimized for parallel execution using the mapping G {yields} {und G}, which can be performed semi-automatically. This approach is widely applicable to many types of high-performance computing systems, such as graphics processing units or clusters comprised of nodes that contain one or more such units. Phase I Accomplishments - Phase I research decomposed/profiled computational particle dynamics simulation code for rocket fuel combustion into low and high computational cost regions (respectively, mainly sequential and mainly parallel kernels), with analysis of space and time complexity. Using the research team's expertise in algorithm-to-architecture mappings, the high-cost kernels were transformed, parallelized, and implemented on Nvidia Fermi GPUs. Measured speedups (GPU with respect to single-core CPU) were approximately 20-32X for realistic model parameters, without final optimization. Error analysis showed no loss of computational accuracy. Commercial Applications and Other Benefits - The proposed research will constitute a breakthrough in solution of problems related to efficient parallel computation of particle and fluid dynamics simulations. These problems occur throughout DOE, military and commercial sectors: the potential payoff is high. We plan to license or sell the solution to contractors for military and domestic applications such as disaster simulation (aerodynamic and hydrodynamic), Government agencies (hydrological and environmental simulations), and medical applications (e.g., in tomographic image reconstruction). Keywords - High-performance Computing, Graphic Processing Unit, Fluid/Particle Simulation. Summary for Members of Congress - Department of Energy has many simulation codes that must compute faster, to be effective. The Phase I research parallelized particle/fluid simulations for rocket combustion, for high-performance computing systems.« less

DISSIPATION OF PARALLEL AND OBLIQUE ALFVÉN-CYCLOTRON WAVES—IMPLICATIONS FOR HEATING OF ALPHA PARTICLES IN THE SOLAR WIND

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maneva, Y. G.; Poedts, Stefaan; Viñas, Adolfo F.

2015-11-20

We perform 2.5D hybrid simulations with massless fluid electrons and kinetic particle-in-cell ions to study the temporal evolution of ion temperatures, temperature anisotropies, and velocity distribution functions in relation to the dissipation and turbulent evolution of a broadband spectrum of parallel and obliquely propagating Alfvén-cyclotron waves. The purpose of this paper is to study the relative role of parallel versus oblique Alfvén-cyclotron waves in the observed heating and acceleration of alpha particles in the fast solar wind. We consider collisionless homogeneous multi-species plasma, consisting of isothermal electrons, isotropic protons, and a minor component of drifting α particles in a finite-βmore » fast stream near the Earth. The kinetic ions are modeled by initially isotropic Maxwellian velocity distribution functions, which develop nonthermal features and temperature anisotropies when a broadband spectrum of low-frequency nonresonant, ω ≤ 0.34 Ω{sub p}, Alfvén-cyclotron waves is imposed at the beginning of the simulations. The initial plasma parameter values, such as ion density, temperatures, and relative drift speeds, are supplied by fast solar wind observations made by the Wind spacecraft at 1 AU. The imposed broadband wave spectra are left-hand polarized and resemble Wind measurements of Alfvénic turbulence in the solar wind. The imposed magnetic field fluctuations for all cases are within the inertial range of the solar wind turbulence and have a Kraichnan-type spectral slope α = −3/2. We vary the propagation angle from θ = 0° to θ = 30° and θ = 60°, and find that the heating of alpha particles is most efficient for the highly oblique waves propagating at 60°, whereas the protons exhibit perpendicular cooling at all propagation angles.« less

Simulation of Silicon Photomultiplier Signals

NASA Astrophysics Data System (ADS)

Seifert, Stefan; van Dam, Herman T.; Huizenga, Jan; Vinke, Ruud; Dendooven, Peter; Lohner, Herbert; Schaart, Dennis R.

2009-12-01

In a silicon photomultiplier (SiPM), also referred to as multi-pixel photon counter (MPPC), many Geiger-mode avalanche photodiodes (GM-APDs) are connected in parallel so as to combine the photon counting capabilities of each of these so-called microcells into a proportional light sensor. The discharge of a single microcell is relatively well understood and electronic models exist to simulate this process. In this paper we introduce an extended model that is able to simulate the simultaneous discharge of multiple cells. This model is used to predict the SiPM signal in response to fast light pulses as a function of the number of fired cells, taking into account the influence of the input impedance of the SiPM preamplifier. The model predicts that the electronic signal is not proportional to the number of fired cells if the preamplifier input impedance is not zero. This effect becomes more important for SiPMs with lower parasitic capacitance (which otherwise is a favorable property). The model is validated by comparing its predictions to experimental data obtained with two different SiPMs (Hamamatsu S10362-11-25u and Hamamatsu S10362-33-25c) illuminated with ps laser pulses. The experimental results are in good agreement with the model predictions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vaezi, P.; Holland, C.; Thakur, S. C.

The Controlled Shear Decorrelation Experiment (CSDX) linear plasma device provides a unique platform for investigating the underlying physics of self-regulating drift-wave turbulence/zonal flow dynamics. A minimal model of 3D drift-reduced nonlocal cold ion fluid equations which evolves density, vorticity, and electron temperature fluctuations, with proper sheath boundary conditions, is used to simulate dynamics of the turbulence in CSDX and its response to changes in parallel boundary conditions. These simulations are then carried out using the BOUndary Turbulence (BOUT++) framework and use equilibrium electron density and temperature profiles taken from experimental measurements. The results show that density gradient-driven drift-waves are themore » dominant instability in CSDX. However, the choice of insulating or conducting endplate boundary conditions affects the linear growth rates and energy balance of the system due to the absence or addition of Kelvin-Helmholtz modes generated by the sheath-driven equilibrium E × B shear and sheath-driven temperature gradient instability. Moreover, nonlinear simulation results show that the boundary conditions impact the turbulence structure and zonal flow formation, resulting in less broadband (more quasi-coherent) turbulence and weaker zonal flow in conducting boundary condition case. These results are qualitatively consistent with earlier experimental observations.« less

Program For Parallel Discrete-Event Simulation

NASA Technical Reports Server (NTRS)

Beckman, Brian C.; Blume, Leo R.; Geiselman, John S.; Presley, Matthew T.; Wedel, John J., Jr.; Bellenot, Steven F.; Diloreto, Michael; Hontalas, Philip J.; Reiher, Peter L.; Weiland, Frederick P.

1991-01-01

User does not have to add any special logic to aid in synchronization. Time Warp Operating System (TWOS) computer program is special-purpose operating system designed to support parallel discrete-event simulation. Complete implementation of Time Warp mechanism. Supports only simulations and other computations designed for virtual time. Time Warp Simulator (TWSIM) subdirectory contains sequential simulation engine interface-compatible with TWOS. TWOS and TWSIM written in, and support simulations in, C programming language.

Xyce release and distribution management : version 1.2.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, Scott Alan; Williamson, Charles Michael

2003-10-01

This document presents a high-level description of the Xyce {trademark} Parallel Electronic Simulator Release and Distribution Management Process. The purpose of this process is to standardize the manner in which all Xyce software products progress toward release and how releases are made available to customers. Rigorous Release Management will assure that Xyce releases are created in such a way that the elements comprising the release are traceable and the release itself is reproducible. Distribution Management describes what is to be done with a Xyce release that is eligible for distribution.

The silicon synapse or, neural net computing.

PubMed

Frenger, P

1989-01-01

Recent developments have rekindled interest in the electronic neural network, a form of parallel computer architecture loosely based on the nervous system of living creatures. This paper describes the elements of neural net computers, reviews the historical milestones in their development, and lists the advantages and disadvantages of their use. Methods for software simulation of neural network systems on existing computers, as well as creation of hardware analogues, are given. The most successful applications of these techniques, involving emulation of biological system responses, are presented. The author's experiences with neural net systems are discussed.

Roos and NACP-02 ion chamber perturbations and water-air stopping-power ratios for clinical electron beams for energies from 4 to 22 MeV

NASA Astrophysics Data System (ADS)

Bailey, M.; Shipley, D. R.; Manning, J. W.

2015-02-01

Empirical fits are developed for depth-compensated wall- and cavity-replacement perturbations in the PTW Roos 34001 and IBA / Scanditronix NACP-02 parallel-plate ionisation chambers, for electron beam qualities from 4 to 22 MeV for depths up to approximately 1.1 × R50,D. These are based on calculations using the Monte Carlo radiation transport code EGSnrc and its user codes with a full simulation of the linac treatment head modelled using BEAMnrc. These fits are used with calculated restricted stopping-power ratios between air and water to match measured depth-dose distributions in water from an Elekta Synergy clinical linear accelerator at the UK National Physical Laboratory. Results compare well with those from recent publications and from the IPEM 2003 electron beam radiotherapy Code of Practice.

THE IBEX RIBBON AND THE PICKUP ION RING STABILITY IN THE OUTER HELIOSHEATH. II. MONTE-CARLO AND PARTICLE-IN-CELL MODEL RESULTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Niemiec, J.; Florinski, V.; Heerikhuisen, J.

2016-08-01

The nearly circular ribbon of energetic neutral atom (ENA) emission discovered by NASA’s Interplanetary Boundary EXplorer satellite ( IBEX ), is most commonly attributed to the effect of charge exchange of secondary pickup ions (PUIs) gyrating about the magnetic field in the outer heliosheath (OHS) and the interstellar space beyond. The first paper in the series (Paper I) presented a theoretical analysis of the pickup process in the OHS and hybrid-kinetic simulations, revealing that the kinetic properties of freshly injected proton rings depend sensitively on the details of their velocity distribution. It was demonstrated that only rings that are notmore » too narrow (parallel thermal spread above a few km s{sup −1}) and not too wide (parallel temperature smaller than the core plasma temperature) could remain stable for a period of time long enough to generate ribbon ENAs. This paper investigates the role of electron dynamics and the extra spatial degree of freedom in the ring ion scattering process with the help of two-dimensional full particle-in-cell (PIC) kinetic simulations. A good agreement is observed between ring evolution under unstable conditions in hybrid and PIC models, and the dominant modes are found to propagate parallel to the magnetic field. We also present more realistic ribbon PUI distributions generated using Monte Carlo simulations of atomic hydrogen in the global heliosphere and examine the effect of both the cold ring-like and the hot “halo” PUIs produced from heliosheath ENAs on the ring stability. It is shown that the second PUI population enhances the fluctuation growth rate, leading to faster isotropization of the solar-wind-derived ring ions.« less

The IBEX Ribbon and the Pickup Ion Ring Stability in the Outer Heliosheath II. Monte-Carlo and Particle-in-cell Model Results

NASA Astrophysics Data System (ADS)

Niemiec, J.; Florinski, V.; Heerikhuisen, J.; Nishikawa, K.-I.

