Science.gov

Sample records for accelerator simulation paradigm

  1. Simulation Accelerator

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Under a NASA SBIR (Small Business Innovative Research) contract, (NAS5-30905), EAI Simulation Associates, Inc., developed a new digital simulation computer, Starlight(tm). With an architecture based on the analog model of computation, Starlight(tm) outperforms all other computers on a wide range of continuous system simulation. This system is used in a variety of applications, including aerospace, automotive, electric power and chemical reactors.

  2. A New Paradigm for Flare Particle Acceleration

    NASA Astrophysics Data System (ADS)

    Guidoni, Silvina E.; Karpen, Judith T.; DeVore, C. Richard

    2017-08-01

    The mechanism that accelerates particles to the energies required to produce the observed high-energy impulsive emission and its spectra in solar flares is not well understood. Here, we propose a first-principle-based model of particle acceleration that produces energy spectra that closely resemble those derived from hard X-ray observations. Our mechanism uses contracting magnetic islands formed during fast reconnection in solar flares to accelerate electrons, as first proposed by Drake et al. (2006) for kinetic-scale plasmoids. We apply these ideas to MHD-scale islands formed during fast reconnection in a simulated eruptive flare. A simple analytic model based on the particles’ adiabatic invariants is used to calculate the energy gain of particles orbiting field lines in our ultrahigh-resolution, 2.5D, MHD numerical simulation of a solar eruption (flare + coronal mass ejection). Then, we analytically model electrons visiting multiple contracting islands to account for the observed high-energy flare emission. Our acceleration mechanism inherently produces sporadic emission because island formation is intermittent. Moreover, a large number of particles could be accelerated in each macroscopic island, which may explain the inferred rates of energetic-electron production in flares. We conclude that island contraction in the flare current sheet is a promising candidate for electron acceleration in solar eruptions. This work was supported in part by the NASA LWS and H-SR programs..

  3. Hardware Accelerated Simulated Radiography

    SciTech Connect

    Laney, D; Callahan, S; Max, N; Silva, C; Langer, S; Frank, R

    2005-04-12

    We present the application of hardware accelerated volume rendering algorithms to the simulation of radiographs as an aid to scientists designing experiments, validating simulation codes, and understanding experimental data. The techniques presented take advantage of 32 bit floating point texture capabilities to obtain validated solutions to the radiative transport equation for X-rays. An unsorted hexahedron projection algorithm is presented for curvilinear hexahedra that produces simulated radiographs in the absorption-only regime. A sorted tetrahedral projection algorithm is presented that simulates radiographs of emissive materials. We apply the tetrahedral projection algorithm to the simulation of experimental diagnostics for inertial confinement fusion experiments on a laser at the University of Rochester. We show that the hardware accelerated solution is faster than the current technique used by scientists.

  4. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a multi-track'' simulation and analysis code can be used for these applications.

  5. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a ``multi-track`` simulation and analysis code can be used for these applications.

  6. Particle acceleration in cosmic plasmas – paradigm change?

    SciTech Connect

    Lytikov, Maxim; Guo, Fan

    2015-07-21

    The presentation begins by considering the requirements on the acceleration mechanism. It is found that at least some particles in high-energy sources are accelerated by magnetic reconnection (and not by shocks). The two paradigms can be distinguished by the hardness of the spectra. Shocks typically produce spectra with p > 2 (relativistic shocks have p ~ 2.2); non-linear shocks & drift acceleration may give p < 2, e.g. p=1.5; B-field dissipation can give p = 1. Then collapse of stressed magnetic X-point in force-free plasma and collapse of a system of magnetic islands are taken up, including Island merger: forced reconnection. Spectra as functions of sigma are shown, and gamma ~ 109 is addressed. It is concluded that reconnection in magnetically-dominated plasma can proceed explosively, is an efficient means of particle acceleration, and is an important (perhaps dominant for some phenomena) mechanism of particle acceleration in high energy sources.

  7. Hardware-Accelerated Simulated Radiography

    SciTech Connect

    Laney, D; Callahan, S; Max, N; Silva, C; Langer, S; Frank, R

    2005-08-04

    We present the application of hardware accelerated volume rendering algorithms to the simulation of radiographs as an aid to scientists designing experiments, validating simulation codes, and understanding experimental data. The techniques presented take advantage of 32-bit floating point texture capabilities to obtain solutions to the radiative transport equation for X-rays. The hardware accelerated solutions are accurate enough to enable scientists to explore the experimental design space with greater efficiency than the methods currently in use. An unsorted hexahedron projection algorithm is presented for curvilinear hexahedral meshes that produces simulated radiographs in the absorption-only regime. A sorted tetrahedral projection algorithm is presented that simulates radiographs of emissive materials. We apply the tetrahedral projection algorithm to the simulation of experimental diagnostics for inertial confinement fusion experiments on a laser at the University of Rochester.

  8. Accelerated dynamics simulations of nanotubes.

    SciTech Connect

    Uberuaga, B. P.; Stuart, S. J.; Voter, A. F.

    2002-01-01

    We report on the application of accelerated dynamics techniques to the study of carbon nanotubes. We have used the parallel replica method and temperature accelerated dynamics simulations are currently in progress. In the parallel replica study, we have stretched tubes at a rate significantly lower than that used in previous studies. In these preliminary results, we find that there are qualitative differences in the rupture of the nanotubes at different temperatures. We plan on extending this investigation to include nanotubes of various chiralities. We also plan on exploring unique geometries of nanotubes.

  9. AESS: Accelerated Exact Stochastic Simulation

    NASA Astrophysics Data System (ADS)

    Jenkins, David D.; Peterson, Gregory D.

    2011-12-01

    The Stochastic Simulation Algorithm (SSA) developed by Gillespie provides a powerful mechanism for exploring the behavior of chemical systems with small species populations or with important noise contributions. Gene circuit simulations for systems biology commonly employ the SSA method, as do ecological applications. This algorithm tends to be computationally expensive, so researchers seek an efficient implementation of SSA. In this program package, the Accelerated Exact Stochastic Simulation Algorithm (AESS) contains optimized implementations of Gillespie's SSA that improve the performance of individual simulation runs or ensembles of simulations used for sweeping parameters or to provide statistically significant results. Program summaryProgram title: AESS Catalogue identifier: AEJW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: University of Tennessee copyright agreement No. of lines in distributed program, including test data, etc.: 10 861 No. of bytes in distributed program, including test data, etc.: 394 631 Distribution format: tar.gz Programming language: C for processors, CUDA for NVIDIA GPUs Computer: Developed and tested on various x86 computers and NVIDIA C1060 Tesla and GTX 480 Fermi GPUs. The system targets x86 workstations, optionally with multicore processors or NVIDIA GPUs as accelerators. Operating system: Tested under Ubuntu Linux OS and CentOS 5.5 Linux OS Classification: 3, 16.12 Nature of problem: Simulation of chemical systems, particularly with low species populations, can be accurately performed using Gillespie's method of stochastic simulation. Numerous variations on the original stochastic simulation algorithm have been developed, including approaches that produce results with statistics that exactly match the chemical master equation (CME) as well as other approaches that approximate the CME. Solution

  10. A Special Chinese Reading Acceleration Training Paradigm: To Enhance the Reading Fluency and Comprehension of Chinese Children with Reading Disabilities

    PubMed Central

    Dai, Li; Zhang, Chenchen; Liu, Xiangping

    2016-01-01

    According to a number of studies, use of a Reading Acceleration Program as reading intervention training has been demonstrated to improve reading speed and comprehension level effectively in most languages and countries. The objective of the current study was to provide further evidence of the effectiveness of a Reading Acceleration Program for Chinese children with reading disabilities using a distinctive Chinese reading acceleration training paradigm. The reading acceleration training paradigm is divided into a non-accelerated reading paradigm, a Character-accelerated reading paradigm and a Words-accelerated reading paradigm. The results of training Chinese children with reading disabilities indicate that the acceleration reading paradigm applies to children with Chinese-reading disabilities. In addition, compared with other reading acceleration paradigms, Words-accelerated reading training is more effective in helping children with reading disabilities read at a high speed while maintaining superior comprehension levels. PMID:28018272

  11. A Special Chinese Reading Acceleration Training Paradigm: To Enhance the Reading Fluency and Comprehension of Chinese Children with Reading Disabilities.

    PubMed

    Dai, Li; Zhang, Chenchen; Liu, Xiangping

    2016-01-01

    According to a number of studies, use of a Reading Acceleration Program as reading intervention training has been demonstrated to improve reading speed and comprehension level effectively in most languages and countries. The objective of the current study was to provide further evidence of the effectiveness of a Reading Acceleration Program for Chinese children with reading disabilities using a distinctive Chinese reading acceleration training paradigm. The reading acceleration training paradigm is divided into a non-accelerated reading paradigm, a Character-accelerated reading paradigm and a Words-accelerated reading paradigm. The results of training Chinese children with reading disabilities indicate that the acceleration reading paradigm applies to children with Chinese-reading disabilities. In addition, compared with other reading acceleration paradigms, Words-accelerated reading training is more effective in helping children with reading disabilities read at a high speed while maintaining superior comprehension levels.

  12. Commnity Petascale Project for Accelerator Science And Simulation: Advancing Computational Science for Future Accelerators And Accelerator Technologies

    SciTech Connect

    Spentzouris, Panagiotis; Cary, John; Mcinnes, Lois Curfman; Mori, Warren; Ng, Cho; Ng, Esmond; Ryne, Robert; /LBL, Berkeley

    2011-10-21

    The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.

  13. Community petascale project for accelerator science and simulation : Advancing computational science for future accelerators and accelerator technologies.

    SciTech Connect

    Spentzouris, P.; Cary, J.; McInnes, L. C.; Mori, W.; Ng, C.; Ng, E.; Ryne, R.

    2008-01-01

    The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R & D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.

  14. Commnity Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

    SciTech Connect

    Spentzouris, Panagiotis; Cary, John; Mcinnes, Lois Curfman; Mori, Warren; Ng, Cho; Ng, Esmond; Ryne, Robert; /LBL, Berkeley

    2008-07-01

    The design and performance optimization of particle accelerators is essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC1 Accelerator Science and Technology project, the SciDAC2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modeling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multi-physics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.

  15. Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

    SciTech Connect

    Spentzouris, P.; Cary, J.; McInnes, L.C.; Mori, W.; Ng, C.; Ng, E.; Ryne, R.; /LBL, Berkeley

    2011-11-14

    The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors. ComPASS is in the first year of executing its plan to develop the next-generation HPC accelerator modeling tools. ComPASS aims to develop an integrated simulation environment that will utilize existing and new accelerator physics modules with petascale capabilities, by employing modern computing and solver technologies. The ComPASS vision is to deliver to accelerator scientists a virtual accelerator and virtual prototyping modeling environment, with the necessary multiphysics, multiscale capabilities. The plan for this development includes delivering accelerator modeling applications appropriate for each stage of the ComPASS software evolution. Such applications are already being used to address challenging problems in accelerator design and optimization. The ComPASS organization

  16. Development of a neural net paradigm that predicts simulator sickness

    SciTech Connect

    Allgood, G.O.

    1993-03-01

    A disease exists that affects pilots and aircrew members who use Navy Operational Flight Training Systems. This malady, commonly referred to as simulator sickness and whose symptomatology closely aligns with that of motion sickness, can compromise the use of these systems because of a reduced utilization factor, negative transfer of training, and reduction in combat readiness. A report is submitted that develops an artificial neural network (ANN) and behavioral model that predicts the onset and level of simulator sickness in the pilots and aircrews who sue these systems. It is proposed that the paradigm could be implemented in real time as a biofeedback monitor to reduce the risk to users of these systems. The model captures the neurophysiological impact of use (human-machine interaction) by developing a structure that maps the associative and nonassociative behavioral patterns (learned expectations) and vestibular (otolith and semicircular canals of the inner ear) and tactile interaction, derived from system acceleration profiles, onto an abstract space that predicts simulator sickness for a given training flight.

  17. Development of a neural net paradigm that predicts simulator sickness

    SciTech Connect

    Allgood, G.O.

    1993-03-01

    A disease exists that affects pilots and aircrew members who use Navy Operational Flight Training Systems. This malady, commonly referred to as simulator sickness and whose symptomatology closely aligns with that of motion sickness, can compromise the use of these systems because of a reduced utilization factor, negative transfer of training, and reduction in combat readiness. A report is submitted that develops an artificial neural network (ANN) and behavioral model that predicts the onset and level of simulator sickness in the pilots and aircrews who sue these systems. It is proposed that the paradigm could be implemented in real time as a biofeedback monitor to reduce the risk to users of these systems. The model captures the neurophysiological impact of use (human-machine interaction) by developing a structure that maps the associative and nonassociative behavioral patterns (learned expectations) and vestibular (otolith and semicircular canals of the inner ear) and tactile interaction, derived from system acceleration profiles, onto an abstract space that predicts simulator sickness for a given training flight.

  18. 20th Space Simulation Conference: The Changing Testing Paradigm

    NASA Technical Reports Server (NTRS)

    Stecher, Joseph L., III (Compiler)

    1999-01-01

    The Institute of Environmental Sciences and Technology's Twentieth Space Simulation Conference, "The Changing Testing Paradigm" provided participants with a forum to acquire and exchange information on the state-of-the-art in space simulation, test technology, atomic oxygen, program/system testing, dynamics testing, contamination, and materials. The papers presented at this conference and the resulting discussions carried out the conference theme "The Changing Testing Paradigm."

  19. 20th Space Simulation Conference: The Changing Testing Paradigm

    NASA Technical Reports Server (NTRS)

    Stecher, Joseph L., III (Compiler)

    1998-01-01

    The Institute of Environmental Sciences' Twentieth Space Simulation Conference, "The Changing Testing Paradigm" provided participants with a forum to acquire and exchange information on the state-of-the-art in space simulation, test technology, atomic oxygen, program/system testing, dynamics testing, contamination, and materials. The papers presented at this conference and the resulting discussions carried out the conference theme "The Changing Testing Paradigm."

  20. Parallel beam dynamics simulation of linear accelerators

    SciTech Connect

    Qiang, Ji; Ryne, Robert D.

    2002-01-31

    In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies.

  1. Effects of Frequency and Motion Paradigm on Perception of Tilt and Translation During Periodic Linear Acceleration

    NASA Technical Reports Server (NTRS)

    Beaton, K. H.; Holly, J. E.; Clement, G. R.; Wood, Scott J.

    2009-01-01

    Previous studies have demonstrated an effect of frequency on the gain of tilt and translation perception. Results from different motion paradigms are often combined to extend the stimulus frequency range. For example, Off-Vertical Axis Rotation (OVAR) and Variable Radius Centrifugation (VRC) are useful to test low frequencies of linear acceleration at amplitudes that would require impractical sled lengths. The purpose of this study was to compare roll-tilt and lateral translation motion perception in 12 healthy subjects across four paradigms: OVAR, VRC, sled translation and rotation about an earth-horizontal axis. Subjects were oscillated in darkness at six frequencies from 0.01875 to 0.6 Hz (peak acceleration equivalent to 10 deg, less for sled motion below 0.15 Hz). Subjects verbally described the amplitude of perceived tilt and translation, and used a joystick to indicate the direction of motion. Consistent with previous reports, tilt perception gain decreased as a function of stimulus frequency in the motion paradigms without concordant canal tilt cues (OVAR, VRC and Sled). Translation perception gain was negligible at low stimulus frequencies and increased at higher frequencies. There were no significant differences between the phase of tilt and translation, nor did the phase significantly vary across stimulus frequency. There were differences in perception gain across the different paradigms. Paradigms that included actual tilt stimuli had the larger tilt gains, and paradigms that included actual translation stimuli had larger translation gains. In addition, the frequency at which there was a crossover of tilt and translation gains appeared to vary across motion paradigm between 0.15 and 0.3 Hz. Since the linear acceleration in the head lateral plane was equivalent across paradigms, differences in gain may be attributable to the presence of linear accelerations in orthogonal directions and/or cognitive aspects based on the expected motion paths.

  2. Effects of Frequency and Motion Paradigm on Perception of Tilt and Translation During Periodic Linear Acceleration

    NASA Technical Reports Server (NTRS)

    Beaton, K. H.; Holly, J. E.; Clement, G. R.; Wood, Scott J.

    2009-01-01

    Previous studies have demonstrated an effect of frequency on the gain of tilt and translation perception. Results from different motion paradigms are often combined to extend the stimulus frequency range. For example, Off-Vertical Axis Rotation (OVAR) and Variable Radius Centrifugation (VRC) are useful to test low frequencies of linear acceleration at amplitudes that would require impractical sled lengths. The purpose of this study was to compare roll-tilt and lateral translation motion perception in 12 healthy subjects across four paradigms: OVAR, VRC, sled translation and rotation about an earth-horizontal axis. Subjects were oscillated in darkness at six frequencies from 0.01875 to 0.6 Hz (peak acceleration equivalent to 10 deg, less for sled motion below 0.15 Hz). Subjects verbally described the amplitude of perceived tilt and translation, and used a joystick to indicate the direction of motion. Consistent with previous reports, tilt perception gain decreased as a function of stimulus frequency in the motion paradigms without concordant canal tilt cues (OVAR, VRC and Sled). Translation perception gain was negligible at low stimulus frequencies and increased at higher frequencies. There were no significant differences between the phase of tilt and translation, nor did the phase significantly vary across stimulus frequency. There were differences in perception gain across the different paradigms. Paradigms that included actual tilt stimuli had the larger tilt gains, and paradigms that included actual translation stimuli had larger translation gains. In addition, the frequency at which there was a crossover of tilt and translation gains appeared to vary across motion paradigm between 0.15 and 0.3 Hz. Since the linear acceleration in the head lateral plane was equivalent across paradigms, differences in gain may be attributable to the presence of linear accelerations in orthogonal directions and/or cognitive aspects based on the expected motion paths.

  3. Transient simulation of ram accelerator flowfields

    NASA Astrophysics Data System (ADS)

    Drabczuk, Randall P.; Rolader, G.; Dash, S.; Sinha, N.; York, B.

    1993-01-01

    This paper describes the development of an advanced computational fluid dynamic (CFD) simulation capability in support of the USAF Armament Directorate ram accelerator research initiative. The state-of-the-art CRAFT computer code has been specialized for high fidelity, transient ram accelerator simulations via inclusion of generalized dynamic gridding, solution adaptive grid clustering, and high pressure thermo-chemistry. Selected ram accelerator simulations are presented that serve to exhibit the CRAFT code capabilities and identify some of the principle research/design Issues.

  4. Transient simulation of ram accelerator flowfields

    NASA Astrophysics Data System (ADS)

    Sinha, N.; York, B. J.; Dash, S. M.; Drabczuk, R.; Rolader, G. E.

    1992-10-01

    This paper describes the development of an advanced computational fluid dynamic (CFD) simulation capability in support of the U.S. Air Force Armament Directorate's ram accelerator research initiative. The state-of-the-art CRAFT computer code has been specialized for high fidelity, transient ram accelerator simulations via inclusion of generalized dynamic gridding, solution adaptive grid clustering, high pressure thermochemistry, etc. Selected ram accelerator simulations are presented which serve to exhibit the CRAFT code's capabilities and identify some of the principal research/design issues.

  5. Enabling technologies for petascale electromagnetic accelerator simulation

    NASA Astrophysics Data System (ADS)

    Lee, Lie-Quan; Akcelik, Volkan; Chen, Sheng; Ge, Lixin; Prudencio, Ernesto; Schussman, Greg; Uplenchwar, Ravi; Ng, Cho; Ko, Kwok; Luo, Xiaojun; Shephard, Mark

    2007-07-01

    The SciDAC2 accelerator project at SLAC aims to simulate an entire three-cryomodule radio frequency (RF) unit of the International Linear Collider (ILC) main Linac. Petascale computing resources supported by advances in Applied Mathematics (AM) and Computer Science (CS) and INCITE Program are essential to enable such very large-scale electromagnetic accelerator simulations required by the ILC Global Design Effort. This poster presents the recent advances and achievements in the areas of CS/AM through collaborations.

  6. Enabling Technologies for Petascale Electromagnetic Accelerator Simulation

    SciTech Connect

    Lee, Lie-Quan; Akcelik, Volkan; Chen, Sheng; Ge, Li-Xin; Prudencio, Ernesto; Schussman, Greg; Uplenchwar, Ravi; Ng, Cho; Ko, Kwok; Luo, Xiaojun; Shephard, Mark; /Rensselaer Poly.

    2007-11-09

    The SciDAC2 accelerator project at SLAC aims to simulate an entire three-cryomodule radio frequency (RF) unit of the International Linear Collider (ILC) main Linac. Petascale computing resources supported by advances in Applied Mathematics (AM) and Computer Science (CS) and INCITE Program are essential to enable such very large-scale electromagnetic accelerator simulations required by the ILC Global Design Effort. This poster presents the recent advances and achievements in the areas of CS/AM through collaborations.

  7. Computer simulations of new dielectric accelerator devices

    SciTech Connect

    Chan, K.C.D. ); Schoessow, P. )

    1990-01-01

    Recently, dielectric wakefield accelerator structures have been successfully demonstrated at the Argonne Advanced Accelerator Test Facility. This paper describes computer simulations of these experiments, including schemes for damping transverse deflecting forces in these devices. These simulations were performed using the MAFIA and ARRAKIS codes. MAFIA is a set of electromagnetic solvers in three dimensions widely used for designing accelerator components. The ARRAKIS codes are time-domain electromagnetic solvers which have recently developed and implemented on massively parallel computers such as the Connection Machine. 6 refs., 5 figs., 1 tab.

  8. Kinetic Simulations of Particle Acceleration at Shocks

    SciTech Connect

    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 shock drift acceleration; and electron DSA is efficient at oblique shocks.

  9. Accelerating Climate Simulations Through Hybrid Computing

    NASA Technical Reports Server (NTRS)

    Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

    2009-01-01

    Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

  10. NUMERICAL SIMULATIONS OF SPICULE ACCELERATION

    SciTech Connect

    Guerreiro, N.; Carlsson, M.; Hansteen, V. E-mail: mats.carlsson@astro.uio.no

    2013-04-01

    Observations in the H{alpha} line of hydrogen and the H and K lines of singly ionized calcium on the solar limb reveal the existence of structures with jet-like behavior, usually designated as spicules. The driving mechanism for such structures remains poorly understood. Sterling et al. shed some light on the problem mimicking reconnection events in the chromosphere with a one-dimensional code by injecting energy with different spatial and temporal distributions and tracing the thermodynamic evolution of the upper chromospheric plasma. They found three different classes of jets resulting from these injections. We follow their approach but improve the physical description by including non-LTE cooling in strong spectral lines and non-equilibrium hydrogen ionization. Increased cooling and conversion of injected energy into hydrogen ionization energy instead of thermal energy both lead to weaker jets and smaller final extent of the spicules compared with Sterling et al. In our simulations we find different behavior depending on the timescale for hydrogen ionization/recombination. Radiation-driven ionization fronts also form.

  11. Accelerated Aging of the M119 Simulator

    NASA Technical Reports Server (NTRS)

    Bixon, Eric R.

    2000-01-01

    This paper addresses the storage requirement, shelf life, and the reliability of M119 Whistling Simulator. Experimental conditions have been determined and the data analysis has been completed for the accelerated testing of the system. A general methodology to evaluate the shelf life of the system as a function of the storage time, temperature, and relative humidity is discussed.

  12. Accelerated simulation methods for plasma kinetics

    NASA Astrophysics Data System (ADS)

    Caflisch, Russel

    2016-11-01

    Collisional kinetics is a multiscale phenomenon due to the disparity between the continuum (fluid) and the collisional (particle) length scales. This paper describes a class of simulation methods for gases and plasmas, and acceleration techniques for improving their speed and accuracy. Starting from the Landau-Fokker-Planck equation for plasmas, the focus will be on a binary collision model that is solved using a Direct Simulation Monte Carlo (DSMC) method. Acceleration of this method is achieved by coupling the particle method to a continuum fluid description. The velocity distribution function f is represented as a combination of a Maxwellian M (the thermal component) and a set of discrete particles fp (the kinetic component). For systems that are close to (local) equilibrium, this reduces the number N of simulated particles that are required to represent f for a given level of accuracy. We present two methods for exploiting this representation. In the first method, equilibration of particles in fp, as well as disequilibration of particles from M, due to the collision process, is represented by a thermalization/dethermalization step that employs an entropy criterion. Efficiency of the representation is greatly increased by inclusion of particles with negative weights. This significantly complicates the simulation, but the second method is a tractable approach for negatively weighted particles. The accelerated simulation method is compared with standard PIC-DSMC method for both spatially homogeneous problems such as a bump-on-tail and inhomogeneous problems such as nonlinear Landau damping.

  13. An exact accelerated stochastic simulation algorithm.

    PubMed

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-04-14

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 23 power of the number of reaction events in a Galton-Watson process.

  14. Quench simulation program for superconducting accelerator magnets

    SciTech Connect

    Seog-Whan Kim

    2001-08-10

    In the design of superconducting magnets for accelerator and the quench protection systems, it is necessary to calculate the current, voltage and temperature during quench. The quench integral value (MIITs) is used to get a rough idea about the quench, but they need numerical calculations to obtain more detailed picture of the quench. A simulation program named KUENCH, which is not based on the MIITs calculation, was developed to calculate voltage, current and temperature of accelerator magnets during quenches. The software and calculation examples are introduced. The example also gives some important information about effects of copper content in the coil and quench protection heaters.

  15. Simulations for Plasma and Laser Acceleration

    NASA Astrophysics Data System (ADS)

    Vay, Jean-Luc; Lehe, RéMi

    Computer simulations have had a profound impact on the design and understanding of past and present plasma acceleration experiments, and will be a key component for turning plasma accelerators from a promising technology into a mainstream scientific tool. In this article, we present an overview of the numerical techniques used with the most popular approaches to model plasma-based accelerators: electromagnetic particle-in-cell, quasistatic and ponderomotive guiding center. The material that is presented is intended to serve as an introduction to the basics of those approaches, and to advances (some of them very recent) that have pushed the state of the art, such as the optimal Lorentz-boosted frame, advanced laser envelope solvers and the elimination of numerical Cherenkov instability. The particle-in-cell method, which has broader interest and is more standardized, is presented in more depth. Additional topics that are cross-cutting, such as azimuthal Fourier decomposition or filtering, are also discussed, as well as potential challenges and remedies in the initialization of simulations and output of data. Examples of simulations using the techniques that are presented have been l out of this article for conciseness, and because simulation results are best understood when presented together, and contrasted with theoretical and/or experimental results, as in other articles of this volume.

  16. Simulations for Plasma and Laser Acceleration

    NASA Astrophysics Data System (ADS)

    Vay, Jean-Luc; Lehe, Rémi

    Computer simulations have had a profound impact on the design and understanding of past and present plasma acceleration experiments, and will be a key component for turning plasma accelerators from a promising technology into a mainstream scientific tool. In this article, we present an overview of the numerical techniques used with the most popular approaches to model plasma-based accelerators: electromagnetic particle-in-cell, quasistatic and ponderomotive guiding center. The material that is presented is intended to serve as an introduction to the basics of those approaches, and to advances (some of them very recent) that have pushed the state of the art, such as the optimal Lorentz-boosted frame, advanced laser envelope solvers and the elimination of numerical Cherenkov instability. The particle-in-cell method, which has broader interest and is more standardized, is presented in more depth. Additional topics that are cross-cutting, such as azimuthal Fourier decomposition or filtering, are also discussed, as well as potential challenges and remedies in the initialization of simulations and output of data. Examples of simulations using the techniques that are presented have been left out of this article for conciseness, and because simulation results are best understood when presented together, and contrasted with theoretical and/or experimental results, as in other articles of this volume.

  17. Accelerated GPU based SPECT Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Garcia, Marie-Paule; Bert, Julien; Benoit, Didier; Bardiès, Manuel; Visvikis, Dimitris

    2016-06-01

    Monte Carlo (MC) modelling is widely used in the field of single photon emission computed tomography (SPECT) as it is a reliable technique to simulate very high quality scans. This technique provides very accurate modelling of the radiation transport and particle interactions in a heterogeneous medium. Various MC codes exist for nuclear medicine imaging simulations. Recently, new strategies exploiting the computing capabilities of graphical processing units (GPU) have been proposed. This work aims at evaluating the accuracy of such GPU implementation strategies in comparison to standard MC codes in the context of SPECT imaging. GATE was considered the reference MC toolkit and used to evaluate the performance of newly developed GPU Geant4-based Monte Carlo simulation (GGEMS) modules for SPECT imaging. Radioisotopes with different photon energies were used with these various CPU and GPU Geant4-based MC codes in order to assess the best strategy for each configuration. Three different isotopes were considered: 99m Tc, 111In and 131I, using a low energy high resolution (LEHR) collimator, a medium energy general purpose (MEGP) collimator and a high energy general purpose (HEGP) collimator respectively. Point source, uniform source, cylindrical phantom and anthropomorphic phantom acquisitions were simulated using a model of the GE infinia II 3/8" gamma camera. Both simulation platforms yielded a similar system sensitivity and image statistical quality for the various combinations. The overall acceleration factor between GATE and GGEMS platform derived from the same cylindrical phantom acquisition was between 18 and 27 for the different radioisotopes. Besides, a full MC simulation using an anthropomorphic phantom showed the full potential of the GGEMS platform, with a resulting acceleration factor up to 71. The good agreement with reference codes and the acceleration factors obtained support the use of GPU implementation strategies for improving computational efficiency

  18. Accelerated GPU based SPECT Monte Carlo simulations.

    PubMed

    Garcia, Marie-Paule; Bert, Julien; Benoit, Didier; Bardiès, Manuel; Visvikis, Dimitris

    2016-06-07

    Monte Carlo (MC) modelling is widely used in the field of single photon emission computed tomography (SPECT) as it is a reliable technique to simulate very high quality scans. This technique provides very accurate modelling of the radiation transport and particle interactions in a heterogeneous medium. Various MC codes exist for nuclear medicine imaging simulations. Recently, new strategies exploiting the computing capabilities of graphical processing units (GPU) have been proposed. This work aims at evaluating the accuracy of such GPU implementation strategies in comparison to standard MC codes in the context of SPECT imaging. GATE was considered the reference MC toolkit and used to evaluate the performance of newly developed GPU Geant4-based Monte Carlo simulation (GGEMS) modules for SPECT imaging. Radioisotopes with different photon energies were used with these various CPU and GPU Geant4-based MC codes in order to assess the best strategy for each configuration. Three different isotopes were considered: (99m) Tc, (111)In and (131)I, using a low energy high resolution (LEHR) collimator, a medium energy general purpose (MEGP) collimator and a high energy general purpose (HEGP) collimator respectively. Point source, uniform source, cylindrical phantom and anthropomorphic phantom acquisitions were simulated using a model of the GE infinia II 3/8" gamma camera. Both simulation platforms yielded a similar system sensitivity and image statistical quality for the various combinations. The overall acceleration factor between GATE and GGEMS platform derived from the same cylindrical phantom acquisition was between 18 and 27 for the different radioisotopes. Besides, a full MC simulation using an anthropomorphic phantom showed the full potential of the GGEMS platform, with a resulting acceleration factor up to 71. The good agreement with reference codes and the acceleration factors obtained support the use of GPU implementation strategies for improving computational

  19. Accelerator simulation activities at the SSCL

    SciTech Connect

    Bourianoff, G.

    1992-11-01

    This paper will attempt to summarize the activities related to accelerator simulation at the SSC laboratory during the recent past. Operational simulations including injection, extraction, and correction, performance prediction of a specified lattice design, in particular, the effect of higher-order multipoles on linear aperture and the effect of power supply ripple on emittance growth in the collider, and lastly, the development and application of advanced techniques to particle tracking, e.g., parallel processing and mapping techniques will be discussed in this paper.

  20. Numerical and laboratory simulations of auroral acceleration

    SciTech Connect

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

    2013-10-15

    The existence of parallel electric fields is an essential ingredient of auroral physics, leading to the acceleration of particles that give rise to the auroral displays. An auroral flux tube is modelled using electrostatic Vlasov simulations, and the results are compared to simulations of a proposed laboratory device that is meant for studies of the plasma physical processes that occur on auroral field lines. The hot magnetospheric plasma is represented by a gas discharge plasma source in the laboratory device, and the cold plasma mimicking the ionospheric plasma is generated by a Q-machine source. In both systems, double layers form with plasma density gradients concentrated on their high potential sides. The systems differ regarding the properties of ion acoustic waves that are heavily damped in the magnetosphere, where the ion population is hot, but weakly damped in the laboratory, where the discharge ions are cold. Ion waves are excited by the ion beam that is created by acceleration in the double layer in both systems. The efficiency of this beam-plasma interaction depends on the acceleration voltage. For voltages where the interaction is less efficient, the laboratory experiment is more space-like.

  1. DIFFUSIVE SHOCK ACCELERATION SIMULATIONS OF RADIO RELICS

    SciTech Connect

    Kang, Hyesung; Ryu, Dongsu; Jones, T. W. E-mail: ryu@canopus.cnu.ac.kr

    2012-09-01

    Recent radio observations have identified a class of structures, so-called radio relics, in clusters of galaxies. The radio emission from these sources is interpreted as synchrotron radiation from GeV electrons gyrating in {mu}G-level magnetic fields. Radio relics, located mostly in the outskirts of clusters, seem to associate with shock waves, especially those developed during mergers. In fact, they seem to be good structures to identify and probe such shocks in intracluster media (ICMs), provided we understand the electron acceleration and re-acceleration at those shocks. In this paper, we describe time-dependent simulations for diffusive shock acceleration at weak shocks that are expected to be found in ICMs. Freshly injected as well as pre-existing populations of cosmic-ray (CR) electrons are considered, and energy losses via synchrotron and inverse Compton are included. We then compare the synchrotron flux and spectral distributions estimated from the simulations with those in two well-observed radio relics in CIZA J2242.8+5301 and ZwCl0008.8+5215. Considering that CR electron injection is expected to be rather inefficient at weak shocks with Mach number M {approx}< a few, the existence of radio relics could indicate the pre-existing population of low-energy CR electrons in ICMs. The implication of our results on the merger shock scenario of radio relics is discussed.

  2. Simulation of Medical Linear Accelerators with PENELOPE

    NASA Astrophysics Data System (ADS)

    Brualla, Lorenzo

    Monte Carlo simulation of clinical linear accelerators (linac) allows accurate estimation of the absorbed dose in a patient. However, its routine use in radiotherapy units has been hindered by the difficulties related to efficient programming of the simulation files and the usually long computation times required. penelope is a Monte Carlo general-purpose radiation transport code that describes the coupled transport of photons, electrons and positrons in arbitrary materials and complex geometries. Although penelope by itself is perfectly suited for the simulation of linacs, it nevertheless imposes a programming effort on the end users wishing to do so. In this chapter a brief review is given on several programs that facilitate the simulation of linacs and computerised tomographies using penelope as the Monte Carlo engine. Variance-reduction techniques implemented in these codes, which allow an efficient simulation of linacs, including multileaf collimators, are also described. The chapter ends with an example of a simulation with penelope of a linac irradiating a highly conformed small electron field used for the treatment of the conjunctival lymphoma of the eye. The example shows the simulation of a linac and a computerised tomography of a segmented eye.

  3. An exact accelerated stochastic simulation algorithm

    NASA Astrophysics Data System (ADS)

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-04-01

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2/3 power of the number of reaction events in a Galton-Watson process.

  4. An exact accelerated stochastic simulation algorithm

    PubMed Central

    Mjolsness, Eric; Orendorff, David; Chatelain, Philippe; Koumoutsakos, Petros

    2009-01-01

    An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present “ER-leap” algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 2∕3 power of the number of reaction events in a Galton–Watson process. PMID:19368432

  5. Accelerated molecular dynamics simulations of protein folding.

    PubMed

    Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

    2015-07-30

    Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

  6. Neoadjuvant paradigm for accelerated drug development: an ideal model in bladder cancer.

    PubMed

    Chism, David D; Woods, Michael E; Milowsky, Matthew I

    2013-01-01

    Neoadjuvant cisplatin-based combination chemotherapy for muscle-invasive bladder cancer (MIBC) has been shown to confer a survival advantage in two randomized clinical trials and a meta-analysis. Despite level 1 evidence supporting its benefit, utilization remains dismal with nearly one-half of patients ineligible for cisplatin-based therapy because of renal dysfunction, impaired performance status, and/or coexisting medical problems. This situation highlights the need for the development of novel therapies for the management of MIBC, a disease with a lethal phenotype. The neoadjuvant paradigm in bladder cancer offers many advantages for accelerated drug development. First, there is a greater likelihood of successful therapy at an earlier disease state that may be characterized by less genomic instability compared with the metastatic setting, with an early readout of activity with results determined in months rather than years. Second, pre- and post-treatment tumor tissue collection in patients with MIBC is performed as the standard of care without the need for research-directed biopsies, allowing for the ability to perform important correlative studies and to monitor tumor response to therapy in "real time." Third, pathological complete response (pT0) predicts for improved outcome in patients with MIBC. Fourth, there is a strong biological rationale with rapidly accumulating evidence for actionable targets in bladder cancer. This review focuses on the neoadjuvant paradigm for accelerated drug development using bladder cancer as the ideal model.