2016-08-01

The nearly circular ribbon of energetic neutral atom (ENA) emission discovered by NASA’s Interplanetary Boundary EXplorer satellite (IBEX), is most commonly attributed to the effect of charge exchange of secondary pickup ions (PUIs) gyrating about the magnetic field in the outer heliosheath (OHS) and the interstellar space beyond. The first paper in the series (Paper I) presented a theoretical analysis of the pickup process in the OHS and hybrid-kinetic simulations, revealing that the kinetic properties of freshly injected proton rings depend sensitively on the details of their velocity distribution. It was demonstrated that only rings that are not too narrow (parallel thermal spread above a few km s-1) and not too wide (parallel temperature smaller than the core plasma temperature) could remain stable for a period of time long enough to generate ribbon ENAs. This paper investigates the role of electron dynamics and the extra spatial degree of freedom in the ring ion scattering process with the help of two-dimensional full particle-in-cell (PIC) kinetic simulations. A good agreement is observed between ring evolution under unstable conditions in hybrid and PIC models, and the dominant modes are found to propagate parallel to the magnetic field. We also present more realistic ribbon PUI distributions generated using Monte Carlo simulations of atomic hydrogen in the global heliosphere and examine the effect of both the cold ring-like and the hot “halo” PUIs produced from heliosheath ENAs on the ring stability. It is shown that the second PUI population enhances the fluctuation growth rate, leading to faster isotropization of the solar-wind-derived ring ions.

Tutorial: Parallel Computing of Simulation Models for Risk Analysis.

PubMed

Reilly, Allison C; Staid, Andrea; Gao, Michael; Guikema, Seth D

2016-10-01

Simulation models are widely used in risk analysis to study the effects of uncertainties on outcomes of interest in complex problems. Often, these models are computationally complex and time consuming to run. This latter point may be at odds with time-sensitive evaluations or may limit the number of parameters that are considered. In this article, we give an introductory tutorial focused on parallelizing simulation code to better leverage modern computing hardware, enabling risk analysts to better utilize simulation-based methods for quantifying uncertainty in practice. This article is aimed primarily at risk analysts who use simulation methods but do not yet utilize parallelization to decrease the computational burden of these models. The discussion is focused on conceptual aspects of embarrassingly parallel computer code and software considerations. Two complementary examples are shown using the languages MATLAB and R. A brief discussion of hardware considerations is located in the Appendix. © 2016 Society for Risk Analysis.

Comparative study of cross-field and field-aligned electron beams in active experiments. [in upper atmosphere

NASA Technical Reports Server (NTRS)

Winglee, R. M.; Pritchett, P. L.

1988-01-01

Beam-plasma interactions associated with the cross-field and field-aligned injection of electron beams from spacecraft were investigated using a two-dimensional (three velocity component) electrostatic particle simulations. It is shown that the beam properties and plasma response can be characterized well by the ratio between the stagnation time and the plasma response time, which depends on the ratio of the ambient plasma density to the beam density, the beam width, the beam energy, and the spacecraft length. It was found that the beams injected across the field lines tend to lose their coherence after about one or two gyrations due to space-charge oscillations induced by the beam, irrespective of the spacecraft charging. These oscillations scatter the beam electrons into a hollow cylinder of a radius equal to a beam electron gyroradius and thickness of the order of two beam Debye lengths. Parallel injected beams are subjected to similar oscillations, which cause the beam to expand to fill a solid cylinder of a comparable thickness.

Understanding of impurity poloidal distribution in the edge pedestal by modelling

NASA Astrophysics Data System (ADS)

Rozhansky, V.; Kaveeva, E.; Molchanov, P.; Veselova, I.; Voskoboynikov, S.; Coster, D.; Fable, E.; Puetterich, T.; Viezzer, E.; Kukushkin, A. S.; Kirk, A.; the ASDEX Upgrade Team

2015-07-01

Simulation of an H-mode ASDEX Upgrade shot with boron impurity was done with the B2SOLPS5.2 transport code. Simulation results were compared with the unique experimental data available for the chosen shot: radial density, electron and ion temperature profiles in the equatorial midplanes, radial electric field profile, radial profiles of the parallel velocity of impurities at the low-field side (LFS) and high-field side (HFS), radial density profiles of impurity ions at LHS and HFS. Simulation results reproduce all available experimental data simultaneously. In particular strong poloidal HFS-LFS asymmetry of B5+ ions was predicted in accordance with the experiment. The simulated HFS B5+ density inside the edge transport barrier is twice larger than that at LFS. This is consistent with the experimental observations where even larger impurity density asymmetry was observed. A similar effect was predicted in the simulation done for the MAST H-mode. Here the HFS density of He2+ is predicted to be 4 times larger than that at LHS. Such a large predicted asymmetry is connected with a larger ratio of HFS and LFS magnetic fields which is typical for spherical tokamaks. The HFS/LFS asymmetry was not measured in the experiment, however modelling qualitatively reproduces the observed change of sign of He+parallel velocity to the counter-current direction at LFS. The understanding of the asymmetry is based on neoclassical effects in plasma with strong gradients. It is demonstrated that simulation results obtained with account of sources of ionization, realistic geometry and turbulent transport are consistent with the simplified analytical approach. Difference from the standard neoclassical theory is emphasized.

Reversible Parallel Discrete-Event Execution of Large-scale Epidemic Outbreak Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perumalla, Kalyan S; Seal, Sudip K

2010-01-01

The spatial scale, runtime speed and behavioral detail of epidemic outbreak simulations together require the use of large-scale parallel processing. In this paper, an optimistic parallel discrete event execution of a reaction-diffusion simulation model of epidemic outbreaks is presented, with an implementation over themore » $$\\mu$$sik simulator. Rollback support is achieved with the development of a novel reversible model that combines reverse computation with a small amount of incremental state saving. Parallel speedup and other runtime performance metrics of the simulation are tested on a small (8,192-core) Blue Gene / P system, while scalability is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes (up to several hundred million individuals in the largest case) are exercised.« less

Sci-Thur PM: YIS - 07: Monte Carlo simulations to obtain several parameters required for electron beam dosimetry.

PubMed

Muir, B; Rogers, D; McEwen, M

2012-07-01

When current dosimetry protocols were written, electron beam data were limited and had uncertainties that were unacceptable for reference dosimetry. Protocols for high-energy reference dosimetry are currently being updated leading to considerable interest in accurate electron beam data. To this end, Monte Carlo simulations using the EGSnrc user-code egs_chamber are performed to extract relevant data for reference beam dosimetry. Calculations of the absorbed dose to water and the absorbed dose to the gas in realistic ion chamber models are performed as a function of depth in water for cobalt-60 and high-energy electron beams between 4 and 22 MeV. These calculations are used to extract several of the parameters required for electron beam dosimetry - the beam quality specifier, R 50 , beam quality conversion factors, k Q and k R50 , the electron quality conversion factor, k' R50 , the photon-electron conversion factor, k ecal , and ion chamber perturbation factors, P Q . The method used has the advantage that many important parameters can be extracted as a function of depth instead of determination at only the reference depth as has typically been done. Results obtained here are in good agreement with measured and other calculated results. The photon-electron conversion factors obtained for a Farmer-type NE2571 and plane-parallel PTW Roos, IBA NACP-02 and Exradin A11 chambers are 0.903, 0.896, 0.894 and 0.906, respectively. These typically differ by less than 0.7% from the contentious TG-51 values but have much smaller systematic uncertainties. These results are valuable for reference dosimetry of high-energy electron beams. © 2012 American Association of Physicists in Medicine.

Electron heating and acceleration during magnetic reconnection

NASA Astrophysics Data System (ADS)

Dahlin, Joel

2017-10-01

Magnetic reconnection is thought to be an important driver of energetic particles in a variety of astrophysical phenomena such as solar flares and magnetospheric storms. However, the observed fraction of energy imparted to a nonthermal component can vary widely in different regimes. We use kinetic particle-in-cell (PIC) simulations to demonstrate the important role of the non-reversing (guide) field in controlling the efficiency of electron acceleration in collisionless reconnection. In reconnection where the guide field is smaller than the reconnecting component, the dominant electron accelerator is a Fermi-type mechanism that preferentially energizes the most energetic particles. In strong guide field reconnection, the field-line contraction that drives the Fermi mechanism becomes weak. Instead, parallel electric fields are primarily responsible for driving electron heating but are ineffective in driving the energetic component of the spectrum. Three-dimensional simulations reveal that the stochastic magnetic field that develops during 3D guide field reconnection plays a vital role in particle acceleration and transport. The reconnection outflows that drive Fermi acceleration also expel accelerating particles from energization regions. In 2D reconnection, electrons are trapped in island cores and acceleration ceases, whereas in 3D the stochastic magnetic field enables energetic electrons to leak out of islands and freely sample regions of energy release. A finite guide field is required to break initial 2D symmetry and facilitate escape from island structures. We show that reconnection with a guide field comparable to the reconnecting field generates the greatest number of energetic electrons, a regime where both (a) the Fermi mechanism is an efficient driver and (b) energetic electrons may freely access acceleration sites. These results have important implications for electron acceleration in solar flares and reconnection-driven dissipation in turbulence.

Electron acceleration by inertial Alfven waves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thompson, B.J.; Lysak, R.L.

1996-03-01

Alfven waves reflected by the ionosphere and by inhomogeneities in the Alfven speed can develop an oscillating parallel electric field when electron inertial effects are included. These waves, which have wavelengths of the order of an Earth radius, can develop a coherent structure spanning distances of several Earth radii along geomagnetic field lines. This system has characteristic frequencies in the range of 1 Hz and can exhibit electric fields capable of accelerating electrons in several senses: via Landua resonance, bounce or transit time resonance as discussed by Andre and Eliasson or through the effective potential drop which appears when themore » transit time of the electrons is much smaller than the wave period, so that the electric fields appear effectively static. A time-dependent model of wave propagation is developed which represents inertial Alfven wave propagation along auroral field lines. The disturbance is modeled as it travels earthward, experiences partial reflections in regions of rapid variation, and finally reflects off a conducting ionosphere to continue propagating antiearthward. The wave experiences partial trapping by the ionospheric and the Alfven speed peaks discussed earlier by Polyakov and Rapoport and Trakhtengerts and Feldstein and later by Lysak. Results of the wave simulation and an accompanying test particle simulation are presented, which indicate that inertial Alfven waves are a possible mechanism for generating electron conic distributions and field-aligned particle precipitation. The model incorporates conservation of energy by allowing electrons to affect the wave via Landau damping, which appears to enhance the effect of the interactions which heat electron populations. 22 refs., 14 figs.« less

A surface code quantum computer in silicon.

PubMed

Hill, Charles D; Peretz, Eldad; Hile, Samuel J; House, Matthew G; Fuechsle, Martin; Rogge, Sven; Simmons, Michelle Y; Hollenberg, Lloyd C L

2015-10-01

The exceptionally long quantum coherence times of phosphorus donor nuclear spin qubits in silicon, coupled with the proven scalability of silicon-based nano-electronics, make them attractive candidates for large-scale quantum computing. However, the high threshold of topological quantum error correction can only be captured in a two-dimensional array of qubits operating synchronously and in parallel-posing formidable fabrication and control challenges. We present an architecture that addresses these problems through a novel shared-control paradigm that is particularly suited to the natural uniformity of the phosphorus donor nuclear spin qubit states and electronic confinement. The architecture comprises a two-dimensional lattice of donor qubits sandwiched between two vertically separated control layers forming a mutually perpendicular crisscross gate array. Shared-control lines facilitate loading/unloading of single electrons to specific donors, thereby activating multiple qubits in parallel across the array on which the required operations for surface code quantum error correction are carried out by global spin control. The complexities of independent qubit control, wave function engineering, and ad hoc quantum interconnects are explicitly avoided. With many of the basic elements of fabrication and control based on demonstrated techniques and with simulated quantum operation below the surface code error threshold, the architecture represents a new pathway for large-scale quantum information processing in silicon and potentially in other qubit systems where uniformity can be exploited.

Numerical simulation and analysis of electromagnetic-wave absorption of a plasma slab created by a direct-current discharge with gridded anode

NASA Astrophysics Data System (ADS)

Yuan, Chengxun; Tian, Ruihuan; Eliseev, S. I.; Bekasov, V. S.; Bogdanov, E. A.; Kudryavtsev, A. A.; Zhou, Zhongxiang

2018-03-01

In this paper, we present investigation of a direct-current discharge with a gridded anode from the point of view of using it as a means of creating plasma coating that could efficiently absorb incident electromagnetic (EM) waves. A single discharge cell consists of two parallel plates, one of which (anode) is gridded. Electrons emitted from the cathode surface are accelerated in the short interelectrode gap and are injected into the post-anode space, where they lose acquired energy on ionization and create plasma. Numerical simulations were used to investigate the discharge structure and obtain spatial distributions of plasma density in the post-anode space. The numerical model of the discharge was based on a simple hybrid approach which takes into account non-local ionization by fast electrons streaming from the cathode sheath. Specially formulated transparency boundary conditions allowed performing simulations in 1D. Simulations were carried out in air at pressures of 10 Torr and higher. Analysis of the discharge structure and discharge formation is presented. It is shown that using cathode materials with lower secondary emission coefficients can allow increasing the thickness of plasma slabs for the same discharge current, which can potentially enhance EM wave absorption. Spatial distributions of electron density obtained during simulations were used to calculate attenuation of an incident EM wave propagating perpendicularly to the plasma slab boundary. It is shown that plasma created by means of a DC discharge with a gridded anode can efficiently absorb EM waves in the low frequency range (6-40 GHz). Increasing gas pressure results in a broader range of wave frequencies (up to 500 GHz) where a considerable attenuation is observed.

On a nonlinear state of the electromagnetic ion/ion cyclotron instability

NASA Astrophysics Data System (ADS)

Cremer, M.; Scholer, M.

We have investigated the nonlinear properties of the electromagnetic ion/ion cyclotron instability (EMIIC) by means of hybrid simulations (macroparticle ions, massless electron fluid). The instability is driven by the relative (super-Alfvénic) streaming of two field-aligned ion beams in a low beta plasma (ion thermal pressure to magnetic field pressure) and may be of importance in the plasma sheet boundary layer. As shown in previously reported simulations the waves propagate obliquely to the magnetic field and heat the ions in the perpendicular direction as the relative beam velocity decreases. By running the simulation to large times it can be shown that the large temperature anisotropy leads to the ion cyclotron instability (IC) with parallel propagating Alfvén ion cyclotron waves. This is confirmed by numerically solving the electromagnetic dispersion relation. An application of this property to the plasma sheet boundary layer is discussed.

Three-dimensional particle-particle simulations: Dependence of relaxation time on plasma parameter

NASA Astrophysics Data System (ADS)

Zhao, Yinjian

2018-05-01

A particle-particle simulation model is applied to investigate the dependence of the relaxation time on the plasma parameter in a three-dimensional unmagnetized plasma. It is found that the relaxation time increases linearly as the plasma parameter increases within the range of the plasma parameter from 2 to 10; when the plasma parameter equals 2, the relaxation time is independent of the total number of particles, but when the plasma parameter equals 10, the relaxation time slightly increases as the total number of particles increases, which indicates the transition of a plasma from collisional to collisionless. In addition, ions with initial Maxwell-Boltzmann (MB) distribution are found to stay in the MB distribution during the whole simulation time, and the mass of ions does not significantly affect the relaxation time of electrons. This work also shows the feasibility of the particle-particle model when using GPU parallel computing techniques.

SOLAR WIND TURBULENCE FROM MHD TO SUB-ION SCALES: HIGH-RESOLUTION HYBRID SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Franci, Luca; Verdini, Andrea; Landi, Simone

2015-05-10

We present results from a high-resolution and large-scale hybrid (fluid electrons and particle-in-cell protons) two-dimensional numerical simulation of decaying turbulence. Two distinct spectral regions (separated by a smooth break at proton scales) develop with clear power-law scaling, each one occupying about a decade in wavenumbers. The simulation results simultaneously exhibit several properties of the observed solar wind fluctuations: spectral indices of the magnetic, kinetic, and residual energy spectra in the magnetohydrodynamic (MHD) inertial range along with a flattening of the electric field spectrum, an increase in magnetic compressibility, and a strong coupling of the cascade with the density and themore » parallel component of the magnetic fluctuations at sub-proton scales. Our findings support the interpretation that in the solar wind, large-scale MHD fluctuations naturally evolve beyond proton scales into a turbulent regime that is governed by the generalized Ohm’s law.« less

Analysis of photoelectron effect on the antenna impedance via Particle-In-Cell simulation

NASA Astrophysics Data System (ADS)

Miyake, Y.; Usui, H.

2008-08-01

We present photoelectron effects on the impedance of electric field antennas used for plasma wave investigations. To illustrate the photoelectron effects, we applied electromagnetic Particle-In-Cell simulation to the self-consistent antenna impedance analysis. We confirmed the formation of a dense photoelectron region around the sunlit surfaces of the antenna and the spacecraft. The dense photoelectrons enhance the real part, and decrease the absolute value of the imaginary part, of antenna impedance at low frequencies. We also showed that the antenna conductance can be analytically calculated from simulation results of the electron current flowing into or out of the antenna. The antenna impedance in the photoelectron environment is represented by a parallel equivalent circuit consisting of a capacitance and a resistance, which is consistent with empirical knowledge. The results also imply that the impedance varies with the spin of the spacecraft, which causes the variation of the photoelectron density around the antenna.

Solar Wind Turbulence from MHD to Sub-ion Scales: High-resolution Hybrid Simulations

NASA Astrophysics Data System (ADS)

Franci, Luca; Verdini, Andrea; Matteini, Lorenzo; Landi, Simone; Hellinger, Petr

2015-05-01

We present results from a high-resolution and large-scale hybrid (fluid electrons and particle-in-cell protons) two-dimensional numerical simulation of decaying turbulence. Two distinct spectral regions (separated by a smooth break at proton scales) develop with clear power-law scaling, each one occupying about a decade in wavenumbers. The simulation results simultaneously exhibit several properties of the observed solar wind fluctuations: spectral indices of the magnetic, kinetic, and residual energy spectra in the magnetohydrodynamic (MHD) inertial range along with a flattening of the electric field spectrum, an increase in magnetic compressibility, and a strong coupling of the cascade with the density and the parallel component of the magnetic fluctuations at sub-proton scales. Our findings support the interpretation that in the solar wind, large-scale MHD fluctuations naturally evolve beyond proton scales into a turbulent regime that is governed by the generalized Ohm’s law.

Feasibility of optically interconnected parallel processors using wavelength division multiplexing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deri, R.J.; De Groot, A.J.; Haigh, R.E.

1996-03-01

New national security demands require enhanced computing systems for nearly ab initio simulations of extremely complex systems and analyzing unprecedented quantities of remote sensing data. This computational performance is being sought using parallel processing systems, in which many less powerful processors are ganged together to achieve high aggregate performance. Such systems require increased capability to communicate information between individual processor and memory elements. As it is likely that the limited performance of today`s electronic interconnects will prevent the system from achieving its ultimate performance, there is great interest in using fiber optic technology to improve interconnect communication. However, little informationmore » is available to quantify the requirements on fiber optical hardware technology for this application. Furthermore, we have sought to explore interconnect architectures that use the complete communication richness of the optical domain rather than using optics as a simple replacement for electronic interconnects. These considerations have led us to study the performance of a moderate size parallel processor with optical interconnects using multiple optical wavelengths. We quantify the bandwidth, latency, and concurrency requirements which allow a bus-type interconnect to achieve scalable computing performance using up to 256 nodes, each operating at GFLOP performance. Our key conclusion is that scalable performance, to {approx}150 GFLOPS, is achievable for several scientific codes using an optical bus with a small number of WDM channels (8 to 32), only one WDM channel received per node, and achievable optoelectronic bandwidth and latency requirements. 21 refs. , 10 figs.« less

Parallel-Processing Test Bed For Simulation Software

NASA Technical Reports Server (NTRS)

Blech, Richard; Cole, Gary; Townsend, Scott

1996-01-01

Second-generation Hypercluster computing system is multiprocessor test bed for research on parallel algorithms for simulation in fluid dynamics, electromagnetics, chemistry, and other fields with large computational requirements but relatively low input/output requirements. Built from standard, off-shelf hardware readily upgraded as improved technology becomes available. System used for experiments with such parallel-processing concepts as message-passing algorithms, debugging software tools, and computational steering. First-generation Hypercluster system described in "Hypercluster Parallel Processor" (LEW-15283).

A parallel finite element simulator for ion transport through three-dimensional ion channel systems.

PubMed

Tu, Bin; Chen, Minxin; Xie, Yan; Zhang, Linbo; Eisenberg, Bob; Lu, Benzhuo

2013-09-15

A parallel finite element simulator, ichannel, is developed for ion transport through three-dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite element solver for a set of Poisson-Nernst-Planck (PNP) equations that describe the electrodiffusion process of ion transport, and a mesh generation tool chain for ion channel systems, which is an essential component for the finite element computations. The finite element method has advantages in modeling irregular geometries and complex boundary conditions. We have built a tool chain to get the surface and volume mesh for ion channel systems, which consists of a set of mesh generation tools. The adaptive finite element solver in our simulator is implemented using the parallel adaptive finite element package Parallel Hierarchical Grid (PHG) developed by one of the authors, which provides the capability of doing large scale parallel computations with high parallel efficiency and the flexibility of choosing high order elements to achieve high order accuracy. The simulator is applied to a real transmembrane protein, the gramicidin A (gA) channel protein, to calculate the electrostatic potential, ion concentrations and I - V curve, with which both primitive and transformed PNP equations are studied and their numerical performances are compared. To further validate the method, we also apply the simulator to two other ion channel systems, the voltage dependent anion channel (VDAC) and α-Hemolysin (α-HL). The simulation results agree well with Brownian dynamics (BD) simulation results and experimental results. Moreover, because ionic finite size effects can be included in PNP model now, we also perform simulations using a size-modified PNP (SMPNP) model on VDAC and α-HL. It is shown that the size effects in SMPNP can effectively lead to reduced current in the channel, and the results are closer to BD simulation results. Copyright © 2013 Wiley Periodicals, Inc.