  7. Centrifuges for microgravity simulation. The Reduced Gravity Paradigm.

    NASA Astrophysics Data System (ADS)

    van Loon, Jack J. W. A.

    2016-07-01

    Due to the cumbersome nature of performing real microgravity - spaceflight research scientists have been searching for alternatives to perform simulated microgravity or partial gravity experiments on Earth. For more than a century one uses the slow rotating clinostat as developed by von Sachs at the end of the nineteenth century. Since then, the fast rotating clinostat, the 3D clinostat or the random positioning machine, the rotating wall vessels, tail suspension and bed rest head down tilt and lately the levitating magnets have been introduced. Several of these simulation systems provide some similarities of the responses and phenotypes as seen in real microgravity experiments. However, one should always realize that we cannot reduce gravity on Earth, other than the relative short duration free fall studies in e.g. drop towers or parabolic aircraft. In this paper we want to explore the possibility to apply centrifuges to simulate microgravity or maybe better to simulate hypo-gravity. This Reduced Gravity Paradigm, RGP is based on the premise that adaptations seen going from a hypergravity level to a lower gravity are similar as changes seen going from unit gravity to microgravity.

  8. Toward GPGPU accelerated human electromechanical cardiac simulations

    PubMed Central

    Vigueras, Guillermo; Roy, Ishani; Cookson, Andrew; Lee, Jack; Smith, Nicolas; Nordsletten, David

    2014-01-01

    In this paper, we look at the acceleration of weakly coupled electromechanics using the graphics processing unit (GPU). Specifically, we port to the GPU a number of components of Heart—a CPU-based finite element code developed for simulating multi-physics problems. On the basis of a criterion of computational cost, we implemented on the GPU the ODE and PDE solution steps for the electrophysiology problem and the Jacobian and residual evaluation for the mechanics problem. Performance of the GPU implementation is then compared with single core CPU (SC) execution as well as multi-core CPU (MC) computations with equivalent theoretical performance. Results show that for a human scale left ventricle mesh, GPU acceleration of the electrophysiology problem provided speedups of 164 × compared with SC and 5.5 times compared with MC for the solution of the ODE model. Speedup of up to 72 × compared with SC and 2.6 × compared with MC was also observed for the PDE solve. Using the same human geometry, the GPU implementation of mechanics residual/Jacobian computation provided speedups of up to 44 × compared with SC and 2.0 × compared with MC. © 2013 The Authors. International Journal for Numerical Methods in Biomedical Engineering published by John Wiley & Sons, Ltd. PMID:24115492

  9. Toward GPGPU accelerated human electromechanical cardiac simulations.

    PubMed

    Vigueras, Guillermo; Roy, Ishani; Cookson, Andrew; Lee, Jack; Smith, Nicolas; Nordsletten, David

    2014-01-01

    In this paper, we look at the acceleration of weakly coupled electromechanics using the graphics processing unit (GPU). Specifically, we port to the GPU a number of components of CHeart--a CPU-based finite element code developed for simulating multi-physics problems. On the basis of a criterion of computational cost, we implemented on the GPU the ODE and PDE solution steps for the electrophysiology problem and the Jacobian and residual evaluation for the mechanics problem. Performance of the GPU implementation is then compared with single core CPU (SC) execution as well as multi-core CPU (MC) computations with equivalent theoretical performance. Results show that for a human scale left ventricle mesh, GPU acceleration of the electrophysiology problem provided speedups of 164 × compared with SC and 5.5 times compared with MC for the solution of the ODE model. Speedup of up to 72 × compared with SC and 2.6 × compared with MC was also observed for the PDE solve. Using the same human geometry, the GPU implementation of mechanics residual/Jacobian computation provided speedups of up to 44 × compared with SC and 2.0 × compared with MC. © 2013 The Authors. International Journal for Numerical Methods in Biomedical Engineering published by John Wiley & Sons, Ltd.

  10. A hierarchical exact accelerated stochastic simulation algorithm

    NASA Astrophysics Data System (ADS)

    Orendorff, David; Mjolsness, Eric

    2012-12-01

    A new algorithm, "HiER-leap" (hierarchical exact reaction-leaping), is derived which improves on the computational properties of the ER-leap algorithm for exact accelerated simulation of stochastic chemical kinetics. Unlike ER-leap, HiER-leap utilizes a hierarchical or divide-and-conquer organization of reaction channels into tightly coupled "blocks" and is thereby able to speed up systems with many reaction channels. Like ER-leap, HiER-leap is based on the use of upper and lower bounds on the reaction propensities to define a rejection sampling algorithm with inexpensive early rejection and acceptance steps. But in HiER-leap, large portions of intra-block sampling may be done in parallel. An accept/reject step is used to synchronize across blocks. This method scales well when many reaction channels are present and has desirable asymptotic properties. The algorithm is exact, parallelizable and achieves a significant speedup over the stochastic simulation algorithm and ER-leap on certain problems. This algorithm offers a potentially important step towards efficient in silico modeling of entire organisms.

  11. Particle Simulations of a Linear Dielectric Wall Proton Accelerator

    SciTech Connect

    Poole, B R; Blackfield, D T; Nelson, S D

    2007-06-12

    The dielectric wall accelerator (DWA) is a compact induction accelerator structure that incorporates the accelerating mechanism, pulse forming structure, and switch structure into an integrated module. The DWA consists of stacked stripline Blumlein assemblies, which can provide accelerating gradients in excess of 100 MeV/meter. Blumleins are switched sequentially according to a prescribed acceleration schedule to maintain synchronism with the proton bunch as it accelerates. A finite difference time domain code (FDTD) is used to determine the applied acceleration field to the proton bunch. Particle simulations are used to model the injector as well as the accelerator stack to determine the proton bunch energy distribution, both longitudinal and transverse dynamic focusing, and emittance growth associated with various DWA configurations.

  12. Numerical simulation of an accelerator injector

    SciTech Connect

    Boyd, J.K.; Caporaso, G.J.; Cole, A.G.

    1985-05-09

    Accelerator injector designs have been evaluated using two computer codes. The first code self consistently follows relativistic particles in two dimensions. Fields are obtained in the Darwin model which includes inductive effects. This code is used to study cathode emission and acceleration to full injector voltage. The second code transports a fixed segment of a beam along the remainder of the beam line. Using these two codes the effects of electrode configuration on emittance, beam quality and beam transport have been studied.

  13. Simulation of a medical linear accelerator for teaching purposes.

    PubMed

    Anderson, Rhys; Lamey, Michael; MacPherson, Miller; Carlone, Marco

    2015-05-08

    Simulation software for medical linear accelerators that can be used in a teaching environment was developed. The components of linear accelerators were modeled to first order accuracy using analytical expressions taken from the literature. The expressions used constants that were empirically set such that realistic response could be expected. These expressions were programmed in a MATLAB environment with a graphical user interface in order to produce an environment similar to that of linear accelerator service mode. The program was evaluated in a systematic fashion, where parameters affecting the clinical properties of medical linear accelerator beams were adjusted independently, and the effects on beam energy and dose rate recorded. These results confirmed that beam tuning adjustments could be simulated in a simple environment. Further, adjustment of service parameters over a large range was possible, and this allows the demonstration of linear accelerator physics in an environment accessible to both medical physicists and linear accelerator service engineers. In conclusion, a software tool, named SIMAC, was developed to improve the teaching of linear accelerator physics in a simulated environment. SIMAC performed in a similar manner to medical linear accelerators. The authors hope that this tool will be valuable as a teaching tool for medical physicists and linear accelerator service engineers.

  14. A linear accelerator for simulated micrometeors.

    NASA Technical Reports Server (NTRS)

    Slattery, J. C.; Becker, D. G.; Hamermesh, B.; Roy, N. L.

    1973-01-01

    Review of the theory, design parameters, and construction details of a linear accelerator designed to impart meteoric velocities to charged microparticles in the 1- to 10-micron diameter range. The described linac is of the Sloan Lawrence type and, in a significant departure from conventional accelerator practice, is adapted to single particle operation by employing a square wave driving voltage with the frequency automatically adjusted from 12.5 to 125 kHz according to the variable velocity of each injected particle. Any output velocity up to about 30 km/sec can easily be selected, with a repetition rate of approximately two particles per minute.

  15. Simulations of a meter-long plasma wakefield accelerator.

    PubMed

    Lee, S; Katsouleas, T; Hemker, R; Mori, W B

    2000-06-01

    Full-scale particle-in-cell simulations of a meter-long plasma wakefield accelerator (PWFA) are presented in two dimensions. The results support the design of a current PWFA experiment in the nonlinear blowout regime where analytic solutions are intractable. A relativistic electron bunch excites a plasma wake that accelerates trailing particles at rates of several hundred MeV/m. A comparison is made of various simulation codes, and a parallel object-oriented code OSIRIS is used to model a full meter of acceleration. Excellent agreement is obtained between the simulations and analytic expressions for the transverse betatron oscillations of the beam. The simulations are used to develop scaling laws for designing future multi-GeV accelerator experiments.

  16. Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators

    SciTech Connect

    Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.

    1999-11-13

    In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design.

  17. Accelerated growth of calcium silicate hydrates: Experiments and simulations

    SciTech Connect

    Nicoleau, Luc

    2011-12-15

    Despite the usefulness of isothermal calorimetry in cement analytics, without any further computations this brings only little information on the nucleation and growth of hydrates. A model originally developed by Garrault et al. is used in this study in order to simulate hydration curves of cement obtained by calorimetry with different known hardening accelerators. The limited basis set of parameters used in this model, having a physical or chemical significance, is valuable for a better understanding of mechanisms underlying in the acceleration of C-S-H precipitation. Alite hydration in presence of four different types of hardening accelerators was investigated. It is evidenced that each accelerator type plays a specific role on one or several growth parameters and that the model may support the development of new accelerators. Those simulations supported by experimental observations enable us to follow the formation of the C-S-H layer around grains and to extract interesting information on its apparent permeability.

  18. Translational Vestibulo-Ocular Reflex and Motion Perception During Interaural Linear Acceleration: Comparison of Different Motion Paradigms

    NASA Technical Reports Server (NTRS)

    Beaton, K. H.; Holly, J. E.; Clement, G. R.; Wood, S. J.

    2011-01-01

    The neural mechanisms to resolve ambiguous tilt-translation motion have been hypothesized to be different for motion perception and eye movements. Previous studies have demonstrated differences in ocular and perceptual responses using a variety of motion paradigms, including Off-Vertical Axis Rotation (OVAR), Variable Radius Centrifugation (VRC), translation along a linear track, and tilt about an Earth-horizontal axis. While the linear acceleration across these motion paradigms is presumably equivalent, there are important differences in semicircular canal cues. The purpose of this study was to compare translation motion perception and horizontal slow phase velocity to quantify consistencies, or lack thereof, across four different motion paradigms. Twelve healthy subjects were exposed to sinusoidal interaural linear acceleration between 0.01 and 0.6 Hz at 1.7 m/s/s (equivalent to 10 tilt) using OVAR, VRC, roll tilt, and lateral translation. During each trial, subjects verbally reported the amount of perceived peak-to-peak lateral translation and indicated the direction of motion with a joystick. Binocular eye movements were recorded using video-oculography. In general, the gain of translation perception (ratio of reported linear displacement to equivalent linear stimulus displacement) increased with stimulus frequency, while the phase did not significantly vary. However, translation perception was more pronounced during both VRC and lateral translation involving actual translation, whereas perceptions were less consistent and more variable during OVAR and roll tilt which did not involve actual translation. For each motion paradigm, horizontal eye movements were negligible at low frequencies and showed phase lead relative to the linear stimulus. At higher frequencies, the gain of the eye movements increased and became more inphase with the acceleration stimulus. While these results are consistent with the hypothesis that the neural computational strategies for

  19. Beam dynamics simulation of a double pass proton linear accelerator

    NASA Astrophysics Data System (ADS)

    Hwang, Kilean; Qiang, Ji

    2017-04-01

    A recirculating superconducting linear accelerator with the advantage of both straight and circular accelerator has been demonstrated with relativistic electron beams. The acceleration concept of a recirculating proton beam was recently proposed [J. Qiang, Nucl. Instrum. Methods Phys. Res., Sect. A 795, 77 (2015, 10.1016/j.nima.2015.05.056)] and is currently under study. In order to further support the concept, the beam dynamics study on a recirculating proton linear accelerator has to be carried out. In this paper, we study the feasibility of a two-pass recirculating proton linear accelerator through the direct numerical beam dynamics design optimization and the start-to-end simulation. This study shows that the two-pass simultaneous focusing without particle losses is attainable including fully 3D space-charge effects through the entire accelerator system.

  20. Accelerating Conservative Parallel Simulation of VHDL Circuits

    DTIC Science & Technology

    1994-12-01

    1993:1). Reasearchers at the Air Force Institute of Technology (AFIT) have been investigating conservative parallel simulation of VHDL circuits for...ered with regard to size, time, and memory consumption. 2A behavior is an executable VHDL process representing a logic gate, source signal, or other...parameters significant to simulation runtime. Candidate parameters include: * number of behaviors * number of interconnections * number of dependencies

  1. Simulation in dermatologic surgery: a new paradigm in training.

    PubMed

    Nicholas, Luke; Toren, Kristen; Bingham, Jonathan; Marquart, Jason

    2013-01-01

    Simulation-based training has become popular in many surgical residencies for acquiring procedural skills, but simulator use is rare in dermatologic training. To evaluate the perceived efficacy of obtaining dermatologic procedural skills using simulators. Opinions of dermatology residents and staff regarding simulator use were assessed using questionnaires completed after a 2-day surgical symposium in which participants were instructed on and practiced with simulators and cadavers. Overall, 93.9% strongly agreed that simulators are helpful in acquiring procedural skills. More than three-quarters of participants agreed that simulators are useful in acquiring, refining, assessing, and learning these skills. Many participants further thought that simulator use would be beneficial in learning anatomy and trouble-shooting techniques. An overwhelming majority of those surveyed believed that training on simulators would be helpful in learning various dermatologic procedures; 90.9% of participants thought that training using simulators should be, at least in part, a mandatory component of residency. It was felt that this training should be conducted at the beginning of residency, with additional with sessions held throughout training. Simulation offers an excellent model for the acquisition and assessment of dermatologic procedural skills. Cost and availability of instructors remain obstacles. Further studies are required to evaluate the implementation and effectiveness of these models. © 2012 by the American Society for Dermatologic Surgery, Inc. Published by Wiley Periodicals, Inc.

  2. ELECTROMAGNETIC SIMULATIONS OF LINEAR PROTON ACCELERATOR STRUCTURES USING DIELECTRIC WALL ACCELERATORS

    SciTech Connect

    Nelson, S; Poole, B; Caporaso, G

    2007-06-15

    Proton accelerator structures for medical applications using Dielectric Wall Accelerator (DWA) technology allow for the utilization of high electric field gradients on the order of 100 MV/m to accelerate the proton bunch. Medical applications involving cancer therapy treatment usually desire short bunch lengths on the order of hundreds of picoseconds in order to limit the extent of the energy deposited in the tumor site (in 3D space, time, and deposited proton charge). Electromagnetic simulations of the DWA structure, in combination with injections of proton bunches have been performed using 3D finite difference codes in combination with particle pushing codes. Electromagnetic simulations of DWA structures includes these effects and also include the details of the switch configuration and how that switch time affects the electric field pulse which accelerates the particle beam.

  3. ELECTROMAGNETIC SIMULATIONS OF DIELECTRIC WALL ACCELERATOR STRUCTURES FOR ELECTRON BEAM ACCELERATION

    SciTech Connect

    Nelson, S D; Poole, B R

    2005-05-05

    Dielectric Wall Accelerator (DWA) technology incorporates the energy storage mechanism, the switching mechanism, and the acceleration mechanism for electron beams. Electromagnetic simulations of DWA structures includes these effects and also details of the switch configuration and how that switch time affects the electric field pulse which accelerates the particle beam. DWA structures include both bi-linear and bi-spiral configurations with field gradients on the order of 20MV/m and the simulations include the effects of the beampipe, the beampipe walls, the DWA High Gradient Insulator (HGI) insulating stack, wakefield impedance calculations, and test particle trajectories with low emittance gain. Design trade-offs include the transmission line impedance (typically a few ohms), equilibration ring optimization, driving switch inductances, and layer-to-layer coupling effects and the associated affect on the acceleration pulse's peak value.

  4. Changing the Paradigm: Simulation, a Method of First Resort

    DTIC Science & Technology

    2011-09-01

    the substantial increases in computing power and memory availability , it was proposed that two additional periods may be examined: the Maturation...throughout the 1990s. It was during this period that the use of simulations for operational wargaming became widespread (Army Modeling & Simulation Office...safety. (For more information, refer to the Acquisition Modeling and Simulation Master Plan available via the OUSD-AT&L website at: www.acq.osd.mil/se

  5. Simulation of electron post-acceleration in a two-stage laser Wakefield accelerator

    SciTech Connect

    Reitsma, A.J.W.; Leemans, W.P.; Esarey, E.; Kamp, L.P.J.; Schep, T.J.

    2002-04-01

    Electron bunches produced in self-modulated laser wakefield experiments usually have a broad energy spectrum, with most electrons at low energy (1-3 MeV) and only a small fraction at high energy. We propose and investigate further acceleration of such bunches in a channel-guided resonant laser wakefield accelerator. Two-dimensional simulations with and without the effects of self-consistent beam loading are performed and compared. These results indicate that it is possible to trap about 40 percent of the injected bunch charge and accelerate this fraction to an average energy of about 50 MeV in a plasma channel of a few mn.

  6. Graphics Processing Unit Acceleration of Gyrokinetic Turbulence Simulations

    NASA Astrophysics Data System (ADS)

    Hause, Benjamin; Parker, Scott

    2012-10-01

    We find a substantial increase in on-node performance using Graphics Processing Unit (GPU) acceleration in gyrokinetic delta-f particle-in-cell simulation. Optimization is performed on a two-dimensional slab gyrokinetic particle simulation using the Portland Group Fortran compiler with the GPU accelerator compiler directives. We have implemented the GPU acceleration on a Core I7 gaming PC with a NVIDIA GTX 580 GPU. We find comparable, or better, acceleration relative to the NERSC DIRAC cluster with the NVIDIA Tesla C2050 computing processor. The Tesla C 2050 is about 2.6 times more expensive than the GTX 580 gaming GPU. Optimization strategies and comparisons between DIRAC and the gaming PC will be presented. We will also discuss progress on optimizing the comprehensive three dimensional general geometry GEM code.

  7. Fully Implict Magneto-hydrodynamics Simulations of Coaxial Plasma Accelerators

    DOE PAGES

    Subramaniam, Vivek; Raja, Laxminarayan L.

    2017-01-05

    The resistive Magneto-Hydrodynamic (MHD) model describes the behavior of a strongly ionized plasma in the presence of external electric and magnetic fields. We developed a fully implicit MHD simulation tool to solve the resistive MHD governing equations in the context of a cell-centered finite-volume scheme. The primary objective of this study is to use the fully-implicit algorithm to obtain insights into the plasma acceleration and jet formation processes in Coaxial Plasma accelerators; electromagnetic acceleration devices that utilize self-induced magnetic fields to accelerate thermal plasmas to large velocities. We also carry out plasma-surface simulations in order to study the impact interactionsmore » when these high velocity plasma jets impinge on target material surfaces. Scaling studies are carried out to establish some basic functional relationships between the target-stagnation conditions and the current discharged between the coaxial electrodes.« less

  8. Simulations of collisionless shocks - Some implications for particle acceleration

    NASA Astrophysics Data System (ADS)

    Burgess, D.

    1992-08-01

    The role of self-consistent plasma simulations is discussed with reference to collisionless shock structure and the extraction of thermal particles to supra-thermal energies. Examples are given from quasi-perpendicular and parallel shock geometries. The cyclic reformation behavior of the quasi-parallel shock, as revealed by simulations, is detailed, and some implications given. Finally, some recent advances are described in the techniques of simulation of strong particle acceleration.

  9. Start-to-end simulation with rare isotope beam for post accelerator of the RAON accelerator

    NASA Astrophysics Data System (ADS)

    Jin, Hyunchang; Jang, Ji-Ho

    2016-09-01

    The RAON accelerator for the Rare Isotope Science Project (RISP) has been developed to create and accelerate various kinds of stable heavy ion beams and rare isotope beams for a wide range of science applications. In the RAON accelerator, the rare isotope beams generated by the Isotope Separation On-Line (ISOL) system will be transported through the post accelerator, namely, from the post Low Energy Beam Transport (LEBT) system and the post Radio Frequency Quadrupole (RFQ) to the superconducting linac (SCL3). The accelerated beams will be put to use in the low energy experimental hall or accelerated again by the superconducting linac (SCL2) in order to be used in the high energy experimental hall. In this paper, we will describe the results of the start-toend simulations with the rare isotope beams generated by the ISOL system in the post accelerator of the RAON accelerator. In addition, the error analysis and correction at the superconducting linac SCL3 will be presented.

  10. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  11. Recirculating Linac Acceleration - End-to-End Simulation

    SciTech Connect

    Alex Bogacz

    2010-03-01

    A conceptual design of a high-pass-number Recirculating Linear Accelerator (RLA) for muons is presented. The scheme involves three superconducting linacs (201 MHz): a single pass linear Pre-accelerator followed by a pair multi-pass (4.5-pass) 'Dogbone' RLAs. Acceleration starts after ionization cooling at 220 MeV/c and proceeds to 12.6 GeV. The Pre-accelerator captures a large muon phase space and accelerates muons to relativistic energies, while adiabatically decreasing the phase-space volume, so that effective acceleration in the RLA is possible. The RLA further compresses and shapes up the longitudinal and transverse phase-spaces, while increasing the energy. Appropriate choice of multi-pass linac optics based on FODO focusing assures large number of passes in the RLA. The proposed 'Dogbone' configuration facilitates simultaneous acceleration of both mu± species through the requirement of mirror symmetric optics of the return 'droplet' arcs. Finally, presented end-to-end simulation validates the efficiency and acceptance of the accelerator system.

  12. Accelerating Subsurface Transport Simulation on Heterogeneous Clusters

    SciTech Connect

    Villa, Oreste; Gawande, Nitin A.; Tumeo, Antonino

    2013-09-23

    Reactive transport numerical models simulate chemical and microbiological reactions that occur along a flowpath. These models have to compute reactions for a large number of locations. They solve the set of ordinary differential equations (ODEs) that describes the reaction for each location through the Newton-Raphson technique. This technique involves computing a Jacobian matrix and a residual vector for each set of equation, and then solving iteratively the linearized system by performing Gaussian Elimination and LU decomposition until convergence. STOMP, a well known subsurface flow simulation tool, employs matrices with sizes in the order of 100x100 elements and, for numerical accuracy, LU factorization with full pivoting instead of the faster partial pivoting. Modern high performance computing systems are heterogeneous machines whose nodes integrate both CPUs and GPUs, exposing unprecedented amounts of parallelism. To exploit all their computational power, applications must use both the types of processing elements. For the case of subsurface flow simulation, this mainly requires implementing efficient batched LU-based solvers and identifying efficient solutions for enabling load balancing among the different processors of the system. In this paper we discuss two approaches that allows scaling STOMP's performance on heterogeneous clusters. We initially identify the challenges in implementing batched LU-based solvers for small matrices on GPUs, and propose an implementation that fulfills STOMP's requirements. We compare this implementation to other existing solutions. Then, we combine the batched GPU solver with an OpenMP-based CPU solver, and present an adaptive load balancer that dynamically distributes the linear systems to solve between the two components inside a node. We show how these approaches, integrated into the full application, provide speed ups from 6 to 7 times on large problems, executed on up to 16 nodes of a cluster with two AMD Opteron 6272

  13. Electron Acceleration in Shock-Shock Interaction: Simulations and Observations

    NASA Astrophysics Data System (ADS)

    Nakanotani, M.; Matsukiyo, S.; Mazelle, C. X.; Hada, T.

    2015-12-01

    Collisionless shock waves play a crucial role in producing high energy particles (cosmic rays) in space. While most of the past studies about particle acceleration assume the presence of a single shock, in space two shocks frequently come close to or even collide with each other. Hietala et al. [2011] observed the collision of an interplanetary shock and the earth's bow shock and the associated acceleration of energetic ions. The kinetic natures of a shock-shock collision has not been well understood. Only the work done by using hybrid simulation was reported by Cargill et al. [1986], in which they focus on a collision of two supercritical shocks and the resultant ion acceleration. We expect similarly that electron acceleration can also occur in shock-shock collision. To investigate the electron acceleration process in a shock-shock collision, we perform one-dimensional full particle-in-cell (PIC) simulations. In the simulation energetic electrons are observed between the two approaching shocks before colliding. These energetic electrons are efficiently accelerated through multiple reflections at the two shocks (Fermi acceleration). The reflected electrons create a temperature anisotropy and excite large amplitude waves upstream via the electron fire hose instability. The large amplitude waves can scatter the energetic electrons in pitch angle so that some of them gain large pitch angles and are easily reflected when they encounter the shocks subsequently. The reflected electrons can sustain, or probably even strengthen, them. We further discuss observational results of an interaction of interplanetary shocks and the earth's bow shock by examining mainly Cluster data. We focus on whether or not electrons are accelerated in the shock-shock interaction.

  14. Simulation Studies of the Pulse Line Ion Accelerator

    NASA Astrophysics Data System (ADS)

    Henestroza, Enrique; Martinez, Roxanne

    2007-11-01

    The Heavy Ion Fusion Science Virtual National Laboratory has been studying the Pulse Line Ion Accelerator (PLIA) concept, motivated by the desire for an inexpensive way to accelerate intense short pulse heavy ion beams to regimes of interest for studies of high energy density matter and fusion ignition conditions. The PLIA uses a slow-wave structure based on a helical winding, on which a voltage pulse is launched and propagated to generate the accelerating fields. The PLIA has the ability to accelerate ion bunches to energies much greater than the peak applied voltage and over distances much larger than the voltage pulse ramp length; furthermore, the PLIA can axially confine the heavy ion beam bunch. These properties make it a good candidate for a high intensity, short bunch injector. We will present self-consistent numerical simulation studies of the beam dynamics in the PLIA.

  15. Acceleration of discrete stochastic biochemical simulation using GPGPU.

    PubMed

    Sumiyoshi, Kei; Hirata, Kazuki; Hiroi, Noriko; Funahashi, Akira

    2015-01-01

    For systems made up of a small number of molecules, such as a biochemical network in a single cell, a simulation requires a stochastic approach, instead of a deterministic approach. The stochastic simulation algorithm (SSA) simulates the stochastic behavior of a spatially homogeneous system. Since stochastic approaches produce different results each time they are used, multiple runs are required in order to obtain statistical results; this results in a large computational cost. We have implemented a parallel method for using SSA to simulate a stochastic model; the method uses a graphics processing unit (GPU), which enables multiple realizations at the same time, and thus reduces the computational time and cost. During the simulation, for the purpose of analysis, each time course is recorded at each time step. A straightforward implementation of this method on a GPU is about 16 times faster than a sequential simulation on a CPU with hybrid parallelization; each of the multiple simulations is run simultaneously, and the computational tasks within each simulation are parallelized. We also implemented an improvement to the memory access and reduced the memory footprint, in order to optimize the computations on the GPU. We also implemented an asynchronous data transfer scheme to accelerate the time course recording function. To analyze the acceleration of our implementation on various sizes of model, we performed SSA simulations on different model sizes and compared these computation times to those for sequential simulations with a CPU. When used with the improved time course recording function, our method was shown to accelerate the SSA simulation by a factor of up to 130.

  16. Scaled simulations of a 10 GeV accelerator

    SciTech Connect

    Cormier-Michel, Estelle; Geddes, C. G. R.; Schroeder, C. B.; Esarey, E.; Leemans, W. P.; Bruhwiler, D. L.; Paul, K.; Cowan, B.

    2009-01-22

    Laser plasma accelerators are able to produce high quality electron beams from 1 MeV to 1 GeV. The next generation of plasma accelerator experiments will likely use a multi-stage approach where a high quality electron bunch is first produced and then injected into an accelerating structure. In this paper we present scaled particle-in-cell simulations of a 10 GeV stage in the quasi-linear regime. We show that physical parameters can be scaled to be able to perform these simulations at reasonable computational cost. Beam loading properties and electron bunch energy gain are calculated. A range of parameter regimes are studied to optimize the quality of the electron bunch at the output of the stage.

  17. Scaled simulations of a 10 GeV accelerator

    SciTech Connect

    Cormier-Michel, Estelle; Geddes, C.G.R; Esarey, E.; Schroeder, C.B.; Bruhwiler, D.L.; Paul, K.; Cowan, B.; Leemans, W.P.

    2008-09-08

    Laser plasma accelerators are able to produce high quality electron beams from 1 MeV to 1 GeV. The next generation of plasma accelerator experiments will likely use a multi-stage approach where a high quality electron bunch is first produced and then injected into an accelerating structure. In this paper we present scaled particle-in-cell simulations of a 10 GeV stage in the quasi-linear regime. We show that physical parameters can be scaled to be able to perform these simulations at reasonable computational cost. Beam loading properties and electron bunch energy gain are calculated. A range of parameter regimes are studied to optimize the quality of the electron bunch at the output of the stage.

  18. Transverse wake field simulations for the ILC acceleration structure

    SciTech Connect

    Solyak, N.; Lunin, A.; Yakovlev, V.; /Fermilab

    2008-06-01

    Details of wake potential simulation in the acceleration structure of ILC, including the RF cavities and input/HOM couplers are presented. Transverse wake potential dependence is described versus the bunch length. Beam emittance dilution caused by main and HOM couplers is estimated, followed by a discussion of possible structural modifications allowing a reduction of transverse wake potential.

  19. Blind protein structure prediction using accelerated free-energy simulations

    PubMed Central

    Perez, Alberto; Morrone, Joseph A.; Brini, Emiliano; MacCallum, Justin L.; Dill, Ken A.

    2016-01-01

    We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition. PMID:27847872

  20. A method of evaluating helmet rotational acceleration protection using the Kingston Impact Simulator (KIS Unit).

    PubMed

    Kis, Mihaly; Saunders, Fraser W; Kis, Mihaly; Irrcher, Isabella; Tator, Charles H; Bishop, Patrick J; ten Hove, Martin W

    2013-11-01

    Helmet use is the primary form of head protection against traumatic brain injury. Although helmet designs have proven to be effective in reducing the incidence of skull fracture and major traumatic brain injury, there is little evidence that helmets protect against concussion. Linear and rotational accelerations are important mechanisms underlying concussion, yet current testing protocols do not account for rotational acceleration. Technical considerations have prevented a valid, accurate, and reproducible testing paradigm. Our objectives were to design a novel helmet-testing methodology that accurately and reliably measures rotational acceleration at injury-relevant impact forces, locations, and planes and to evaluate differences in rotational force protection in commercially available helmets. Laboratory study. The Kingston Impact Simulator (KIS unit) was used to study 10 commercially available hockey helmets. The rotational acceleration force protection was measured in the horizontal, coronal, and sagittal planes at each of 12 predetermined impact locations. Mean peak unhelmeted and helmeted accelerations at all impact locations and planes ranged from 63 to 28.6 g and from 26.8 to 8.0 g, respectively. The percent reduction in rotational acceleration for all test helmets ranged from 6.4% to 84%. Statistically significant differences in rotational acceleration between manufacturers and within a helmet brand were identified. KIS is a novel testing methodology that identifies rotation force protection within and between hockey helmet models and manufacturers at different impact location and planes. This information may be useful in improving future helmet design and construction to provide maximal protection against the forces causing concussion.

  1. Lunar Dust Simulant in Mechanical Component Testing - Paradigm and Practicality

    NASA Technical Reports Server (NTRS)

    Jett, T.; Street, K.; Abel, P.; Richmond, R.

    2008-01-01

    Due to the uniquely harsh lunar surface environment, terrestrial test activities may not adequately represent abrasive wear by lunar dust likely to be experienced in mechanical systems used in lunar exploration. Testing to identify potential moving mechanism problems has recently begun within the NASA Engineering and Safety Center Mechanical Systems Lunar Dust Assessment activity in coordination with the Exploration Technology and Development Program Dust Management Project, and these complimentary efforts will be described. Specific concerns about differences between simulant and lunar dust, and procedures for mechanical component testing with lunar simulant will be considered. In preparing for long term operations within a dusty lunar environment, the three fundamental approaches to keeping mechanical equipment functioning are dust avoidance, dust removal, and dust tolerance, with some combination of the three likely to be found in most engineering designs. Methods to exclude dust from contact with mechanical components would constitute mitigation by dust avoidance, so testing seals for dust exclusion efficacy as a function of particle size provides useful information for mechanism design. Dust of particle size less than a micron is not well documented for impact on lunar mechanical components. Therefore, creating a standardized lunar dust simulant in the particulate size range of ca. 0.1 to 1.0 micrometer is useful for testing effects on mechanical components such as bearings, gears, seals, bushings, and other moving mechanical assemblies. Approaching actual wear testing of mechanical components, it is beneficial to first establish relative wear rates caused by dust on commonly used mechanical component materials. The wear mode due to dust within mechanical components, such as abrasion caused by dust in grease(s), needs to be considered, as well as the effects of vacuum, lunar thermal cycle, and electrostatics on wear rate.

  2. Simulations of ion acceleration at non-relativistic shocks. I. Acceleration efficiency

    SciTech Connect

    Caprioli, D.; Spitkovsky, A.

    2014-03-10

    We use two-dimensional and three-dimensional hybrid (kinetic ions-fluid electrons) simulations to investigate particle acceleration and magnetic field amplification at non-relativistic astrophysical shocks. We show that diffusive shock acceleration operates for quasi-parallel configurations (i.e., when the background magnetic field is almost aligned with the shock normal) and, for large sonic and Alfvénic Mach numbers, produces universal power-law spectra ∝p {sup –4}, where p is the particle momentum. The maximum energy of accelerated ions increases with time, and it is only limited by finite box size and run time. Acceleration is mainly efficient for parallel and quasi-parallel strong shocks, where 10%-20% of the bulk kinetic energy can be converted to energetic particles and becomes ineffective for quasi-perpendicular shocks. Also, the generation of magnetic turbulence correlates with efficient ion acceleration and vanishes for quasi-perpendicular configurations. At very oblique shocks, ions can be accelerated via shock drift acceleration, but they only gain a factor of a few in momentum and their maximum energy does not increase with time. These findings are consistent with the degree of polarization and the morphology of the radio and X-ray synchrotron emission observed, for instance, in the remnant of SN 1006. We also discuss the transition from thermal to non-thermal particles in the ion spectrum (supra-thermal region) and we identify two dynamical signatures peculiar of efficient particle acceleration, namely, the formation of an upstream precursor and the alteration of standard shock jump conditions.

  3. Accelerating the paradigm shift toward inclusion of pregnant women in drug research: Ethical and regulatory considerations.

    PubMed

    White, Amina

    2015-11-01

    Although there has been long-standing reluctance to include pregnant women as clinical trial participants, increasing recognition of profound gaps in research on the safety and efficacy of drugs often prescribed to pregnant women calls into question the practice of routinely excluding them. This article presents compelling reasons for including pregnant women in clinical research, highlights certain regulatory barriers to the inclusion of pregnant women, and proposes that professional societies with expertise in obstetrics and maternal-fetal medicine can be instrumental in hastening the paradigm shift from the systematic exclusion of pregnant women in research to a one of responsible and fair inclusion. Published by Elsevier Inc.

  4. Monte Carlo simulation of particle acceleration at astrophysical shocks

    NASA Technical Reports Server (NTRS)

    Campbell, Roy K.

    1989-01-01

    A Monte Carlo code was developed for the simulation of particle acceleration at astrophysical shocks. The code is implemented in Turbo Pascal on a PC. It is modularized and structured in such a way that modification and maintenance are relatively painless. Monte Carlo simulations of particle acceleration at shocks follow the trajectories of individual particles as they scatter repeatedly across the shock front, gaining energy with each crossing. The particles are assumed to scatter from magnetohydrodynamic (MHD) turbulence on both sides of the shock. A scattering law is used which is related to the assumed form of the turbulence, and the particle and shock parameters. High energy cosmic ray spectra derived from Monte Carlo simulations have observed power law behavior just as the spectra derived from analytic calculations based on a diffusion equation. This high energy behavior is not sensitive to the scattering law used. In contrast with Monte Carlo calculations diffusive calculations rely on the initial injection of supra-thermal particles into the shock environment. Monte Carlo simulations are the only known way to describe the extraction of particles directly from the thermal pool. This was the triumph of the Monte Carlo approach. The question of acceleration efficiency is an important one in the shock acceleration game. The efficiency of shock waves efficient to account for the observed flux of high energy galactic cosmic rays was examined. The efficiency of the acceleration process depends on the thermal particle pick-up and hence the low energy scattering in detail. One of the goals is the self-consistent derivation of the accelerated particle spectra and the MHD turbulence spectra. Presumably the upstream turbulence, which scatters the particles so they can be accelerated, is excited by the streaming accelerated particles and the needed downstream turbulence is convected from the upstream region. The present code is to be modified to include a better

  5. Monte Carlo simulation of particle acceleration at astrophysical shocks

    NASA Technical Reports Server (NTRS)

    Campbell, Roy K.