3-DIMENSIONAL Optoelectronic

NASA Astrophysics Data System (ADS)

Krishnamoorthy, Ashok Venketaraman

This thesis covers the design, analysis, optimization, and implementation of optoelectronic (N,M,F) networks. (N,M,F) networks are generic space-division networks that are well suited to implementation using optoelectronic integrated circuits and free-space optical interconnects. An (N,M,F) networks consists of N input channels each having a fanout F_{rm o}, M output channels each having a fanin F_{rm i}, and Log_{rm K}(N/F) stages of K x K switches. The functionality of the fanout, switching, and fanin stages depends on the specific application. Three applications of optoelectronic (N,M,F) networks are considered. The first is an optoelectronic (N,1,1) content -addressable memory system that achieves associative recall on two-dimensional images retrieved from a parallel-access optical memory. The design and simulation of the associative memory are discussed, and an experimental emulation of a prototype system using images from a parallel-readout optical disk is presented. The system design provides superior performance to existing electronic content-addressable memory chips in terms of capacity and search rate, and uses readily available optical disk and VLSI technologies. Next, a scalable optoelectronic (N,M,F) neural network that uses free-space holographic optical interconnects is presented. The neural architecture minimizes the number of optical transmitters needed, and provides accurate electronic fanin with low signal skew, and dendritic-type fan-in processing capability in a compact layout. Optimal data-encoding methods and circuit techniques are discussed. The implementation of an prototype optoelectronic neural system, and its application to a simple recognition task is demonstrated. Finally, the design, analysis, and optimization of a (N,N,F) self-routing, packet-switched multistage interconnection network is described. The network is suitable for parallel computing and broadband switching applications. The tradeoff between optical and electronic interconnects is examined quantitatively by varying the electronic switch size K. The performance of the (N,N,F) network versus the fanning parameter F, is also analyzed. It is shown that the optoelectronic (N,N,F) networks provide a range of performance-cost alternatives, and offer superior performance-per-cost to fully electronic switching networks and to previous networks designs.

Applications of New Surrogate Global Optimization Algorithms including Efficient Synchronous and Asynchronous Parallelism for Calibration of Expensive Nonlinear Geophysical Simulation Models.

NASA Astrophysics Data System (ADS)

Shoemaker, C. A.; Pang, M.; Akhtar, T.; Bindel, D.

2016-12-01

New parallel surrogate global optimization algorithms are developed and applied to objective functions that are expensive simulations (possibly with multiple local minima). The algorithms can be applied to most geophysical simulations, including those with nonlinear partial differential equations. The optimization does not require simulations be parallelized. Asynchronous (and synchronous) parallel execution is available in the optimization toolbox "pySOT". The parallel algorithms are modified from serial to eliminate fine grained parallelism. The optimization is computed with open source software pySOT, a Surrogate Global Optimization Toolbox that allows user to pick the type of surrogate (or ensembles), the search procedure on surrogate, and the type of parallelism (synchronous or asynchronous). pySOT also allows the user to develop new algorithms by modifying parts of the code. In the applications here, the objective function takes up to 30 minutes for one simulation, and serial optimization can take over 200 hours. Results from Yellowstone (NSF) and NCSS (Singapore) supercomputers are given for groundwater contaminant hydrology simulations with applications to model parameter estimation and decontamination management. All results are compared with alternatives. The first results are for optimization of pumping at many wells to reduce cost for decontamination of groundwater at a superfund site. The optimization runs with up to 128 processors. Superlinear speed up is obtained for up to 16 processors, and efficiency with 64 processors is over 80%. Each evaluation of the objective function requires the solution of nonlinear partial differential equations to describe the impact of spatially distributed pumping and model parameters on model predictions for the spatial and temporal distribution of groundwater contaminants. The second application uses an asynchronous parallel global optimization for groundwater quality model calibration. The time for a single objective function evaluation varies unpredictably, so efficiency is improved with asynchronous parallel calculations to improve load balancing. The third application (done at NCSS) incorporates new global surrogate multi-objective parallel search algorithms into pySOT and applies it to a large watershed calibration problem.

Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

DTIC Science & Technology

2012-10-01

using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

Look-ahead Dynamic Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-10-20

Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.

Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Candel, A.; Kabel, A.; Lee, L.

Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

Laser-induced extreme magnetic field in nanorod targets

NASA Astrophysics Data System (ADS)

Lécz, Zsolt; Andreev, Alexander

2018-03-01

The application of nano-structured target surfaces in laser-solid interaction has attracted significant attention in the last few years. Their ability to absorb significantly more laser energy promises a possible route for advancing the currently established laser ion acceleration concepts. However, it is crucial to have a better understanding of field evolution and electron dynamics during laser-matter interactions before the employment of such exotic targets. This paper focuses on the magnetic field generation in nano-forest targets consisting of parallel nanorods grown on plane surfaces. A general scaling law for the self-generated quasi-static magnetic field amplitude is given and it is shown that amplitudes up to 1 MT field are achievable with current technology. Analytical results are supported by three-dimensional particle-in-cell simulations. Non-parallel arrangements of nanorods has also been considered which result in the generation of donut-shaped azimuthal magnetic fields in a larger volume.

Laser-driven collimated tens-GeV monoenergetic protons from mass-limited target plus preformed channel

NASA Astrophysics Data System (ADS)

Zheng, F. L.; Wu, S. Z.; Wu, H. C.; Zhou, C. T.; Cai, H. B.; Yu, M. Y.; Tajima, T.; Yan, X. Q.; He, X. T.

2013-01-01

Proton acceleration by ultra-intense laser pulse irradiating a target with cross-section smaller than the laser spot size and connected to a parabolic density channel is investigated. The target splits the laser into two parallel propagating parts, which snowplow the back-side plasma electrons along their paths, creating two adjacent parallel wakes and an intense return current in the gap between them. The radiation-pressure pre-accelerated target protons trapped in the wake fields now undergo acceleration as well as collimation by the quasistatic wake electrostatic and magnetic fields. Particle-in-cell simulations show that stable long-distance acceleration can be realized, and a 30 fs monoenergetic ion beam of >10 GeV peak energy and <2° divergence can be produced by a circularly polarized laser pulse at an intensity of about 1022 W/cm2.

Every factor helps: Rapid Ptychographic Reconstruction

NASA Astrophysics Data System (ADS)

Nashed, Youssef

2015-03-01

Recent advances in microscopy, specifically higher spatial resolution and data acquisition rates, require faster and more robust phase retrieval reconstruction methods. Ptychography is a phase retrieval technique for reconstructing the complex transmission function of a specimen from a sequence of diffraction patterns in visible light, X-ray, and electron microscopes. As technical advances allow larger fields to be imaged, computational challenges arise for reconstructing the correspondingly larger data volumes. Waiting to postprocess datasets offline results in missed opportunities. Here we present a parallel method for real-time ptychographic phase retrieval. It uses a hybrid parallel strategy to divide the computation between multiple graphics processing units (GPUs). A final specimen reconstruction is then achieved by different techniques to merge sub-dataset results into a single complex phase and amplitude image. Results are shown on a simulated specimen and real datasets from X-ray experiments conducted at a synchrotron light source.

Radiation from Accelerated Particles in Shocks and Reconnections

NASA Technical Reports Server (NTRS)

Nishikawa, K.-I.; Zhang, B.; Niemiec, J.; Medvedev, M.; Hardee, P.; Mizuno, Y.; Nordlund, A.; Frederiksen, J. T.; Sol, H.; Pohl, M.;

Electron acceleration by magnetic islands in a dynamically evolved coronal current sheet

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Shaohua, E-mail: shzhang@mail.iggcas.ac.cn; Wang, Bin; Meng, Lifei

2016-03-25

This work simulated the electron acceleration by magnetic islands in a drastically evolved solar coronal current sheet via the combined 2.5-dimensional (2.5D) resistive Magnetohydrodynamics (MHD) and guiding-center approximation test-particle methods. With high magnetic Reynolds number of 105, the long–thin current sheet is evolved into a chain of magnetic islands, growing in size and coalescing with each other, due to tearing instability. The acceleration of electrons is studied in one typical phase when several large magnetic islands are formed. The results show that the electrons with an initial Maxwell distribution evolve into a heavy-tailed distribution and more than 20% of themore » electrons can be accelerated higher than 200 keV within 0.1 second and some of them can even be energized up to MeV ranges. The most energetic electrons have a tendency to be around the outer regions of the magnetic islands or to be located in the small secondary magnetic islands. We find that the acceleration and spatial distributions of the energetic electrons is caused by the trapping effect of the magnetic islands and the distributions of the parallel electric field E{sub p}.« less

Real-world hydrologic assessment of a fully-distributed hydrological model in a parallel computing environment

NASA Astrophysics Data System (ADS)

Vivoni, Enrique R.; Mascaro, Giuseppe; Mniszewski, Susan; Fasel, Patricia; Springer, Everett P.; Ivanov, Valeriy Y.; Bras, Rafael L.

2011-10-01

SummaryA major challenge in the use of fully-distributed hydrologic models has been the lack of computational capabilities for high-resolution, long-term simulations in large river basins. In this study, we present the parallel model implementation and real-world hydrologic assessment of the Triangulated Irregular Network (TIN)-based Real-time Integrated Basin Simulator (tRIBS). Our parallelization approach is based on the decomposition of a complex watershed using the channel network as a directed graph. The resulting sub-basin partitioning divides effort among processors and handles hydrologic exchanges across boundaries. Through numerical experiments in a set of nested basins, we quantify parallel performance relative to serial runs for a range of processors, simulation complexities and lengths, and sub-basin partitioning methods, while accounting for inter-run variability on a parallel computing system. In contrast to serial simulations, the parallel model speed-up depends on the variability of hydrologic processes. Load balancing significantly improves parallel speed-up with proportionally faster runs as simulation complexity (domain resolution and channel network extent) increases. The best strategy for large river basins is to combine a balanced partitioning with an extended channel network, with potential savings through a lower TIN resolution. Based on these advances, a wider range of applications for fully-distributed hydrologic models are now possible. This is illustrated through a set of ensemble forecasts that account for precipitation uncertainty derived from a statistical downscaling model.

Total fluid pressure imbalance in the scrape-off layer of tokamak plasmas

DOE PAGES

Churchill, Randy M.; Canik, John M.; Chang, C. S.; ...

2017-03-10

Simulations using the fully kinetic neoclassical code XGCa (X-point included guiding-center axisymmetric) were undertaken to explore the impact of kinetic effects on scrape-off layer (SOL) physics in DIII-D H-mode plasmas. XGCa is a total-f, gyrokinetic code which self-consistently calculates the axisymmetric electrostatic potential and plasma dynamics, and includes modules for Monte Carlo neutral transport. Previously presented XGCa results showed several noteworthy features, including large variations of ion density and pressure along field lines in the SOL, experimentally relevant levels of SOL parallel ion flow (Mach number similar to 0.5), skewed ion distributions near the sheath entrance leading to subsonic flowmore » there, and elevated sheath potentials (Churchill 2016 Nucl. Mater. Energy 1-6). In this paper, we explore in detail the question of pressure balance in the SOL, as it was observed in the simulation that there was a large deviation from a simple total pressure balance (the sum of ion and electron static pressure plus ion inertia). It will be shown that both the contributions from the ion viscosity (driven by ion temperature anisotropy) and neutral source terms can be substantial, and should be retained in the parallel momentum equation in the SOL, but still falls short of accounting for the observed fluid pressure imbalance in the XGCa simulation results.« less

Satisfiability Test with Synchronous Simulated Annealing on the Fujitsu AP1000 Massively-Parallel Multiprocessor

NASA Technical Reports Server (NTRS)

Sohn, Andrew; Biswas, Rupak

1996-01-01

Solving the hard Satisfiability Problem is time consuming even for modest-sized problem instances. Solving the Random L-SAT Problem is especially difficult due to the ratio of clauses to variables. This report presents a parallel synchronous simulated annealing method for solving the Random L-SAT Problem on a large-scale distributed-memory multiprocessor. In particular, we use a parallel synchronous simulated annealing procedure, called Generalized Speculative Computation, which guarantees the same decision sequence as sequential simulated annealing. To demonstrate the performance of the parallel method, we have selected problem instances varying in size from 100-variables/425-clauses to 5000-variables/21,250-clauses. Experimental results on the AP1000 multiprocessor indicate that our approach can satisfy 99.9 percent of the clauses while giving almost a 70-fold speedup on 500 processors.