    1989-01-01

    A Monte Carlo code was developed for the simulation of particle acceleration at astrophysical shocks. The code is implemented in Turbo Pascal on a PC. It is modularized and structured in such a way that modification and maintenance are relatively painless. Monte Carlo simulations of particle acceleration at shocks follow the trajectories of individual particles as they scatter repeatedly across the shock front, gaining energy with each crossing. The particles are assumed to scatter from magnetohydrodynamic (MHD) turbulence on both sides of the shock. A scattering law is used which is related to the assumed form of the turbulence, and the particle and shock parameters. High energy cosmic ray spectra derived from Monte Carlo simulations have observed power law behavior just as the spectra derived from analytic calculations based on a diffusion equation. This high energy behavior is not sensitive to the scattering law used. In contrast with Monte Carlo calculations diffusive calculations rely on the initial injection of supra-thermal particles into the shock environment. Monte Carlo simulations are the only known way to describe the extraction of particles directly from the thermal pool. This was the triumph of the Monte Carlo approach. The question of acceleration efficiency is an important one in the shock acceleration game. The efficiency of shock waves efficient to account for the observed flux of high energy galactic cosmic rays was examined. The efficiency of the acceleration process depends on the thermal particle pick-up and hence the low energy scattering in detail. One of the goals is the self-consistent derivation of the accelerated particle spectra and the MHD turbulence spectra. Presumably the upstream turbulence, which scatters the particles so they can be accelerated, is excited by the streaming accelerated particles and the needed downstream turbulence is convected from the upstream region. The present code is to be modified to include a better

  6. Beam Dynamics Design and Simulation in Ion Linear Accelerators (

    SciTech Connect

    Ostroumov, Peter N.; Asseev, Vladislav N.; Mustapha, and Brahim

    2006-08-01

    Orginally, the ray tracing code TRACK has been developed to fulfill the many special requirements for the Rare Isotope Accelerator Facility known as RIA. Since no available beam-dynamics code met all the necessary requirements, modifications to the code TRACK were introduced to allow end-to-end (from the ion souce to the production target) simulations of the RIA machine, TRACK is a general beam-dynamics code and can be applied for the design, commissioning and operation of modern ion linear accelerators and beam transport systems.

  7. Ritanserin facilitates anxiety in a simulated public-speaking paradigm.

    PubMed

    Guimarães, F S; Mbaya, P S; Deakin, J F

    1997-01-01

    The effects of ritanserin, a 5-HT2A/2C (5-hydroxytryptamine) antagonist, have been investigated in simulated public speaking with healthy volunteers. The aim was to investigate the role of 5-HT in subjective experimental anxiety. There were three experimental groups each comprising four or five males and 11 females. Subjects received placebo, ritanserin 2.5 or 10 mg, p.o. They rated themselves using the Spielberger State-Trait Anxiety Inventory and visual analogue scales factored into anxiety, sedation and discontentment scores. Autonomic measures included skin conductance and heart rate. Subjects were told, 75 min after drug or placebo ingestion, without prior warning, to prepare a 4-min speech. Measures were taken before, during and after the speech. Ritanserin prolonged the anxiety induced by the procedure on the subjective ratings but had minimal effect on autonomic responses to the procedure. The result contrasts with an anxiolytic-like effect of ritanserin on aversively conditioned autonomic responses. The present finding is compatible with animal behavioural evidence that 5-HT has distinct and opposing roles in modulating conditioned and unconditioned anxiety.

  8. Accelerating sino-atrium computer simulations with graphic processing units.

    PubMed

    Zhang, Hong; Xiao, Zheng; Lin, Shien-fong

    2015-01-01

    Sino-atrial node cells (SANCs) play a significant role in rhythmic firing. To investigate their role in arrhythmia and interactions with the atrium, computer simulations based on cellular dynamic mathematical models are generally used. However, the large-scale computation usually makes research difficult, given the limited computational power of Central Processing Units (CPUs). In this paper, an accelerating approach with Graphic Processing Units (GPUs) is proposed in a simulation consisting of the SAN tissue and the adjoining atrium. By using the operator splitting method, the computational task was made parallel. Three parallelization strategies were then put forward. The strategy with the shortest running time was further optimized by considering block size, data transfer and partition. The results showed that for a simulation with 500 SANCs and 30 atrial cells, the execution time taken by the non-optimized program decreased 62% with respect to a serial program running on CPU. The execution time decreased by 80% after the program was optimized. The larger the tissue was, the more significant the acceleration became. The results demonstrated the effectiveness of the proposed GPU-accelerating methods and their promising applications in more complicated biological simulations.

  9. Acceleration of block-matching algorithms using a custom instruction-based paradigm on a Nios II microprocessor

    NASA Astrophysics Data System (ADS)

    González, Diego; Botella, Guillermo; García, Carlos; Prieto, Manuel; Tirado, Francisco

    2013-12-01

    This contribution focuses on the optimization of matching-based motion estimation algorithms widely used for video coding standards using an Altera custom instruction-based paradigm and a combination of synchronous dynamic random access memory (SDRAM) with on-chip memory in Nios II processors. A complete profile of the algorithms is achieved before the optimization, which locates code leaks, and afterward, creates a custom instruction set, which is then added to the specific design, enhancing the original system. As well, every possible memory combination between on-chip memory and SDRAM has been tested to achieve the best performance. The final throughput of the complete designs are shown. This manuscript outlines a low-cost system, mapped using very large scale integration technology, which accelerates software algorithms by converting them into custom hardware logic blocks and showing the best combination between on-chip memory and SDRAM for the Nios II processor.

  10. Note: Numerical simulation and experimental validation of accelerating voltage formation for a pulsed electron accelerator

    SciTech Connect

    Egorov, I.

    2014-06-15

    This paper describes the development of a computation model of a pulsed voltage generator for a repetitive electron accelerator. The model is based on a principle circuit of the generator, supplemented with the parasitics elements of the construction. Verification of the principle model was achieved by comparison of simulation with experimental results, where reasonable agreement was demonstrated for a wide range of generator load resistance.

  11. Monte Carlo simulations of particle acceleration at oblique shocks

    NASA Technical Reports Server (NTRS)

    Baring, Matthew G.; Ellison, Donald C.; Jones, Frank C.

    1994-01-01

    The Fermi shock acceleration mechanism may be responsible for the production of high-energy cosmic rays in a wide variety of environments. Modeling of this phenomenon has largely focused on plane-parallel shocks, and one of the most promising techniques for its study is the Monte Carlo simulation of particle transport in shocked fluid flows. One of the principal problems in shock acceleration theory is the mechanism and efficiency of injection of particles from the thermal gas into the accelerated population. The Monte Carlo technique is ideally suited to addressing the injection problem directly, and previous applications of it to the quasi-parallel Earth bow shock led to very successful modeling of proton and heavy ion spectra, as well as other observed quantities. Recently this technique has been extended to oblique shock geometries, in which the upstream magnetic field makes a significant angle Theta(sub B1) to the shock normal. Spectral resutls from test particle Monte Carlo simulations of cosmic-ray acceleration at oblique, nonrelativistic shocks are presented. The results show that low Mach number shocks have injection efficiencies that are relatively insensitive to (though not independent of) the shock obliquity, but that there is a dramatic drop in efficiency for shocks of Mach number 30 or more as the obliquity increases above 15 deg. Cosmic-ray distributions just upstream of the shock reveal prominent bumps at energies below the thermal peak; these disappear far upstream but might be observable features close to astrophysical shocks.

  12. New Developments in the Simulation of Advanced Accelerator Concepts

    SciTech Connect

    Paul, K.; Cary, J.R.; Cowan, B.; Bruhwiler, D.L.; Geddes, C.G.R.; Mullowney, P.J.; Messmer, P.; Esarey, E.; Cormier-Michel, E.; Leemans, W.P.; Vay, J.-L.

    2008-09-10

    Improved computational methods are essential to the diverse and rapidly developing field of advanced accelerator concepts. We present an overview of some computational algorithms for laser-plasma concepts and high-brightness photocathode electron sources. In particular, we discuss algorithms for reduced laser-plasma models that can be orders of magnitude faster than their higher-fidelity counterparts, as well as important on-going efforts to include relevant additional physics that has been previously neglected. As an example of the former, we present 2D laser wakefield accelerator simulations in an optimal Lorentz frame, demonstrating>10 GeV energy gain of externally injected electrons over a 2 m interaction length, showing good agreement with predictions from scaled simulations and theory, with a speedup factor of ~;;2,000 as compared to standard particle-in-cell.

  13. Simulation of cardiovascular response to acceleration stress following weightless exposure

    NASA Technical Reports Server (NTRS)

    Srinivasan, R.; Leonard, J. I.

    1983-01-01

    Physiological adjustments taking place during space flight tend to reduce the tolerance of the crew to headward (+Gz) acceleration experienced during the reentry phase of the flight. This reduced tolerance to acceleration stress apparently arises from an adaptation to the microgravity environment of space, including a decrease in the total circulating blood volume. Countermeasures such as anti-g garments have long been known to improve the tolerance to headward g-force, but their effectiveness in space flight has not been fully evaluated. The simulation study presented in this paper is concerned with the response of the cardiovascular system to g-stress following cardiovascular deconditioning, resulting from exposure to weightlessness, or any of its ground-based experimental analogs. The results serve to demonstrate the utility of mathematical modeling and computer simulation for studying the causes of orthostatic intolerance and the remedial measures to lessen it.

  14. SIMULATING AN ACCELERATION SCHEDULE FOR NDCX-II

    SciTech Connect

    Sharp, W.M.; Friedman, A.; Grote, D.P.; Henestroza, E.; Leitner, M.A.; Waldron, W.L.

    2009-05-01

    The Virtual National Laboratory for Heavy-Ion Fusion Science is developing a physics design for NDCX-II, an experiment to study warm dense matter heated by ions. Present plans call for using 34 induction cells to accelerate 45 nC of Li+ ions to more than 3 MeV, followed by neutralized drift-compression. To heat targets to the desired temperatures, the beam must be compressed to a millimeter-scale radius and a duration of about 1 ns. A novel NDCX-II acceleration schedule has been developed using an interactive one-dimensional particle-in-cell simulation ASP to model the longitudinal physics and axisymmetric WARP simulations to validate the 1-D model and add transverse focusing. Three-dimensional Warp runs have been used recently to study the sensitivity to misalignments in the focusing solenoids.

  15. The Particle Accelerator Simulation Code PyORBIT

    SciTech Connect

    Gorlov, Timofey V; Holmes, Jeffrey A; Cousineau, Sarah M; Shishlo, Andrei P

    2015-01-01

    The particle accelerator simulation code PyORBIT is presented. The structure, implementation, history, parallel and simulation capabilities, and future development of the code are discussed. The PyORBIT code is a new implementation and extension of algorithms of the original ORBIT code that was developed for the Spallation Neutron Source accelerator at the Oak Ridge National Laboratory. The PyORBIT code has a two level structure. The upper level uses the Python programming language to control the flow of intensive calculations performed by the lower level code implemented in the C++ language. The parallel capabilities are based on MPI communications. The PyORBIT is an open source code accessible to the public through the Google Open Source Projects Hosting service.

  16. Simulating An Acceleration Schedule For NDCX-II

    SciTech Connect

    Sharp, W M; Friedman, A; Grote, D P; Henestroza, E; Leitner, M A; Waldron, W L

    2009-05-18

    The Virtual National Laboratory for Heavy-Ion Fusion Science is developing a physics design for NDCX-II, an experiment to study warm dense matter heated by ions. Present plans call for using 34 induction cells to accelerate 45 nC of Li{sup +} ions to more than 3 MeV, followed by neutralized drift-compression. To heat targets to the desired temperatures, the beam must be compressed to a millimeter-scale radius and a duration of about 1 ns. A novel NDCX-II acceleration schedule has been developed using an interactive one-dimensional particle-in-cell simulation ASP to model the longitudinal physics and axisymmetric WARP simulations to validate the 1-D model and add transverse focusing. Three-dimensional Warp runs have been used recently to study the sensitivity to misalignments in the focusing solenoids.

  17. New Developments in the Simulation of Advanced Accelerator Concepts

    SciTech Connect

    Bruhwiler, David L.; Cary, John R.; Cowan, Benjamin M.; Paul, Kevin; Mullowney, Paul J.; Messmer, Peter; Geddes, Cameron G. R.; Esarey, Eric; Cormier-Michel, Estelle; Leemans, Wim; Vay, Jean-Luc

    2009-01-22

    Improved computational methods are essential to the diverse and rapidly developing field of advanced accelerator concepts. We present an overview of some computational algorithms for laser-plasma concepts and high-brightness photocathode electron sources. In particular, we discuss algorithms for reduced laser-plasma models that can be orders of magnitude faster than their higher-fidelity counterparts, as well as important on-going efforts to include relevant additional physics that has been previously neglected. As an example of the former, we present 2D laser wakefield accelerator simulations in an optimal Lorentz frame, demonstrating >10 GeV energy gain of externally injected electrons over a 2 m interaction length, showing good agreement with predictions from scaled simulations and theory, with a speedup factor of {approx}2,000 as compared to standard particle-in-cell.

  18. Synergia: a modern tool for accelerator physics simulation

    SciTech Connect

    Spentzouris, P.; Amundson, J.; /Fermilab

    2004-10-01

    High precision modeling of space-charge effects, together with accurate treatment of single-particle dynamics, is essential for designing future accelerators as well as optimizing the performance of existing machines. Synergia is a high-fidelity parallel beam dynamics simulation package with fully three dimensional space-charge capabilities and a higher order optics implementation. We describe the computational techniques, the advanced human interface, and the parallel performance obtained using large numbers of macroparticles.

  19. Community Petascale Project for Accelerator Science and Simulation

    SciTech Connect

    Warren B. Mori

    2013-02-01

    The UCLA Plasma Simulation Group is a major partner of the "Community Petascale Project for Accelerator Science and Simulation. This is the final technical report. We include an overall summary, a list of publications and individual progress reports for each years. During the past five years we have made tremendous progress in enhancing the capabilities of OSIRIS and QuickPIC, in developing new algorithms and data structures for PIC codes to run on GPUS and many future core architectures, and in using these codes to model experiments and in making new scientific discoveries. Here we summarize some highlights for which SciDAC was a major contributor.

  20. Accelerating particle-in-cell simulations using multilevel Monte Carlo

    NASA Astrophysics Data System (ADS)

    Ricketson, Lee

    2015-11-01

    Particle-in-cell (PIC) simulations have been an important tool in understanding plasmas since the dawn of the digital computer. Much more recently, the multilevel Monte Carlo (MLMC) method has accelerated particle-based simulations of a variety of systems described by stochastic differential equations (SDEs), from financial portfolios to porous media flow. The fundamental idea of MLMC is to perform correlated particle simulations using a hierarchy of different time steps, and to use these correlations for variance reduction on the fine-step result. This framework is directly applicable to the Langevin formulation of Coulomb collisions, as demonstrated in previous work, but in order to apply to PIC simulations of realistic scenarios, MLMC must be generalized to incorporate self-consistent evolution of the electromagnetic fields. We present such a generalization, with rigorous results concerning its accuracy and efficiency. We present examples of the method in the collisionless, electrostatic context, and discuss applications and extensions for the future.

  1. Accelerating gravitational microlensing simulations using the Xeon Phi coprocessor

    NASA Astrophysics Data System (ADS)

    Chen, B.; Kantowski, R.; Dai, X.; Baron, E.; Van der Mark, P.

    2017-04-01

    Recently Graphics Processing Units (GPUs) have been used to speed up very CPU-intensive gravitational microlensing simulations. In this work, we use the Xeon Phi coprocessor to accelerate such simulations and compare its performance on a microlensing code with that of NVIDIA's GPUs. For the selected set of parameters evaluated in our experiment, we find that the speedup by Intel's Knights Corner coprocessor is comparable to that by NVIDIA's Fermi family of GPUs with compute capability 2.0, but less significant than GPUs with higher compute capabilities such as the Kepler. However, the very recently released second generation Xeon Phi, Knights Landing, is about 5.8 times faster than the Knights Corner, and about 2.9 times faster than the Kepler GPU used in our simulations. We conclude that the Xeon Phi is a very promising alternative to GPUs for modern high performance microlensing simulations.

  2. Simulating synchrotron radiation in accelerators including diffuse and specular reflections

    NASA Astrophysics Data System (ADS)

    Dugan, G.; Sagan, D.

    2017-02-01

    An accurate calculation of the synchrotron radiation flux within the vacuum chamber of an accelerator is needed for a number of applications. These include simulations of electron cloud effects and the design of radiation masking systems. To properly simulate the synchrotron radiation, it is important to include the scattering of the radiation at the vacuum chamber walls. To this end, a program called synrad3d has been developed which simulates the production and propagation of synchrotron radiation using a collection of photons. Photons generated by a charged particle beam are tracked from birth until they strike the vacuum chamber wall where the photon is either absorbed or scattered. Both specular and diffuse scattering is simulated. If a photon is scattered, it is further tracked through multiple encounters with the wall until it is finally absorbed. This paper describes the synrad3d program, with a focus on the details of its scattering model, and presents some examples of the program's use.

  3. Design of Accelerator Online Simulator Server Using Structured Data

    SciTech Connect

    Shen, Guobao; Chu, Chungming; Wu, Juhao; Kraimer, Martin; /Argonne

    2012-07-06

    Model based control plays an important role for a modern accelerator during beam commissioning, beam study, and even daily operation. With a realistic model, beam behaviour can be predicted and therefore effectively controlled. The approach used by most current high level application environments is to use a built-in simulation engine and feed a realistic model into that simulation engine. Instead of this traditional monolithic structure, a new approach using a client-server architecture is under development. An on-line simulator server is accessed via network accessible structured data. With this approach, a user can easily access multiple simulation codes. This paper describes the design, implementation, and current status of PVData, which defines the structured data, and PVAccess, which provides network access to the structured data.

  4. Introducing a new paradigm for accelerators and large experimental apparatus control systems

    NASA Astrophysics Data System (ADS)

    Catani, L.; Zani, F.; Bisegni, C.; Di Pirro, G.; Foggetta, L.; Mazzitelli, G.; Stecchi, A.

    2012-11-01

    The integration of web technologies and web services has been, in the recent years, one of the major trends in upgrading and developing distributed control systems for accelerators and large experimental apparatuses. Usually, web technologies have been introduced to complement the control systems with smart add-ons and user friendly services or, for instance, to safely allow access to the control system to users from remote sites. Despite this still narrow spectrum of employment, some software technologies developed for high-performance web services, although originally intended and optimized for these particular applications, deserve some features suggesting a deeper integration in a control system and, eventually, their use to develop some of the control system’s core components. In this paper, we present the conceptual design of a new control system for a particle accelerator and associated machine data acquisition system, based on a synergic combination of a nonrelational key/value database and network distributed object caching. The use of these technologies, to implement respectively continuous data archiving and data distribution between components, brought about the definition of a new control system concept offering a number of interesting features such as a high level of abstraction of services and components and their integration in a framework that can be seen as a comprehensive service provider that both graphical user interface applications and front-end controllers join for accessing and, to some extent, expanding its functionalities.

  5. COMPASS, the COMmunity Petascale Project for Accelerator Science And Simulation, a Broad Computational Accelerator Physics Initiative

    SciTech Connect

    Cary, J.R.; Spentzouris, P.; Amundson, J.; McInnes, L.; Borland, M.; Mustapha, B.; Norris, B.; Ostroumov, P.; Wang, Y.; Fischer, W.; Fedotov, A.; Ben-Zvi, I.; Ryne, R.; Esarey, E.; Geddes, C.; Qiang, J.; Ng, E.; Li, S.; Ng, C.; Lee, R.; Merminga, L.; /Jefferson Lab /Tech-X, Boulder /UCLA /Colorado U. /Maryland U. /Southern California U.

    2007-11-09

    Accelerators are the largest and most costly scientific instruments of the Department of Energy, with uses across a broad range of science, including colliders for particle physics and nuclear science and light sources and neutron sources for materials studies. COMPASS, the Community Petascale Project for Accelerator Science and Simulation, is a broad, four-office (HEP, NP, BES, ASCR) effort to develop computational tools for the prediction and performance enhancement of accelerators. The tools being developed can be used to predict the dynamics of beams in the presence of optical elements and space charge forces, the calculation of electromagnetic modes and wake fields of cavities, the cooling induced by comoving beams, and the acceleration of beams by intense fields in plasmas generated by beams or lasers. In SciDAC-1, the computational tools had multiple successes in predicting the dynamics of beams and beam generation. In SciDAC-2 these tools will be petascale enabled to allow the inclusion of an unprecedented level of physics for detailed prediction.

  6. COMPASS, the COMmunity Petascale project for Accelerator Science and Simulation, a board computational accelerator physics initiative

    SciTech Connect

    Cary, J.R.; Spentzouris, P.; Amundson, J.; McInnes, L.; Borland, M.; Mustapha, B.; Ostroumov, P.; Wang, Y.; Fischer, W.; Fedotov, A.; Ben-Zvi, I.; Ryne, R.; Esarey, E.; Geddes, C.; Qiang, J.; Ng, E.; Li, S.; Ng, C.; Lee, R.; Merminga, L.; Wang, H.; Bruhwiler, D.L.; Dechow, D.; Mullowney, P.; Messmer, P.; Nieter, C.; Ovtchinnikov, S.; Paul, K.; Stoltz, P.; Wade-Stein, D.; Mori, W.B.; Decyk, V.; Huang, C.K.; Lu, W.; Tzoufras, M.; Tsung, F.; Zhou, M.; Werner, G.R.; Antonsen, T.; Katsouleas, T.; Morris, B.

    2007-07-16

    Accelerators are the largest and most costly scientific instruments of the Department of Energy, with uses across a broad range of science, including colliders for particle physics and nuclear science and light sources and neutron sources for materials studies. COMPASS, the Community Petascale Project for Accelerator Science and Simulation, is a broad, four-office (HEP, NP, BES, ASCR) effort to develop computational tools for the prediction and performance enhancement of accelerators. The tools being developed can be used to predict the dynamics of beams in the presence of optical elements and space charge forces, the calculation of electromagnetic modes and wake fields of cavities, the cooling induced by comoving beams, and the acceleration of beams by intense fields in plasmas generated by beams or lasers. In SciDAC-1, the computational tools had multiple successes in predicting the dynamics of beams and beam generation. In SciDAC-2 these tools will be petascale enabled to allow the inclusion of an unprecedented level of physics for detailed prediction.

  7. COMPASS, the COMmunity Petascale Project for Accelerator Science and Simulation, a broad computational accelerator physics initiative

    SciTech Connect

    J.R. Cary; P. Spentzouris; J. Amundson; L. McInnes; M. Borland; B. Mustapha; B. Norris; P. Ostroumov; Y. Wang; W. Fischer; A. Fedotov; I. Ben-Zvi; R. Ryne; E. Esarey; C. Geddes; J. Qiang; E. Ng; S. Li; C. Ng; R. Lee; L. Merminga; H. Wang; D.L. Bruhwiler; D. Dechow; P. Mullowney; P. Messmer; C. Nieter; S. Ovtchinnikov; K. Paul; P. Stoltz; D. Wade-Stein; W.B. Mori; V. Decyk; C.K. Huang; W. Lu; M. Tzoufras; F. Tsung; M. Zhou; G.R. Werner; T. Antonsen; T. Katsouleas

    2007-06-01

    Accelerators are the largest and most costly scientific instruments of the Department of Energy, with uses across a broad range of science, including colliders for particle physics and nuclear science and light sources and neutron sources for materials studies. COMPASS, the Community Petascale Project for Accelerator Science and Simulation, is a broad, four-office (HEP, NP, BES, ASCR) effort to develop computational tools for the prediction and performance enhancement of accelerators. The tools being developed can be used to predict the dynamics of beams in the presence of optical elements and space charge forces, the calculation of electromagnetic modes and wake fields of cavities, the cooling induced by comoving beams, and the acceleration of beams by intense fields in plasmas generated by beams or lasers. In SciDAC-1, the computational tools had multiple successes in predicting the dynamics of beams and beam generation. In SciDAC-2 these tools will be petascale enabled to allow the inclusion of an unprecedented level of physics for detailed prediction.

  8. Simulating Electron Clouds in Heavy-Ion Accelerators

    SciTech Connect

    Cohen, R.H.; Friedman, A.; Kireeff Covo, M.; Lund, S.M.; Molvik,A.W.; Bieniosek, F.M.; Seidl, P.A.; Vay, J-L.; Stoltz, P.; Veitzer, S.

    2005-04-07

    Contaminating clouds of electrons are a concern for most accelerators of positive-charged particles, but there are some unique aspects of heavy-ion accelerators for fusion and high-energy density physics which make modeling such clouds especially challenging. In particular, self-consistent electron and ion simulation is required, including a particle advance scheme which can follow electrons in regions where electrons are strongly-, weakly-, and un-magnetized. They describe their approach to such self-consistency, and in particular a scheme for interpolating between full-orbit (Boris) and drift-kinetic particle pushes that enables electron time steps long compared to the typical gyro period in the magnets. They present tests and applications: simulation of electron clouds produced by three different kinds of sources indicates the sensitivity of the cloud shape to the nature of the source; first-of-a-kind self-consistent simulation of electron-cloud experiments on the High-Current Experiment (HCX) at Lawrence Berkeley National Laboratory, in which the machine can be flooded with electrons released by impact of the ion beam and an end plate, demonstrate the ability to reproduce key features of the ion-beam phase space; and simulation of a two-stream instability of thin beams in a magnetic field demonstrates the ability of the large-timestep mover to accurately calculate the instability.

  9. Electromagnetic metamaterial simulations using a GPU-accelerated FDTD method

    NASA Astrophysics Data System (ADS)

    Seok, Myung-Su; Lee, Min-Gon; Yoo, SeokJae; Park, Q.-Han

    2015-12-01

    Metamaterials composed of artificial subwavelength structures exhibit extraordinary properties that cannot be found in nature. Designing artificial structures having exceptional properties plays a pivotal role in current metamaterial research. We present a new numerical simulation scheme for metamaterial research. The scheme is based on a graphic processing unit (GPU)-accelerated finite-difference time-domain (FDTD) method. The FDTD computation can be significantly accelerated when GPUs are used instead of only central processing units (CPUs). We explain how the fast FDTD simulation of large-scale metamaterials can be achieved through communication optimization in a heterogeneous CPU/GPU-based computer cluster. Our method also includes various advanced FDTD techniques: the non-uniform grid technique, the total-field/scattered-field (TFSF) technique, the auxiliary field technique for dispersive materials, the running discrete Fourier transform, and the complex structure setting. We demonstrate the power of our new FDTD simulation scheme by simulating the negative refraction of light in a coaxial waveguide metamaterial.

  10. A universal postprocessing toolkit for accelerator simulation and data analysis.

    SciTech Connect

    Borland, M.

    1998-12-16

    The Self-Describing Data Sets (SDDS) toolkit comprises about 70 generally-applicable programs sharing a common data protocol. At the Advanced Photon Source (APS), SDDS performs the vast majority of operational data collection and processing, most data display functions, and many control functions. In addition, a number of accelerator simulation codes use SDDS for all post-processing and data display. This has three principle advantages: first, simulation codes need not provide customized post-processing tools, thus simplifying development and maintenance. Second, users can enhance code capabilities without changing the code itself, by adding SDDS-based pre- and post-processing. Third, multiple codes can be used together more easily, by employing SDDS for data transfer and adaptation. Given its broad applicability, the SDDS file protocol is surprisingly simple, making it quite easy for simulations to generate SDDS-compliant data. This paper discusses the philosophy behind SDDS, contrasting it with some recent trends, and outlines the capabilities of the toolkit. The paper also gives examples of using SDDS for accelerator simulation.

  11. Graphics Processing Unit Acceleration of Gyrokinetic Turbulence Simulations

    NASA Astrophysics Data System (ADS)

    Hause, Benjamin; Parker, Scott; Chen, Yang

    2013-10-01

    We find a substantial increase in on-node performance using Graphics Processing Unit (GPU) acceleration in gyrokinetic delta-f particle-in-cell simulation. Optimization is performed on a two-dimensional slab gyrokinetic particle simulation using the Portland Group Fortran compiler with the OpenACC compiler directives and Fortran CUDA. Mixed implementation of both Open-ACC and CUDA is demonstrated. CUDA is required for optimizing the particle deposition algorithm. We have implemented the GPU acceleration on a third generation Core I7 gaming PC with two NVIDIA GTX 680 GPUs. We find comparable, or better, acceleration relative to the NERSC DIRAC cluster with the NVIDIA Tesla C2050 computing processor. The Tesla C 2050 is about 2.6 times more expensive than the GTX 580 gaming GPU. We also see enormous speedups (10 or more) on the Titan supercomputer at Oak Ridge with Kepler K20 GPUs. Results show speed-ups comparable or better than that of OpenMP models utilizing multiple cores. The use of hybrid OpenACC, CUDA Fortran, and MPI models across many nodes will also be discussed. Optimization strategies will be presented. We will discuss progress on optimizing the comprehensive three dimensional general geometry GEM code.

  12. A GPU Accelerated Simulation Program for Electron Cooling Process

    NASA Astrophysics Data System (ADS)

    Zhang, He; Huang, He; Li, Rui; Chen, Jie; Luo, Li-Shi

    2015-04-01

    Electron cooling is essential to achieve high luminosity in the medium energy electron ion collider (MIEC) project at Jefferson Lab. Bunched electron beam with energy above 50 MeV is used to cool coasting and/or bunched ion beams. Although the conventional electron cooling technique has been widely used, such an implementation in MEIC is still challenging. We are developing a simulation program for the electron cooling process to fulfill the need of the electron cooling system design for MEIC. The program simulates the evolution of the ion beam under the intrabeam scattering (IBS) effect and the electron cooling effect using Monte Carlo method. To accelerate the calculation, the program is developed on a GPU platform. We will present some preliminary simulation results. Work supported by the Department of Energy, Laboratory Directed Research and Development Funding, under Contract No. DE-AC05-06OR23177.

  13. LEGO - A Class Library for Accelerator Design and Simulation

    SciTech Connect

    Cai, Yunhai

    1998-11-19

    An object-oriented class library of accelerator design and simulation is designed and implemented in a simple and modular fashion. All physics of single-particle dynamics is implemented based on the Hamiltonian in the local frame of the component. Symplectic integrators are used to approximate the integration of the Hamiltonian. A differential algebra class is introduced to extract a Taylor map up to arbitrary order. Analysis of optics is done in the same way both for the linear and non-linear cases. Recently, Monte Carlo simulation of synchrotron radiation has been added into the library. The code is used to design and simulate the lattices of the PEP-II and SPEAR3. And it is also used for the commissioning of the PEP-II. Some examples of how to use the library will be given.

  14. DEM simulation of granular flows in a centrifugal acceleration field

    NASA Astrophysics Data System (ADS)

    Cabrera, Miguel Angel; Peng, Chong; Wu, Wei

    2017-04-01

    The main purpose of mass-flow experimental models is abstracting distinctive features of natural granular flows, and allow its systematic study in the laboratory. In this process, particle size, space, time, and stress scales must be considered for the proper representation of specific phenomena [5]. One of the most challenging tasks in small scale models, is matching the range of stresses and strains among the particle and fluid media observed in a field event. Centrifuge modelling offers an alternative to upscale all gravity-driven processes, and it has been recently employed in the simulation of granular flows [1, 2, 3, 6, 7]. Centrifuge scaling principles are presented in Ref. [4], collecting a wide spectrum of static and dynamic models. However, for the case of kinematic processes, the non-uniformity of the centrifugal acceleration field plays a major role (i.e., Coriolis and inertial effects). In this work, we discuss a general formulation for the centrifugal acceleration field, implemented in a discrete element model framework (DEM), and validated with centrifuge experimental results. Conventional DEM simulations relate the volumetric forces as a function of the gravitational force Gp = mpg. However, in the local coordinate system of a rotating centrifuge model, the cylindrical centrifugal acceleration field needs to be included. In this rotating system, the centrifugal acceleration of a particle depends on the rotating speed of the centrifuge, as well as the position and speed of the particle in the rotating model. Therefore, we obtain the formulation of centrifugal acceleration field by coordinate transformation. The numerical model is validated with a series of centrifuge experiments of monodispersed glass beads, flowing down an inclined plane at different acceleration levels and slope angles. Further discussion leads to the numerical parameterization necessary for simulating equivalent granular flows under an augmented acceleration field. The premise of

  15. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    PubMed

    Mücksch, Christian; Urbassek, Herbert M

    2014-01-01

    The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s) and experiment (up to hours), and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  16. Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics

    PubMed Central

    Mücksch, Christian; Urbassek, Herbert M.

    2013-01-01

    The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ( s) and experiment (up to hours), and the accordingly different ‘final’ adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. PMID:23755156

  17. Fast acceleration of 2D wave propagation simulations using modern computational accelerators.

    PubMed

    Wang, Wei; Xu, Lifan; Cavazos, John; Huang, Howie H; Kay, Matthew

    2014-01-01

    Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than 150x speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least 200x faster than the sequential implementation and 30x faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of 120x with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of

  18. Fast Acceleration of 2D Wave Propagation Simulations Using Modern Computational Accelerators

    PubMed Central

    Wang, Wei; Xu, Lifan; Cavazos, John; Huang, Howie H.; Kay, Matthew

    2014-01-01

    Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least faster than the sequential implementation and faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of wave propagation in

  19. Relativistic Klystron Two-Beam Accelerator Simulation Code Development

    NASA Astrophysics Data System (ADS)

    Lidia, Steven; Ryne, Robert

    1997-05-01

    We present recent work on the development and testing of a 3-D simu- lation code for relativistic klystron two-beam accelerators (RK-TBAs). This new code utilizes symplectic integration techniques to push macro- particles, coupled to a circuit equation framework that advances the fields in the cavities. Space charge effects are calculated using a Green's function approach, and pipe wall effects are included in the electrostatic approximation. We present simulations of the LBNL/LLNL RK-TBA device, emphasizing cavity power development and beam dynamics, including the high- and low-frequency beam break-up instabilities.

  20. Accelerating Climate and Weather Simulations through Hybrid Computing

    NASA Technical Reports Server (NTRS)

    Zhou, Shujia; Cruz, Carlos; Duffy, Daniel; Tucker, Robert; Purcell, Mark

    2011-01-01

    Unconventional multi- and many-core processors (e.g. IBM (R) Cell B.E.(TM) and NVIDIA (R) GPU) have emerged as effective accelerators in trial climate and weather simulations. Yet these climate and weather models typically run on parallel computers with conventional processors (e.g. Intel, AMD, and IBM) using Message Passing Interface. To address challenges involved in efficiently and easily connecting accelerators to parallel computers, we investigated using IBM's Dynamic Application Virtualization (TM) (IBM DAV) software in a prototype hybrid computing system with representative climate and weather model components. The hybrid system comprises two Intel blades and two IBM QS22 Cell B.E. blades, connected with both InfiniBand(R) (IB) and 1-Gigabit Ethernet. The system significantly accelerates a solar radiation model component by offloading compute-intensive calculations to the Cell blades. Systematic tests show that IBM DAV can seamlessly offload compute-intensive calculations from Intel blades to Cell B.E. blades in a scalable, load-balanced manner. However, noticeable communication overhead was observed, mainly due to IP over the IB protocol. Full utilization of IB Sockets Direct Protocol and the lower latency production version of IBM DAV will reduce this overhead.

  1. Acceleration of cardiac tissue simulation with graphic processing units.

    PubMed

    Sato, Daisuke; Xie, Yuanfang; Weiss, James N; Qu, Zhilin; Garfinkel, Alan; Sanderson, Allen R

    2009-09-01

    In this technical note we show the promise of using graphic processing units (GPUs) to accelerate simulations of electrical wave propagation in cardiac tissue, one of the more demanding computational problems in cardiology. We have found that the computational speed of two-dimensional (2D) tissue simulations with a single commercially available GPU is about 30 times faster than with a single 2.0 GHz Advanced Micro Devices (AMD) Opteron processor. We have also simulated wave conduction in the three-dimensional (3D) anatomic heart with GPUs where we found the computational speed with a single GPU is 1.6 times slower than with a 32-central processing unit (CPU) Opteron cluster. However, a cluster with two or four GPUs is faster than the CPU-based cluster. These results demonstrate that a commodity personal computer is able to perform a whole heart simulation of electrical wave conduction within times that enable the investigators to interact more easily with their simulations.

  2. PIC simulations on the termination shock: Microstructure and electron acceleration

    NASA Astrophysics Data System (ADS)

    Matsukiyo, S.; Scholer, M.