Efficient parallelization of analytic bond-order potentials for large-scale atomistic simulations

NASA Astrophysics Data System (ADS)

Teijeiro, C.; Hammerschmidt, T.; Drautz, R.; Sutmann, G.

2016-07-01

Analytic bond-order potentials (BOPs) provide a way to compute atomistic properties with controllable accuracy. For large-scale computations of heterogeneous compounds at the atomistic level, both the computational efficiency and memory demand of BOP implementations have to be optimized. Since the evaluation of BOPs is a local operation within a finite environment, the parallelization concepts known from short-range interacting particle simulations can be applied to improve the performance of these simulations. In this work, several efficient parallelization methods for BOPs that use three-dimensional domain decomposition schemes are described. The schemes are implemented into the bond-order potential code BOPfox, and their performance is measured in a series of benchmarks. Systems of up to several millions of atoms are simulated on a high performance computing system, and parallel scaling is demonstrated for up to thousands of processors.

Parallel simulation of tsunami inundation on a large-scale supercomputer

NASA Astrophysics Data System (ADS)

Oishi, Y.; Imamura, F.; Sugawara, D.

2013-12-01

An accurate prediction of tsunami inundation is important for disaster mitigation purposes. One approach is to approximate the tsunami wave source through an instant inversion analysis using real-time observation data (e.g., Tsushima et al., 2009) and then use the resulting wave source data in an instant tsunami inundation simulation. However, a bottleneck of this approach is the large computational cost of the non-linear inundation simulation and the computational power of recent massively parallel supercomputers is helpful to enable faster than real-time execution of a tsunami inundation simulation. Parallel computers have become approximately 1000 times faster in 10 years (www.top500.org), and so it is expected that very fast parallel computers will be more and more prevalent in the near future. Therefore, it is important to investigate how to efficiently conduct a tsunami simulation on parallel computers. In this study, we are targeting very fast tsunami inundation simulations on the K computer, currently the fastest Japanese supercomputer, which has a theoretical peak performance of 11.2 PFLOPS. One computing node of the K computer consists of 1 CPU with 8 cores that share memory, and the nodes are connected through a high-performance torus-mesh network. The K computer is designed for distributed-memory parallel computation, so we have developed a parallel tsunami model. Our model is based on TUNAMI-N2 model of Tohoku University, which is based on a leap-frog finite difference method. A grid nesting scheme is employed to apply high-resolution grids only at the coastal regions. To balance the computation load of each CPU in the parallelization, CPUs are first allocated to each nested layer in proportion to the number of grid points of the nested layer. Using CPUs allocated to each layer, 1-D domain decomposition is performed on each layer. In the parallel computation, three types of communication are necessary: (1) communication to adjacent neighbours for the finite difference calculation, (2) communication between adjacent layers for the calculations to connect each layer, and (3) global communication to obtain the time step which satisfies the CFL condition in the whole domain. A preliminary test on the K computer showed the parallel efficiency on 1024 cores was 57% relative to 64 cores. We estimate that the parallel efficiency will be considerably improved by applying a 2-D domain decomposition instead of the present 1-D domain decomposition in future work. The present parallel tsunami model was applied to the 2011 Great Tohoku tsunami. The coarsest resolution layer covers a 758 km × 1155 km region with a 405 m grid spacing. A nesting of five layers was used with the resolution ratio of 1/3 between nested layers. The finest resolution region has 5 m resolution and covers most of the coastal region of Sendai city. To complete 2 hours of simulation time, the serial (non-parallel) computation took approximately 4 days on a workstation. To complete the same simulation on 1024 cores of the K computer, it took 45 minutes which is more than two times faster than real-time. This presentation discusses the updated parallel computational performance and the efficient use of the K computer when considering the characteristics of the tsunami inundation simulation model in relation to the characteristics and capabilities of the K computer.

Off-equatorial current-driven instabilities ahead of approaching dipolarization fronts

NASA Astrophysics Data System (ADS)

Zhang, Xu; Angelopoulos, V.; Pritchett, P. L.; Liu, Jiang

2017-05-01

Recent kinetic simulations have revealed that electromagnetic instabilities near the ion gyrofrequency and slightly away from the equatorial plane can be driven by a current parallel to the magnetic field prior to the arrival of dipolarization fronts. Such instabilities are important because of their potential contribution to global electromagnetic energy conversion near dipolarization fronts. Of the several instabilities that may be consistent with such waves, the most notable are the current-driven electromagnetic ion cyclotron instability and the current-driven kink-like instability. To confirm the existence and characteristics of these instabilities, we used observations by two Time History of Events and Macroscale Interactions during Substorms satellites, one near the neutral sheet observing dipolarization fronts and the other at the boundary layer observing precursor waves and currents. We found that such instabilities with monochromatic signatures are rare, but one of the few cases was selected for further study. Two different instabilities, one at about 0.3 Hz and the other at a much lower frequency, 0.02 Hz, were seen in the data from the off-equatorial spacecraft. A parallel current attributed to an electron beam coexisted with the waves. Our instability analysis attributes the higher-frequency instability to a current-driven ion cyclotron instability and the lower frequency instability to a kink-like instability. The current-driven kink-like instability we observed is consistent with the instabilities observed in the simulation. We suggest that the currents needed to excite these low-frequency instabilities are so intense that the associated electron beams are easily thermalized and hence difficult to observe.

Methodology of modeling and measuring computer architectures for plasma simulations

NASA Technical Reports Server (NTRS)

Wang, L. P. T.

1977-01-01

A brief introduction to plasma simulation using computers and the difficulties on currently available computers is given. Through the use of an analyzing and measuring methodology - SARA, the control flow and data flow of a particle simulation model REM2-1/2D are exemplified. After recursive refinements the total execution time may be greatly shortened and a fully parallel data flow can be obtained. From this data flow, a matched computer architecture or organization could be configured to achieve the computation bound of an application problem. A sequential type simulation model, an array/pipeline type simulation model, and a fully parallel simulation model of a code REM2-1/2D are proposed and analyzed. This methodology can be applied to other application problems which have implicitly parallel nature.

Massively parallel quantum computer simulator

NASA Astrophysics Data System (ADS)

De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

2007-01-01

We describe portable software to simulate universal quantum computers on massive parallel computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray X1E, a SGI Altix 3700 and clusters of PCs running Windows XP. We study the performance of the software by simulating quantum computers containing up to 36 qubits, using up to 4096 processors and up to 1 TB of memory. Our results demonstrate that the simulator exhibits nearly ideal scaling as a function of the number of processors and suggest that the simulation software described in this paper may also serve as benchmark for testing high-end parallel computers.

PENTACLE: Parallelized particle-particle particle-tree code for planet formation

NASA Astrophysics Data System (ADS)

Iwasawa, Masaki; Oshino, Shoichi; Fujii, Michiko S.; Hori, Yasunori

2017-10-01

We have newly developed a parallelized particle-particle particle-tree code for planet formation, PENTACLE, which is a parallelized hybrid N-body integrator executed on a CPU-based (super)computer. PENTACLE uses a fourth-order Hermite algorithm to calculate gravitational interactions between particles within a cut-off radius and a Barnes-Hut tree method for gravity from particles beyond. It also implements an open-source library designed for full automatic parallelization of particle simulations, FDPS (Framework for Developing Particle Simulator), to parallelize a Barnes-Hut tree algorithm for a memory-distributed supercomputer. These allow us to handle 1-10 million particles in a high-resolution N-body simulation on CPU clusters for collisional dynamics, including physical collisions in a planetesimal disc. In this paper, we show the performance and the accuracy of PENTACLE in terms of \\tilde{R}_cut and a time-step Δt. It turns out that the accuracy of a hybrid N-body simulation is controlled through Δ t / \\tilde{R}_cut and Δ t / \\tilde{R}_cut ˜ 0.1 is necessary to simulate accurately the accretion process of a planet for ≥106 yr. For all those interested in large-scale particle simulations, PENTACLE, customized for planet formation, will be freely available from https://github.com/PENTACLE-Team/PENTACLE under the MIT licence.

Numerical characteristics of quantum computer simulation

NASA Astrophysics Data System (ADS)

Chernyavskiy, A.; Khamitov, K.; Teplov, A.; Voevodin, V.; Voevodin, Vl.

2016-12-01

The simulation of quantum circuits is significantly important for the implementation of quantum information technologies. The main difficulty of such modeling is the exponential growth of dimensionality, thus the usage of modern high-performance parallel computations is relevant. As it is well known, arbitrary quantum computation in circuit model can be done by only single- and two-qubit gates, and we analyze the computational structure and properties of the simulation of such gates. We investigate the fact that the unique properties of quantum nature lead to the computational properties of the considered algorithms: the quantum parallelism make the simulation of quantum gates highly parallel, and on the other hand, quantum entanglement leads to the problem of computational locality during simulation. We use the methodology of the AlgoWiki project (algowiki-project.org) to analyze the algorithm. This methodology consists of theoretical (sequential and parallel complexity, macro structure, and visual informational graph) and experimental (locality and memory access, scalability and more specific dynamic characteristics) parts. Experimental part was made by using the petascale Lomonosov supercomputer (Moscow State University, Russia). We show that the simulation of quantum gates is a good base for the research and testing of the development methods for data intense parallel software, and considered methodology of the analysis can be successfully used for the improvement of the algorithms in quantum information science.

Visualization and Tracking of Parallel CFD Simulations

NASA Technical Reports Server (NTRS)

Vaziri, Arsi; Kremenetsky, Mark

1995-01-01

We describe a system for interactive visualization and tracking of a 3-D unsteady computational fluid dynamics (CFD) simulation on a parallel computer. CM/AVS, a distributed, parallel implementation of a visualization environment (AVS) runs on the CM-5 parallel supercomputer. A CFD solver is run as a CM/AVS module on the CM-5. Data communication between the solver, other parallel visualization modules, and a graphics workstation, which is running AVS, are handled by CM/AVS. Partitioning of the visualization task, between CM-5 and the workstation, can be done interactively in the visual programming environment provided by AVS. Flow solver parameters can also be altered by programmable interactive widgets. This system partially removes the requirement of storing large solution files at frequent time steps, a characteristic of the traditional 'simulate (yields) store (yields) visualize' post-processing approach.