    2013-05-01

    The ability of the termination shock as a particle accelerator is totally unknown. Voyager data and recent kinetic numerical simulations revealed that the compression ratio of the termination shock is rather low due to the presence of pickup ions, i.e., the termination shock appears to be a weak shock. Nevertheless, two Voyager spacecraft observed not only high energy ions called termination shock particles, which are non-thermal but less energetic compared to the so-called anomalous cosmic rays, but also high energy electrons. In this study we focus especially on microstructure of the termination shock and the associated electron acceleration process by performing one-dimensional full particle-in-cell (PIC) simulations for a variety of parameters. For typical solar wind parameters at the termination shock, a shock potential has no sharp ramp with the spatial scale of the order of electron inertial length which is suitable for the injection of anomalous cosmic ray acceleration. Solar wind ions are not so much heated, which is consistent with Voyager spacecraft data. If a shock angle is close to 90 deg., a shock is almost time stationary or weakly breathing when a relative pickup ion density is 30%, while it becomes non-stationary if the relative pickup ion density is 20%. When the shock angle becomes oblique, a self-reformation occurs due to the interaction of solar wind ions and whistler precursors. Here, the shock angle is defined as the angle between upstream magnetic field and shock normal. For the case with relatively low beta solar wind plasma (electron beta is 0.1 and solar wind ion temperature equals to electron temperature), modified two-stream instability (MTSI) gets excited in the extended foot sustained by reflected pickup ions, and both solar wind electrons and ions are heated. If the solar wind plasma temperature gets five times higher, on the other hand, the MTSI is weakened and the pre-heating of the solar wind plasma in the extended foot is

  3. Simulation of PEP-II Accelerator Backgrounds Using TURTLE

    SciTech Connect

    Barlow, R.J.; Fieguth, T.; Kozanecki, W.; Majewski, S.A.; Roudeau, P.; Stocchi, A.; /Orsay, LAL

    2006-02-15

    We present studies of accelerator-induced backgrounds in the BaBar detector at the SLAC B-Factory, carried out using LPTURTLE, a modified version of the DECAY TURTLE simulation package. Lost-particle backgrounds in PEP-II are dominated by a combination of beam-gas bremstrahlung, beam-gas Coulomb scattering, radiative-Bhabha events and beam-beam blow-up. The radiation damage and detector occupancy caused by the associated electromagnetic shower debris can limit the usable luminosity. In order to understand and mitigate such backgrounds, we have performed a full program of beam-gas and luminosity-background simulations, that include the effects of the detector solenoidal field, detailed modeling of limiting apertures in both collider rings, and optimization of the betatron collimation scheme in the presence of large transverse tails.

  4. Wakefield Simulations for the Laser Acceleration Experiment at SLAC

    SciTech Connect

    Ng, Johnny

    2012-04-18

    Laser-driven acceleration in dielectric photonic band gap structures can provide gradients on the order of GeV/m. The small transverse dimension of the structure, on the order of the laser wavelength, presents interesting wakefield-related issues. Higher order modes can seriously degrade beam quality, and a detailed understanding is needed to mitigate such effects. On the other hand, wakefields also provide a direct way to probe the interaction of a relativistic bunch with the synchronous modes supported by the structure. Simulation studies have been carried out as part of the effort to understand the impact on beam dynamics, and to compare with data from beam experiments designed to characterize candidate structures. In this paper, we present simulation results of wakefields excited by a sub-wavelength bunch in optical photonic band gap structures.

  5. GPU Accelerated Numerical Simulation of Viscous Flow Down a Slope

    NASA Astrophysics Data System (ADS)

    Gygax, Remo; Räss, Ludovic; Omlin, Samuel; Podladchikov, Yuri; Jaboyedoff, Michel

    2014-05-01

    Numerical simulations are an effective tool in natural risk analysis. They are useful to determine the propagation and the runout distance of gravity driven movements such as debris flows or landslides. To evaluate these processes an approach on analogue laboratory experiments and a GPU accelerated numerical simulation of the flow of a viscous liquid down an inclined slope is considered. The physical processes underlying large gravity driven flows share certain aspects with the propagation of debris mass in a rockslide and the spreading of water waves. Several studies have shown that the numerical implementation of the physical processes of viscous flow produce a good fit with the observation of experiments in laboratory in both a quantitative and a qualitative way. When considering a process that is this far explored we can concentrate on its numerical transcription and the application of the code in a GPU accelerated environment to obtain a 3D simulation. The objective of providing a numerical solution in high resolution by NVIDIA-CUDA GPU parallel processing is to increase the speed of the simulation and the accuracy on the prediction. The main goal is to write an easily adaptable and as short as possible code on the widely used platform MATLAB, which will be translated to C-CUDA to achieve higher resolution and processing speed while running on a NVIDIA graphics card cluster. The numerical model, based on the finite difference scheme, is compared to analogue laboratory experiments. This way our numerical model parameters are adjusted to reproduce the effective movements observed by high-speed camera acquisitions during the laboratory experiments.

  6. Simulating synchrotron radiation in accelerators including diffuse and specular reflections

    DOE PAGES

    Dugan, G.; Sagan, D.

    2017-02-24

    An accurate calculation of the synchrotron radiation flux within the vacuum chamber of an accelerator is needed for a number of applications. These include simulations of electron cloud effects and the design of radiation masking systems. To properly simulate the synchrotron radiation, it is important to include the scattering of the radiation at the vacuum chamber walls. To this end, a program called synrad3d has been developed which simulates the production and propagation of synchrotron radiation using a collection of photons. Photons generated by a charged particle beam are tracked from birth until they strike the vacuum chamber wall wheremore » the photon is either absorbed or scattered. Both specular and diffuse scattering is simulated. If a photon is scattered, it is further tracked through multiple encounters with the wall until it is finally absorbed. This paper describes the synrad3d program, with a focus on the details of its scattering model, and presents some examples of the program’s use.« less

  7. Measuring listening effort: driving simulator vs. simple dual-task paradigm

    PubMed Central

    Wu, Yu-Hsiang; Aksan, Nazan; Rizzo, Matthew; Stangl, Elizabeth; Zhang, Xuyang; Bentler, Ruth

    2014-01-01

    Objectives The dual-task paradigm has been widely used to measure listening effort. The primary objectives of the study were to (1) investigate the effect of hearing aid amplification and a hearing aid directional technology on listening effort measured by a complicated, more real world dual-task paradigm, and (2) compare the results obtained with this paradigm to a simpler laboratory-style dual-task paradigm. Design The listening effort of adults with hearing impairment was measured using two dual-task paradigms, wherein participants performed a speech recognition task simultaneously with either a driving task in a simulator or a visual reaction-time task in a sound-treated booth. The speech materials and road noises for the speech recognition task were recorded in a van traveling on the highway in three hearing aid conditions: unaided, aided with omni directional processing (OMNI), and aided with directional processing (DIR). The change in the driving task or the visual reaction-time task performance across the conditions quantified the change in listening effort. Results Compared to the driving-only condition, driving performance declined significantly with the addition of the speech recognition task. Although the speech recognition score was higher in the OMNI and DIR conditions than in the unaided condition, driving performance was similar across these three conditions, suggesting that listening effort was not affected by amplification and directional processing. Results from the simple dual-task paradigm showed a similar trend: hearing aid technologies improved speech recognition performance, but did not affect performance in the visual reaction-time task (i.e., reduce listening effort). The correlation between listening effort measured using the driving paradigm and the visual reaction-time task paradigm was significant. The finding showing that our older (56 to 85 years old) participants’ better speech recognition performance did not result in reduced

  8. Measuring listening effort: driving simulator versus simple dual-task paradigm.

    PubMed

    Wu, Yu-Hsiang; Aksan, Nazan; Rizzo, Matthew; Stangl, Elizabeth; Zhang, Xuyang; Bentler, Ruth

    2014-01-01

    The dual-task paradigm has been widely used to measure listening effort. The primary objectives of the study were to (1) investigate the effect of hearing aid amplification and a hearing aid directional technology on listening effort measured by a complicated, more real world dual-task paradigm and (2) compare the results obtained with this paradigm to a simpler laboratory-style dual-task paradigm. The listening effort of adults with hearing impairment was measured using two dual-task paradigms, wherein participants performed a speech recognition task simultaneously with either a driving task in a simulator or a visual reaction-time task in a sound-treated booth. The speech materials and road noises for the speech recognition task were recorded in a van traveling on the highway in three hearing aid conditions: unaided, aided with omnidirectional processing (OMNI), and aided with directional processing (DIR). The change in the driving task or the visual reaction-time task performance across the conditions quantified the change in listening effort. Compared to the driving-only condition, driving performance declined significantly with the addition of the speech recognition task. Although the speech recognition score was higher in the OMNI and DIR conditions than in the unaided condition, driving performance was similar across these three conditions, suggesting that listening effort was not affected by amplification and directional processing. Results from the simple dual-task paradigm showed a similar trend: hearing aid technologies improved speech recognition performance, but did not affect performance in the visual reaction-time task (i.e., reduce listening effort). The correlation between listening effort measured using the driving paradigm and the visual reaction-time task paradigm was significant. The finding showing that our older (56 to 85 years old) participants' better speech recognition performance did not result in reduced listening effort was not

  9. Final Progress Report - Heavy Ion Accelerator Theory and Simulation

    SciTech Connect

    Haber, Irving

    2009-10-31

    The use of a beam of heavy ions to heat a target for the study of warm dense matter physics, high energy density physics, and ultimately to ignite an inertial fusion pellet, requires the achievement of beam intensities somewhat greater than have traditionally been obtained using conventional accelerator technology. The research program described here has substantially contributed to understanding the basic nonlinear intense-beam physics that is central to the attainment of the requisite intensities. Since it is very difficult to reverse intensity dilution, avoiding excessive dilution over the entire beam lifetime is necessary for achieving the required beam intensities on target. The central emphasis in this research has therefore been on understanding the nonlinear mechanisms that are responsible for intensity dilution and which generally occur when intense space-charge-dominated beams are not in detailed equilibrium with the external forces used to confine them. This is an important area of study because such lack of detailed equilibrium can be an unavoidable consequence of the beam manipulations such as acceleration, bunching, and focusing necessary to attain sufficient intensity on target. The primary tool employed in this effort has been the use of simulation, particularly the WARP code, in concert with experiment, to identify the nonlinear dynamical characteristics that are important in practical high intensity accelerators. This research has gradually made a transition from the study of idealized systems and comparisons with theory, to study the fundamental scaling of intensity dilution in intense beams, and more recently to explicit identification of the mechanisms relevant to actual experiments. This work consists of two categories; work in direct support beam physics directly applicable to NDCX and a larger effort to further the general understanding of space-charge-dominated beam physics.

  10. Monte Carlo simulation of a clinical linear accelerator.

    PubMed

    Lin, S Y; Chu, T C; Lin, J P

    2001-12-01

    The effects of the physical parameters of an electron beam from a Siemens PRIMUS clinical linear accelerator (linac) on the dose distribution in water were investigated by Monte Carlo simulation. The EGS4 user code, OMEGA/BEAM, was used in this study. Various incident electron beams, for example, with different energies, spot sizes and distances from the point source, were simulated using the detailed linac head structure in the 6 MV photon mode. Approximately 10 million particles were collected in the scored plane, which was set under the reticle to form the so-called phase space file. The phase space file served as a source for simulating the dose distribution in water using DOSXYZ. Dose profiles at Dmax (1.5 cm) and PDD curves were calculated following simulating about 1 billion histories for dose profiles and 500 million histories for percent depth dose (PDD) curves in a 30 x 30 x 30 cm3 water phantom. The simulation results were compared with the data measured by a CEA film and an ion chamber. The results show that the dose profiles are influenced by the energy and the spot size, while PDD curves are primarily influenced by the energy of the incident beam. The effect of the distance from the point source on the dose profile is not significant and is recommended to be set at infinity. We also recommend adjusting the beam energy by using PDD curves and, then, adjusting the spot size by using the dose profile to maintain the consistency of the Monte Carlo results and measured data.

  11. Trypsinogen activation as observed in accelerated molecular dynamics simulations

    PubMed Central

    Boechi, Leonardo; Pierce, Levi; Komives, Elizabeth A; McCammon, J Andrew

    2014-01-01

    Serine proteases are involved in many fundamental physiological processes, and control of their activity mainly results from the fact that they are synthetized in an inactive form that becomes active upon cleavage. Three decades ago Martin Karplus’s group performed the first molecular dynamics simulations of trypsin, the most studied member of the serine protease family, to address the transition from the zymogen to its active form. Based on the computational power available at the time, only high frequency fluctuations, but not the transition steps, could be observed. By performing accelerated molecular dynamics (aMD) simulations, an interesting approach that increases the configurational sampling of atomistic simulations, we were able to observe the N-terminal tail insertion, a crucial step of the transition mechanism. Our results also support the hypothesis that the hydrophobic effect is the main force guiding the insertion step, although substantial enthalpic contributions are important in the activation mechanism. As the N-terminal tail insertion is a conserved step in the activation of serine proteases, these results afford new perspective on the underlying thermodynamics of the transition from the zymogen to the active enzyme. PMID:25131668

  12. Requirements for Simulating Space Radiation With Particle Accelerators

    NASA Technical Reports Server (NTRS)

    Schimmerling, W.; Wilson, J. W.; Cucinotta, F.; Kim, M-H Y.

    2004-01-01

    Interplanetary space radiation consists of fully ionized nuclei of atomic elements with high energy for which only the few lowest energy ions can be stopped in shielding materials. The health risk from exposure to these ions and their secondary radiations generated in the materials of spacecraft and planetary surface enclosures is a major limiting factor in the management of space radiation risk. Accurate risk prediction depends on a knowledge of basic radiobiological mechanisms and how they are modified in the living tissues of a whole organism. To a large extent, this knowledge is not currently available. It is best developed at ground-based laboratories, using particle accelerator beams to simulate the components of space radiation. Different particles, in different energy regions, are required to study different biological effects, including beams of argon and iron nuclei in the energy range 600 to several thousand MeV/nucleon and carbon beams in the energy range of approximately 100 MeV/nucleon to approximately 1000 MeV/nucleon. Three facilities, one each in the United States, in Germany and in Japan, currently have the partial capability to satisfy these constraints. A facility has been proposed using the Brookhaven National Laboratory Booster Synchrotron in the United States; in conjunction with other on-site accelerators, it will be able to provide the full range of heavy ion beams and energies required. International cooperation in the use of these facilities is essential to the development of a safe international space program.

  13. Dark Current Simulation for Linear Collider Accelerator Structures

    SciTech Connect

    Ng, C.K.; Li, Z.; Zhan, X.; Srinivas, V.; Wang, J.; Ko, K.; /SLAC

    2011-08-25

    The dynamics of field-emitted electrons in the traveling wave fields of a constant gradient (tapered) disk-loaded waveguide is followed numerically. Previous simulations have been limited to constant impedance (uniform) structures for sake of simplicity since only the fields in a unit cell is needed. Using a finite element field solver on a parallel computer, the fields in the tapered structure can now be readily generated. We will obtain the characteristics of the dark current emitted from both structure types and compare the two results with and without the effect of secondary electrons. The NLC and JLC detuned structures are considered to study if dark current may pose a problem for high gradient acceleration in the next generation of Linear Colliders.

  14. Mesoscopic simulations of accelerated polymer drift in microfluidic capillaries

    NASA Astrophysics Data System (ADS)

    Berkenbos, A.; Lowe, C. P.

    2007-10-01

    We use a mesoscopic simulation technique to study the transport of polymers in dilute solution flowing through a cylindrical tube. The simulations use an explicit solvent model to include all the relevant hydrodynamic couplings and a coarse grained ideal chain model for the polymers (appropriate for systems near the theta temperature). For the interactions between the solvent and the tube wall we use a novel method that ensures continuity of the stress at the interface. We show that the results for the polymer drift velocity are independent of the degree of coarse graining. Further, for the case where the size of the chains is small but not negligible compared to the tube radius, our results are in excellent agreement with experiment. However, they also show that in this regime, the "accelerated" drift, relative to the average solvent flow velocity, is described by the steric effect of the tube wall excluding the polymer center of mass from sampling the full cross section of the tube. Hydrodynamic interactions have a negligible influence in this regime. Consequently, the agreement between experiment and theories that approximates the former but includes the latter is fortunate. When the undisturbed polymer radius approaches or exceeds the tube radius, the hydrodynamic interactions do have a significant effect. They reduce the drift velocity, in qualitative agreement with theoretical predictions. The accelerated drift still approaches the maximum value, one would expect based on a Poiseuille flow but more slowly than if one neglects hydrodynamics. Finally, we propose an empirical fit that accurately describes data in the intermediate regime.

  15. The simulated gambling paradigm applied to young adults: an examination of university students' performance.

    PubMed

    Caroselli, Jerome Silvio; Hiscock, Merrill; Scheibel, Randall S; Ingram, Fred

    2006-01-01

    Simulated gambling tasks have become popular as sensitive tools for identifying individuals with real-time impairment in decision making. Various clinical samples, especially patients with damage to the ventromedial prefrontal cortex, perform poorly on these tasks. The patients typically persist in choosing risky (disadvantageous) card decks instead of switching to safer (advantageous) decks. In terms of Damasio's (1994) somatic marker hypothesis, the poor performance stems from defective integration of emotional and rational aspects of decision making. Less information is available about performance in healthy populations, particularly young adults. After administering a computerized gambling task to 141 university students, we found that individuals in this population also tend to prefer disadvantageous decks to advantageous decks. The results indicate that performance is governed primarily by the frequency of positive outcomes on a trial-by-trial basis rather than by the accumulation of winnings in the longer term. These findings are discussed in light of the cognitive literature pertaining to the simulated gambling paradigm.

  16. A new paradigm for reproducing and analyzing N-body simulations of planetary systems

    NASA Astrophysics Data System (ADS)

    Rein, Hanno; Tamayo, Daniel

    2017-01-01

    The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they can only be replicated in an approximate or statistical sense. Even if authors share their full source code and initial conditions, differences in compilers, libraries, operating systems or hardware often lead to qualitatively different results. We provide a new set of easy-to-use, open-source tools that address the above issues, allowing for exact (bit-by-bit) reproducibility of N-body experiments. In addition to generating completely reproducible integrations, we show that our framework also offers novel and innovative ways to analyze these simulations. As an example, we present a high-accuracy integration of the Solar System spanning 10 Gyrs, requiring several weeks to run on a modern CPU. In our framework we can not only easily access simulation data at predefined intervals for which we save snapshots, but at any time during the integration. We achieve this by integrating an on-demand reconstructed simulation forward in time from the nearest snapshot. This allows us to extract arbitrary quantities at any point in the saved simulation exactly (bit-by-bit), and within seconds rather than weeks. We believe that the tools we present in this paper offer a new paradigm for how N-body simulations are run, analyzed, and shared across the community.

  17. A new paradigm for reproducing and analyzing N-body simulations of planetary systems

    NASA Astrophysics Data System (ADS)

    Rein, Hanno; Tamayo, Daniel

    2017-05-01

    The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they can only be replicated in an approximate or statistical sense. Even if authors share their full source code and initial conditions, differences in compilers, libraries, operating systems or hardware often lead to qualitatively different results. We provide a new set of easy-to-use, open-source tools that address the above issues, allowing for exact (bit-by-bit) reproducibility of N-body experiments. In addition to generating completely reproducible integrations, we show that our framework also offers novel and innovative ways to analyse these simulations. As an example, we present a high-accuracy integration of the Solar system spanning 10 Gyr, requiring several weeks to run on a modern CPU. In our framework, we can not only easily access simulation data at predefined intervals for which we save snapshots, but at any time during the integration. We achieve this by integrating an on-demand reconstructed simulation forward in time from the nearest snapshot. This allows us to extract arbitrary quantities at any point in the saved simulation exactly (bit-by-bit), and within seconds rather than weeks. We believe that the tools we present in this paper offer a new paradigm for how N-body simulations are run, analysed and shared across the community.

  18. The computer simulation of laser proton acceleration for hadron therapy

    NASA Astrophysics Data System (ADS)

    Lykov, Vladimir; Baydin, Grigory

    2008-11-01

    The ions acceleration by intensive ultra-short laser pulses has interest in views of them possible applications for proton radiography, production of medical isotopes and hadron therapy. The 3D relativistic PIC-code LegoLPI is developed at RFNC-VNIITF for modeling of intensive laser interaction with plasma. The LegoLPI-code simulations were carried out to find the optimal conditions for generation of proton beams with parameters necessary for hadrons therapy. The performed simulations show that optimal for it may be two-layer foil of aluminum and polyethylene with thickness 100 nm and 50 nm accordingly. The maximum efficiency of laser energy transformation into 200 MeV protons is achieved on irradiating these foils by 30 fs laser pulse with intensity about 2.10^22 W/cm^2. The conclusion is made that lasers with peak power about 0.5-1PW and average power 0.5-1 kW are needed for generation of proton beams with parameters necessary for proton therapy.

  19. Accelerated prompt gamma estimation for clinical proton therapy simulations

    NASA Astrophysics Data System (ADS)

    Huisman, Brent F. B.; Létang, J. M.; Testa, É.; Sarrut, D.

    2016-11-01

    There is interest in the particle therapy community in using prompt gammas (PGs), a natural byproduct of particle treatment, for range verification and eventually dose control. However, PG production is a rare process and therefore estimation of PGs exiting a patient during a proton treatment plan executed by a Monte Carlo (MC) simulation converges slowly. Recently, different approaches to accelerating the estimation of PG yield have been presented. Sterpin et al (2015 Phys. Med. Biol. 60 4915-46) described a fast analytic method, which is still sensitive to heterogeneities. El Kanawati et al (2015 Phys. Med. Biol. 60 8067-86) described a variance reduction method (pgTLE) that accelerates the PG estimation by precomputing PG production probabilities as a function of energy and target materials, but has as a drawback that the proposed method is limited to analytical phantoms. We present a two-stage variance reduction method, named voxelized pgTLE (vpgTLE), that extends pgTLE to voxelized volumes. As a preliminary step, PG production probabilities are precomputed once and stored in a database. In stage 1, we simulate the interactions between the treatment plan and the patient CT with low statistic MC to obtain the spatial and spectral distribution of the PGs. As primary particles are propagated throughout the patient CT, the PG yields are computed in each voxel from the initial database, as a function of the current energy of the primary, the material in the voxel and the step length. The result is a voxelized image of PG yield, normalized to a single primary. The second stage uses this intermediate PG image as a source to generate and propagate the number of PGs throughout the rest of the scene geometry, e.g. into a detection device, corresponding to the number of primaries desired. We achieved a gain of around 103 for both a geometrical heterogeneous phantom and a complete patient CT treatment plan with respect to analog MC, at a convergence level of 2% relative

  20. The interaction between atmospheric gravity waves and large-scale flows: an efficient description beyond the non-acceleration paradigm

    NASA Astrophysics Data System (ADS)

    Achatz, U.; Boeloeni, G.; Ribstein, B.; Sgoff, C.; Wei, J.

    2016-12-01

    With the aim of contributing to the improvement of subgrid-scale gravity wave (GW) parameterizations in numerical-weather-prediction and climate models, the comparative relevance in GW drag of direct GW-mean-flow interactions and turbulent wave breakdown are investigated. Of equal interest is how well Wentzel-Kramer-Brillouin (WKB) theory can capture direct wave-mean-flow interactions, that are excluded by applying the steady-state approximation. WKB is implemented in a very efficient Lagrangian ray-tracing approach that considers wave action density in phase-space, thereby avoiding numerical instabilities due to caustics. It is supplemented by a simple wave-breaking scheme based on a static-instability saturation criterion. Idealized test cases of horizontally homogeneous GW packets are considered where wave-resolving Large-Eddy Simulations (LES) provide the reference. In all of theses cases the WKB simulations including direct GW-mean-flow interactions reproduce the LES data, to a good accuracy, already without wave-breaking scheme. The latter provides a next-order correction that is useful for fully capturing the total-energy balance between wave and mean flow. Moreover, a steady-state WKB implementation, as used in present GW parameterizations, and where turbulence provides, by the non-interaction paradigm, the only possibility to affect the mean flow, is much less able to yield reliable results. The GW energy is damped too strongly and induces an oversimplified mean flow. This argues for WKB approaches to GW parameterization that take wave transience into account. The presentation might be supplemented by a report on other recent developments from the DFG research unit MS-GWaves (https://ms-gwaves.iau.uni-frankfurt.de/index.php) on the multi-scale dynamics of gravity waves, e.g. with regard to spontaneous imbalance or the GW-tropopause interaction.

  1. The interaction between atmospheric gravity waves and large-scale flows: an efficient description beyond the non-acceleration paradigm

    NASA Astrophysics Data System (ADS)

    Bölöni, Gergely; Ribstein, Bruno; Muraschko, Jewgenija; Sgoff, Christine; Wei, Junhong; Achatz, Ulrich

    2017-04-01

    With the aim of contributing to the improvement of subgrid-scale gravity wave (GW) parameterizations in numerical-weather-prediction and climate models, the comparative relevance in GW drag of direct GW-mean-flow interactions and turbulent wave breakdown are investigated. Of equal interest is how well Wentzel-Kramer-Brillouin (WKB) theory can capture direct wave-mean-flow interactions, that are excluded by applying the steady-state approximation. WKB is implemented in a very efficient Lagrangian ray-tracing approach that considers wave action density in phase-space, thereby avoiding numerical instabilities due to caustics (Muraschko et al., 2015, Quart. J. Roy. Meteor. Soc., 141, 676-697). It is supplemented by a simple wave-breaking scheme based on a static-instability saturation criterion. Idealized test cases of horizontally homogeneous GW packets are considered where wave-resolving Large-Eddy Simulations (LES) provide the reference. In all of theses cases the WKB simulations including direct GW-mean-flow interactions reproduce the LES data, to a good accuracy, already without wave-breaking scheme. The latter provides a next-order correction that is useful for fully capturing the total-energy balance between wave and mean flow. Moreover, a steady-state WKB implementation, as used in present GW parameterizations, and where turbulence provides, by the non-interaction paradigm, the only possibility to affect the mean flow, is much less able to yield reliable results. The GW energy is damped too strongly and induces an oversimplified mean flow. This argues for WKB approaches to GW parameterization that take wave transience into account (Bölöni et al., 2016 J. Atmos. Sci., 73, 4833-4852).

  2. Saturn: A large area x-ray simulation accelerator

    SciTech Connect

    Bloomquist, D.D.; Stinnett, R.W.; McDaniel, D.H.; Lee, J.R.; Sharpe, A.W.; Halbleib, J.A.; Schlitt, L.G.; Spence, P.W.; Corcoran, P.

    1987-01-01

    Saturn is the result of a major metamorphosis of the Particle Beam Fusion Accelerator-I (PBFA-I) from an ICF research facility to the large-area x-ray source of the Simulation Technology Laboratory (STL) project. Renamed Saturn, for its unique multiple-ring diode design, the facility is designed to take advantage of the numerous advances in pulsed power technology made by the ICF program in recent years and much of the existing PBFA-I support system. Saturn will include significant upgrades in the energy storage and pulse-forming sections. The 36 magnetically insulated transmission lines (MITLs) that provided power flow to the ion diode of PBFA-I were replaced by a system of vertical triplate water transmission lines. These lines are connected to three horizontal triplate disks in a water convolute section. Power will flow through an insulator stack into radial MITLs that drive the three-ring diode. Saturn is designed to operate with a maximum of 750 kJ coupled to the three-ring e-beam diode with a peak power of 25 TW to provide an x-ray exposure capability of 5 x 10/sup 12/ rads/s (Si) and 5 cal/g (Au) over 500 cm/sup 2/.

  3. GPUPEGAS: A NEW GPU-ACCELERATED HYDRODYNAMIC CODE FOR NUMERICAL SIMULATIONS OF INTERACTING GALAXIES

    SciTech Connect

    Kulikov, Igor

    2014-09-01

    In this paper, a new scalable hydrodynamic code, GPUPEGAS (GPU-accelerated Performance Gas Astrophysical Simulation), for the simulation of interacting galaxies is proposed. The details of a parallel numerical method co-design are described. A speed-up of 55 times was obtained within a single GPU accelerator. The use of 60 GPU accelerators resulted in 96% parallel efficiency. A collisionless hydrodynamic approach has been used for modeling of stars and dark matter. The scalability of the GPUPEGAS code is shown.

  4. A multi-paradigm modeling framework to simulate dynamic reciprocity in a bioreactor.

    PubMed

    Kaul, Himanshu; Cui, Zhanfeng; Ventikos, Yiannis

    2013-01-01

    Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications.

  5. A Multi-Paradigm Modeling Framework to Simulate Dynamic Reciprocity in a Bioreactor

    PubMed Central

    Kaul, Himanshu; Cui, Zhanfeng; Ventikos, Yiannis

    2013-01-01

    Despite numerous technology advances, bioreactors are still mostly utilized as functional black-boxes where trial and error eventually leads to the desirable cellular outcome. Investigators have applied various computational approaches to understand the impact the internal dynamics of such devices has on overall cell growth, but such models cannot provide a comprehensive perspective regarding the system dynamics, due to limitations inherent to the underlying approaches. In this study, a novel multi-paradigm modeling platform capable of simulating the dynamic bidirectional relationship between cells and their microenvironment is presented. Designing the modeling platform entailed combining and coupling fully an agent-based modeling platform with a transport phenomena computational modeling framework. To demonstrate capability, the platform was used to study the impact of bioreactor parameters on the overall cell population behavior and vice versa. In order to achieve this, virtual bioreactors were constructed and seeded. The virtual cells, guided by a set of rules involving the simulated mass transport inside the bioreactor, as well as cell-related probabilistic parameters, were capable of displaying an array of behaviors such as proliferation, migration, chemotaxis and apoptosis. In this way the platform was shown to capture not only the impact of bioreactor transport processes on cellular behavior but also the influence that cellular activity wields on that very same local mass transport, thereby influencing overall cell growth. The platform was validated by simulating cellular chemotaxis in a virtual direct visualization chamber and comparing the simulation with its experimental analogue. The results presented in this paper are in agreement with published models of similar flavor. The modeling platform can be used as a concept selection tool to optimize bioreactor design specifications. PMID:23555740

  6. Accelerated Molecular Dynamics Simulations of Reactive Hydrocarbon Systems

    SciTech Connect

    Stuart, Steven J.

    2014-02-25

    The research activities in this project consisted of four different sub-projects. Three different accelerated dynamics techniques (parallel replica dynamics, hyperdynamics, and temperature-accelerated dynamics) were applied to the modeling of pyrolysis of hydrocarbons. In addition, parallel replica dynamics was applied to modeling of polymerization.

  7. Internet of Things: a possible change in the distributed modeling and simulation architecture paradigm

    NASA Astrophysics Data System (ADS)

    Riecken, Mark; Lessmann, Kurt; Schillero, David

    2016-05-01

    The Data Distribution Service (DDS) was started by the Object Management Group (OMG) in 2004. Currently, DDS is one of the contenders to support the Internet of Things (IoT) and the Industrial IOT (IIoT). DDS has also been used as a distributed simulation architecture. Given the anticipated proliferation of IoT and II devices, along with the explosive growth of sensor technology, can we expect this to have an impact on the broader community of distributed simulation? If it does, what is the impact and which distributed simulation domains will be most affected? DDS shares many of the same goals and characteristics of distributed simulation such as the need to support scale and an emphasis on Quality of Service (QoS) that can be tailored to meet the end user's needs. In addition, DDS has some built-in features such as security that are not present in traditional distributed simulation protocols. If the IoT and II realize their potential application, we predict a large base of technology to be built around this distributed data paradigm, much of which could be directly beneficial to the distributed M&S community. In this paper we compare some of the perceived gaps and shortfalls of current distributed M&S technology to the emerging capabilities of DDS built around the IoT. Although some trial work has been conducted in this area, we propose a more focused examination of the potential of these new technologies and their applicability to current and future problems in distributed M&S. The Internet of Things (IoT) and its data communications mechanisms such as the Data Distribution System (DDS) share properties in common with distributed modeling and simulation (M&S) and its protocols such as the High Level Architecture (HLA) and the Test and Training Enabling Architecture (TENA). This paper proposes a framework based on the sensor use case for how the two communities of practice (CoP) can benefit from one another and achieve greater capability in practical distributed

  8. Final Report for "Community Petascale Project for Accelerator Science and Simulations".

    SciTech Connect

    Cary, J. R.; Bruhwiler, D. L.; Stoltz, P. H.; Cormier-Michel, E.; Cowan, B.; Schwartz, B. T.; Bell, G.; Paul, K.; Veitzer, S.

    2013-04-19

    This final report describes the work that has been accomplished over the past 5 years under the Community Petascale Project for Accelerator and Simulations (ComPASS) at Tech-X Corporation. Tech-X had been involved in the full range of ComPASS activities with simulation of laser plasma accelerator concepts, mainly in collaboration with LOASIS program at LBNL, simulation of coherent electron cooling in collaboration with BNL, modeling of electron clouds in high intensity accelerators, in collaboration with researchers at Fermilab and accurate modeling of superconducting RF cavity in collaboration with Fermilab, JLab and Cockcroft Institute in the UK.

  9. Simulation of SEP Acceleration and Transport at CME-driven Shocks

    SciTech Connect

    Kota, J.; Jokipii, J.R.; Manchester, W.B.; Zeeuw, D.L. de; Gombosi, T.I.

    2005-08-01

    Our code of solar energetic particle (SEP) acceleration and transport developed in Arizona is combined with the realistic CME simulations of Michigan, using the solar wind and magnetic field data of the Michigan CME-simulation as input to the SEP code. We suggest that, in addition to the acceleration at the shock significant acceleration may also occur in the sheet behind the shock, where magnetic field lines are compressed as they are bent around the expanding cloud. We consider field aligned motion and cast the proper Fokker-Planck equation into a non-inertial comoving frame, that follows field lines as they evolve. Illustrative simulation results are presented.

  10. Computational Materials Science and Chemistry: Accelerating Discovery and Innovation through Simulation-Based Engineering and Science

    SciTech Connect

    Crabtree, George; Glotzer, Sharon; McCurdy, Bill; Roberto, Jim

    2010-07-26

    enabled the development of computer simulations and models of unprecedented fidelity. We are at the threshold of a new era where the integrated synthesis, characterization, and modeling of complex materials and chemical processes will transform our ability to understand and design new materials and chemistries with predictive power. In turn, this predictive capability will transform technological innovation by accelerating the development and deployment of new materials and processes in products and manufacturing. Harnessing the potential of computational science and engineering for the discovery and development of materials and chemical processes is essential to maintaining leadership in these foundational fields that underpin energy technologies and industrial competitiveness. Capitalizing on the opportunities presented by simulation-based engineering and science in materials and chemistry will require an integration of experimental capabilities with theoretical and computational modeling; the development of a robust and sustainable infrastructure to support the development and deployment of advanced computational models; and the assembly of a community of scientists and engineers to implement this integration and infrastructure. This community must extend to industry, where incorporating predictive materials science and chemistry into design tools can accelerate the product development cycle and drive economic competitiveness. The confluence of new theories, new materials synthesis capabilities, and new computer platforms has created an unprecedented opportunity to implement a "materials-by-design" paradigm with wide-ranging benefits in technological innovation and scientific discovery. The Workshop on Computational Materials Science and Chemistry for Innovation was convened in Bethesda, Maryland, on July 26-27, 2010. Sponsored by the Department of Energy (DOE) Offices of Advanced Scientific Computing Research and Basic Energy Sciences, the workshop brought together

  11. Accelerating Monte Carlo simulations of photon transport in a voxelized geometry using a massively parallel graphics processing unit.

    PubMed

    Badal, Andreu; Badano, Aldo

    2009-11-01

    It is a known fact that Monte Carlo simulations of radiation transport are computationally intensive and may require long computing times. The authors introduce a new paradigm for the acceleration of Monte Carlo simulations: The use of a graphics processing unit (GPU) as the main computing device instead of a central processing unit (CPU). A GPU-based Monte Carlo code that simulates photon transport in a voxelized geometry with the accurate physics models from PENELOPE has been developed using the CUDATM programming model (NVIDIA Corporation, Santa Clara, CA). An outline of the new code and a sample x-ray imaging simulation with an anthropomorphic phantom are presented. A remarkable 27-fold speed up factor was obtained using a GPU compared to a single core CPU. The reported results show that GPUs are currently a good alternative to CPUs for the simulation of radiation transport. Since the performance of GPUs is currently increasing at a faster pace than that of CPUs, the advantages of GPU-based software are likely to be more pronounced in the future.

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

    SciTech Connect

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei

    2014-05-14

    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 the 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

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

    NASA Astrophysics Data System (ADS)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

    2014-05-01

    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 the 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 × 106-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

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

    PubMed

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

    2014-05-14

    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 the 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(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

  15. Advanced visualization technology for terascale particle accelerator simulations

    SciTech Connect

    Ma, K-L; Schussman, G.; Wilson, B.; Ko, K.; Qiang, J.; Ryne, R.

    2002-11-16

    This paper presents two new hardware-assisted rendering techniques developed for interactive visualization of the terascale data generated from numerical modeling of next generation accelerator designs. The first technique, based on a hybrid rendering approach, makes possible interactive exploration of large-scale particle data from particle beam dynamics modeling. The second technique, based on a compact texture-enhanced representation, exploits the advanced features of commodity graphics cards to achieve perceptually effective visualization of the very dense and complex electromagnetic fields produced from the modeling of reflection and transmission properties of open structures in an accelerator design. Because of the collaborative nature of the overall accelerator modeling project, the visualization technology developed is for both desktop and remote visualization settings. We have tested the techniques using both time varying particle data sets containing up to one billion particle s per time step and electromagnetic field data sets with millions of mesh elements.

  16. Numerical simulations of the superdetonative ram accelerator combusting flow field

    NASA Technical Reports Server (NTRS)

    Soetrisno, Moeljo; Imlay, Scott T.; Roberts, Donald W.

    1993-01-01

    The effects of projectile canting and fins on the ram accelerator combusting flowfield and the possible cause of the ram accelerator unstart are investigated by performing axisymmetric, two-dimensional, and three-dimensional calculations. Calculations are performed using the INCA code for solving Navier-Stokes equations and a guasi-global combustion model of Westbrook and Dryer (1981, 1984), which includes N2 and nine reacting species (CH4, CO, CO2, H2, H, O2, O, OH, and H2O), which are allowed to undergo a 12-step reaction. It is found that, without canting, interactions between the fins, boundary layers, and combustion fronts are insufficient to unstart the projectile at superdetonative velocities. With canting, the projectile will unstart at flow conditions where it appears to accelerate without canting. Unstart occurs at some critical canting angle. It is also found that three-dimensionality plays an important role in the overall combustion process.

  17. Numerical simulations of the superdetonative ram accelerator combusting flow field

    NASA Technical Reports Server (NTRS)

    Soetrisno, Moeljo; Imlay, Scott T.; Roberts, Donald W.

    1993-01-01

    The effects of projectile canting and fins on the ram accelerator combusting flowfield and the possible cause of the ram accelerator unstart are investigated by performing axisymmetric, two-dimensional, and three-dimensional calculations. Calculations are performed using the INCA code for solving Navier-Stokes equations and a guasi-global combustion model of Westbrook and Dryer (1981, 1984), which includes N2 and nine reacting species (CH4, CO, CO2, H2, H, O2, O, OH, and H2O), which are allowed to undergo a 12-step reaction. It is found that, without canting, interactions between the fins, boundary layers, and combustion fronts are insufficient to unstart the projectile at superdetonative velocities. With canting, the projectile will unstart at flow conditions where it appears to accelerate without canting. Unstart occurs at some critical canting angle. It is also found that three-dimensionality plays an important role in the overall combustion process.

  18. Accelerating simulation of ensembles of locally differing optical structures via a Schur complement domain decomposition.

    PubMed

    Verweij, Sacha; Liu, Victor; Fan, Shanhui

    2014-11-15

    We present a Schur complement domain decomposition method that can significantly accelerate simulation of ensembles of locally differing optical structures. We apply the method to design a multi-spatial-mode photonic crystal waveguide splitter that exhibits high transmission and preservation of modal content, showing design acceleration by more than a factor of 20.

  19. Reactor for simulation and acceleration of solar ultraviolet damage

    NASA Technical Reports Server (NTRS)

    Laue, E.; Gupta, A.

    1979-01-01

    An environmental test chamber providing acceleration of UV radiation and precise temperature control (+ or -)1 C was designed, constructed and tested. This chamber allows acceleration of solar ultraviolet up to 30 suns while maintaining temperature of the absorbing surface at 30 C - 60 C. This test chamber utilizes a filtered medium pressure mercury arc as the source of radiation, and a combination of selenium radiometer and silicon radiometer to monitor solar ultraviolet (295-340 nm) and total radiant power output, respectively. Details of design and construction and operational procedures are presented along with typical test data.

  20. Acceleration techniques for dependability simulation. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Barnette, James David

    1995-01-01

    As computer systems increase in complexity, the need to project system performance from the earliest design and development stages increases. We have to employ simulation for detailed dependability studies of large systems. However, as the complexity of the simulation model increases, the time required to obtain statistically significant results also increases. This paper discusses an approach that is application independent and can be readily applied to any process-based simulation model. Topics include background on classical discrete event simulation and techniques for random variate generation and statistics gathering to support simulation.

  1. Constraint methods that accelerate free-energy simulations of biomolecules

    SciTech Connect

    Perez, Alberto; MacCallum, Justin L.; Coutsias, Evangelos A.; Dill, Ken A.

    2015-12-28

    Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

  2. Constraint methods that accelerate free-energy simulations of biomolecules.

    PubMed

    Perez, Alberto; MacCallum, Justin L; Coutsias, Evangelos A; Dill, Ken A

    2015-12-28

    Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

  3. Constraint methods that accelerate free-energy simulations of biomolecules

    PubMed Central

    MacCallum, Justin L.; Dill, Ken A.

    2015-01-01

    Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann’s law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions. PMID:26723628

  4. Constraint methods that accelerate free-energy simulations of biomolecules

    NASA Astrophysics Data System (ADS)

    Perez, Alberto; MacCallum, Justin L.; Coutsias, Evangelos A.; Dill, Ken A.

    2015-12-01

    Atomistic molecular dynamics simulations of biomolecules are critical for generating narratives about biological mechanisms. The power of atomistic simulations is that these are physics-based methods that satisfy Boltzmann's law, so they can be used to compute populations, dynamics, and mechanisms. But physical simulations are computationally intensive and do not scale well to the sizes of many important biomolecules. One way to speed up physical simulations is by coarse-graining the potential function. Another way is to harness structural knowledge, often by imposing spring-like restraints. But harnessing external knowledge in physical simulations is problematic because knowledge, data, or hunches have errors, noise, and combinatoric uncertainties. Here, we review recent principled methods for imposing restraints to speed up physics-based molecular simulations that promise to scale to larger biomolecules and motions.

  5. Acceleration of a QM/MM-QMC simulation using GPU.

    PubMed

    Uejima, Yutaka; Terashima, Tomoharu; Maezono, Ryo

    2011-07-30

    We accelerated an ab initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a (single core CPU with double precision), getting 23.6 (11.0) times faster calculations in single (double) precision treatments on GPU. The energy deviation caused by the single precision treatment was found to be within the accuracy required in the calculation, ∼10(-5) hartree. The accelerated computational nodes mounting GPU are combined to form a hybrid MPI cluster on which we confirmed the performance linearly scales to the number of nodes.

  6. Particle Acceleration in the Low Corona Over Broad Longitudes: Coupling MHD and 3D Particle Simulations

    NASA Astrophysics Data System (ADS)

    Gorby, M.; Schwadron, N.; Torok, T.; Downs, C.; Lionello, R.; Linker, J.; Titov, V. S.; Mikic, Z.; Riley, P.; Desai, M. I.; Dayeh, M. A.

    2014-12-01

    Recent work on the coupling between the Energetic Particle Radiation Environment Module (EPREM, a 3D energetic particle model) and Magnetohydrodynamics Around a Sphere (MAS, an MHD code developed at Predictive Science, Inc.) has demonstrated the efficacy of compression regions around fast coronal mass ejections (CMEs) for particle acceleration low in the corona (˜ 3 - 6 solar radii). These couplings show rapid particle acceleration over a broad longitudinal extent (˜ 80 degrees) resulting from the pile-up of magnetic flux in the compression regions and their subsequent expansion. The challenge for forming large SEP events in such compression-acceleration scenarios is to have enhanced scattering within the acceleration region while also allowing for efficient escape of accelerated particles downstream (away from the Sun) from the compression region. We present here the most recent simulation results including energetic particle and CME plasma profiles, the subsequent flux and dosages at 1AU, and an analysis of the compressional regions as efficient accelerators.

  7. Effects of dimensionality on kinetic simulations of laser-ion acceleration in the transparency regime

    DOE PAGES

    Stark, David James; Yin, Lin; Albright, Brian James; ...

    2017-05-03

    A particle-in-cell study of laser-ion acceleration mechanisms in the transparency regime illustrates how two-dimensional (2D) S and P simulations (laser polarization in and out of the simulation plane, respectively) capture different physics characterizing these systems, visible in their entirety in often cost-prohibitive three-dimensional (3D) simulations. The electron momentum anisotropy induced in the target by the laser pulse is dramatically different in the two 2D cases, manifested in differences in target expansion timescales, electric field strengths, and density thresholds for the onset of relativistically induced transparency. In particular, 2D-P simulations exhibit dramatically greater electron heating in the simulation plane, whereas 2D-Smore » ones show a much more isotropic energy distribution, similar to 3D. An ion trajectory analysis allows one to isolate the fields responsible for ion acceleration and to characterize the acceleration regimes in time and space. The artificial longitudinal electron heating in 2D-P exaggerates the effectiveness of target-normal sheath acceleration into its dominant acceleration mechanism throughout the laser-plasma interaction, whereas 2D-S and 3D both have sizable populations accelerated preferentially during transparency.« less

  8. Accelerated Laboratory Research Experience in Psychology through Simulation.

    ERIC Educational Resources Information Center

    Chatfield, Douglas C.; Cruse, Bradley H.

    1986-01-01

    Describes implementation of computer simulation to aid in training psychology students in research methodology. Four skills required in research are reviewed; the simulation's context and the software used are described; and student activities, including submission of articles to online class journals and students' responses to the method, are…

  9. Effects of dimensionality on computer simulations of laser-ion acceleration: When are three-dimensional simulations needed?

    NASA Astrophysics Data System (ADS)

    Yin, L.; Stark, D. J.; Albright, B. J.

    2016-10-01

    Laser-ion acceleration via relativistic induced transparency provides an effective means to accelerate ions to tens of MeV/nucleon over distances of 10s of μm. These ion sources may enable a host of applications, from fast ignition and x-rays sources to medical treatments. Understanding whether two-dimensional (2D) PIC simulations can capture the relevant 3D physics is important to the development of a predictive capability for short-pulse laser-ion acceleration and for economical design studies for applications of these accelerators. In this work, PIC simulations are performed in 3D and in 2D where the direction of the laser polarization is in the simulation plane (2D-P) and out-of-plane (2D-S). Our studies indicate modeling sensitivity to dimensionality and laser polarization. Differences arise in energy partition, electron heating, ion peak energy, and ion spectral shape. 2D-P simulations are found to over-predict electron heating and ion peak energy. The origin of these differences and the extent to which 2D simulations may capture the key acceleration dynamics will be discussed. Work performed under the auspices of the U.S. DOE by the LANS, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. Funding provided by the Los Alamos National Laboratory Directed Research and Development Program.

  10. Numerical Simulations of the NRL Collective Particle Accelerator.

    DTIC Science & Technology

    1983-11-01

    observable experimentally. It is worth noting as well that an IREB propagating through a rippled magnetic field can produce significant microwave ...insulation, diode operation, microwave tube design, etc. MAGIC is an intermediate size code (about 20,000 statements), and is highly optimized both for user...ACCELERATOR PHASE-SPACE PLOT OF P1 VS. XI AT TIMlE ’.20E-09 SEC SPECIES NUMBER 1 OIM RATIO -1.759E+11 X2 WINDOW l.OOE-02 TO 2.40E-02 *109P2 WINDOW -1.OOE+l0 TO

  11. Lattice Boltzmann accelerated direct simulation Monte Carlo for dilute gas flow simulations

    NASA Astrophysics Data System (ADS)

    Di Staso, G.; Clercx, H. J. H.; Succi, S.; Toschi, F.

    2016-11-01

    Hybrid particle-continuum computational frameworks permit the simulation of gas flows by locally adjusting the resolution to the degree of non-equilibrium displayed by the flow in different regions of space and time. In this work, we present a new scheme that couples the direct simulation Monte Carlo (DSMC) with the lattice Boltzmann (LB) method in the limit of isothermal flows. The former handles strong non-equilibrium effects, as they typically occur in the vicinity of solid boundaries, whereas the latter is in charge of the bulk flow, where non-equilibrium can be dealt with perturbatively, i.e. according to Navier-Stokes hydrodynamics. The proposed concurrent multiscale method is applied to the dilute gas Couette flow, showing major computational gains when compared with the full DSMC scenarios. In addition, it is shown that the coupling with LB in the bulk flow can speed up the DSMC treatment of the Knudsen layer with respect to the full DSMC case. In other words, LB acts as a DSMC accelerator. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  12. Lattice Boltzmann accelerated direct simulation Monte Carlo for dilute gas flow simulations.

    PubMed

    Di Staso, G; Clercx, H J H; Succi, S; Toschi, F

    2016-11-13

    Hybrid particle-continuum computational frameworks permit the simulation of gas flows by locally adjusting the resolution to the degree of non-equilibrium displayed by the flow in different regions of space and time. In this work, we present a new scheme that couples the direct simulation Monte Carlo (DSMC) with the lattice Boltzmann (LB) method in the limit of isothermal flows. The former handles strong non-equilibrium effects, as they typically occur in the vicinity of solid boundaries, whereas the latter is in charge of the bulk flow, where non-equilibrium can be dealt with perturbatively, i.e. according to Navier-Stokes hydrodynamics. The proposed concurrent multiscale method is applied to the dilute gas Couette flow, showing major computational gains when compared with the full DSMC scenarios. In addition, it is shown that the coupling with LB in the bulk flow can speed up the DSMC treatment of the Knudsen layer with respect to the full DSMC case. In other words, LB acts as a DSMC accelerator.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

  13. 3-D RPIC simulations of relativistic jets: Particle acceleration, magnetic field generation, and emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.

    2006-01-01

    Nonthermal radiation observed from astrophysical systems containing (relativistic) jets and shocks, e.g., supernova remnants, active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the .shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields 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. We will review recent PIC simulations which show particle acceleration in jets.

  14. 3-D RPIC simulations of relativistic jets: Particle acceleration, magnetic field generation, and emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.

    2006-01-01

    Nonthermal radiation observed from astrophysical systems containing (relativistic) jets and shocks, e.g., supernova remnants, active galactic nuclei (AGNs), gamma-ray bursts (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments. Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets show that acceleration occurs within the downstream jet, rather than by the scattering of particles back and forth across the shock as in Fermi acceleration. Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., the Buneman instability, other two-streaming instability, and the Weibel instability) created in the .shocks are responsible for particle (electron, positron, and ion) acceleration. The simulation results show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields. These magnetic fields 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. We will review recent PIC simulations which show particle acceleration in jets.

  15. Simulation of Laser Wake Field Acceleration using a 2.5D PIC Code

    SciTech Connect

    An, W. M.; Hua, J. F.; Huang, W. H.; Tang, Ch. X.; Lin, Y. Z.

    2006-11-27

    A 2.5D PIC simulation code is developed to study the LWFA( Laser WakeField Acceleration ). The electron self-injection and the generation of mono-energetic electron beam in LWFA is briefly discussed through the simulation. And the experiment of this year at SILEX-I laser facility is also introduced.

  16. Acceleration of Radiance for Lighting Simulation by Using Parallel Computing with OpenCL

    SciTech Connect

    Zuo, Wangda; McNeil, Andrew; Wetter, Michael; Lee, Eleanor

    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.

  17. A seat cushion to provide realistic acceleration cues for aircraft simulators

    NASA Technical Reports Server (NTRS)

    Ashworth, B. R.

    1976-01-01

    A seat cushion to provide acceleration cues for aircraft simulator pilots was built, performance tested, and evaluated. The four cell seat, using a thin air cushion with highly responsive pressure control, attempts to reproduce the same events which occur in an aircraft seat under acceleration loading. The pressure controller provides seat cushion responses which are considered adequate for current high performance aircraft simulations. The initial tests of the seat cushions have resulted in excellent pilot opinion of the cushion's ability to provide realistic and useful cues to the simulator pilot.

  18. ELECTROMAGNETIC AND THERMAL SIMULATIONS FOR THE SWITCH REGION OF A COMPACT PROTON ACCELERATOR

    SciTech Connect

    Wang, L; Caporaso, G J; Sullivan, J S

    2007-06-15

    A compact proton accelerator for medical applications is being developed at Lawrence Livermore National Laboratory. The accelerator architecture is based on the dielectric wall accelerator (DWA) concept. One critical area to consider is the switch region. Electric field simulations and thermal calculations of the switch area were performed to help determine the operating limits of rmed SiC switches. Different geometries were considered for the field simulation including the shape of the thin Indium solder meniscus between the electrodes and SiC. Electric field simulations were also utilized to demonstrate how the field stress could be reduced. Both transient and steady steady-state thermal simulations were analyzed to find the average power capability of the switches.

  19. Simulation Studies of the Dielectric Grating as an Accelerating and Focusing Structure

    SciTech Connect

    Soong, Ken; Peralta, E.A.; Byer, R.L.; Colby, E.; /SLAC

    2011-08-12

    A grating-based design is a promising candidate for a laser-driven dielectric accelerator. Through simulations, we show the merits of a readily fabricated grating structure as an accelerating component. Additionally, we show that with a small design perturbation, the accelerating component can be converted into a focusing structure. The understanding of these two components is critical in the successful development of any complete accelerator. The concept of accelerating electrons with the tremendous electric fields found in lasers has been proposed for decades. However, until recently the realization of such an accelerator was not technologically feasible. Recent advances in the semiconductor industry, as well as advances in laser technology, have now made laser-driven dielectric accelerators imminent. The grating-based accelerator is one proposed design for a dielectric laser-driven accelerator. This design, which was introduced by Plettner, consists of a pair of opposing transparent binary gratings, illustrated in Fig. 1. The teeth of the gratings serve as a phase mask, ensuring a phase synchronicity between the electromagnetic field and the moving particles. The current grating accelerator design has the drive laser incident perpendicular to the substrate, which poses a laser-structure alignment complication. The next iteration of grating structure fabrication seeks to monolithically create an array of grating structures by etching the grating's vacuum channel into a fused silica wafer. With this method it is possible to have the drive laser confined to the plane of the wafer, thus ensuring alignment of the laser-and-structure, the two grating halves, and subsequent accelerator components. There has been previous work using 2-dimensional finite difference time domain (2D-FDTD) calculations to evaluate the performance of the grating accelerator structure. However, this work approximates the grating as an infinite structure and does not accurately model a

  20. FEM Techniques for High Stress Detection in Accelerated Fatigue Simulation

    NASA Astrophysics Data System (ADS)

    Veltri, M.

    2016-09-01

    This work presents the theory and a numerical validation study in support to a novel method for a priori identification of fatigue critical regions, with the aim to accelerate durability design in large FEM problems. The investigation is placed in the context of modern full-body structural durability analysis, where a computationally intensive dynamic solution could be required to identify areas with potential for fatigue damage initiation. The early detection of fatigue critical areas can drive a simplification of the problem size, leading to sensible improvement in solution time and model handling while allowing processing of the critical areas in higher detail. The proposed technique is applied to a real life industrial case in a comparative assessment with established practices. Synthetic damage prediction quantification and visualization techniques allow for a quick and efficient comparison between methods, outlining potential application benefits and boundaries.

  1. Accelerated simulation study of space charge effects in quadrupole ion traps using GPU techniques.

    PubMed

    Xiong, Xingchuang; Xu, Wei; Fang, Xiang; Deng, Yulin; Ouyang, Zheng

    2012-10-01

    Space charge effects play important roles in the performance of various types of mass analyzers. Simulation of space charge effects is often limited by the computation capability. In this study, we evaluate the method of using graphics processing unit (GPU) to accelerate ion trajectory simulation. Simulation using GPU has been compared with multi-core central processing unit (CPU), and an acceleration of about 390 times have been obtained using a single computer for simulation of up to 10(5) ions in quadrupole ion traps. Characteristics of trapped ions can be investigated at detailed levels within a reasonable simulation time. Space charge effects on the trapping capacities of linear and 3D ion traps, ion cloud shapes, ion motion frequency shift, mass spectrum peak coalescence effects between two ion clouds of close m/z are studied with the ion trajectory simulation using GPU.

  2. Accelerated Simulation Study of Space Charge Effects in Quadrupole Ion Traps Using GPU Techniques

    NASA Astrophysics Data System (ADS)

    Xiong, Xingchuang; Xu, Wei; Fang, Xiang; Deng, Yulin; Ouyang, Zheng

    2012-10-01

    Space charge effects play important roles in the performance of various types of mass analyzers. Simulation of space charge effects is often limited by the computation capability. In this study, we evaluate the method of using graphics processing unit (GPU) to accelerate ion trajectory simulation. Simulation using GPU has been compared with multi-core central processing unit (CPU), and an acceleration of about 390 times have been obtained using a single computer for simulation of up to 105 ions in quadrupole ion traps. Characteristics of trapped ions can be investigated at detailed levels within a reasonable simulation time. Space charge effects on the trapping capacities of linear and 3D ion traps, ion cloud shapes, ion motion frequency shift, mass spectrum peak coalescence effects between two ion clouds of close m/z are studied with the ion trajectory simulation using GPU.

  3. Numerical simulation of solar cosmic ray acceleration in reconnecting current sheets

    NASA Astrophysics Data System (ADS)

    Balabin, Yury; Podgorny, Igor; Podgorny, Alexander; Vashenyuk, Eduard

    The set of neutron monitors measurements reveals two components of relativistic protons that accompaniment a flare. The prompt component of relativistic protons is created simultaneously with flare hard X-ray radiation. It possesses information about the mechanism of particle acceleration in a flare up to 10 GeV. Prompt component shows the exponential spectrum with W0 order of 0.5 GeV. The possibility of particle acceleration in a current sheet has been considered in the frame of the elctrodynamical solar flare model. Particles can get energy during acceleration in the Lorenz electric field along a singular line. The similar mechanism of acceleration has been observed in the powerful pinch discharge. In previous simulation works it has been shown that exponential spectrum appears, if the electric field is applied along a magnetic symmetrical X-type singular line. Such simulation can be considered as a first step for reality, because the real field distribution is much more complicated. Now numerical simulations have been carried out for the real magnetic and electric configurations calculated in MHD numerical experiments for the famous Bastille flare. The result of simulation shows that the spectrum of accelerated protons during a flare indeed is the exponential one. From comparison of simulation results with observable spectra of solar protons the rate of reconnection of order of 107 cm/s for W0 0.5 GeV is estimated.

  4. Pertuzumab and its accelerated approval: evolving treatment paradigms and new challenges in the management of HER2-positive breast cancer.

    PubMed

    O'Sullivan, Ciara C; Connolly, Roisin M

    2014-03-01

    The addition of trastuzumab, a monoclonal antibody to human epidermal growth factor receptor 2 (HER2), to standard chemotherapy in patients with HER2-positive breast cancer has resulted in major improvements in breast cancer outcomes, including improved survival, in both the adjuvant and metastatic settings. However, some patients experience disease relapse despite adjuvant trastuzumab-containing therapy, and resistance to trastuzumab develops in the majority of patients in the metastatic setting. An understanding of the molecular mechanisms underlying trastuzumab resistance has aided the development of novel HER2-targeted therapies. In June 2012, the HER2 dimerization inhibitor pertuzumab was approved by the US Food and Drug Administration (FDA) for use with chemotherapy and trastuzumab in the first-line treatment of metastatic HER2-positive breast cancer. In September 2013, accelerated approval was granted for use of pertuzumab in the neoadjuvant setting, representing a landmark decision by the FDA. This article discusses the development of pertuzumab to date, with a particular focus on the accelerated approval decision. We highlight the need to identify reliable biomarkers of sensitivity and resistance to HER2-targeted therapy, which would make possible the individualization of treatment for patients with HER2-positive breast cancer.

  5. Numerical Simulations of Particle Acceleration at Interplanetary Quasi-perpendicular Shocks

    NASA Astrophysics Data System (ADS)

    Kong, F.-J.; Qin, G.; Zhang, L.-H.

    2017-08-01

    Using test particle simulations we study particle acceleration at highly perpendicular ({θ }{Bn}≥slant 75^\\circ ) shocks under conditions of modeling magnetic turbulence. We adopt a backward-in-time method to solve the Newton-Lorentz equation using the observed shock parameters for quasi-perpendicular interplanetary shocks, and compare the simulation results with ACE/EPAM observations to obtain the injection energy and timescale of particle acceleration. With our modeling and observations, we find that a large upstream speed is responsible for efficient particle acceleration. Our results also show that the quasi-perpendicular shocks are capable of accelerating thermal particles to high energies of the order of MeV for both kappa and Maxwellian upstream distributions, which may originate from the fact that in our model, the local background magnetic field has a component parallel to the shock normal.

  6. Computer simulation of the coupling slots effects for on-axis coupled accelerating structures.

    NASA Astrophysics Data System (ADS)

    Salakhoutdinov, A. F.; Shvedunov, V. I.

    1997-05-01

    The presence of coupling elements in accelerating structures leads to the violation of axial symmetry of accelerating field and it may cause displacement, defocusing and non-linear distortion of phase space. As a result the growth of transverse emittance occures. From the other hand, these effects may be used for designing of RF- focusing accelerating structure for electron accelerators of various types. The numerical simulation of electrodynamical properties of on-axis coupled accelerating structure taking into account the coupling slots have been made. The characteristics of fields excited within the coupling cell have been investigated. The numerical estimations of various multipolarity components of transverse forces acting upon a particle inside the coupling cell have been achieved.

  7. Beam dynamics simulations of post low energy beam transport section in RAON heavy ion accelerator

    SciTech Connect

    Jin, Hyunchang Jang, Ji-Ho; Jang, Hyojae; Hong, In-Seok

    2016-02-15

    RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.

  8. The operant reserve: a computer simulation in (accelerated) real time.

    PubMed

    Catania, A Charles

    2005-05-31

    In Skinner's Reflex Reserve theory, reinforced responses added to a reserve depleted by responding. It could not handle the finding that partial reinforcement generated more responding than continuous reinforcement, but it would have worked if its growth had depended not just on the last response but also on earlier responses preceding a reinforcer, each weighted by delay. In that case, partial reinforcement generates steady states in which reserve decrements produced by responding balance increments produced when reinforcers follow responding. A computer simulation arranged schedules for responses produced with probabilities proportional to reserve size. Each response subtracted a fixed amount from the reserve and added an amount weighted by the reciprocal of the time to the next reinforcer. Simulated cumulative records and quantitative data for extinction, random-ratio, random-interval, and other schedules were consistent with those of real performances, including some effects of history. The model also simulated rapid performance transitions with changed contingencies that did not depend on molar variables or on differential reinforcement of inter-response times. The simulation can be extended to inhomogeneous contingencies by way of continua of reserves arrayed along response and time dimensions, and to concurrent performances and stimulus control by way of different reserves created for different response classes.

  9. Numerical Simulation of Laser-Driven In-Tube Accelerator Operation

    SciTech Connect

    Ohnishi, N.; Ogino, Y.; Sawada, K.; Ohtani, T.; Mori, K.; Sasoh, A.

    2006-05-02

    To achieve a higher thrust performance in the laser-driven in-tube accelerator operation, numerical analysises have been carried out. The computational code covers from the generation of the blast wave to its interactions with the projectile and the acceleration wall. The thrust history and the momentum coupling coefficient evaluated from the numerical simulation depend on the fill pressure and the projectile shape. The confinement effect can be clearly found using the projectile attached with a shroud.

  10. New "Tau-Leap" Strategy for Accelerated Stochastic Simulation.

    PubMed

    Ramkrishna, Doraiswami; Shu, Che-Chi; Tran, Vu

    2014-12-10

    The "Tau-Leap" strategy for stochastic simulations of chemical reaction systems due to Gillespie and co-workers has had considerable impact on various applications. This strategy is reexamined with Chebyshev's inequality for random variables as it provides a rigorous probabilistic basis for a measured τ-leap thus adding significantly to simulation efficiency. It is also shown that existing strategies for simulation times have no probabilistic assurance that they satisfy the τ-leap criterion while the use of Chebyshev's inequality leads to a specified degree of certainty with which the τ-leap criterion is satisfied. This reduces the loss of sample paths which do not comply with the τ-leap criterion. The performance of the present algorithm is assessed, with respect to one discussed by Cao et al. (J. Chem. Phys.2006, 124, 044109), a second pertaining to binomial leap (Tian and Burrage J. Chem. Phys.2004, 121, 10356; Chatterjee et al. J. Chem. Phys.2005, 122, 024112; Peng et al. J. Chem. Phys.2007, 126, 224109), and a third regarding the midpoint Poisson leap (Peng et al., 2007; Gillespie J. Chem. Phys.2001, 115, 1716). The performance assessment is made by estimating the error in the histogram measured against that obtained with the so-called stochastic simulation algorithm. It is shown that the current algorithm displays notably less histogram error than its predecessor for a fixed computation time and, conversely, less computation time for a fixed accuracy. This computational advantage is an asset in repetitive calculations essential for modeling stochastic systems. The importance of stochastic simulations is derived from diverse areas of application in physical and biological sciences, process systems, and economics, etc. Computational improvements such as those reported herein are therefore of considerable significance.

  11. Capture and Control of Laser-Accelerated Proton Beams: Experiment and Simulation

    SciTech Connect

    Nurnberg, F; Alber, I; Harres, K; Schollmeier, M; Roth, M; Barth, W; Eickhoff, H; Hofmann, I; Friedman, A; Grote, D; Logan, B G

    2009-05-13

    This paper summarizes the ongoing studies on the possibilities for transport and RF capture of laser-accelerated proton beams in conventional accelerator structures. First results on the capture of laser-accelerated proton beams are presented, supported by Trace3D, CST particle studio and Warp simulations. Based on these results, the development of the pulsed high-field solenoid is guided by our desire to optimize the output particle number for this highly divergent beam with an exponential energy spectrum. A future experimental test stand is proposed to do studies concerning the application as a new particle source.

  12. 3D Simulations for a Micron-Scale, Dielectric-Based Acceleration Experiment

    SciTech Connect

    Yoder, R. B.; Travish, G.; Xu Jin; Rosenzweig, J. B.

    2009-01-22

    An experimental program to demonstrate a dielectric, slab-symmetric accelerator structure has been underway for the past two years. These resonant devices are driven by a side-coupled 800-nm laser and can be configured to maintain the field profile necessary for synchronous acceleration and focusing of relativistic or nonrelativistic particles. We present 3D simulations of various versions of the structure geometry, including a metal-walled structure relevant to ongoing cold tests on resonant properties, and an all-dielectric structure to be constructed for a proof-of-principle acceleration experiment.

  13. Microparticle accelerator of unique design. [for micrometeoroid impact and cratering simulation

    NASA Technical Reports Server (NTRS)

    Vedder, J. F.

    1978-01-01

    A microparticle accelerator has been devised for micrometeoroid impact and cratering simulation; the device produces high-velocity (0.5-15 km/sec), micrometer-sized projectiles of any cohesive material. In the source, an electrodynamic levitator, single particles are charged by ion bombardment in high vacuum. The vertical accelerator has four drift tubes, each initially at a high negative voltage. After injection of the projectile, each tube is grounded in turn at a time determined by the voltage and charge/mass ratio to give four acceleration stages with a total voltage equivalent to about 1.7 MV.

  14. Linear Accelerator and Gamma Knife-Based Stereotactic Cranial Radiosurgery: Challenges and Successes of Existing Quality Assurance Guidelines and Paradigms

    SciTech Connect

    Goetsch, Steven J.

    2008-05-01

    Intracranial stereotactic radiosurgery has been practiced since 1951. The technique has expanded from a single dedicated unit in Stockholm in 1968 to hundreds of centers performing an estimated 100,000 Gamma Knife and linear accelerator cases in 2005. The radiation dosimetry of small photon fields used in this technique has been well explored in the past 15 years. Quality assurance recommendations have been promulgated in refereed reports and by several national and international professional societies since 1991. The field has survived several reported treatment errors and incidents, generally reacting by strengthening standards and precautions. An increasing number of computer-controlled and robotic-dedicated treatment units are expanding the field and putting patients at risk of unforeseen errors. Revisions and updates to previously published quality assurance documents, and especially to radiation dosimetry protocols, are now needed to ensure continued successful procedures that minimize the risk of serious errors.

  15. GPU accelerated numerical simulations of viscoelastic phase separation model.

    PubMed

    Yang, Keda; Su, Jiaye; Guo, Hongxia

    2012-07-05

    We introduce a complete implementation of viscoelastic model for numerical simulations of the phase separation kinetics in dynamic asymmetry systems such as polymer blends and polymer solutions on a graphics processing unit (GPU) by CUDA language and discuss algorithms and optimizations in details. From studies of a polymer solution, we show that the GPU-based implementation can predict correctly the accepted results and provide about 190 times speedup over a single central processing unit (CPU). Further accuracy analysis demonstrates that both the single and the double precision calculations on the GPU are sufficient to produce high-quality results in numerical simulations of viscoelastic model. Therefore, the GPU-based viscoelastic model is very promising for studying many phase separation processes of experimental and theoretical interests that often take place on the large length and time scales and are not easily addressed by a conventional implementation running on a single CPU.

  16. Accelerated discovery of OLED materials through atomic-scale simulation

    NASA Astrophysics Data System (ADS)

    Halls, Mathew D.; Giesen, David J.; Hughes, Thomas F.; Goldberg, Alexander; Cao, Yixiang; Kwak, H. Shaun; Mustard, Thomas J.; Gavartin, Jacob

    2016-09-01

    Organic light-emitting diode (OLED) devices are under widespread investigation to displace or complement inorganic optoelectronic devices for solid-state lighting and active displays. The materials in these devices are selected or designed according to their intrinsic and extrinsic electronic properties with concern for efficient charge injection and transport, and desired stability and light emission characteristics. The chemical design space for OLED materials is enormous and there is need for the development of computational approaches to help identify the most promising solutions for experimental development. In this work we will present examples of simulation approaches available to efficiently screen libraries of potential OLED materials; including first-principles prediction of key intrinsic properties, and classical simulation of amorphous morphology and stability. Also, an alternative to exhaustive computational screening is introduced based on a biomimetic evolutionary framework; evolving the molecular structure in the calculated OLED property design space.

  17. Mainstreaming Modeling and Simulation to Accelerate Public Health Innovation

    PubMed Central

    Sepulveda, Martin-J.; Mabry, Patricia L.

    2014-01-01

    Dynamic modeling and simulation are systems science tools that examine behaviors and outcomes resulting from interactions among multiple system components over time. Although there are excellent examples of their application, they have not been adopted as mainstream tools in population health planning and policymaking. Impediments to their use include the legacy and ease of use of statistical approaches that produce estimates with confidence intervals, the difficulty of multidisciplinary collaboration for modeling and simulation, systems scientists’ inability to communicate effectively the added value of the tools, and low funding for population health systems science. Proposed remedies include aggregation of diverse data sets, systems science training for public health and other health professionals, changing research incentives toward collaboration, and increased funding for population health systems science projects. PMID:24832426

  18. Simulation of imaging radar using graphics hardware acceleration

    NASA Astrophysics Data System (ADS)

    Peinecke, Niklas; Döhler, Hans-Ullrich; Korn, Bernd R.

    2008-04-01

    Extending previous works by Doehler and Bollmeyer we describe a new implementation of an imaging radar simulator. Our approach is based on using modern computer graphics hardware making heavy use of recent technologies like vertex and fragment shaders. Furthermore, to allow for a nearly realistic image we generate radar shadows implementing shadow map techniques in the programmable graphics hardware. The particular implementation is tailored to imitate millimeter wave (MMW) radar but could be extended for other types of radar systems easily.

  19. Community Project for Accelerator Science and Simulation (ComPASS)

    SciTech Connect

    Simmons, Christopher; Carey, Varis

    2016-10-12

    After concluding our initial exercise (solving a simplified statistical inverse problem with unknown parameter laser intensity) of coupling Vorpal and our parallel statistical library QUESO, we shifted the application focus to DLA. Our efforts focused on developing a Gaussian process (GP) emulator within QUESO for efficient optimization of power couplers within woodpiles. The smaller simulation size (compared with LPA) allows for sufficient “training runs” to develop a reasonable GP statistical emulator for a parameter space of moderate dimension.

  20. Biocellion: accelerating computer simulation of multicellular biological system models

    PubMed Central

    Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

    2014-01-01

    Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

  1. Investigation on Accelerating Dust Storm Simulation via Domain Decomposition Methods

    NASA Astrophysics Data System (ADS)

    Yu, M.; Gui, Z.; Yang, C. P.; Xia, J.; Chen, S.

    2014-12-01

    Dust storm simulation is a data and computing intensive process, which requires high efficiency and adequate computing resources. To speed up the process, high performance computing is widely adopted. By partitioning a large study area into small subdomains according to their geographic location and executing them on different computing nodes in a parallel fashion, the computing performance can be significantly improved. However, it is still a question worthy of consideration that how to allocate these subdomain processes into computing nodes without introducing imbalanced task loads and unnecessary communications among computing nodes. Here we propose a domain decomposition and allocation framework that can carefully leverage the computing cost and communication cost for each computing node to minimize total execution time and reduce overall communication cost for the entire system. The framework is tested in the NMM (Nonhydrostatic Mesoscale Model)-dust model, where a 72-hour processes of the dust load are simulated. Performance result using the proposed scheduling method is compared with the one using default scheduling methods of MPI. Results demonstrate that the system improves the performance of simulation by 20% up to 80%.