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

PubMed

Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

2014-06-14

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

Anisotropic electron temperature measurements without knowing the spectral transmissivity for a JT-60SA Thomson scattering diagnostic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tojo, H.; Hatae, T.; Yatsuka, E.

2012-10-15

This paper focuses on a method for measuring the electron temperature (T{sub e}) without knowing the transmissivity using Thomson scattering diagnostic with a double-pass scattering system. Application of this method for measuring the anisotropic T{sub e}, i.e., the T{sub e} in the directions parallel (T{sub e Double-Vertical-Line Double-Vertical-Line }) and perpendicular (T{sub e Up-Tack }) to the magnetic field, is proposed. Simulations based on the designed parameters for a JT-60SA indicate the feasibility of the measurements except in certain T{sub e} ranges, e.g., T{sub e Double-Vertical-Line Double-Vertical-Line }{approx} 3.5T{sub e Up-Tack} at 120 Degree-Sign of the scattering angle.

Design of object-oriented distributed simulation classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D. (Principal Investigator)

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package is being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for 'Numerical Propulsion Simulation System'. NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT 'Actor' model of a concurrent object and uses 'connectors' to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Design of Object-Oriented Distributed Simulation Classes

NASA Technical Reports Server (NTRS)

Schoeffler, James D.

1995-01-01

Distributed simulation of aircraft engines as part of a computer aided design package being developed by NASA Lewis Research Center for the aircraft industry. The project is called NPSS, an acronym for "Numerical Propulsion Simulation System". NPSS is a flexible object-oriented simulation of aircraft engines requiring high computing speed. It is desirable to run the simulation on a distributed computer system with multiple processors executing portions of the simulation in parallel. The purpose of this research was to investigate object-oriented structures such that individual objects could be distributed. The set of classes used in the simulation must be designed to facilitate parallel computation. Since the portions of the simulation carried out in parallel are not independent of one another, there is the need for communication among the parallel executing processors which in turn implies need for their synchronization. Communication and synchronization can lead to decreased throughput as parallel processors wait for data or synchronization signals from other processors. As a result of this research, the following have been accomplished. The design and implementation of a set of simulation classes which result in a distributed simulation control program have been completed. The design is based upon MIT "Actor" model of a concurrent object and uses "connectors" to structure dynamic connections between simulation components. Connectors may be dynamically created according to the distribution of objects among machines at execution time without any programming changes. Measurements of the basic performance have been carried out with the result that communication overhead of the distributed design is swamped by the computation time of modules unless modules have very short execution times per iteration or time step. An analytical performance model based upon queuing network theory has been designed and implemented. Its application to realistic configurations has not been carried out.

Partitioning and packing mathematical simulation models for calculation on parallel computers

NASA Technical Reports Server (NTRS)

Arpasi, D. J.; Milner, E. J.

1986-01-01

The development of multiprocessor simulations from a serial set of ordinary differential equations describing a physical system is described. Degrees of parallelism (i.e., coupling between the equations) and their impact on parallel processing are discussed. The problem of identifying computational parallelism within sets of closely coupled equations that require the exchange of current values of variables is described. A technique is presented for identifying this parallelism and for partitioning the equations for parallel solution on a multiprocessor. An algorithm which packs the equations into a minimum number of processors is also described. The results of the packing algorithm when applied to a turbojet engine model are presented in terms of processor utilization.

Vectorization for Molecular Dynamics on Intel Xeon Phi Corpocessors

NASA Astrophysics Data System (ADS)

Yi, Hongsuk

2014-03-01

Many modern processors are capable of exploiting data-level parallelism through the use of single instruction multiple data (SIMD) execution. The new Intel Xeon Phi coprocessor supports 512 bit vector registers for the high performance computing. In this paper, we have developed a hierarchical parallelization scheme for accelerated molecular dynamics simulations with the Terfoff potentials for covalent bond solid crystals on Intel Xeon Phi coprocessor systems. The scheme exploits multi-level parallelism computing. We combine thread-level parallelism using a tightly coupled thread-level and task-level parallelism with 512-bit vector register. The simulation results show that the parallel performance of SIMD implementations on Xeon Phi is apparently superior to their x86 CPU architecture.

SU-F-J-146: Experimental Validation of 6 MV Photon PDD in Parallel Magnetic Field Calculated by EGSnrc

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghila, A; Steciw, S; Fallone, B

Purpose: Integrated linac-MR systems are uniquely suited for real time tumor tracking during radiation treatment. Understanding the magnetic field dose effects and incorporating them in treatment planning is paramount for linac-MR clinical implementation. We experimentally validated the EGSnrc dose calculations in the presence of a magnetic field parallel to the radiation beam travel. Methods: Two cylindrical bore electromagnets produced a 0.21 T magnetic field parallel to the central axis of a 6 MV photon beam. A parallel plate ion chamber was used to measure the PDD in a polystyrene phantom, placed inside the bore in two setups: phantom top surfacemore » coinciding with the magnet bore center (183 cm SSD), and with the magnet bore’s top surface (170 cm SSD). We measured the field of the magnet at several points and included the exact dimensions of the coils to generate a 3D magnetic field map in a finite element model. BEAMnrc and DOSXYZnrc simulated the PDD experiments in parallel magnetic field (i.e. 3D magnetic field included) and with no magnetic field. Results: With the phantom surface at the top of the electromagnet, the surface dose increased by 10% (compared to no-magnetic field), due to electrons being focused by the smaller fringe fields of the electromagnet. With the phantom surface at the bore center, the surface dose increased by 30% since extra 13 cm of air column was in relatively higher magnetic field (>0.13T) in the magnet bore. EGSnrc Monte Carlo code correctly calculated the radiation dose with and without the magnetic field, and all points passed the 2%, 2 mm Gamma criterion when the ion chamber’s entrance window and air cavity were included in the simulated phantom. Conclusion: A parallel magnetic field increases the surface and buildup dose during irradiation. The EGSnrc package can model these magnetic field dose effects accurately. Dr. Fallone is a co-founder and CEO of MagnetTx Oncology Solutions (under discussions to license Alberta bi-planar linac MR for commercialization).« less

Acceleration of Radiance for Lighting Simulation by Using Parallel Computing with OpenCL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuo, Wangda; McNeil, Andrew; Wetter, Michael

2011-09-06

We report on the acceleration of annual daylighting simulations for fenestration systems in the Radiance ray-tracing program. The algorithm was optimized to reduce both the redundant data input/output operations and the floating-point operations. To further accelerate the simulation speed, the calculation for matrix multiplications was implemented using parallel computing on a graphics processing unit. We used OpenCL, which is a cross-platform parallel programming language. Numerical experiments show that the combination of the above measures can speed up the annual daylighting simulations 101.7 times or 28.6 times when the sky vector has 146 or 2306 elements, respectively.

Streaming parallel GPU acceleration of large-scale filter-based spiking neural networks.

PubMed

Slażyński, Leszek; Bohte, Sander

2012-01-01

The arrival of graphics processing (GPU) cards suitable for massively parallel computing promises affordable large-scale neural network simulation previously only available at supercomputing facilities. While the raw numbers suggest that GPUs may outperform CPUs by at least an order of magnitude, the challenge is to develop fine-grained parallel algorithms to fully exploit the particulars of GPUs. Computation in a neural network is inherently parallel and thus a natural match for GPU architectures: given inputs, the internal state for each neuron can be updated in parallel. We show that for filter-based spiking neurons, like the Spike Response Model, the additive nature of membrane potential dynamics enables additional update parallelism. This also reduces the accumulation of numerical errors when using single precision computation, the native precision of GPUs. We further show that optimizing simulation algorithms and data structures to the GPU's architecture has a large pay-off: for example, matching iterative neural updating to the memory architecture of the GPU speeds up this simulation step by a factor of three to five. With such optimizations, we can simulate in better-than-realtime plausible spiking neural networks of up to 50 000 neurons, processing over 35 million spiking events per second.

Cyclotron Acceleration of Relativistic Electrons through Landau Resonance with Obliquely Propagating Whistler Mode Chorus Emissions

NASA Astrophysics Data System (ADS)

Omura, Y.; Hsieh, Y. K.; Foster, J. C.; Erickson, P. J.; Kletzing, C.; Baker, D. N.

2017-12-01

A recent test particle simulation of obliquely propagating whistler mode wave-particle interaction [Hsieh and Omura, 2017] shows that the perpendicular wave electric field can play a significant role in trapping and accelerating relativistic electrons through Landau resonance. A further theoretical and numerical investigation verifies that there occurs nonlinear wave trapping of relativistic electrons by the nonlinear Lorentz force of the perpendicular wave magnetic field. An electron moving with a parallel velocity equal to the parallel phase velocity of an obliquely propagating wave basically see a stationary wave phase. Since the electron position is displaced from its gyrocenter by a distance ρ*sin(φ), where ρ is the gyroradius and φ is the gyrophase, the wave phase is modulated with the gyromotion, and the stationary wave fields as seen by the electron are expanded as series of Bessel functions Jn with phase variations n*φ. The J1 components of the wave electric and magnetic fields rotate in the right-hand direction with the gyrofrequency, and they can be in resonance with the electron undergoing the gyromotion, resulting in effective electron acceleration and pitch angle scattering. We have performed a subpacket analysis of chorus waveforms observed by the Van Allen Probes [Foster et al., 2017], and calculated the energy gain by the cyclotron acceleration through Landau resonance. We compare the efficiencies of accelerations by cyclotron and Landau resonances in typical events of rapid electron acceleration observed by the Van Allen Probes.References:[1] Hsieh, Y.-K., and Y. Omura (2017), Nonlinear dynamics of electrons interacting with oblique whistler mode chorus in the magnetosphere, J. Geophys. Res. Space Physics, 122, 675-694, doi:10.1002/2016JA023255.[2] Foster, J. C., P. J. Erickson, Y. Omura, D. N. Baker, C. A. Kletzing, and S. G. Claudepierre (2017), Van Allen Probes observations of prompt MeV radiation belt electron acceleration in nonlinear interactions with VLF chorus, J. Geophys. Res. Space Physics, 122, 324-339, doi:10.1002/2016JA023429.

A parallel Monte Carlo code for planar and SPECT imaging: implementation, verification and applications in (131)I SPECT.

PubMed

Dewaraja, Yuni K; Ljungberg, Michael; Majumdar, Amitava; Bose, Abhijit; Koral, Kenneth F

2002-02-01

This paper reports the implementation of the SIMIND Monte Carlo code on an IBM SP2 distributed memory parallel computer. Basic aspects of running Monte Carlo particle transport calculations on parallel architectures are described. Our parallelization is based on equally partitioning photons among the processors and uses the Message Passing Interface (MPI) library for interprocessor communication and the Scalable Parallel Random Number Generator (SPRNG) to generate uncorrelated random number streams. These parallelization techniques are also applicable to other distributed memory architectures. A linear increase in computing speed with the number of processors is demonstrated for up to 32 processors. This speed-up is especially significant in Single Photon Emission Computed Tomography (SPECT) simulations involving higher energy photon emitters, where explicit modeling of the phantom and collimator is required. For (131)I, the accuracy of the parallel code is demonstrated by comparing simulated and experimental SPECT images from a heart/thorax phantom. Clinically realistic SPECT simulations using the voxel-man phantom are carried out to assess scatter and attenuation correction.