  2. Modern Simulation and Optimization Tools for Non-Scaling FFAGs and Related Accelerators

    SciTech Connect

    C. Johnstone; M. Berz; K. Makino

    2010-11-04

    With the U.S. experimental effort in HEP largely located at laboratories supporting the operations of large, highly specialized accelerators, the understanding and prediction of high energy particle accelerators becomes critical to the overall success of the DOE HEP program. One area in which small businesses can contribute to the ongoing success of the U.S. program in HEP is through innovations in computer techniques and sophistication in the modeling of high-energy accelerators. A specific newly identified problem lies in the simulation and optimization of FFAGs and related devices, for which currently available tools originally developed for other purposes provide only approximate and inefficient simulation. We propose to develop a set of tools for this purpose based on modern techniques and simulation approaches.

  3. Acceleration of heavy and light particles in turbulence: Comparison between experiments and direct numerical simulations

    NASA Astrophysics Data System (ADS)

    Volk, R.; Calzavarini, E.; Verhille, G.; Lohse, D.; Mordant, N.; Pinton, J.-F.; Toschi, F.

    2008-08-01

    We compare experimental data and numerical simulations for the dynamics of inertial particles with finite density in turbulence. In the experiment, bubbles and solid particles are optically tracked in a turbulent flow of water using an Extended Laser Doppler Velocimetry technique. The probability density functions (PDF) of particle accelerations and their auto-correlation in time are computed. Numerical results are obtained from a direct numerical simulation in which a suspension of passive pointwise particles is tracked, with the same finite density and the same response time as in the experiment. We observe a good agreement for both the variance of acceleration and the autocorrelation time scale of the dynamics; small discrepancies on the shape of the acceleration PDF are observed. We discuss the effects induced by the finite size of the particles, not taken into account in the present numerical simulations.

  4. Particle in cell simulation of laser-accelerated proton beams for radiation therapy.

    PubMed

    Fourkal, E; Shahine, B; Ding, M; Li, J S; Tajima, T; Ma, C M

    2002-12-01

    In this article we present the results of particle in cell (PIC) simulations of laser plasma interaction for proton acceleration for radiation therapy treatments. We show that under optimal interaction conditions protons can be accelerated up to relativistic energies of 300 MeV by a petawatt laser field. The proton acceleration is due to the dragging Coulomb force arising from charge separation induced by the ponderomotive pressure (light pressure) of high-intensity laser. The proton energy and phase space distribution functions obtained from the PIC simulations are used in the calculations of dose distributions using the GEANT Monte Carlo simulation code. Because of the broad energy and angular spectra of the protons, a compact particle selection and beam collimation system will be needed to generate small beams of polyenergetic protons for intensity modulated proton therapy.

  5. Balancing a simulated inverted pendulum through motor imagery: an EEG-based real-time control paradigm.

    PubMed

    Yue, Jingwei; Zhou, Zongtan; Jiang, Jun; Liu, Yadong; Hu, Dewen

    2012-08-30

    Most brain-computer interfaces (BCIs) are non-time-restraint systems. However, the method used to design a real-time BCI paradigm for controlling unstable devices is still a challenging problem. This paper presents a real-time feedback BCI paradigm for controlling an inverted pendulum on a cart (IPC). In this paradigm, sensorimotor rhythms (SMRs) were recorded using 15 active electrodes placed on the surface of the subject's scalp. Subsequently, common spatial pattern (CSP) was used as the basic filter to extract spatial patterns. Finally, linear discriminant analysis (LDA) was used to translate the patterns into control commands that could stabilize the simulated inverted pendulum. Offline trainings were employed to teach the subjects to execute corresponding mental tasks, such as left/right hand motor imagery. Five subjects could successfully balance the online inverted pendulum for more than 35s. The results demonstrated that BCIs are able to control nonlinear unstable devices. Furthermore, the demonstration and extension of real-time continuous control might be useful for the real-life application and generalization of BCI.

  6. TEP and Lichtenstein anatomy: does simulation accelerate acquisition among interns?

    PubMed

    Rowse, P G; Ruparel, R K; Abdelsattar, J M; AlJamal, Y N; Dy, B M; Farley, D R

    2016-06-01

    The anatomy of the inguinal region is notoriously challenging to master. We sought to teach open inguinal hernia (OIH) and totally extraperitoneal (TEP) anatomy with simulation models among general surgery (GS) interns. Low-fidelity OIH and TEP models were constructed out of cardboard, plastic bins, fabric, and yarn. GS interns (n = 30) participated in a 3-h hernia session including a pretest, anatomy lecture, simulated OIH and TEP hernia repair, and posttest. Pre- and posttest scores were based on a difficult 30-point exam which included didactic questions (10 points), drawing relevant TEP (10 points), and OIH (10 points) anatomy. Participants were surveyed following the session. Median pretest scores were 13 % (range 0-60 %). Median posttest scores improved to 47 % (range 20-93 %, p < 0.001). Median number of structures drawn in the TEP image improved from 2 (range 0-14) to 11 (range 1-21, p < 0.001). Median number of structures drawn in the OIH image improved from 3 (range 0-15) to 7 (range 1-19, p < 0.001). 67 % (12/18) demonstrated improvement in knowledge of abdominal wall layers. 23 % (7/30) knew the triangles of pain/doom on the pretest vs. 77 % (23/30) on the posttest. Mean Likert scores favored session enjoyability (4.5), not a waste of training time (4.4), and improved understanding of OIH and TEP anatomy (4.4, 4.2). Low-fidelity simulators can be used to teach and assess knowledge of TEP and OIH anatomy. While enjoyable and useful, one 3-h session does not create master hernia surgeons or expert anatomists out of novice trainees.

  7. MO-F-16A-02: Simulation of a Medical Linear Accelerator for Teaching Purposes

    SciTech Connect

    Carlone, M; Lamey, M; Anderson, R; MacPherson, M

    2014-06-15

    Purpose: Detailed functioning of linear accelerator physics is well known. Less well developed is the basic understanding of how the adjustment of the linear accelerator's electrical components affects the resulting radiation beam. Other than the text by Karzmark, there is very little literature devoted to the practical understanding of linear accelerator functionality targeted at the radiotherapy clinic level. The purpose of this work is to describe a simulation environment for medical linear accelerators with the purpose of teaching linear accelerator physics. Methods: Varian type lineacs were simulated. Klystron saturation and peak output were modelled analytically. The energy gain of an electron beam was modelled using load line expressions. The bending magnet was assumed to be a perfect solenoid whose pass through energy varied linearly with solenoid current. The dose rate calculated at depth in water was assumed to be a simple function of the target's beam current. The flattening filter was modelled as an attenuator with conical shape, and the time-averaged dose rate at a depth in water was determined by calculating kerma. Results: Fifteen analytical models were combined into a single model called SIMAC. Performance was verified systematically by adjusting typical linac control parameters. Increasing klystron pulse voltage increased dose rate to a peak, which then decreased as the beam energy was further increased due to the fixed pass through energy of the bending magnet. Increasing accelerator beam current leads to a higher dose per pulse. However, the energy of the electron beam decreases due to beam loading and so the dose rate eventually maximizes and the decreases as beam current was further increased. Conclusion: SIMAC can realistically simulate the functionality of a linear accelerator. It is expected to have value as a teaching tool for both medical physicists and linear accelerator service personnel.

  8. Modern approaches to accelerator simulation and on-line control

    SciTech Connect

    Lee, M.; Clearwater, S.; Theil, E.; Paxson, V.

    1987-02-01

    COMFORT-PLUS consists of three parts: (1) COMFORT (Control Of Machine Function, ORbits, and Trajectories), which computes the machine lattice functions and transport matrices along a beamline; (2) PLUS (Prediction from Lattice Using Simulation) which finds or compensates for errors in the beam parameters or machine elements; and (3) a highly graphical interface to PLUS. The COMFORT-PLUS package has been developed on a SUN-3 workstation. The structure and use of COMFORT-PLUS are described, and an example of the use of the package is presented. (LEW)

  9. Accelerated GPU simulation of compressible flow by the discontinuous evolution Galerkin method

    NASA Astrophysics Data System (ADS)

    Block, B. J.; Lukáčová-Medvid'ová, M.; Virnau, P.; Yelash, L.

    2012-08-01

    The aim of the present paper is to report on our recent results for GPU accelerated simulations of compressible flows. For numerical simulation the adaptive discontinuous Galerkin method with the multidimensional bicharacteristic based evolution Galerkin operator has been used. For time discretization we have applied the explicit third order Runge-Kutta method. Evaluation of the genuinely multidimensional evolution operator has been accelerated using the GPU implementation. We have obtained a speedup up to 30 (in comparison to a single CPU core) for the calculation of the evolution Galerkin operator on a typical discretization mesh consisting of 16384 mesh cells.

  10. Benchmarking the codes VORPAL, OSIRIS, and QuickPIC with Laser Wakefield Acceleration Simulations

    SciTech Connect

    Paul, K.; Bruhwiler, D. L.; Cowan, B.; Cary, J. R.; Huang, C.; Mori, W. B.; Tsung, F. S.; Cormier-Michel, E.; Geddes, C. G. R.; Esarey, E.; Fonseca, R. A.; Martins, S. F.; Silva, L. O.

    2009-01-22

    Three-dimensional laser wakefield acceleration (LWFA) simulations have recently been performed to benchmark the commonly used particle-in-cell (PIC) codes VORPAL, OSIRIS, and QuickPIC. The simulations were run in parallel on over 100 processors, using parameters relevant to LWFA with ultra-short Ti-Sapphire laser pulses propagating in hydrogen gas. Both first-order and second-order particle shapes were employed. We present the results of this benchmarking exercise, and show that accelerating gradients from full PIC agree for all values of a{sub 0} and that full and reduced PIC agree well for values of a{sub 0} approaching 4.

  11. A comparison of acceleration control and pulse control in simulated spacecraft docking maneuvers

    NASA Technical Reports Server (NTRS)

    Brody, Adam R.; Ellis, Stephen R.

    1991-01-01

    Results are reported from a study designed to compare acceleration control with pulse control in simulated spacecraft docking maneuvers. Nine commercial airline pilots served as test subjects and the simulated remote dockings of an orbital maneuvering vehicle (OMV) to a space station were initiated from 50, 100, and 150 meters along the station's minus velocity vector. The trials were grouped into blocks of 18 consisting of six repetitions of the three ranges. It was found that mission duration was lower with pulse mode, while fuel consumption was lower with acceleration mode. It is suggested that this result is most likely specific to the thruster values that are being used.

  12. Electric field simulation and measurement of a pulse line ion accelerator

    NASA Astrophysics Data System (ADS)

    Shen, Xiao-Kang; Zhang, Zi-Min; Cao, Shu-Chun; Zhao, Hong-Wei; Wang, Bo; Shen, Xiao-Li; Zhao, Quan-Tang; Liu, Ming; Jing, Yi

    2012-07-01

    An oil dielectric helical pulse line to demonstrate the principles of a Pulse Line Ion Accelerator (PLIA) has been designed and fabricated. The simulation of the axial electric field of an accelerator with CST code has been completed and the simulation results show complete agreement with the theoretical calculations. To fully understand the real value of the electric field excited from the helical line in PLIA, an optical electric integrated electric field measurement system was adopted. The measurement result shows that the real magnitude of axial electric field is smaller than that calculated, probably due to the actual pitch of the resister column which is much less than that of helix.

  13. Benchmarking the codes VORPAL, OSIRIS, and QuickPIC with Laser Wakefield Acceleration Simulations

    SciTech Connect

    Paul, Kevin; Huang, C.; Bruhwiler, D.L.; Mori, W.B.; Tsung, F.S.; Cormier-Michel, E.; Geddes, C.G.R.; Cowan, B.; Cary, J.R.; Esarey, E.; Fonseca, R.A.; Martins, S.F.; Silva, L.O.

    2008-09-08

    Three-dimensional laser wakefield acceleration (LWFA) simulations have recently been performed to benchmark the commonly used particle-in-cell (PIC) codes VORPAL, OSIRIS, and QuickPIC. The simulations were run in parallel on over 100 processors, using parameters relevant to LWFA with ultra-short Ti-Sapphire laser pulses propagating in hydrogen gas. Both first-order and second-order particle shapes were employed. We present the results of this benchmarking exercise, and show that accelerating gradients from full PIC agree for all values of a0 and that full and reduced PIC agree well for values of a0 approaching 4.

  14. SU-E-T-512: Electromagnetic Simulations of the Dielectric Wall Accelerator

    SciTech Connect

    Uselmann, A; Mackie, T

    2014-06-01

    Purpose: To characterize and parametrically study the key components of a dielectric wall accelerator through electromagnetic modeling and particle tracking. Methods: Electromagnetic and particle tracking simulations were performed using a commercial code (CST Microwave Studio, CST Inc.) utilizing the finite integration technique. A dielectric wall accelerator consists of a series of stacked transmission lines sequentially fired in synchrony with an ion pulse. Numerous properties of the stacked transmission lines, including geometric, material, and electronic properties, were analyzed and varied in order to assess their impact on the transverse and axial electric fields. Additionally, stacks of transmission lines were simulated in order to quantify the parasitic effect observed in closely packed lines. Particle tracking simulations using the particle-in-cell method were performed on the various stacks to determine the impact of the above properties on the resultant phase space of the ions. Results: Examination of the simulation results show that novel geometries can shape the accelerating pulse in order to reduce the energy spread and increase the average energy of accelerated ions. Parasitic effects were quantified for various geometries and found to vary with distance from the end of the transmission line and along the beam axis. An optimal arrival time of an ion pulse relative to the triggering of the transmission lines for a given geometry was determined through parametric study. Benchmark simulations of single transmission lines agree well with published experimental results. Conclusion: This work characterized the behavior of the transmission lines used in a dielectric wall accelerator and used this information to improve them in novel ways. Utilizing novel geometries, we were able to improve the accelerating gradient and phase space of the accelerated particle bunch. Through simulation, we were able to discover and optimize design issues with the device at

  15. WarpIV: In situ visualization and analysis of ion accelerator simulations

    DOE PAGES

    Rubel, Oliver; Loring, Burlen; Vay, Jean -Luc; ...

    2016-05-09

    The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analyticsmore » to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. Furthermore, this supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.« less

  16. WarpIV: In situ visualization and analysis of ion accelerator simulations

    SciTech Connect

    Rubel, Oliver; Loring, Burlen; Vay, Jean -Luc; Grote, David P.; Lehe, Remi; Bulanov, Stepan; Vincenti, Henri; Bethel, E. Wes

    2016-05-09

    The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analytics to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. Furthermore, this supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.

  17. WarpIV: In Situ Visualization and Analysis of Ion Accelerator Simulations.

    PubMed

    Rubel, Oliver; Loring, Burlen; Vay, Jean-Luc; Grote, David P; Lehe, Remi; Bulanov, Stepan; Vincenti, Henri; Bethel, E Wes

    2016-01-01

    The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analytics to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. This supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.

  18. WarpIV: In situ visualization and analysis of ion accelerator simulations

    SciTech Connect

    Rubel, Oliver; Loring, Burlen; Vay, Jean -Luc; Grote, David P.; Lehe, Remi; Bulanov, Stepan; Vincenti, Henri; Bethel, E. Wes

    2016-05-09

    The generation of short pulses of ion beams through the interaction of an intense laser with a plasma sheath offers the possibility of compact and cheaper ion sources for many applications--from fast ignition and radiography of dense targets to hadron therapy and injection into conventional accelerators. To enable the efficient analysis of large-scale, high-fidelity particle accelerator simulations using the Warp simulation suite, the authors introduce the Warp In situ Visualization Toolkit (WarpIV). WarpIV integrates state-of-the-art in situ visualization and analysis using VisIt with Warp, supports management and control of complex in situ visualization and analysis workflows, and implements integrated analytics to facilitate query- and feature-based data analytics and efficient large-scale data analysis. WarpIV enables for the first time distributed parallel, in situ visualization of the full simulation data using high-performance compute resources as the data is being generated by Warp. The authors describe the application of WarpIV to study and compare large 2D and 3D ion accelerator simulations, demonstrating significant differences in the acceleration process in 2D and 3D simulations. WarpIV is available to the public via https://bitbucket.org/berkeleylab/warpiv. The Warp In situ Visualization Toolkit (WarpIV) supports large-scale, parallel, in situ visualization and analysis and facilitates query- and feature-based analytics, enabling for the first time high-performance analysis of large-scale, high-fidelity particle accelerator simulations while the data is being generated by the Warp simulation suite. Furthermore, this supplemental material https://extras.computer.org/extra/mcg2016030022s1.pdf provides more details regarding the memory profiling and optimization and the Yee grid recentering optimization results discussed in the main article.

  19. Accelerated Monte Carlo models to simulate fluorescence spectra from layered tissues.

    PubMed

    Swartling, Johannes; Pifferi, Antonio; Enejder, Annika M K; Andersson-Engels, Stefan

    2003-04-01

    Two efficient Monte Carlo models are described, facilitating predictions of complete time-resolved fluorescence spectra from a light-scattering and light-absorbing medium. These are compared with a third, conventional fluorescence Monte Carlo model in terms of accuracy, signal-to-noise statistics, and simulation time. The improved computation efficiency is achieved by means of a convolution technique, justified by the symmetry of the problem. Furthermore, the reciprocity principle for photon paths, employed in one of the accelerated models, is shown to simplify the computations of the distribution of the emitted fluorescence drastically. A so-called white Monte Carlo approach is finally suggested for efficient simulations of one excitation wavelength combined with a wide range of emission wavelengths. The fluorescence is simulated in a purely scattering medium, and the absorption properties are instead taken into account analytically afterward. This approach is applicable to the conventional model as well as to the two accelerated models. Essentially the same absolute values for the fluorescence integrated over the emitting surface and time are obtained for the three models within the accuracy of the simulations. The time-resolved and spatially resolved fluorescence exhibits a slight overestimation at short delay times close to the source corresponding to approximately two grid elements for the accelerated models, as a result of the discretization and the convolution. The improved efficiency is most prominent for the reverse-emission accelerated model, for which the simulation time can be reduced by up to two orders of magnitude.

  20. Acceleration of Markov chain Monte Carlo simulations through sequential updating

    NASA Astrophysics Data System (ADS)

    Ren, Ruichao; Orkoulas, G.

    2006-02-01

    Strict detailed balance is not necessary for Markov chain Monte Carlo simulations to converge to the correct equilibrium distribution. In this work, we propose a new algorithm which only satisfies the weaker balance condition, and it is shown analytically to have better mobility over the phase space than the Metropolis algorithm satisfying strict detailed balance. The new algorithm employs sequential updating and yields better sampling statistics than the Metropolis algorithm with random updating. We illustrate the efficiency of the new algorithm on the two-dimensional Ising model. The algorithm is shown to identify the correct equilibrium distribution and to converge faster than the Metropolis algorithm with strict detailed balance. The main advantages of the new algorithm are its simplicity and the feasibility of parallel implementation through domain decomposition.

  1. Direct numerical simulation of turbulence using GPU accelerated supercomputers

    NASA Astrophysics Data System (ADS)

    Khajeh-Saeed, Ali; Blair Perot, J.

    2013-02-01

    Direct numerical simulations of turbulence are optimized for up to 192 graphics processors. The results from two large GPU clusters are compared to the performance of corresponding CPU clusters. A number of important algorithm changes are necessary to access the full computational power of graphics processors and these adaptations are discussed. It is shown that the handling of subdomain communication becomes even more critical when using GPU based supercomputers. The potential for overlap of MPI communication with GPU computation is analyzed and then optimized. Detailed timings reveal that the internal calculations are now so efficient that the operations related to MPI communication are the primary scaling bottleneck at all but the very largest problem sizes that can fit on the hardware. This work gives a glimpse of the CFD performance issues will dominate many hardware platform in the near future.

  2. Accelerated Monte Carlo simulations with restricted Boltzmann machines

    NASA Astrophysics Data System (ADS)

    Huang, Li; Wang, Lei

    2017-01-01

    Despite their exceptional flexibility and popularity, Monte Carlo methods often suffer from slow mixing times for challenging statistical physics problems. We present a general strategy to overcome this difficulty by adopting ideas and techniques from the machine learning community. We fit the unnormalized probability of the physical model to a feed-forward neural network and reinterpret the architecture as a restricted Boltzmann machine. Then, exploiting its feature detection ability, we utilize the restricted Boltzmann machine to propose efficient Monte Carlo updates to speed up the simulation of the original physical system. We implement these ideas for the Falicov-Kimball model and demonstrate an improved acceptance ratio and autocorrelation time near the phase transition point.

  3. Acceleration in other axes affects +Gz tolerance: dynamic centrifuge simulation of agile flight.

    PubMed

    Albery, William B

    2004-01-01

    Modern, thrust-vectored jet aircraft have the capability of developing multi-axis accelerations, especially during the performance of "supermaneuvers." These "agile" aircraft are capable of unconventional flight. The human consequences of this agile flight environment are unknown. This multi-axis acceleration environment was studied on the Dynamic Environment Simulator gimbaled centrifuge. There were nine relaxed, unprotected subjects who were exposed to either lateral (+/- 1, +/- 2 Gy), transverse chest-to-back (+1, 2.5, or 4 Gx), or back-to-chest (-1 Gx) sustained acceleration. Positive C (+Gz) acceleration was then added beginning at 1.0 Gz by gradual onset (0.1 Gz x s(-1)) until the subjects lost nearly all of their vision. Baseline +Gz-only relaxed tolerances were measured before and after all combined Gy/Gz and Gx/Gz exposures. Heart rate, percent cerebral oxygen saturation, and cerebral blood volumes were collected during each exposure. Adding moderate transverse (+Gx) acceleration significantly reduced +Gz tolerance. Relaxed, unprotected +Gz tolerance was reduced approximately 0.25 G when 1.0 or 2.5 Gx was added to the increasing +Gz exposure. Adding moderate lateral Gy significantly increased +Gz tolerance. Relaxed, unprotected +Gz tolerance was increased approximately 0.5 G when +2 Gy or -2 Gy was added to the -Gz exposure. The decrease in cerebral blood volume was significantly less when +Gz was added to -1 Gx compared with the addition of +Gz to +Gx. Multi-axis sustained accelerations, such as those experienced during thrust-vectored aircraft maneuvers, can either enhance or reduce the +Gz tolerance of the pilot depending on the direction of the net gravitoinertial force. Gy acceleration in conjunction with Gz acceleration can enhance G tolerance. Gx acceleration in addition to Gz acceleration can reduce G tolerance.

  4. Particle-in-cell simulation of x-ray wakefield acceleration and betatron radiation in nanotubes

    SciTech Connect

    Zhang, Xiaomei; Tajima, Toshiki; Farinella, Deano; Shin, Youngmin; Mourou, Gerard; Wheeler, Jonathan; Taborek, Peter; Chen, Pisin; Dollar, Franklin; Shen, Baifei

    2016-10-18

    Though wakefield acceleration in crystal channels has been previously proposed, x-ray wakefield acceleration has only recently become a realistic possibility since the invention of the single-cycled optical laser compression technique. We investigate the acceleration due to a wakefield induced by a coherent, ultrashort x-ray pulse guided by a nanoscale channel inside a solid material. By two-dimensional particle-in-cell computer simulations, we show that an acceleration gradient of TeV/cm is attainable. This is about 3 orders of magnitude stronger than that of the conventional plasma-based wakefield accelerations, which implies the possibility of an extremely compact scheme to attain ultrahigh energies. In addition to particle acceleration, this scheme can also induce the emission of high energy photons at ~O(10–100) MeV. Here, our simulations confirm such high energy photon emissions, which is in contrast with that induced by the optical laser driven wakefield scheme. In addition to this, the significantly improved emittance of the energetic electrons has been discussed.

  5. Particle-in-cell simulation of x-ray wakefield acceleration and betatron radiation in nanotubes

    DOE PAGES

    Zhang, Xiaomei; Tajima, Toshiki; Farinella, Deano; ...

    2016-10-18

    Though wakefield acceleration in crystal channels has been previously proposed, x-ray wakefield acceleration has only recently become a realistic possibility since the invention of the single-cycled optical laser compression technique. We investigate the acceleration due to a wakefield induced by a coherent, ultrashort x-ray pulse guided by a nanoscale channel inside a solid material. By two-dimensional particle-in-cell computer simulations, we show that an acceleration gradient of TeV/cm is attainable. This is about 3 orders of magnitude stronger than that of the conventional plasma-based wakefield accelerations, which implies the possibility of an extremely compact scheme to attain ultrahigh energies. In additionmore » to particle acceleration, this scheme can also induce the emission of high energy photons at ~O(10–100) MeV. Here, our simulations confirm such high energy photon emissions, which is in contrast with that induced by the optical laser driven wakefield scheme. In addition to this, the significantly improved emittance of the energetic electrons has been discussed.« less

  6. Particle-in-cell simulation of x-ray wakefield acceleration and betatron radiation in nanotubes

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaomei; Tajima, Toshiki; Farinella, Deano; Shin, Youngmin; Mourou, Gerard; Wheeler, Jonathan; Taborek, Peter; Chen, Pisin; Dollar, Franklin; Shen, Baifei

    2016-10-01

    Though wakefield acceleration in crystal channels has been previously proposed, x-ray wakefield acceleration has only recently become a realistic possibility since the invention of the single-cycled optical laser compression technique. We investigate the acceleration due to a wakefield induced by a coherent, ultrashort x-ray pulse guided by a nanoscale channel inside a solid material. By two-dimensional particle-in-cell computer simulations, we show that an acceleration gradient of TeV /cm is attainable. This is about 3 orders of magnitude stronger than that of the conventional plasma-based wakefield accelerations, which implies the possibility of an extremely compact scheme to attain ultrahigh energies. In addition to particle acceleration, this scheme can also induce the emission of high energy photons at ˜O (10 - 100 ) MeV . Our simulations confirm such high energy photon emissions, which is in contrast with that induced by the optical laser driven wakefield scheme. In addition to this, the significantly improved emittance of the energetic electrons has been discussed.

  7. A multiscale approach to accelerate pore-scale simulation of porous electrodes

    NASA Astrophysics Data System (ADS)

    Zheng, Weibo; Kim, Seung Hyun

    2017-04-01

    A new method to accelerate pore-scale simulation of porous electrodes is presented. The method combines the macroscopic approach with pore-scale simulation by decomposing a physical quantity into macroscopic and local variations. The multiscale method is applied to the potential equation in pore-scale simulation of a Proton Exchange Membrane Fuel Cell (PEMFC) catalyst layer, and validated with the conventional approach for pore-scale simulation. Results show that the multiscale scheme substantially reduces the computational cost without sacrificing accuracy.

  8. The interaction between atmospheric gravity waves and large-scale flows: an efficient description beyond the non-acceleration paradigm

    NASA Astrophysics Data System (ADS)

    Ribstein, Bruno; Bölöni, Gergely; Muraschko, Jewgenija; Sgoff, Christine; Wei, Junhong; Achatz, Ulrich

    2016-11-01

    With the aim of contributing to the improvement of subgrid-scale gravity wave (GW) parameterizations in numerical-weather-prediction and climate models, the comparative relevance in GW drag of direct GW-mean-flow interactions and turbulent wave breakdown are investigated. Of equal interest is how well Wentzel-Kramer-Brillouin (WKB) theory can capture direct wave-mean-flow interactions, that are excluded by applying the steady-state approximation. WKB is implemented in a very efficient Lagrangian ray-tracing approach that considers wave action density in phasespace, thereby avoiding numerical instabilities due to caustics. It is supplemented by a simple wave-breaking scheme based on a static-instability saturation criterion. Idealized test cases of horizontally homogeneous GW packets are considered where wave-resolving Large-Eddy Simulations (LES) provide the reference. In all of theses cases the WKB simulations including direct GW-mean-flow interactions reproduce the LES data, to a good accuracy, already without wave-breaking scheme. The latter provides a next-order correction that is useful for fully capturing the total-energy balance between wave and mean flow. This is not the case when a steady-state WKB implementation is used, as used in present GW parameterizations.

  9. Measurements and simulation of controlled beamfront motion in the Laser Controlled Collective Accelerator

    SciTech Connect

    Yao, R.L.; Destler, W.W.; Striffler, C.D.; Rodgers, J.; Scgalov, Z.

    1989-01-01

    In the Laser Controlled Collective Accelerator, an intense electron beam is injected at a current above the vacuum space charge limit into an initially evacuated drift tube. A plasma channel, produced by time-sequenced, multiple laser beam ionization of a solid target on the drift tube wall, provides the necessary neutralization to allow for effective beam propagation. By controlling the rate of production of the plasma channel as a function of time down the drift tube, control of the electron beamfront can be achieved. Recent experimental measurements of controlled beamfront motion in this configuration are presented, along with results of ion acceleration experiments conducted using two different accelerating gradients. These results are compared with numerical simulations of the system in which both controlled beamfront motion and ion acceleration is observed consistent with both design expectations and experimental results. 5 refs., 6 figs.

  10. A selective review of simulated driving studies: Combining naturalistic and hybrid paradigms, analysis approaches, and future directions.

    PubMed

    Calhoun, V D; Pearlson, G D

    2012-01-02

    Naturalistic paradigms such as movie watching or simulated driving that mimic closely real-world complex activities are becoming more widely used in functional magnetic resonance imaging (fMRI) studies both because of their ability to robustly stimulate brain connectivity and the availability of analysis methods which are able to capitalize on connectivity within and among intrinsic brain networks identified both during a task and in resting fMRI data. In this paper we review over a decade of work from our group and others on the use of simulated driving paradigms to study both the healthy brain as well as the effects of acute alcohol administration on functional connectivity during such paradigms. We briefly review our initial work focused on the configuration of the driving simulator and the analysis strategies. We then describe in more detail several recent studies from our group including a hybrid study examining distracted driving and compare resulting data with those from a separate visual oddball task (Fig. 6). The analysis of these data was performed primarily using a combination of group independent component analysis (ICA) and the general linear model (GLM) and in the various studies we highlight novel findings which result from an analysis of either 1) within-network connectivity, 2) inter-network connectivity, also called functional network connectivity, or 3) the degree to which the modulation of the various intrinsic networks were associated with the alcohol administration and the task context. Despite the fact that the behavioral effects of alcohol intoxication are relatively well known, there is still much to discover on how acute alcohol exposure modulates brain function in a selective manner, associated with behavioral alterations. Through the above studies, we have learned more regarding the impact of acute alcohol intoxication on organization of the brain's intrinsic connectivity networks during performance of a complex, real-world cognitive

  11. A Selective Review of Simulated Driving Studies: Combining Naturalistic and Hybrid Paradigms, Analysis Approaches, and Future Directions

    PubMed Central

    Calhoun, V. D.; Pearlson, G. D.

    2011-01-01

    Naturalistic paradigms such as movie watching or simulated driving that mimic closely real-world complex activities are becoming more widely used in functional magnetic resonance imaging (fMRI) studies both because of their ability to robustly stimulate brain connectivity and the availability of analysis methods which are able to capitalize on connectivity within and among intrinsic brain networks identified both during a task and in resting fMRI data. In this paper we review over a decade of work from our group and others on the use of simulated driving paradigms to study both the healthy brain as well as the effects of acute alcohol administration on functional connectivity during such paradigms. We briefly review our initial work focused on the configuration of the driving simulator and the analysis strategies. We then describe in more detail several recent studies from our group including a hybrid study examining distracted driving and compare resulting data with those from a separate visual oddball task. The analysis of these data were performed primarily using a combination of group independent component analysis (ICA) and the general linear model (GLM) and in the various studies we highlight novel findings which result from an analysis of either 1) within-network connectivity, 2) inter-network connectivity, also called functional network connectivity, or 3) the degree to which the modulation of the various intrinsic networks were associated with the alcohol administration and the task context. Despite the fact that the behavioral effects of alcohol intoxication are relatively well known, there is still much to discover on how acute alcohol exposure modulates brain function in a selective manner, associated with behavioral alterations. Through the above studies, we have learned more regarding the impact of acute alcohol intoxication on organization of the brain’s intrinsic connectivity networks during performance of a complex, real-world cognitive operation

  12. The impact of accelerator processors for high-throughput molecular modeling and simulation.

    PubMed

    Giupponi, G; Harvey, M J; De Fabritiis, G

    2008-12-01

    The recent introduction of cost-effective accelerator processors (APs), such as the IBM Cell processor and Nvidia's graphics processing units (GPUs), represents an important technological innovation which promises to unleash the full potential of atomistic molecular modeling and simulation for the biotechnology industry. Present APs can deliver over an order of magnitude more floating-point operations per second (flops) than standard processors, broadly equivalent to a decade of Moore's law growth, and significantly reduce the cost of current atom-based molecular simulations. In conjunction with distributed and grid-computing solutions, accelerated molecular simulations may finally be used to extend current in silico protocols by the use of accurate thermodynamic calculations instead of approximate methods and simulate hundreds of protein-ligand complexes with full molecular specificity, a crucial requirement of in silico drug discovery workflows.

  13. Particle-in-cell simulations of plasma accelerators and electron-neutral collisions

    SciTech Connect

    Bruhwiler, David L.; Giacone, Rodolfo E.; Cary, John R.; Verboncoeur, John P.; Mardahl, Peter; Esarey, Eric; Leemans, W.P.; Shadwick, B.A.

    2001-10-01

    We present 2-D simulations of both beam-driven and laser-driven plasma wakefield accelerators, using the object-oriented particle-in-cell code XOOPIC, which is time explicit, fully electromagnetic, and capable of running on massively parallel supercomputers. Simulations of laser-driven wakefields with low ({approx}10{sup 16} W/cm{sup 2}) and high ({approx}10{sup 18} W/cm{sup 2}) peak intensity laser pulses are conducted in slab geometry, showing agreement with theory and fluid simulations. Simulations of the E-157 beam wakefield experiment at the Stanford Linear Accelerator Center, in which a 30 GeV electron beam passes through 1 m of preionized lithium plasma, are conducted in cylindrical geometry, obtaining good agreement with previous work. We briefly describe some of the more significant modifications of XOOPIC required by this work, and summarize the issues relevant to modeling relativistic electron-neutral collisions in a particle-in-cell code.

  14. Simulator for an Accelerator-Driven Subcritical Fissile Solution System

    SciTech Connect

    Klein, Steven Karl; Day, Christy M.; Determan, John C.

    2015-09-14

    LANL has developed a process to generate a progressive family of system models for a fissile solution system. This family includes a dynamic system simulation comprised of coupled nonlinear differential equations describing the time evolution of the system. Neutron kinetics, radiolytic gas generation and transport, and core thermal hydraulics are included in the DSS. Extensions to explicit operation of cooling loops and radiolytic gas handling are embedded in these systems as is a stability model. The DSS may then be converted to an implementation in Visual Studio to provide a design team the ability to rapidly estimate system performance impacts from a variety of design decisions. This provides a method to assist in optimization of the system design. Once design has been generated in some detail the C++ version of the system model may then be implemented in a LabVIEW user interface to evaluate operator controls and instrumentation and operator recognition and response to off-normal events. Taken as a set of system models the DSS, Visual Studio, and LabVIEW progression provides a comprehensive set of design support tools.

  15. Accelerated finite element elastodynamic simulations using the GPU

    SciTech Connect

    Huthwaite, Peter

    2014-01-15

    An approach is developed to perform explicit time domain finite element simulations of elastodynamic problems on the graphical processing unit, using Nvidia's CUDA. Of critical importance for this problem is the arrangement of nodes in memory, allowing data to be loaded efficiently and minimising communication between the independently executed blocks of threads. The initial stage of memory arrangement is partitioning the mesh; both a well established ‘greedy’ partitioner and a new, more efficient ‘aligned’ partitioner are investigated. A method is then developed to efficiently arrange the memory within each partition. The software is applied to three models from the fields of non-destructive testing, vibrations and geophysics, demonstrating a memory bandwidth of very close to the card's maximum, reflecting the bandwidth-limited nature of the algorithm. Comparison with Abaqus, a widely used commercial CPU equivalent, validated the accuracy of the results and demonstrated a speed improvement of around two orders of magnitude. A software package, Pogo, incorporating these developments, is released open source, downloadable from (http://www.pogo-fea.com/) to benefit the community. -- Highlights: •A novel memory arrangement approach is discussed for finite elements on the GPU. •The mesh is partitioned then nodes are arranged efficiently within each partition. •Models from ultrasonics, vibrations and geophysics are run. •The code is significantly faster than an equivalent commercial CPU package. •Pogo, the new software package, is released open source.

  16. 3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Hededal, C. B.; Fishman, G. J.

    2006-01-01

    Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

  17. 3-D RPIC Simulations of Relativistic Jets: Particle Acceleration, Magnetic Field Generation, and Emission

    NASA Technical Reports Server (NTRS)

    Nishikawa, K.-I.; Mizuno, Y.; Hardee, P.; Hededal, C. B.; Fishman, G. J.

    2006-01-01

    Recent PIC simulations using injected relativistic electron-ion (electro-positron) jets into ambient plasmas show that acceleration occurs in relativistic shocks. The Weibel instability created in shocks is responsible for particle acceleration, and generation and amplification of highly inhomogeneous, small-scale magnetic fields. These magnetic fields contribute to the electron's transverse deflection in relativistic jets. The "jitter" radiation from deflected electrons has different properties than the synchrotron radiation which is calculated in a uniform magnetic field. This jitter radiation may be important to understand the complex time evolution and spectral structure in relativistic jets and gamma-ray bursts. We will present recent PIC simulations which show particle acceleration and magnetic field generation. We will also calculate associated self-consistent emission from relativistic shocks.

  18. Accelerating Monte Carlo simulations with an NVIDIA ® graphics processor

    NASA Astrophysics Data System (ADS)

    Martinsen, Paul; Blaschke, Johannes; Künnemeyer, Rainer; Jordan, Robert

    2009-10-01

    can be expensive, but recent advances in consumer grade graphics cards have opened the possibility of high-performance desktop parallel-computing. Solution method: In this pair of programmes we have implemented the Monte Carlo algorithm described by Prahl et al. [2] for photon transport in infinite scattering media to compare the performance of two readily accessible architectures: a standard desktop PC and a consumer grade graphics card from NVIDIA. Restrictions: The graphics card implementation uses single precision floating point numbers for all calculations. Only photon transport from an isotropic point-source is supported. The graphics-card version has no user interface. The simulation parameters must be set in the source code. The desktop version has a simple user interface; however some properties can only be accessed through an ActiveX client (such as Matlab). Additional comments: The random number library used has a LGPL ( http://www.gnu.org/copyleft/lesser.html) licence. Running time: Runtime can range from minutes to months depending on the number of photons simulated and the optical properties of the medium. References:http://www.nvidia.com/object/cuda_home.html. S. Prahl, M. Keijzer, Sl. Jacques, A. Welch, SPIE Institute Series 5 (1989) 102.

  19. Numerical simulations of Rayleigh-Taylor (RT) turbulence with complex acceleration history

    NASA Astrophysics Data System (ADS)

    Ramaprabhu, Praveen; Dimonte, Guy; Andrews, Malcolm

    2007-11-01

    Complex acceleration histories of an RT unstable interface are important in validating turbulent mix models. Of particular interest are alternating stages of acceleration and deceleration, since the the associated demixing is a discriminating test of such models. We have performed numerical simulations of a turbulent RT mixing layer subjected to two stages of acceleration separated by a stage of deceleration. The profile was chosen from earlier Linear Electric Motor experiments with which we compare our results. The acceleration phases produce classical RT unstable growth (t^2) with growth rates comparable to earlier results of turbulent RT simulations. The calculations are challenging as dominant bubbles become shredded as they reverse direction in response to the reversal in g, placing increased demands on numerical resolution. The shredding to small scales is accompanied by a peaking of the molecular mixing during the RT stable stage. In general, we find that simulations agree with experiments when initialized with broadband initial perturbations, but not for an annular shell. Other effects such as the presence of surface tension in the LEM experiments (but not in our simulations) further complicate this picture.

  20. Biodynamic Assessment of Pilot Knee-Board Configurations During Simulated T-38 Catapult Acceleration

    DTIC Science & Technology

    2015-04-01

    0041 Biodynamic Assessment of Pilot Knee -Board Configurations During Simulated T-38 Catapult Acceleration Mr. Chris Perry Mr. Chris...distribution unlimited. STINFO COPY AIR FORCE RESEARCH LABORATORY 711 HUMAN PERFORMANCE WING, HUMAN EFFECTIVENESS DIRECTORATE, WRIGHT...PATTERSON AIR FORCE BASE, OH 45433 AIR FORCE MATERIEL COMMAND UNITED STATES AIR FORCE NOTICE AND SIGNATURE PAGE Using Government drawings

  1. Simulation prediction and experiment setup of vacuum laser acceleration at Brookhaven National Lab-Accelerator Test Facility

    NASA Astrophysics Data System (ADS)

    Shao, L.; Cline, D.; Ding, X.; Ho, Y. K.; Kong, Q.; Xu, J. J.; Pogorelsky, I.; Yakimenko, V.; Kusche, K.

    2013-02-01

    This paper presents the pre-experiment plan and prediction of the first stage of vacuum laser acceleration (VLA) collaborating by UCLA, Fudan University and ATF-BNL. This first stage experiment is a proof-of-principle to support our previously posted novel VLA theory. Simulations show that based on ATF's current experimental conditions the electron beam with initial energy of 15 MeV can get net energy gain from an intense CO2 laser beam. The difference in electron beam energy spread is observable by the ATF beam line diagnostics system. Further, this energy spread expansion effect increases along with an increase in laser intensity. The proposal has been approved by the ATF committee and the experiment will be our next project.

  2. Laser-wakefield accelerators for medical phase contrast imaging: Monte Carlo simulations and experimental studies

    NASA Astrophysics Data System (ADS)

    Cipiccia, S.; Reboredo, D.; Vittoria, Fabio A.; Welsh, G. H.; Grant, P.; Grant, D. W.; Brunetti, E.; Wiggins, S. M.; Olivo, A.; Jaroszynski, D. A.

    2015-05-01

    X-ray phase contrast imaging (X-PCi) is a very promising method of dramatically enhancing the contrast of X-ray images of microscopic weakly absorbing objects and soft tissue, which may lead to significant advancement in medical imaging with high-resolution and low-dose. The interest in X-PCi is giving rise to a demand for effective simulation methods. Monte Carlo codes have been proved a valuable tool for studying X-PCi including coherent effects. The laser-plasma wakefield accelerators (LWFA) is a very compact particle accelerator that uses plasma as an accelerating medium. Accelerating gradient in excess of 1 GV/cm can be obtained, which makes them over a thousand times more compact than conventional accelerators. LWFA are also sources of brilliant betatron radiation, which are promising for applications including medical imaging. We present a study that explores the potential of LWFA-based betatron sources for medical X-PCi and investigate its resolution limit using numerical simulations based on the FLUKA Monte Carlo code, and present preliminary experimental results.

  3. Ion Beam Transport Simulations for the 1.7 MV Tandem Accelerator at the Michigan Ion Beam Laboratory

    NASA Astrophysics Data System (ADS)

    Naab, F. U.; Toader, O. F.; Was, G. S.

    The Michigan Ion Beam Laboratory houses a 1.7 MV tandem accelerator. For many years this accelerator was configured to run with three ion sources: a TORoidal Volume Ion Source (TORVIS), a Duoplasmatron source and a Sputter source. In this article we describe an application we have created using the SIMION® code to simulate the trajectories of ion beams produced with these sources through the accelerator. The goal of this work is to have an analytical tool to understand the effect of each electromagnetic component on the ion trajectories. This effect is shown in detailed drawings. Each ion trajectory simulation starts at the aperture of the ion source and ends at the position of the target. Using these simulations, new accelerator operators or users quickly understand how the accelerator system works. Furthermore, these simulations allow analysis of modifications in the ion beam optics of the accelerator by adding, removing or replacing components or changing their relative positions.

  4. Two-stage light-gas magnetoplasma accelerator for hypervelocity impact simulation

    NASA Astrophysics Data System (ADS)

    Khramtsov, P. P.; Vasetskij, V. A.; Makhnach, A. I.; Grishenko, V. M.; Chernik, M. Yu; Shikh, I. A.; Doroshko, M. V.

    2016-11-01

    The development of macroparticles acceleration methods for high-speed impact simulation in a laboratory is an actual problem due to increasing of space flights duration and necessity of providing adequate spacecraft protection against micrometeoroid and space debris impacts. This paper presents results of experimental study of a two-stage light- gas magnetoplasma launcher for acceleration of a macroparticle, in which a coaxial plasma accelerator creates a shock wave in a high-pressure channel filled with light gas. Graphite and steel spheres with diameter of 2.5-4 mm were used as a projectile and were accelerated to the speed of 0.8-4.8 km/s. A launching of particle occurred in vacuum. For projectile velocity control the speed measuring method was developed. The error of this metod does not exceed 5%. The process of projectile flight from the barrel and the process of a particle collision with a target were registered by use of high-speed camera. The results of projectile collision with elements of meteoroid shielding are presented. In order to increase the projectile velocity, the high-pressure channel should be filled with hydrogen. However, we used helium in our experiments for safety reasons. Therefore, we can expect that the range of mass and velocity of the accelerated particles can be extended by use of hydrogen as an accelerating gas.

  5. Multi-species first-principles simulations of particle acceleration at shocks

    NASA Astrophysics Data System (ADS)

    Caprioli, Damiano

    Astrophysical shocks are known to be prominent sources of non-thermal particles and emission. In particular, strong shocks at supernova remnant blast waves are thought to accelerate Galactic cosmic rays (CRs) up to about 10^17eV via diffusive shock acceleration (DSA). The chemical composition of Galactic CRs, now measured with great accuracy by payloads and satellites, is reminiscent of that of the typical interstellar medium, although with some significant deviations. Observations reveal: 1) an electron/proton ratio of about 1% at about 10 GeV, (2) a general enhancement of the refractory elements relative to the volatile ones, (3) among the volatile elements, an enhancement of the heavier elements relative to the lighter ones, and (4) a discrepant hardening of CR nuclei heavier than hydrogen. Such peculiar trends contain precious information about the dependence of the acceleration process on the particle mass/charge ratio, a trend that has no theoretical counterpart in the DSA theory, yet. Building on our recent successes in modeling electron and proton DSA at non-relativistic astrophysical shocks via first-principles kinetic simulations, we will perform multispecies particle-in-cells simulations of such systems also including nuclei heavier than hydrogen, in order to investigate thermalization, injection, and acceleration of species with different mass/charge ratio. We will also analyze how the simulation outputs compare with the observed CR abundances, in order to build a model for DSA that accounts for the relative acceleration efficiency of energetic electrons, protons, and heavier ions. Finally, we will assess the possible contribution of accelerated heavy ions, especially helium, to the generation of magnetic turbulence via CR-driven instabilities - crucial to foster rapid particle energgization- and to the hadronic gamma-ray emission from young supernova remnants.

  6. Simulation and analysis of TE wave propagation for measurement of electron cloud densities in particle accelerators

    NASA Astrophysics Data System (ADS)

    Sonnad, Kiran G.; Hammond, Kenneth C.; Schwartz, Robert M.; Veitzer, Seth A.

    2014-08-01

    The use of transverse electric (TE) waves has proved to be a powerful, noninvasive method for estimating the densities of electron clouds formed in particle accelerators. Results from the plasma simulation program VSim have served as a useful guide for experimental studies related to this method, which have been performed at various accelerator facilities. This paper provides results of the simulation and modeling work done in conjunction with experimental efforts carried out at the Cornell electron storage ring “Test Accelerator” (CESRTA). This paper begins with a discussion of the phase shift induced by electron clouds in the transmission of RF waves, followed by the effect of reflections along the beam pipe, simulation of the resonant standing wave frequency shifts and finally the effects of external magnetic fields, namely dipoles and wigglers. A derivation of the dispersion relationship of wave propagation for arbitrary geometries in field free regions with a cold, uniform cloud density is also provided.

  7. D-leaping: Accelerating stochastic simulation algorithms for reactions with delays

    SciTech Connect

    Bayati, Basil; Chatelain, Philippe; Koumoutsakos, Petros

    2009-09-01

    We propose a novel, accelerated algorithm for the approximate stochastic simulation of biochemical systems with delays. The present work extends existing accelerated algorithms by distributing, in a time adaptive fashion, the delayed reactions so as to minimize the computational effort while preserving their accuracy. The accuracy of the present algorithm is assessed by comparing its results to those of the corresponding delay differential equations for a representative biochemical system. In addition, the fluctuations produced from the present algorithm are comparable to those from an exact stochastic simulation with delays. The algorithm is used to simulate biochemical systems that model oscillatory gene expression. The results indicate that the present algorithm is competitive with existing works for several benchmark problems while it is orders of magnitude faster for certain systems of biochemical reactions.

  8. Three-dimensional simulations of high-current beams in induction accelerators with WARP3d

    SciTech Connect

    Grote, D.P.; Friedman, A.; Haber, I.

    1995-09-01

    For many issues relevant to acceleration and propagation of heavy-ion beams for inertial confinement fusion, understanding the behavior of the beam requires the self-consistent inclusion of the self-fields of the beams in multiple dimensions. For these reasons, the three-dimensional simulation code WARP3d A.Friedman was developed. The code combines the particle-in-cell plasma simulation technique with a realistic description of the elements which make up an accelerator. In this paper, the general structure of the code is reviewed and details of two ongoing applications are presented along with a discussion of simulation techniques used. The most important results of this work are presented.

  9. Accelerated stochastic and hybrid methods for spatial simulations of reaction diffusion systems

    NASA Astrophysics Data System (ADS)

    Rossinelli, Diego; Bayati, Basil; Koumoutsakos, Petros

    2008-01-01

    Spatial distributions characterize the evolution of reaction-diffusion models of several physical, chemical, and biological systems. We present two novel algorithms for the efficient simulation of these models: Spatial τ-Leaping ( Sτ-Leaping), employing a unified acceleration of the stochastic simulation of reaction and diffusion, and Hybrid τ-Leaping ( Hτ-Leaping), combining a deterministic diffusion approximation with a τ-Leaping acceleration of the stochastic reactions. The algorithms are validated by solving Fisher's equation and used to explore the role of the number of particles in pattern formation. The results indicate that the present algorithms have a nearly constant time complexity with respect to the number of events (reaction and diffusion), unlike the exact stochastic simulation algorithm which scales linearly.

  10. Using graphics processing units to accelerate perturbation Monte Carlo simulation in a turbid medium

    NASA Astrophysics Data System (ADS)

    Cai, Fuhong; He, Sailing

    2012-04-01

    We report a fast perturbation Monte Carlo (PMC) algorithm accelerated by graphics processing units (GPU). The two-step PMC simulation [Opt. Lett. 36, 2095 (2011)] is performed by storing the seeds instead of the photon's trajectory, and thus the requirement in computer random-access memory (RAM) becomes minimal. The two-step PMC is extremely suitable for implementation onto GPU. In a standard simulation of spatially-resolved photon migration in the turbid media, the acceleration ratio between using GPU and using conventional CPU is about 1000. Furthermore, since in the two-step PMC algorithm one records the effective seeds, which is associated to the photon that reaches a region of interest in this letter, and then re-run the MC simulation based on the recorded effective seeds, radiative transfer equation (RTE) can be solved by two-step PMC not only with an arbitrary change in the absorption coefficient, but also with large change in the scattering coefficient.

  11. Using graphics processing units to accelerate perturbation Monte Carlo simulation in a turbid medium.

    PubMed

    Cai, Fuhong; He, Sailing

    2012-04-01

    We report a fast perturbation Monte Carlo (PMC) algorithm accelerated by graphics processing units (GPU). The two-step PMC simulation [Opt. Lett. 36, 2095 (2011)] is performed by storing the seeds instead of the photon's trajectory, and thus the requirement in computer random-access memory (RAM) becomes minimal. The two-step PMC is extremely suitable for implementation onto GPU. In a standard simulation of spatially-resolved photon migration in the turbid media, the acceleration ratio between using GPU and using conventional CPU is about 1000. Furthermore, since in the two-step PMC algorithm one records the effective seeds, which is associated to the photon that reaches a region of interest in this letter, and then re-run the MC simulation based on the recorded effective seeds, radiative transfer equation (RTE) can be solved by two-step PMC not only with an arbitrary change in the absorption coefficient, but also with large change in the scattering coefficient.

  12. Center of Mass Acceleration Feedback Control for Standing by Functional Neuromuscular Stimulation – a Simulation Study

    PubMed Central

    Audu, Musa L.; Kirsch, Robert F.; Triolo, Ronald J.

    2013-01-01

    The potential efficacy of total body center of mass (COM) acceleration for feedback control of standing balance by functional neuromuscular stimulation (FNS) following spinal cord injury (SCI) was investigated. COM acceleration may be a viable alternative to conventional joint kinematics due to its rapid responsiveness, focal representation of COM dynamics, and ease of measurement. A computational procedure was developed using an anatomically-realistic, three-dimensional, bipedal biomechanical model to determine optimal patterns of muscle excitations to produce targeted effects upon COM acceleration from erect stance. The procedure was verified with electromyographic data collected from standing able-bodied subjects undergoing systematic perturbations. Using 16 muscle groups targeted by existing implantable neuroprostheses, data were generated to train an artificial neural network (ANN)-based controller in simulation. During forward simulations, proportional feedback of COM acceleration drove the ANN to produce muscle excitation patterns countering the effects of applied perturbations. Feedback gains were optimized to minimize upper extremity (UE) loading required to stabilize against disturbances. Compared to the clinical case of maximum constant excitation, the controller reduced UE loading by 43% in resisting external perturbations and by 51% during simulated one-arm reaching. Future work includes performance assessment against expected measurement errors and developing user-specific control systems. PMID:22773529

  13. [AUTONOMIC CONTROL OF HEART RATE, BLOOD LACTATE AND ACCELERATION DURING COMBAT SIMULATION IN TAEKWONDO ELITE ATHLETES].

    PubMed

    Cerda-Kohler, Hugo; Aguayo Fuentealba, Juan Carlos; Francino Barrera, Giovanni; Guajardo-Sandoval, Adrián; Jorquera Aguilera, Carlos; Báez-San Martín, Eduardo

    2015-09-01

    the aim of the study was to measure the heart rate recovery, blood lactate and movement acceleration during simulated taekwondo competition. twelve male subjects who belong to the national team, with at least five years of experience participated in this research. They performed a simulated combat to evaluate the following variables: (i) Blood lactate after one minute recovery between each round, (ii) Heart rate recovery (HRR) at thirty and sixty seconds in each minute rest between rounds, (iii) Peak acceleration (ACCp) in each round performed. The significance level was set at p < 005. the results showed no significant differences between winners and losers in the HRR at both, thirty and sixty seconds (p > 0.05), blood lactate (p > 0.05), peak acceleration (p > 0.05) and the average acceleration of combat (p = 0.18). There was no correlation between delta lactate and ACCp (r = 0.01; p = 0.93), delta lactate and HRR (r = -0.23; p = 0.18), and ACCp and HRR (r = 0.003; p = 0.98). these data suggest that studied variables would not be decisive in the simulated combat outcomes. Other factors such as technical-tactical or psychological variables could have a significant impact on athletic performance. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  14. Design and Optimization of Large Accelerator Systems through High-Fidelity Electromagnetic Simulations

    SciTech Connect

    Ng, Cho; Akcelik, Volkan; Candel, Arno; Chen, Sheng; Ge, Lixin; Kabel, Andreas; Lee, Lie-Quan; Li, Zenghai; Prudencio, Ernesto; Schussman, Greg; Uplenchwar1, Ravi; Xiao1, Liling; Ko1, Kwok; Austin, T.; Cary, J.R.; Ovtchinnikov, S.; Smith, D.N.; Werner, G.R.; Bellantoni, L.; /SLAC /TechX Corp. /Fermilab

    2008-08-01

    SciDAC1, with its support for the 'Advanced Computing for 21st Century Accelerator Science and Technology' (AST) project, witnessed dramatic advances in electromagnetic (EM) simulations for the design and optimization of important accelerators across the Office of Science. In SciDAC2, EM simulations continue to play an important role in the 'Community Petascale Project for Accelerator Science and Simulation' (ComPASS), through close collaborations with SciDAC CETs/Institutes in computational science. Existing codes will be improved and new multi-physics tools will be developed to model large accelerator systems with unprecedented realism and high accuracy using computing resources at petascale. These tools aim at targeting the most challenging problems facing the ComPASS project. Supported by advances in computational science research, they have been successfully applied to the International Linear Collider (ILC) and the Large Hadron Collider (LHC) in High Energy Physics (HEP), the JLab 12-GeV Upgrade in Nuclear Physics (NP), as well as the Spallation Neutron Source (SNS) and the Linac Coherent Light Source (LCLS) in Basic Energy Sciences (BES).

  15. Experiments in sensing transient rotational acceleration cues on a flight simulator

    NASA Technical Reports Server (NTRS)

    Parrish, R. V.

    1979-01-01

    Results are presented for two transient motion sensing experiments which were motivated by the identification of an anomalous roll cue (a 'jerk' attributed to an acceleration spike) in a prior investigation of realistic fighter motion simulation. The experimental results suggest the consideration of several issues for motion washout and challenge current sensory system modeling efforts. Although no sensory modeling effort is made it is argued that such models must incorporate the ability to handle transient inputs of short duration (some of which are less than the accepted latency times for sensing), and must represent separate channels for rotational acceleration and velocity sensing.

  16. Design and Model Simulations of an Inverse Cerenkov Accelerator Using an Inverse Free Electron Laser Prebuncher

    NASA Astrophysics Data System (ADS)

    Kimura, W. D.; Babzien, M.; Cline, D. B.; Fiorito, R. B.; Gallardo, J. C.; Kusche, K. P.; Liu, Y.; Pogorelsky, I. V.; Quimby, D. C.; Rule, D. W.; Sandweiss, J.; Skaritka, J.; van Steenbergen, A.; Yakimenko, V.

    1997-05-01

    An experiment to use an inverse free electron laser (IFEL) to prebunch at optical wavelengths the electrons entering into an inverse Cerenkov accelerator (ICA) is being prepared at the BNL Accelerator Test Facility (ATF). The detailed design and simulations for this experiment will be presented. Microbunches on the order of 2 microns in length separated by 10.6 microns are predicted. Under the anticipated ATF conditions, space charge effects should not be an issue. Characterizing the microbunches and maintaining the proper phase relation between the IFEL and ICA modules are important issues that will also be discussed.

  17. Solving Large Sparse Linear Systems in End-to-end Accelerator Structure Simulations

    SciTech Connect

    Lee, L

    2004-01-23

    This paper presents a case study of solving very large sparse linear systems in end-to-end accelerator structure simulations. Both direct solvers and iterative solvers are investigated. A parallel multilevel preconditioner based on hierarchical finite element basis functions is considered and has been implemented to accelerate the convergence of iterative solvers. A linear system with matrix size 93,147,736 and with 3,964,961,944 non-zeros from 3D electromagnetic finite element discretization has been solved in less than 8 minutes with 1024 CPUs on the NERSC IBM SP. The resource utilization as well as the application performance for these solvers is discussed.

  18. Laser ion acceleration toward future ion beam cancer therapy - Numerical simulation study -

    PubMed Central

    Kawata, Shigeo; Izumiyama, Takeshi; Nagashima, Toshihiro; Takano, Masahiro; Barada, Daisuke; Kong, Qing; Gu, Yan Jun; Wang, Ping Xiao; Ma, Yan Yun; Wang, Wei Min

    2013-01-01

    Background: Ion beam has been used in cancer treatment, and has a unique preferable feature to deposit its main energy inside a human body so that cancer cell could be killed by the ion beam. However, conventional ion accelerator tends to be huge in its size and its cost. In this paper a future intense-laser ion accelerator is proposed to make the ion accelerator compact. Subjects and methods: An intense femtosecond pulsed laser was employed to accelerate ions. The issues in the laser ion accelerator include the energy efficiency from the laser to the ions, the ion beam collimation, the ion energy spectrum control, the ion beam bunching and the ion particle energy control. In the study particle computer simulations were performed to solve the issues, and each component was designed to control the ion beam quality. Results: When an intense laser illuminates a target, electrons in the target are accelerated and leave from the target; temporarily a strong electric field is formed between the high-energy electrons and the target ions, and the target ions are accelerated. The energy efficiency from the laser to ions was improved by using a solid target with a fine sub-wavelength structure or by a near-critical density gas plasma. The ion beam collimation was realized by holes behind the solid target. The control of the ion energy spectrum and the ion particle energy, and the ion beam bunching were successfully realized by a multi-stage laser-target interaction. Conclusions: The present study proposed a novel concept for a future compact laser ion accelerator, based on each component study required to control the ion beam quality and parameters. PMID:24155555

  19. Developing high energy, stable laser wakefield accelerators: particle simulations and experiments

    NASA Astrophysics Data System (ADS)

    Geddes, Cameron

    2006-10-01

    Laser driven wakefield accelerators produce accelerating fields thousands of times those achievable in conventional radiofrequency accelerators, and recent experiments have produced high energy electron bunches with low emittance and energy spread. Challenges now include control and reproducibility of the electron beam, further improvements in energy spread, and scaling to higher energies. We present large-scale particle in cell simulations together with recent experiments towards these goals. In LBNL experiments the relativistically intense drive pulse was guided over more than 10 diffraction ranges by plasma channels. Guiding beyond the diffraction range improved efficiency by allowing use of a smaller laser spot size (and hence higher intensities) over long propagation distances. At a drive pulse power of 9 TW, electrons were trapped from the plasma and beams of percent energy spread containing > 200pC charge above 80 MeV with normalized emittance estimated at < 2 π-mm-mrad were produced. Energies have now been scaled to 1 GeV using 40 TW of laser power. Particle simulations and data showed that the high quality bunch in recent experiments was formed when beam loading turned off injection after initial self trapping, creating a bunch of electrons isolated in phase space. A narrow energy spread beam was then obtained by extracting the bunch as it outran the accelerating phase of the wake. Large scale simulations coupled with experiments are now under way to better understand the optimization of such accelerators including production of reproducible electron beams and scaling to energies beyond a GeV. Numerical resolution and two and three dimensional effects are discussed as well as diagnostics for application of the simulations to experiments. Effects including injection and beam dynamics as well as pump laser depletion and reshaping will be described, with application to design of future experiments. Supported by DOE grant DE-AC02-05CH11231 and by an INCITE

  20. The changing paradigm for integrated simulation in support of Command and Control (C2)

    NASA Astrophysics Data System (ADS)

    Riecken, Mark; Hieb, Michael

    2016-05-01

    Modern software and network technologies are on the verge of enabling what has eluded the simulation and operational communities for more than two decades, truly integrating simulation functionality into operational Command and Control (C2) capabilities. This deep integration will benefit multiple stakeholder communities from experimentation and test to training by providing predictive and advanced analytics. There is a new opportunity to support operations with simulation once a deep integration is achieved. While it is true that doctrinal and acquisition issues remain to be addressed, nonetheless it is increasingly obvious that few technical barriers persist. How will this change the way in which common simulation and operational data is stored and accessed? As the Services move towards single networks, will there be technical and policy issues associated with sharing those operational networks with simulation data, even if the simulation data is operational in nature (e.g., associated with planning)? How will data models that have traditionally been simulation only be merged in with operational data models? How will the issues of trust be addressed?

  1. Mean-state acceleration of cloud-resolving models and large eddy simulations

    DOE PAGES

    Jones, C. R.; Bretherton, C. S.; Pritchard, M. S.

    2015-10-29

    In this study, large eddy simulations and cloud-resolving models (CRMs) are routinely used to simulate boundary layer and deep convective cloud processes, aid in the development of moist physical parameterization for global models, study cloud-climate feedbacks and cloud-aerosol interaction, and as the heart of superparameterized climate models. These models are computationally demanding, placing practical constraints on their use in these applications, especially for long, climate-relevant simulations. In many situations, the horizontal-mean atmospheric structure evolves slowly compared to the turnover time of the most energetic turbulent eddies. We develop a simple scheme to reduce this time scale separation to accelerate themore » evolution of the mean state. Using this approach we are able to accelerate the model evolution by a factor of 2–16 or more in idealized stratocumulus, shallow and deep cumulus convection without substantial loss of accuracy in simulating mean cloud statistics and their sensitivity to climate change perturbations. As a culminating test, we apply this technique to accelerate the embedded CRMs in the Superparameterized Community Atmosphere Model by a factor of 2, thereby showing that the method is robust and stable to realistic perturbations across spatial and temporal scales typical in a GCM.« less

  2. Mean-state acceleration of cloud-resolving models and large eddy simulations

    SciTech Connect

    Jones, C. R.; Bretherton, C. S.; Pritchard, M. S.

    2015-10-29

    In this study, large eddy simulations and cloud-resolving models (CRMs) are routinely used to simulate boundary layer and deep convective cloud processes, aid in the development of moist physical parameterization for global models, study cloud-climate feedbacks and cloud-aerosol interaction, and as the heart of superparameterized climate models. These models are computationally demanding, placing practical constraints on their use in these applications, especially for long, climate-relevant simulations. In many situations, the horizontal-mean atmospheric structure evolves slowly compared to the turnover time of the most energetic turbulent eddies. We develop a simple scheme to reduce this time scale separation to accelerate the evolution of the mean state. Using this approach we are able to accelerate the model evolution by a factor of 2–16 or more in idealized stratocumulus, shallow and deep cumulus convection without substantial loss of accuracy in simulating mean cloud statistics and their sensitivity to climate change perturbations. As a culminating test, we apply this technique to accelerate the embedded CRMs in the Superparameterized Community Atmosphere Model by a factor of 2, thereby showing that the method is robust and stable to realistic perturbations across spatial and temporal scales typical in a GCM.

  3. Two-fluid electromagnetic simulations of plasma-jet acceleration with detailed equation-of-state

    SciTech Connect

    Thoma, C.; Welch, D. R.; Clark, R. E.; Bruner, N.; MacFarlane, J. J.; Golovkin, I. E.

    2011-10-15

    We describe a new particle-based two-fluid fully electromagnetic algorithm suitable for modeling high density (n{sub i} {approx} 10{sup 17} cm{sup -3}) and high Mach number laboratory plasma jets. In this parameter regime, traditional particle-in-cell (PIC) techniques are challenging due to electron timescale and lengthscale constraints. In this new approach, an implicit field solve allows the use of large timesteps while an Eulerian particle remap procedure allows simulations to be run with very few particles per cell. Hall physics and charge separation effects are included self-consistently. A detailed equation of state (EOS) model is used to evolve the ion charge state and introduce non-ideal gas behavior. Electron cooling due to radiation emission is included in the model as well. We demonstrate the use of these new algorithms in 1D and 2D Cartesian simulations of railgun (parallel plate) jet accelerators using He and Ar gases. The inclusion of EOS and radiation physics reduces the electron temperature, resulting in higher calculated jet Mach numbers in the simulations. We also introduce a surface physics model for jet accelerators in which a frictional drag along the walls leads to axial spreading of the emerging jet. The simulations demonstrate that high Mach number jets can be produced by railgun accelerators for a variety of applications, including high energy density physics experiments.

  4. Plasma flow and fast particles in a hypervelocity accelerator - A color presentation. [micrometeoroid simulation

    NASA Technical Reports Server (NTRS)

    Igenbergs, E. B.; Cour-Palais, B.; Fisher, E.; Stehle, O.

    1975-01-01

    A new concept for particle acceleration for micrometeoroid simulation was developed at NASA Marshall Space Flight Center, using a high-density self-luminescent fast plasma flow to accelerate glass beads (with a diameter up to 1.0 mm) to velocities between 15-20 km/sec. After a short introduction to the operation of the hypervelocity range, the eight-converter-camera unit used for the photographs of the plasma flow and the accelerated particles is described. These photographs are obtained with an eight-segment reflecting pyramidal beam splitter. Wratten filters were mounted between the beam splitter and the converter tubes of the cameras. The photographs, which were recorded on black and white film, were used to make the matrices for the dye-color process, which produced the prints shown.

  5. Plasma flow and fast particles in a hypervelocity accelerator - A color presentation. [micrometeoroid simulation

    NASA Technical Reports Server (NTRS)

    Igenbergs, E. B.; Cour-Palais, B.; Fisher, E.; Stehle, O.

    1975-01-01

    A new concept for particle acceleration for micrometeoroid simulation was developed at NASA Marshall Space Flight Center, using a high-density self-luminescent fast plasma flow to accelerate glass beads (with a diameter up to 1.0 mm) to velocities between 15-20 km/sec. After a short introduction to the operation of the hypervelocity range, the eight-converter-camera unit used for the photographs of the plasma flow and the accelerated particles is described. These photographs are obtained with an eight-segment reflecting pyramidal beam splitter. Wratten filters were mounted between the beam splitter and the converter tubes of the cameras. The photographs, which were recorded on black and white film, were used to make the matrices for the dye-color process, which produced the prints shown.

  6. Particle-in-cell/accelerator code for space-charge dominated beam simulation

    SciTech Connect

    2012-05-08

    Warp is a multidimensional discrete-particle beam simulation program designed to be applicable where the beam space-charge is non-negligible or dominant. It is being developed in a collaboration among LLNL, LBNL and the University of Maryland. It was originally designed and optimized for heave ion fusion accelerator physics studies, but has received use in a broader range of applications, including for example laser wakefield accelerators, e-cloud studies in high enery accelerators, particle traps and other areas. At present it incorporates 3-D, axisymmetric (r,z) planar (x-z) and transverse slice (x,y) descriptions, with both electrostatic and electro-magnetic fields, and a beam envelope model. The code is guilt atop the Python interpreter language.

  7. Simulation analysis for effects of bone loss on acceleration tolerance of human lumbar vertebra

    NASA Astrophysics Data System (ADS)

    Ma, Honglei; Zhang, Feng; Zhu, Yu; Xiao, Yanhua; Wazir, Abrar

    2014-02-01

    The purpose of the present study was to analyze and predict the changes in acceleration tolerance of human vertebra as a result of bone loss caused by long-term space flight. A human L3-L4 vertebra FEM model was constructed, in which the cancellous bone was separated, and surrounding ligaments were also taken into account. The simulation results demonstrated that bone loss has more of an effect on the acceleration tolerance in x-direction. The results serve to aid in the creation of new acceleration tolerance standards, ensuring astronauts return home safely after long-term space flight. This study shows that more attention should be focused on the bone degradation of crew members and to create new protective designs for space capsules in the future.

  8. Forward and adjoint spectral-element simulations of seismic wave propagation using hardware accelerators

    NASA Astrophysics Data System (ADS)

    Peter, Daniel; Videau, Brice; Pouget, Kevin; Komatitsch, Dimitri

    2015-04-01

    Improving the resolution of tomographic images is crucial to answer important questions on the nature of Earth's subsurface structure and internal processes. Seismic tomography is the most prominent approach where seismic signals from ground-motion records are used to infer physical properties of internal structures such as compressional- and shear-wave speeds, anisotropy and attenuation. Recent advances in regional- and global-scale seismic inversions move towards full-waveform inversions which require accurate simulations of seismic wave propagation in complex 3D media, providing access to the full 3D seismic wavefields. However, these numerical simulations are computationally very expensive and need high-performance computing (HPC) facilities for further improving the current state of knowledge. During recent years, many-core architectures such as graphics processing units (GPUs) have been added to available large HPC systems. Such GPU-accelerated computing together with advances in multi-core central processing units (CPUs) can greatly accelerate scientific applications. There are mainly two possible choices of language support for GPU cards, the CUDA programming environment and OpenCL language standard. CUDA software development targets NVIDIA graphic cards while OpenCL was adopted mainly by AMD graphic cards. In order to employ such hardware accelerators for seismic wave propagation simulations, we incorporated a code generation tool BOAST into an existing spectral-element code package SPECFEM3D_GLOBE. This allows us to use meta-programming of computational kernels and generate optimized source code for both CUDA and OpenCL languages, running simulations on either CUDA or OpenCL hardware accelerators. We show here applications of forward and adjoint seismic wave propagation on CUDA/OpenCL GPUs, validating results and comparing performances for different simulations and hardware usages.

  9. 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.

  10. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

    PubMed Central

    2011-01-01

    We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment. PMID:21494425

  11. Toward a new paradigm in hospital-based pediatric education: the development of an onsite simulator program.

    PubMed

    Weinstock, Peter H; Kappus, Liana J; Kleinman, Monica E; Grenier, Barry; Hickey, Patricia; Burns, Jeffrey P

    2005-11-01

    The low incidence of crises in pediatrics, coupled with logistic issues and restricted work hours for trainees, hinders opportunities for frequent practice of crisis management and teamwork skills. We hypothesized that a dedicated simulator suite contiguous to the intensive care unit (ICU) would enhance the frequency and breadth of critical-incident training for a range of clinicians. Descriptive study. A tertiary-care pediatric teaching hospital. A realistic pediatric simulator suite was constructed 100 feet from the ICU, at a total base cost of $290,000. The simulation room is an exact replica of an ICU bed space, incorporating high-fidelity mannequin simulators. To capture an even wider audience, a portable unit was also created. Leaders from seven departments-critical care, cardiac intensive care, emergency medicine, transport medicine, anesthesia, respiratory care, and general pediatrics-completed instructor training to ensure effective debriefing techniques. Pediatric staff, including 100% of critical care fellows, 86% of nurses, 90% of respiratory therapists, and 74% of pediatric house staff, participated in >1500 learning encounters per year. All individuals were trained during their normal workday in the hospital. Courses in crisis resource management, skills acquisition, annual review, orientation, and trauma management (1,116, 98, 90, 60, and 60 encounters per year, respectively) were all designed by a multidisciplinary committee to ensure goal-directed education to a range of audiences. Annual costs were on par with those at other centers (approximately 44 dollars per trainee encounter). An onsite and comprehensive simulation program can significantly increase the opportunities for clinicians from multiple disciplines, in the course of their daily routines, to repetitively practice responses to pediatric medical crises. After an initial capital investment, the training appears to be cost-effective. Hospital-based simulator suites may point the way

  12. Radiation belt electron acceleration during the 17 March 2015 geomagnetic storm: Observations and simulations

    NASA Astrophysics Data System (ADS)

    Li, W.; Ma, Q.; Thorne, R. M.; Bortnik, J.; Zhang, X.-J.; Li, J.; Baker, D. N.; Reeves, G. D.; Spence, H. E.; Kletzing, C. A.; Kurth, W. S.; Hospodarsky, G. B.; Blake, J. B.; Fennell, J. F.; Kanekal, S. G.; Angelopoulos, V.; Green, J. C.; Goldstein, J.