Numerical simulation of current-free double layers created in a helicon plasma device

NASA Astrophysics Data System (ADS)

Rao, Sathyanarayan; Singh, Nagendra

2012-09-01

Two-dimensional simulations reveal that when radially confined source plasma with magnetized electrons and unmagnetized ions expands into diverging magnetic field B, a current-free double layer (CFDL) embedded in a conical density structure forms, as experimentally measured in the Australian helicon plasma device (HPD). The magnetized electrons follow the diverging B while the unmagnetized ions tend to flow directly downstream of the source, resulting in a radial electric field (E⊥) structure, which couples the ion and electron flows. Ions are transversely (radially) accelerated by E⊥ on the high potential side of the double layer in the CFDL. The accelerated ions are trapped near the conical surface, where E⊥ reverses direction. The potential structure of the CFDL is U-shaped and the plasma density is enhanced on the conical surface. The plasma density is severely depleted downstream of the parallel potential drop (φ||o) in the CFDL; the density depletion and the potential drop are related by quasi-neutrality condition, including the divergence in the magnetic field and in the plasma flow in the conical structure. The potential and density structures, the CFDL spatial size, its electric field strengths and the electron and ion velocities and energy distributions in the CFDL are found to be in good agreements with those measured in the Australian experiment. The applicability of our results to measured axial potential profiles in magnetic nozzle experiments in HPDs is discussed.

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL)

NASA Technical Reports Server (NTRS)

Carroll, Chester C.; Owen, Jeffrey E.

1988-01-01

A direct-execution parallel architecture for the Advanced Continuous Simulation Language (ACSL) is presented which overcomes the traditional disadvantages of simulations executed on a digital computer. The incorporation of parallel processing allows the mapping of simulations into a digital computer to be done in the same inherently parallel manner as they are currently mapped onto an analog computer. The direct-execution format maximizes the efficiency of the executed code since the need for a high level language compiler is eliminated. Resolution is greatly increased over that which is available with an analog computer without the sacrifice in execution speed normally expected with digitial computer simulations. Although this report covers all aspects of the new architecture, key emphasis is placed on the processing element configuration and the microprogramming of the ACLS constructs. The execution times for all ACLS constructs are computed using a model of a processing element based on the AMD 29000 CPU and the AMD 29027 FPU. The increase in execution speed provided by parallel processing is exemplified by comparing the derived execution times of two ACSL programs with the execution times for the same programs executed on a similar sequential architecture.

Accelerating the Gillespie Exact Stochastic Simulation Algorithm using hybrid parallel execution on graphics processing units.

PubMed

Komarov, Ivan; D'Souza, Roshan M

2012-01-01

The Gillespie Stochastic Simulation Algorithm (GSSA) and its variants are cornerstone techniques to simulate reaction kinetics in situations where the concentration of the reactant is too low to allow deterministic techniques such as differential equations. The inherent limitations of the GSSA include the time required for executing a single run and the need for multiple runs for parameter sweep exercises due to the stochastic nature of the simulation. Even very efficient variants of GSSA are prohibitively expensive to compute and perform parameter sweeps. Here we present a novel variant of the exact GSSA that is amenable to acceleration by using graphics processing units (GPUs). We parallelize the execution of a single realization across threads in a warp (fine-grained parallelism). A warp is a collection of threads that are executed synchronously on a single multi-processor. Warps executing in parallel on different multi-processors (coarse-grained parallelism) simultaneously generate multiple trajectories. Novel data-structures and algorithms reduce memory traffic, which is the bottleneck in computing the GSSA. Our benchmarks show an 8×-120× performance gain over various state-of-the-art serial algorithms when simulating different types of models.

An analytic formula for the relativistic incoherent Thomson backscattering spectrum for a drifting bi-Maxwellian plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Naito, O.

2015-08-15

An analytic formula has been derived for the relativistic incoherent Thomson backscattering spectrum for a drifting anisotropic plasma when the scattering vector is parallel to the drifting direction. The shape of the scattering spectrum is insensitive to the electron temperature perpendicular to the scattering vector, but its amplitude may be modulated. As a result, while the measured temperature correctly represents the electron distribution parallel to the scattering vector, the electron density may be underestimated when the perpendicular temperature is higher than the parallel temperature. Since the scattering spectrum in shorter wavelengths is greatly enhanced by the existence of drift, themore » diagnostics might be used to measure local electron current density in fusion plasmas.« less

Traffic Simulations on Parallel Computers Using Domain Decomposition Techniques

DOT National Transportation Integrated Search

1995-01-01

Large scale simulations of Intelligent Transportation Systems (ITS) can only be acheived by using the computing resources offered by parallel computing architectures. Domain decomposition techniques are proposed which allow the performance of traffic...

GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

PubMed

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

2015-07-01

GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

On extending parallelism to serial simulators

NASA Technical Reports Server (NTRS)

Nicol, David; Heidelberger, Philip

1994-01-01

This paper describes an approach to discrete event simulation modeling that appears to be effective for developing portable and efficient parallel execution of models of large distributed systems and communication networks. In this approach, the modeler develops submodels using an existing sequential simulation modeling tool, using the full expressive power of the tool. A set of modeling language extensions permit automatically synchronized communication between submodels; however, the automation requires that any such communication must take a nonzero amount off simulation time. Within this modeling paradigm, a variety of conservative synchronization protocols can transparently support conservative execution of submodels on potentially different processors. A specific implementation of this approach, U.P.S. (Utilitarian Parallel Simulator), is described, along with performance results on the Intel Paragon.

Simulation of external and internal electrostatic discharges at the spacecraft system test level

NASA Technical Reports Server (NTRS)

Whittlesey, A.; Leung, P.

1984-01-01

Environmental test activities concerned with space plasma-caused charging and discharing phenomena are discussed. It is pointed out that the origin of such an electrostatic discharge (ESD) is charging of spacecraft dielectrics by an energetic plasma in geosynchronous orbit, Jupiter's magnetosphere, or other similar space environments. In dealing with environmental testing problems, it is necessary to define the location and magnitude of any ESD's in preparation for a subsequent simulation of the given conditions. Questions of external and internal charging are discussed separately. The environmental hazard from an external discharge can be assessed by viewing the dielectric surface as one side of a parallel plate capacitor. In the case of internal charging, the level of environmental concern depends on the higher energy spectrum of the ambient electrons.

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S.

2017-11-01

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Giannozzi, P; Andreussi, O; Brumme, T; Bunau, O; Buongiorno Nardelli, M; Calandra, M; Car, R; Cavazzoni, C; Ceresoli, D; Cococcioni, M; Colonna, N; Carnimeo, I; Dal Corso, A; de Gironcoli, S; Delugas, P; DiStasio, R A; Ferretti, A; Floris, A; Fratesi, G; Fugallo, G; Gebauer, R; Gerstmann, U; Giustino, F; Gorni, T; Jia, J; Kawamura, M; Ko, H-Y; Kokalj, A; Küçükbenli, E; Lazzeri, M; Marsili, M; Marzari, N; Mauri, F; Nguyen, N L; Nguyen, H-V; Otero-de-la-Roza, A; Paulatto, L; Poncé, S; Rocca, D; Sabatini, R; Santra, B; Schlipf, M; Seitsonen, A P; Smogunov, A; Timrov, I; Thonhauser, T; Umari, P; Vast, N; Wu, X; Baroni, S

2017-10-24

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Andreussi, Oliviero; Brumme, Thomas; Bunau, Oana; Buongiorno Nardelli, Marco; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Cococcioni, Matteo; Colonna, Nicola; Carnimeo, Ivan; Dal Corso, Andrea; de Gironcoli, Stefano; Delugas, Pietro; DiStasio, Robert; Ferretti, Andrea; Floris, Andrea; Fratesi, Guido; Fugallo, Giorgia; Gebauer, Ralph; Gerstmann, Uwe; Giustino, Feliciano; Gorni, Tommaso; Jia, Junteng; Kawamura, Mitsuaki; Ko, Hsin-Yu; Kokalj, Anton; Küçükbenli, Emine; Lazzeri, Michele; Marsili, Margherita; Marzari, Nicola; Mauri, Francesco; Nguyen, Ngoc Linh; Nguyen, Huy-Viet; Otero-de-la-Roza, Alberto; Paulatto, Lorenzo; Poncé, Samuel; Giannozzi, Paolo; Rocca, Dario; Sabatini, Riccardo; Santra, Biswajit; Schlipf, Martin; Seitsonen, Ari Paavo; Smogunov, Alexander; Timrov, Iurii; Thonhauser, Timo; Umari, Paolo; Vast, Nathalie; Wu, Xifan; Baroni, Stefano

2017-09-27

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.

Global Magnetohydrodynamic Simulation Using High Performance FORTRAN on Parallel Computers

NASA Astrophysics Data System (ADS)

Ogino, T.

High Performance Fortran (HPF) is one of modern and common techniques to achieve high performance parallel computation. We have translated a 3-dimensional magnetohydrodynamic (MHD) simulation code of the Earth's magnetosphere from VPP Fortran to HPF/JA on the Fujitsu VPP5000/56 vector-parallel supercomputer and the MHD code was fully vectorized and fully parallelized in VPP Fortran. The entire performance and capability of the HPF MHD code could be shown to be almost comparable to that of VPP Fortran. A 3-dimensional global MHD simulation of the earth's magnetosphere was performed at a speed of over 400 Gflops with an efficiency of 76.5 VPP5000/56 in vector and parallel computation that permitted comparison with catalog values. We have concluded that fluid and MHD codes that are fully vectorized and fully parallelized in VPP Fortran can be translated with relative ease to HPF/JA, and a code in HPF/JA may be expected to perform comparably to the same code written in VPP Fortran.

Electron heating in a Monte Carlo model of a high Mach number, supercritical, collisionless shock

NASA Technical Reports Server (NTRS)

Ellison, Donald C.; Jones, Frank C.

1987-01-01

Preliminary work in the investigation of electron injection and acceleration at parallel shocks is presented. A simple model of electron heating that is derived from a unified shock model which includes the effects of an electrostatic potential jump is described. The unified shock model provides a kinetic description of the injection and acceleration of ions and a fluid description of electron heating at high Mach number, supercritical, and parallel shocks.

The cost of conservative synchronization in parallel discrete event simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1990-01-01

The performance of a synchronous conservative parallel discrete-event simulation protocol is analyzed. The class of simulation models considered is oriented around a physical domain and possesses a limited ability to predict future behavior. A stochastic model is used to show that as the volume of simulation activity in the model increases relative to a fixed architecture, the complexity of the average per-event overhead due to synchronization, event list manipulation, lookahead calculations, and processor idle time approach the complexity of the average per-event overhead of a serial simulation. The method is therefore within a constant factor of optimal. The analysis demonstrates that on large problems--those for which parallel processing is ideally suited--there is often enough parallel workload so that processors are not usually idle. The viability of the method is also demonstrated empirically, showing how good performance is achieved on large problems using a thirty-two node Intel iPSC/2 distributed memory multiprocessor.

A New Parallel Boundary Condition for Turbulence Simulations in Stellarators

NASA Astrophysics Data System (ADS)

Martin, Mike F.; Landreman, Matt; Dorland, William; Xanthopoulos, Pavlos

2017-10-01

For gyrokinetic simulations of core turbulence, the ``twist-and-shift'' parallel boundary condition (Beer et al., PoP, 1995), which involves a shift in radial wavenumber proportional to the global shear and a quantization of the simulation domain's aspect ratio, is the standard choice. But as this condition was derived under the assumption of axisymmetry, ``twist-and-shift'' as it stands is formally incorrect for turbulence simulations in stellarators. Moreover, for low-shear stellarators like W7X and HSX, the use of a global shear in the traditional boundary condition places an inflexible constraint on the aspect ratio of the domain, requiring more grid points to fully resolve its extent. Here, we present a parallel boundary condition for ``stellarator-symmetric'' simulations that relies on the local shear along a field line. This boundary condition is similar to ``twist-and-shift'', but has an added flexibility in choosing the parallel length of the domain based on local shear consideration in order to optimize certain parameters such as the aspect ratio of the simulation domain.

The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations

PubMed Central

Boršnik, Urban; Miller, Benjamin T.; Brooks, Bernard R.; Janežič, Dušanka

2011-01-01

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used. PMID:21793007

Parallelizing Timed Petri Net simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1993-01-01

The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

Parallel computing method for simulating hydrological processesof large rivers under climate change

NASA Astrophysics Data System (ADS)

Wang, H.; Chen, Y.

2016-12-01

Climate change is one of the proverbial global environmental problems in the world.Climate change has altered the watershed hydrological processes in time and space distribution, especially in worldlarge rivers.Watershed hydrological process simulation based on physically based distributed hydrological model can could have better results compared with the lumped models.However, watershed hydrological process simulation includes large amount of calculations, especially in large rivers, thus needing huge computing resources that may not be steadily available for the researchers or at high expense, this seriously restricted the research and application. To solve this problem, the current parallel method are mostly parallel computing in space and time dimensions.They calculate the natural features orderly thatbased on distributed hydrological model by grid (unit, a basin) from upstream to downstream.This articleproposes ahigh-performancecomputing method of hydrological process simulation with high speedratio and parallel efficiency.It combinedthe runoff characteristics of time and space of distributed hydrological model withthe methods adopting distributed data storage, memory database, distributed computing, parallel computing based on computing power unit.The method has strong adaptability and extensibility,which means it canmake full use of the computing and storage resources under the condition of limited computing resources, and the computing efficiency can be improved linearly with the increase of computing resources .This method can satisfy the parallel computing requirements ofhydrological process simulation in small, medium and large rivers.

Possible Dynamically Gated Conductance along Heme Wires in Bacterial Multiheme Cytochromes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Dayle MA; Rosso, Kevin M.

2014-07-24

The staggered cross decaheme configuration of electron transfer co-factors in the outer-membrane cytochrome MtrF may serve as a prototype for conformationally-gated multi-heme electron transport. Derived from the bacterium Shewanella oneidensis, the staggered cross configuration reveals intersecting c-type octaheme and tetraheme “wires” containing thermodynamic “hills” and “valleys”, suggesting that the protein structure may include a dynamical mechanism for conductance and pathway switching depending on enzymatic functional need. Recent molecular simulations have established the pair-wise electronic couplings, redox potentials, and reorganization energies to predict the maximum conductance along the various heme wire pathways by sequential hopping of a single electron (PNAS (2014)more » 11,611-616). Here, we expand this information with classical molecular and statistical mechanics calculations of large-amplitude protein dynamics in MtrF, to address its potential to modulate pathway conductance, including assessment of the effect of the total charge state. Explicit solvent molecular dynamics simulations of fully oxidized and fully reduced MtrF employing ten independent 50-ns simulations at 300 K and 1 atm showed that reduced MtrF is more expanded and explores more conformational space than oxidized MtrF, and that heme reduction leads to increased heme solvent exposure. The slowest mode of collective decaheme motion is 90% similar between the oxidized and reduced states, and consists primarily of inter-heme separation with minor rotational contributions. The frequency of this motion is 1.7×107 s 1 for fully-oxidized and fully-reduced MtrF, respectively, slower than the downhill electron transfer rates between stacked heme pairs at the octaheme termini and faster than the electron transfer rates between parallel hemes in the tetraheme chain. This implies that MtrF uses slow conformational fluctuations to modulate electron flow along the octaheme pathway, apparently for the purpose of increasing the residence time of electrons on lowest potential hemes 4 and 9. This apparent gating mechanism should increase the success rate of electron transfer from MtrF to low potential environmental acceptors via these two solvent-exposed hemes.« less

Porting LAMMPS to GPUs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, William Michael; Plimpton, Steven James; Wang, Peng

2010-03-01

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

Particle-in-cell simulation of an electronegative plasma under direct current bias studied in a large range of electronegativity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oudini, N.; Laboratoire des plasmas de Decharges, Centre de Developement des Technologies Avancees, Cite du 20 Aout BP 17 Baba Hassen, 16081 Algiers; Raimbault, J.-L.

2013-04-15

A one-dimensional electronegative plasma situated between two symmetrical parallel electrodes under DC bias is studied by Particle-In-Cell simulation with Monte Carlo Collisions. By varying the electronegativity {alpha}{identical_to}n{sub -}/n{sub e} from the limit of electron-ion plasmas (negative ion free) to ion-ion plasmas (electron free), the sheaths formation, the negative ion flux flowing towards the electrodes, and the particle velocities at the sheath edges are investigated. Depending on {alpha}, it is shown that the electronegative plasma behavior can be described by four regimes. In the lowest regime of {alpha}, i.e., {alpha} < 50, negative ions are confined by two positive sheaths withinmore » the plasma, while in the higher regimes of {alpha}, a negative sheath is formed and the negative ion flux can be extracted from the bulk plasma. In the two intermediate regimes of {alpha}, i.e., 50 < {alpha} < 10{sup 5}, both the electron and the negative ion fluxes are involved in the neutralization of the positive ions flux that leaves the plasma. In particular, we show that the velocity of the negative ions entering the negative sheath is affected by the presence of the electrons, and is not given by the modified Bohm velocity generally accepted for electronegative plasmas. For extremely high electronegativity, i.e., {alpha} > 10{sup 5}, the presence of electrons in the plasma is marginal and the electronegative plasma can be considered as an ion-ion plasma (electron free).« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deline, Chris; Meydbray, Jenya; Donovan, Matt

The 2012 NREL report 'Photovoltaic Shading Testbed for Module-Level Power Electronics' provides a standard methodology for estimating the performance benefit of distributed power electronics under partial shading conditions. Since the release of the report, experiments have been conducted for a number of products and for different system configurations. Drawing from these experiences, updates to the test and analysis methods are recommended. Proposed changes in data processing have the benefit of reducing the sensitivity to measurement errors and weather variability, as well as bringing the updated performance score in line with measured and simulated values of the shade recovery benefit ofmore » distributed PV power electronics. Also, due to the emergence of new technologies including sub-module embedded power electronics, the shading method has been extended to include power electronics that operate at a finer granularity than the module level. An update to the method is proposed to account for these emerging technologies that respond to shading differently than module-level devices. The partial shading test remains a repeatable test procedure that attempts to simulate shading situations as would be experienced by typical residential or commercial rooftop photovoltaic (PV) systems. Performance data for multiple products tested using this method are discussed, based on equipment from Enphase, Solar Edge, Maxim Integrated and SMA. In general, the annual recovery of shading losses from the module-level electronics evaluated is 25-35%, with the major difference between different trials being related to the number of parallel strings in the test installation rather than differences between the equipment tested. Appendix D data has been added in this update.« less

Research in parallel computing

NASA Technical Reports Server (NTRS)

Ortega, James M.; Henderson, Charles

1994-01-01

This report summarizes work on parallel computations for NASA Grant NAG-1-1529 for the period 1 Jan. - 30 June 1994. Short summaries on highly parallel preconditioners, target-specific parallel reductions, and simulation of delta-cache protocols are provided.

Quantitative resonant soft x-ray reflectivity of ultrathin anisotropic organic layers: Simulation and experiment of PTCDA on Au.

PubMed

Capelli, R; Mahne, N; Koshmak, K; Giglia, A; Doyle, B P; Mukherjee, S; Nannarone, S; Pasquali, L

2016-07-14

Resonant soft X-ray reflectivity at the carbon K edge, with linearly polarized light, was used to derive quantitative information of film morphology, molecular arrangement, and electronic orbital anisotropies of an ultrathin 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) film on Au(111). The experimental spectra were simulated by computing the propagation of the electromagnetic field in a trilayer system (vacuum/PTCDA/Au), where the organic film was treated as an anisotropic medium. Optical constants were derived from the calculated (through density functional theory) absorption cross sections of the single molecule along the three principal molecular axes. These were used to construct the dielectric tensor of the film, assuming the molecules to be lying flat with respect to the substrate and with a herringbone arrangement parallel to the substrate plane. Resonant soft X-ray reflectivity proved to be extremely sensitive to film thickness, down to the single molecular layer. The best agreement between simulation and experiment was found for a film of 1.6 nm, with flat laying configuration of the molecules. The high sensitivity to experimental geometries in terms of beam incidence and light polarization was also clarified through simulations. The optical anisotropies of the organic film were experimentally determined and through the comparison with calculations, it was possible to relate them to the orbital symmetry of the empty electronic states.

Development of the Next Generation of Biogeochemistry Simulations Using EMSL's NWChem Molecular Modeling Software

NASA Astrophysics Data System (ADS)

Bylaska, E. J.; Kowalski, K.; Apra, E.; Govind, N.; Valiev, M.

2017-12-01

Methods of directly simulating the behavior of complex strongly interacting atomic systems (molecular dynamics, Monte Carlo) have provided important insight into the behavior of nanoparticles, biogeochemical systems, mineral/fluid systems, nanoparticles, actinide systems and geofluids. The limitation of these methods to even wider applications is the difficulty of developing accurate potential interactions in these systems at the molecular level that capture their complex chemistry. The well-developed tools of quantum chemistry and physics have been shown to approach the accuracy required. However, despite the continuous effort being put into improving their accuracy and efficiency, these tools will be of little value to condensed matter problems without continued improvements in techniques to traverse and sample the high-dimensional phase space needed to span the ˜10^12 time scale differences between molecular simulation and chemical events. In recent years, we have made considerable progress in developing electronic structure and AIMD methods tailored to treat biochemical and geochemical problems, including very efficient implementations of many-body methods, fast exact exchange methods, electron-transfer methods, excited state methods, QM/MM, and new parallel algorithms that scale to +100,000 cores. The poster will focus on the fundamentals of these methods and the realities in terms of system size, computational requirements and simulation times that are required for their application to complex biogeochemical systems.