    2016-06-01

    Various physical processes are known to cause acceleration, loss, and transport of energetic electrons in the Earth's radiation belts, but their quantitative roles in different time and space need further investigation. During the largest storm over the past decade (17 March 2015), relativistic electrons experienced fairly rapid acceleration up to ~7 MeV within 2 days after an initial substantial dropout, as observed by Van Allen Probes. In the present paper, we evaluate the relative roles of various physical processes during the recovery phase of this large storm using a 3-D diffusion simulation. By quantitatively comparing the observed and simulated electron evolution, we found that chorus plays a critical role in accelerating electrons up to several MeV near the developing peak location and produces characteristic flat-top pitch angle distributions. By only including radial diffusion, the simulation underestimates the observed electron acceleration, while radial diffusion plays an important role in redistributing electrons and potentially accelerates them to even higher energies. Moreover, plasmaspheric hiss is found to provide efficient pitch angle scattering losses for hundreds of keV electrons, while its scattering effect on > 1 MeV electrons is relatively slow. Although an additional loss process is required to fully explain the overestimated electron fluxes at multi-MeV, the combined physical processes of radial diffusion and pitch angle and energy diffusion by chorus and hiss reproduce the observed electron dynamics remarkably well, suggesting that quasi-linear diffusion theory is reasonable to evaluate radiation belt electron dynamics during this big storm.

  13. The Q Continuum Simulation: Harnessing the Power of GPU Accelerated Supercomputers

    NASA Astrophysics Data System (ADS)

    Heitmann, Katrin; Frontiere, Nicholas; Sewell, Chris; Habib, Salman; Pope, Adrian; Finkel, Hal; Rizzi, Silvio; Insley, Joe; Bhattacharya, Suman

    2015-08-01

    Modeling large-scale sky survey observations is a key driver for the continuing development of high-resolution, large-volume, cosmological simulations. We report the first results from the “Q Continuum” cosmological N-body simulation run carried out on the GPU-accelerated supercomputer Titan. The simulation encompasses a volume of {(1300 {Mpc})}3 and evolves more than half a trillion particles, leading to a particle mass resolution of {m}{{p}}≃ 1.5\\cdot {10}8 {M}⊙ . At this mass resolution, the Q Continuum run is currently the largest cosmology simulation available. It enables the construction of detailed synthetic sky catalogs, encompassing different modeling methodologies, including semi-analytic modeling and sub-halo abundance matching in a large, cosmological volume. Here we describe the simulation and outputs in detail and present first results for a range of cosmological statistics, such as mass power spectra, halo mass functions, and halo mass-concentration relations for different epochs. We also provide details on challenges connected to running a simulation on almost 90% of Titan, one of the fastest supercomputers in the world, including our usage of Titan’s GPU accelerators.

  14. The Q Continuum Simulation: Harnessing the Power of GPU Accelerated Supercomputers

    SciTech Connect

    Heitmann, Katrin; Frontiere, Nicholas; Sewell, Chris; Habib, Salman; Pope, Adrian; Finkel, Hal; Rizzi, Silvio; Insley, Joe; Bhattacharya, Suman

    2015-08-21

    Modeling large-scale sky survey observations is a key driver for the continuing development of high-resolution, large-volume, cosmological simulations. We report the first results from the "Q Continuum" cosmological N-body simulation run carried out on the GPU-accelerated supercomputer Titan. The simulation encompasses a volume of (1300 Mpc)(3) and evolves more than half a trillion particles, leading to a particle mass resolution of m(p) similar or equal to 1.5 . 10(8) M-circle dot. At thismass resolution, the Q Continuum run is currently the largest cosmology simulation available. It enables the construction of detailed synthetic sky catalogs, encompassing different modeling methodologies, including semi-analytic modeling and sub-halo abundance matching in a large, cosmological volume. Here we describe the simulation and outputs in detail and present first results for a range of cosmological statistics, such as mass power spectra, halo mass functions, and halo mass-concentration relations for different epochs. We also provide details on challenges connected to running a simulation on almost 90% of Titan, one of the fastest supercomputers in the world, including our usage of Titan's GPU accelerators.

  15. Particle-in-cell Simulation of Electron Acceleration in Solar Coronal Jets

    NASA Astrophysics Data System (ADS)

    Baumann, G.; Nordlund, Å.

    2012-11-01

    We investigate electron acceleration resulting from three-dimensional magnetic reconnection between an emerging, twisted magnetic flux rope and a pre-existing weak, open magnetic field. We first follow the rise of an unstable, twisted flux tube with a resistive MHD simulation where the numerical resolution is enhanced by using fixed mesh refinement. As in previous MHD investigations of similar situations, the rise of the flux tube into the pre-existing inclined coronal magnetic field results in the formation of a solar coronal jet. A snapshot of the MHD model is then used as an initial and boundary condition for a particle-in-cell simulation, using up to half a billion cells and over 20 billion charged particles. Particle acceleration occurs mainly in the reconnection current sheet, with accelerated electrons displaying a power law in the energy probability distribution with an index of around -1.5. The main acceleration mechanism is a systematic electric field, striving to maintaining the electric current in the current sheet against losses caused by electrons not being able to stay in the current sheet for more than a few seconds at a time.

  16. Simulation of Cosmic Ray Acceleration, Propagation and Interaction in SNR Environment

    NASA Astrophysics Data System (ADS)

    Lee, S. H.; Kamae, T.; Ellison, D. C.

    2007-07-01

    Recent studies of young supernova remnants (SNRs) with Chandra, XMM, Suzaku and HESS have revealed complex morphologies and spectral features of the emission sites. The critical question of the relative importance of the two competing gamma-ray emission mechanisms in SNRs; inverse-Compton scattering by high-energy electrons and pion production by energetic protons, may be resolved by GLAST-LAT. To keep pace with the improved observations, we are developing a 3D model of particle acceleration, diffusion, and interaction in a SNR where broad-band emission from radio to multi-TeV energies, produced by shock accelerated electrons and ions, can be simulated for a given topology of shock fronts, magnetic field, and ISM densities. The 3D model takes as input, the particle spectra predicted by a hydrodynamic simulation of SNR evolution where nonlinear diffusive shock acceleration is coupled to the remnant dynamics (e.g., Ellison, Decourchelle & Ballet; Ellison & Cassam-Chenai Ellison, Berezhko & Baring). We will present preliminary models of the Galactic Ridge SNR RX J1713-3946 for selected choices of SNR parameters, magnetic field topology, and ISM density distributions. When constrained by broad-band observations, our models should predict the extent of coupling between spectral shape and morphology and provide direct information on the acceleration efficiency of cosmic-ray electrons and ions in SNRs.

  17. Magnetic-Island Contraction and Particle Acceleration in Simulated Eruptive Solar Flares

    NASA Technical Reports Server (NTRS)

    Guidoni, S. E.; Devore, C. R.; Karpen, J. T.; Lynch, B. J.

    2016-01-01

    The mechanism that accelerates particles to the energies required to produce the observed high-energy impulsive emission in solar flares is not well understood. Drake et al. proposed a mechanism for accelerating electrons in contracting magnetic islands formed by kinetic reconnection in multi-layered current sheets (CSs). We apply these ideas to sunward-moving flux ropes (2.5D magnetic islands) formed during fast reconnection in a simulated eruptive flare. A simple analytic model is used to calculate the energy gain of particles orbiting the field lines of the contracting magnetic islands in our ultrahigh-resolution 2.5D numerical simulation. We find that the estimated energy gains in a single island range up to a factor of five. This is higher than that found by Drake et al. for islands in the terrestrial magnetosphere and at the heliopause, due to strong plasma compression that occurs at the flare CS. In order to increase their energy by two orders of magnitude and plausibly account for the observed high-energy flare emission, the electrons must visit multiple contracting islands. This mechanism should produce sporadic emission because island formation is intermittent. Moreover, a large number of particles could be accelerated in each magneto hydro dynamic-scale island, which may explain the inferred rates of energetic-electron production in flares. We conclude that island contraction in the flare CS is a promising candidate for electron acceleration in solar eruptions.

  18. Magnetic-island Contraction and Particle Acceleration in Simulated Eruptive Solar Flares

    NASA Astrophysics Data System (ADS)

    Guidoni, S. E.; DeVore, C. R.; Karpen, J. T.; Lynch, B. J.

    2016-03-01

    The mechanism that accelerates particles to the energies required to produce the observed high-energy impulsive emission in solar flares is not well understood. Drake et al. proposed a mechanism for accelerating electrons in contracting magnetic islands formed by kinetic reconnection in multi-layered current sheets (CSs). We apply these ideas to sunward-moving flux ropes (2.5D magnetic islands) formed during fast reconnection in a simulated eruptive flare. A simple analytic model is used to calculate the energy gain of particles orbiting the field lines of the contracting magnetic islands in our ultrahigh-resolution 2.5D numerical simulation. We find that the estimated energy gains in a single island range up to a factor of five. This is higher than that found by Drake et al. for islands in the terrestrial magnetosphere and at the heliopause, due to strong plasma compression that occurs at the flare CS. In order to increase their energy by two orders of magnitude and plausibly account for the observed high-energy flare emission, the electrons must visit multiple contracting islands. This mechanism should produce sporadic emission because island formation is intermittent. Moreover, a large number of particles could be accelerated in each magnetohydrodynamic-scale island, which may explain the inferred rates of energetic-electron production in flares. We conclude that island contraction in the flare CS is a promising candidate for electron acceleration in solar eruptions.

  19. MAGNETIC-ISLAND CONTRACTION AND PARTICLE ACCELERATION IN SIMULATED ERUPTIVE SOLAR FLARES

    SciTech Connect

    Guidoni, S. E.; DeVore, C. R.; Karpen, J. T.; Lynch, B. J.

    2016-03-20

    The mechanism that accelerates particles to the energies required to produce the observed high-energy impulsive emission in solar flares is not well understood. Drake et al. proposed a mechanism for accelerating electrons in contracting magnetic islands formed by kinetic reconnection in multi-layered current sheets (CSs). We apply these ideas to sunward-moving flux ropes (2.5D magnetic islands) formed during fast reconnection in a simulated eruptive flare. A simple analytic model is used to calculate the energy gain of particles orbiting the field lines of the contracting magnetic islands in our ultrahigh-resolution 2.5D numerical simulation. We find that the estimated energy gains in a single island range up to a factor of five. This is higher than that found by Drake et al. for islands in the terrestrial magnetosphere and at the heliopause, due to strong plasma compression that occurs at the flare CS. In order to increase their energy by two orders of magnitude and plausibly account for the observed high-energy flare emission, the electrons must visit multiple contracting islands. This mechanism should produce sporadic emission because island formation is intermittent. Moreover, a large number of particles could be accelerated in each magnetohydrodynamic-scale island, which may explain the inferred rates of energetic-electron production in flares. We conclude that island contraction in the flare CS is a promising candidate for electron acceleration in solar eruptions.

  20. Magnetic-Island Contraction and Particle Acceleration in Simulated Eruptive Solar Flares

    NASA Technical Reports Server (NTRS)

    Guidoni, S. E.; Devore, C. R.; Karpen, J. T.; Lynch, B. J.

    2016-01-01

    The mechanism that accelerates particles to the energies required to produce the observed high-energy impulsive emission in solar flares is not well understood. Drake et al. proposed a mechanism for accelerating electrons in contracting magnetic islands formed by kinetic reconnection in multi-layered current sheets (CSs). We apply these ideas to sunward-moving flux ropes (2.5D magnetic islands) formed during fast reconnection in a simulated eruptive flare. A simple analytic model is used to calculate the energy gain of particles orbiting the field lines of the contracting magnetic islands in our ultrahigh-resolution 2.5D numerical simulation. We find that the estimated energy gains in a single island range up to a factor of five. This is higher than that found by Drake et al. for islands in the terrestrial magnetosphere and at the heliopause, due to strong plasma compression that occurs at the flare CS. In order to increase their energy by two orders of magnitude and plausibly account for the observed high-energy flare emission, the electrons must visit multiple contracting islands. This mechanism should produce sporadic emission because island formation is intermittent. Moreover, a large number of particles could be accelerated in each magneto hydro dynamic-scale island, which may explain the inferred rates of energetic-electron production in flares. We conclude that island contraction in the flare CS is a promising candidate for electron acceleration in solar eruptions.

  1. Extremely high paw accelerations during paw shake in the cat: A mechanism revealed by computer simulations

    NASA Astrophysics Data System (ADS)

    Klishko, Alexander; Cofer, David; Edwards, Donald; Prilutsky, Boris

    2008-03-01

    Paw shake response is a reflex aimed at removing an irritating stimulus from the paw by imparting to it high periodic accelerations (>10 g). These values seem too high to be produced by distal muscles exclusively. According to Prilutsky et al. (2005), resultant hip moments during paw shake are much greater than distal joint moments, whereas distal joint velocities and accelerations exceed those of the proximal joints. The goal of this study was to examine how proximal hip muscles could contribute to high paw accelerations. Using software AnimatLab, we developed a 2D model of the cat hindlimb consisting of 5 rigid segments with 4 hinge joints and 11 muscles spanning all joints. The muscles were assumed passive except for those crossing the hip. When in simulations the hip muscles were reciprocally activated to periodically flex and extend the hip joint with a typical paw shake frequency of 10 Hz, the hindlimb segments demonstrated motion resembling experimental observations: linear and angular velocities and accelerations of the distal segments exceeded several fold the values of the proximal segments. Simulated paw shake revealed features of a whip-like motion.

  2. Finite element analysis of head-neck kinematics under simulated rear impact at different accelerations.

    PubMed

    Zhang, Qing Hang; Tan, Soon Huat; Teo, Ee Chon

    2008-07-01

    The information on the variation of ligament strains over time after rear impact has been seldom investigated. In the current study, a detailed three-dimensional C0-C7 finite element model of the whole head-neck complex developed previously was modified to include T1 vertebra. Rear impact of half sine-pulses with peak values of 3.5g, 5g, 6.5g and 8g respectively were applied to the inferior surface of the T1 vertebral body to validate the simulated variations of the intervertebral segmental rotations and to investigate the ligament tensions of the cervical spine under different levels of accelerations. The simulated kinematics of the head-neck complex showed relatively good agreement with the experimental data with most of the predicted peak values falling within one standard deviation of the experimental data. Under rear impact, the whole C0-T1 structure formed an S-shaped curvature with flexion at the upper levels and extension at the lower levels at early stage after impact, during which the lower cervical levels might experience hyperextensions. The predicted high resultant strain of the capsular ligaments, even at low impact acceleration compared with other ligament groups, suggests their susceptibility to injury. The peak impact acceleration has a significant effect on the potential injury of ligaments. Under higher accelerations, most ligaments will reach failure strain in a much shorter time immediately after impact.

  3. [Preparation of hydroxyapatite coating in concentrated simulated body fluid by accelerated biomimetic synthesis].

    PubMed

    Li, Yadong; Liu, Jingxiao; Shi, Fei; Tang, Nailing; Yu, Ling

    2007-12-01

    In the present work, NiTi alloy substrates were activated by three different pretreatment processes. 5 X SBF1 and 5 X SBF2 concentrated simulated body fluids were prepared with citric acid buffer reagent, and then calcium phosphate coatings were formed quickly on NiTi alloy surface by accelerated biomimetic synthesis after pretreatment. The microstructure, composition and surface morphology of calcium phosphate coatings were studied. The results indicate that calcium phosphate coatings possess porous and net structure, which are composed of precipitated spherical particles with diameter less than 3 microm. The analysis of XRD shows that the main component of calcium phosphate coatings is hydroxyapatite, whereas the concentrated 5 x SBF simulated body fluid, which is in the absence of Mg2+ and HCO3- crystal growth inhibitors, apparently accelerates the growth rate of hydroxyapatite coatings.

  4. Load management strategy for Particle-In-Cell simulations in high energy particle acceleration

    NASA Astrophysics Data System (ADS)

    Beck, A.; Frederiksen, J. T.; Dérouillat, J.

    2016-09-01

    In the wake of the intense effort made for the experimental CILEX project, numerical simulation campaigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These simulations bring, of course, important insight into the fundamental physics at play. As a by-product, they also characterize the quality of our theoretical and numerical models. In this paper, we compare the results given by different codes and point out algorithmic limitations both in terms of physical accuracy and computational performances. These limitations are illustrated in the context of electron laser wakefield acceleration (LWFA). The main limitation we identify in state-of-the-art Particle-In-Cell (PIC) codes is computational load imbalance. We propose an innovative algorithm to deal with this specific issue as well as milestones towards a modern, accurate high-performance PIC code for high energy particle acceleration.

  5. Acquisition, retention and transfer of simulated laparoscopic tasks using fNIR and a contextual interference paradigm.

    PubMed

    Shewokis, Patricia A; Shariff, Faiz U; Liu, Yichuan; Ayaz, Hasan; Castellanos, Andres; Lind, D Scott

    2017-02-01

    Using functional near infrared spectroscopy, a noninvasive, optical brain imaging tool that monitors changes in hemodynamics within the prefrontal cortex (PFC), we assessed performance and cognitive effort during the acquisition, retention and transfer of multiple simulated laparoscopic tasks by novice learners within a contextual interference paradigm. Third-year medical students (n = 10) were randomized to either a blocked or random practice schedule. Across 3 days, students performed 108 acquisition trials of 3 laparoscopic tasks on the LapSim(®) simulator followed by delayed retention and transfer tests. Performance metrics (Global score, Total time) and hemodynamic responses (total hemoglobin (μm)) were assessed during skill acquisition, retention and transfer. All acquisition tasks resulted in significant practice schedule X trial block interactions for the left medial anterior PFC. During retention and transfer, random performed the skills in less time and had lower total hemoglobin change in the right dorsolateral PFC than blocked. Compared with blocked, random practice resulted in enhanced learning through better performance and less cognitive load for retention and transfer of simulated laparoscopic tasks. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Equation-based languages – A new paradigm for building energy modeling, simulation and optimization

    SciTech Connect

    Wetter, Michael; Bonvini, Marco; Nouidui, Thierry S.

    2016-04-01

    Most of the state-of-the-art building simulation programs implement models in imperative programming languages. This complicates modeling and excludes the use of certain efficient methods for simulation and optimization. In contrast, equation-based modeling languages declare relations among variables, thereby allowing the use of computer algebra to enable much simpler schematic modeling and to generate efficient code for simulation and optimization. We contrast the two approaches in this paper. We explain how such manipulations support new use cases. In the first of two examples, we couple models of the electrical grid, multiple buildings, HVAC systems and controllers to test a controller that adjusts building room temperatures and PV inverter reactive power to maintain power quality. In the second example, we contrast the computing time for solving an optimal control problem for a room-level model predictive controller with and without symbolic manipulations. As a result, exploiting the equation-based language led to 2, 200 times faster solution

  7. The changing face of surgical education: simulation as the new paradigm.

    PubMed

    Scott, Daniel J; Cendan, Juan C; Pugh, Carla M; Minter, Rebecca M; Dunnington, Gary L; Kozar, Rosemary A

    2008-06-15

    Surgical simulation has evolved considerably over the past two decades and now plays a major role in training efforts designed to foster the acquisition of new skills and knowledge outside of the clinical environment. Numerous driving forces have fueled this fundamental change in educational methods, including concerns over patient safety and the need to maximize efficiency within the context of limited work hours and clinical exposure. The importance of simulation has been recognized by the major stake-holders in surgical education, and the Residency Review Committee has mandated that all programs implement skills training curricula in 2008. Numerous issues now face educators who must use these novel training methods. It is important that these individuals have a solid understanding of content, development, research, and implementation aspects regarding simulation. This paper highlights presentations about these topics from a panel of experts convened at the 2008 Academic Surgical Congress.

  8. Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units.

    PubMed

    Fang, Qianqian; Boas, David A

    2009-10-26

    We report a parallel Monte Carlo algorithm accelerated by graphics processing units (GPU) for modeling time-resolved photon migration in arbitrary 3D turbid media. By taking advantage of the massively parallel threads and low-memory latency, this algorithm allows many photons to be simulated simultaneously in a GPU. To further improve the computational efficiency, we explored two parallel random number generators (RNG), including a floating-point-only RNG based on a chaotic lattice. An efficient scheme for boundary reflection was implemented, along with the functions for time-resolved imaging. For a homogeneous semi-infinite medium, good agreement was observed between the simulation output and the analytical solution from the diffusion theory. The code was implemented with CUDA programming language, and benchmarked under various parameters, such as thread number, selection of RNG and memory access pattern. With a low-cost graphics card, this algorithm has demonstrated an acceleration ratio above 300 when using 1792 parallel threads over conventional CPU computation. The acceleration ratio drops to 75 when using atomic operations. These results render the GPU-based Monte Carlo simulation a practical solution for data analysis in a wide range of diffuse optical imaging applications, such as human brain or small-animal imaging.

  9. The Acceleration of Thermal Ions at a Strong, Quasi-Parallel Interplanetary Shock: A Hybrid Simulation

    NASA Astrophysics Data System (ADS)

    Giacalone, Joe

    2017-09-01

    Using a self-consistent hybrid simulation, with kinetic protons and fluid electrons, we investigate the acceleration of thermal protons and minor ions (alphas, 3He ++, and C5+) by a quasi-parallel collisionless shock. The results are compared to spacecraft observations of a strong interplanetary shock seen by the Advanced Composition Explorer on DOY 94, 2001, which was associated with significant increases in the flux of > 50 keV/nuc ions. Our simulation uses similar plasma and shock parameters to those observed. The densities of minor ions for two of the species (alphas and C5+) were based on observations at thermal energies for this shock, and we used a nominal value for the density of 3He ++, since no observations at thermal energies was available to us. Acceleration of the ions by the shock leads to a high-energy tail in the distribution in the post-shock plasma for all ion species. We find that by extrapolating the simulated tails to the higher energies measured by ACE/EPAM and ACE/ULEIS, the intensity matches well the observations for protons, alphas, and carbon. This suggests that thermal solar wind, accelerated directly at the shock, is a significant source of the observed high-energy protons and these minor ions.

  10. Particle-in-Cell Code BEAMPATH for Beam Dynamics Simulations in Linear Accelerators and Beamlines

    SciTech Connect

    Batygin, Y.

    2004-10-28

    A code library BEAMPATH for 2 - dimensional and 3 - dimensional space charge dominated beam dynamics study in linear particle accelerators and beam transport lines is developed. The program is used for particle-in-cell simulation of axial-symmetric, quadrupole-symmetric and z-uniform beams in a channel containing RF gaps, radio-frequency quadrupoles, multipole lenses, solenoids and bending magnets. The programming method includes hierarchical program design using program-independent modules and a flexible combination of modules to provide the most effective version of the structure for every specific case of simulation. Numerical techniques as well as the results of beam dynamics studies are presented.

  11. Forced detection Monte Carlo algorithms for accelerated blood vessel image simulations.

    PubMed

    Fredriksson, Ingemar; Larsson, Marcus; Strömberg, Tomas

    2009-03-01

    Two forced detection (FD) variance reduction Monte Carlo algorithms for image simulations of tissue-embedded objects with matched refractive index are presented. The principle of the algorithms is to force a fraction of the photon weight to the detector at each and every scattering event. The fractional weight is given by the probability for the photon to reach the detector without further interactions. Two imaging setups are applied to a tissue model including blood vessels, where the FD algorithms produce identical results as traditional brute force simulations, while being accelerated with two orders of magnitude. Extending the methods to include refraction mismatches is discussed.

  12. Hub-based simulation and graphics hardware accelerated visualization for nanotechnology applications.

    PubMed

    Qiao, Wei; McLennan, Michael; Kennell, Rick; Ebert, David S; Klimeck, Gerhard

    2006-01-01

    The Network for Computational Nanotechnology (NCN) has developed a science gateway at nanoHUB.org for nanotechnology education and research. Remote users can browse through online seminars and courses, and launch sophisticated nanotechnology simulation tools, all within their web browser. Simulations are supported by a middleware that can route complex jobs to grid supercomputing resources. But what is truly unique about the middleware is the way that it uses hardware accelerated graphics to support both problem setup and result visualization. This paper describes the design and integration of a remote visualization framework into the nanoHUB for interactive visual analytics of nanotechnology simulations. Our services flexibly handle a variety of nanoscience simulations, render them utilizing graphics hardware acceleration in a scalable manner, and deliver them seamlessly through the middleware to the user. Rendering is done only on-demand, as needed, so each graphics hardware unit can simultaneously support many user sessions. Additionally, a novel node distribution scheme further improves our system's scalability. Our approach is not only efficient but also cost-effective. Only a half-dozen render nodes are anticipated to support hundreds of active tool sessions on the nanoHUB. Moreover, this architecture and visual analytics environment provides capabilities that can serve many areas of scientific simulation and analysis beyond nanotechnology with its ability to interactively analyze and visualize multivariate scalar and vector fields.

  13. Simulations of ion acceleration at non-relativistic shocks. II. Magnetic field amplification

    SciTech Connect

    Caprioli, D.; Spitkovsky, A.

    2014-10-10

    We use large hybrid simulations to study ion acceleration and generation of magnetic turbulence due to the streaming of particles that are self-consistently accelerated at non-relativistic shocks. When acceleration is efficient, we find that the upstream magnetic field is significantly amplified. The total amplification factor is larger than 10 for shocks with Alfvénic Mach number M = 100, and scales with the square root of M. The spectral energy density of excited magnetic turbulence is determined by the energy distribution of accelerated particles, and for moderately strong shocks (M ≲ 30) agrees well with the prediction of resonant streaming instability, in the framework of quasilinear theory of diffusive shock acceleration. For M ≳ 30, instead, Bell's non-resonant hybrid (NRH) instability is predicted and found to grow faster than resonant instability. NRH modes are excited far upstream by escaping particles, and initially grow without disrupting the current, their typical wavelengths being much shorter than the current ions' gyroradii. Then, in the nonlinear stage, most unstable modes migrate to larger and larger wavelengths, eventually becoming resonant in wavelength with the driving ions, which start diffuse. Ahead of strong shocks we distinguish two regions, separated by the free-escape boundary: the far upstream, where field amplification is provided by the current of escaping ions via NRH instability, and the shock precursor, where energetic particles are effectively magnetized, and field amplification is provided by the current in diffusing ions. The presented scalings of magnetic field amplification enable the inclusion of self-consistent microphysics into phenomenological models of ion acceleration at non-relativistic shocks.

  14. The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation.

    PubMed

    Baron, Riccardo; McCammon, J Andrew; Mattevi, Andrea

    2009-12-01

    Oxygen biocatalysis and regulation is crucial to a variety of biochemical processes in nature. Oxygen-binding proteins cover only a limited part of oxygen biocatalysis, which involves numerous examples of oxygen-consuming biocatalysts with low oxygen affinities. The integration of experiments with powerful biomolecular simulation opens appealing possibilities to investigate crucial questions on the fascinating relationship between enzyme dynamics and oxygen biocatalysis in new protein structures.

  15. Equation-based languages – A new paradigm for building energy modeling, simulation and optimization

    DOE PAGES

    Wetter, Michael; Bonvini, Marco; Nouidui, Thierry S.

    2016-04-01

    Most of the state-of-the-art building simulation programs implement models in imperative programming languages. This complicates modeling and excludes the use of certain efficient methods for simulation and optimization. In contrast, equation-based modeling languages declare relations among variables, thereby allowing the use of computer algebra to enable much simpler schematic modeling and to generate efficient code for simulation and optimization. We contrast the two approaches in this paper. We explain how such manipulations support new use cases. In the first of two examples, we couple models of the electrical grid, multiple buildings, HVAC systems and controllers to test a controller thatmore » adjusts building room temperatures and PV inverter reactive power to maintain power quality. In the second example, we contrast the computing time for solving an optimal control problem for a room-level model predictive controller with and without symbolic manipulations. As a result, exploiting the equation-based language led to 2, 200 times faster solution« less

  16. Automated detection and analysis of particle beams in laser-plasma accelerator simulations

    SciTech Connect

    Ushizima, Daniela Mayumi; Geddes, C.G.; Cormier-Michel, E.; Bethel, E. Wes; Jacobsen, J.; Prabhat, ,; R.ubel, O.; Weber, G,; Hamann, B.

    2010-05-21

    Numerical simulations of laser-plasma wakefield (particle) accelerators model the acceleration of electrons trapped in plasma oscillations (wakes) left behind when an intense laser pulse propagates through the plasma. The goal of these simulations is to better understand the process involved in plasma wake generation and how electrons are trapped and accelerated by the wake. Understanding of such accelerators, and their development, offer high accelerating gradients, potentially reducing size and cost of new accelerators. One operating regime of interest is where a trapped subset of electrons loads the wake and forms an isolated group of accelerated particles with low spread in momentum and position, desirable characteristics for many applications. The electrons trapped in the wake may be accelerated to high energies, the plasma gradient in the wake reaching up to a gigaelectronvolt per centimeter. High-energy electron accelerators power intense X-ray radiation to terahertz sources, and are used in many applications including medical radiotherapy and imaging. To extract information from the simulation about the quality of the beam, a typical approach is to examine plots of the entire dataset, visually determining the adequate parameters necessary to select a subset of particles, which is then further analyzed. This procedure requires laborious examination of massive data sets over many time steps using several plots, a routine that is unfeasible for large data collections. Demand for automated analysis is growing along with the volume and size of simulations. Current 2D LWFA simulation datasets are typically between 1GB and 100GB in size, but simulations in 3D are of the order of TBs. The increase in the number of datasets and dataset sizes leads to a need for automatic routines to recognize particle patterns as particle bunches (beam of electrons) for subsequent analysis. Because of the growth in dataset size, the application of machine learning techniques for

  17. Ant colony method to control variance reduction techniques in the Monte Carlo simulation of clinical electron linear accelerators

    NASA Astrophysics Data System (ADS)

    García-Pareja, S.; Vilches, M.; Lallena, A. M.

    2007-09-01

    The ant colony method is used to control the application of variance reduction techniques to the simulation of clinical electron linear accelerators of use in cancer therapy. In particular, splitting and Russian roulette, two standard variance reduction methods, are considered. The approach can be applied to any accelerator in a straightforward way and permits, in addition, to investigate the "hot" regions of the accelerator, an information which is basic to develop a source model for this therapy tool.

  18. Proton and Helium Injection Into First Order Fermi Acceleration at Shocks: Hybrid Simulation and Analysis

    NASA Astrophysics Data System (ADS)

    Dudnikova, Galina; Malkov, Mikhail; Sagdeev, Roald; Liseykina, Tatjana; Hanusch, Adrian

    2016-10-01

    Elemental composition of galactic cosmic rays (CR) probably holds the key to their origin. Most likely, they are accelerated at collisionless shocks in supernova remnants, but the acceleration mechanism is not entirely understood. One complicated problem is ``injection'', a process whereby the shock selects a tiny fraction of particles to keep on crossing its front and gain more energy. Comparing the injection rates of particles with different mass to charge ratio is a powerful tool for studying this process. Recent advances in measurements of CR He/p ratio have provided particularly important new clues. We performed a series of hybrid simulations and analyzed a joint injection of protons and Helium, in conjunction with upstream waves they generate. The emphasis of this work is on the bootstrap aspects of injection manifested in particle confinement to the shock and, therefore, their continuing acceleration by the self-driven waves. The waves are initially generated by He and protons in separate spectral regions, and their interaction plays a crucial role in particle acceleration. The work is ongoing and new results will be reported along with their analysis and comparison with the latest data from the AMS-02 space-based spectrometer. Work supported Grant RFBR 16-01-00209, NASA ATP-program under Award NNX14AH36G, and by the US Department of Energy under Award No. DE-FG02-04ER54738.

  19. Dynamic Monte Carlo simulations of double crystallization accelerated in microdomains of diblock copolymers

    NASA Astrophysics Data System (ADS)

    Li, Yuan; Ma, Yu; Li, Juan; Jiang, Xiaoming; Hu, Wenbing

    2012-03-01

    We report dynamic Monte Carlo simulations of microphase separated diblock copolymers, to investigate how crystallization of one species could accelerate the subsequent crystallization of another species. Although the lattice copolymer model brings a boundary constraint to the long periods of microdomains, the single-molecular-level force balance between two blocks and its change can be revealed in this simple approach. We found two contrastable acceleration mechanisms: (1) the metastable lamellar crystals of one species become thicker at higher crystallization temperatures, sacrificing its microphase interfacial area to make a larger coil-stretching of another amorphous species and hence to accelerate subsequent crystallization of the latter with a more favorable conformation. (2) While in the case allowing chain-sliding in the crystal, the equilibrated lamellar crystals of one species become thinner at higher temperatures, sacrificing its thermal stability to gain a higher conformational entropy of another amorphous species and hence to accelerate subsequent crystallization of the latter with a stronger tension at the block junction. Parallel situations of experiments have been discussed.

  20. GPU-accelerated Tersoff potentials for massively parallel Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Nguyen, Trung Dac

    2017-03-01

    The Tersoff potential is one of the empirical many-body potentials that has been widely used in simulation studies at atomic scales. Unlike pair-wise potentials, the Tersoff potential involves three-body terms, which require much more arithmetic operations and data dependency. In this contribution, we have implemented the GPU-accelerated version of several variants of the Tersoff potential for LAMMPS, an open-source massively parallel Molecular Dynamics code. Compared to the existing MPI implementation in LAMMPS, the GPU implementation exhibits a better scalability and offers a speedup of 2.2X when run on 1000 compute nodes on the Titan supercomputer. On a single node, the speedup ranges from 2.0 to 8.0 times, depending on the number of atoms per GPU and hardware configurations. The most notable features of our GPU-accelerated version include its design for MPI/accelerator heterogeneous parallelism, its compatibility with other functionalities in LAMMPS, its ability to give deterministic results and to support both NVIDIA CUDA- and OpenCL-enabled accelerators. Our implementation is now part of the GPU package in LAMMPS and accessible for public use.

  1. Using the k-d Tree Data Structure to Accelerate Monte Carlo Simulations.

    PubMed

    Chen, Qile P; Xue, Bai; Siepmann, J Ilja

    2017-04-11

    The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble. Simulations for TraPPE-UA ethanol in the NpT ensemble and for the rigid TIP4P water model in the Gibbs ensemble gain slightly in efficiency with the k-d tree, whereas simulations for TIP4P water in the NpT ensemble do not benefit from the use of the k-d tree. The speed-up can be attributed to the reduction in the number of distance calculations in the range search from scaling as [Formula: see text] to [Formula: see text]. In addition, these tests suggest that the efficiency gain from the use of the k-d tree data structure depends on the flexibility of the molecular model (requiring configurational-bias MC moves to sample changes in conformation), on the ensemble (with open ensembles requiring special MC moves to aid particle transfers), and on the number of interaction sites per molecule (with compact multisite models not seeing an efficiency gain). Overall, the use of the k-d tree data structure can substantially enhance MC simulation efficiency for a variety of systems, and it will enable simulations for larger system sizes in the future.

  2. Issues for Simulation of Galactic Cosmic Ray Exposures for Radiobiological Research at Ground-Based Accelerators

    PubMed Central

    Kim, Myung-Hee Y.; Rusek, Adam; Cucinotta, Francis A.

    2015-01-01

    For radiobiology research on the health risks of galactic cosmic rays (GCR) ground-based accelerators have been used with mono-energetic beams of single high charge, Z and energy, E (HZE) particles. In this paper, we consider the pros and cons of a GCR reference field at a particle accelerator. At the NASA Space Radiation Laboratory (NSRL), we have proposed a GCR simulator, which implements a new rapid switching mode and higher energy beam extraction to 1.5 GeV/u, in order to integrate multiple ions into a single simulation within hours or longer for chronic exposures. After considering the GCR environment and energy limitations of NSRL, we performed extensive simulation studies using the stochastic transport code, GERMcode (GCR Event Risk Model) to define a GCR reference field using 9 HZE particle beam–energy combinations each with a unique absorber thickness to provide fragmentation and 10 or more energies of proton and 4He beams. The reference field is shown to well represent the charge dependence of GCR dose in several energy bins behind shielding compared to a simulated GCR environment. However, a more significant challenge for space radiobiology research is to consider chronic GCR exposure of up to 3 years in relation to simulations with animal models of human risks. We discuss issues in approaches to map important biological time scales in experimental models using ground-based simulation, with extended exposure of up to a few weeks using chronic or fractionation exposures. A kinetics model of HZE particle hit probabilities suggests that experimental simulations of several weeks will be needed to avoid high fluence rate artifacts, which places limitations on the experiments to be performed. Ultimately risk estimates are limited by theoretical understanding, and focus on improving knowledge of mechanisms and development of experimental models to improve this understanding should remain the highest priority for space radiobiology research. PMID:26090339

  3. Issues for Simulation of Galactic Cosmic Ray Exposures for Radiobiological Research at Ground-Based Accelerators.

    PubMed

    Kim, Myung-Hee Y; Rusek, Adam; Cucinotta, Francis A

    2015-01-01

    For radiobiology research on the health risks of galactic cosmic rays (GCR) ground-based accelerators have been used with mono-energetic beams of single high charge, Z and energy, E (HZE) particles. In this paper, we consider the pros and cons of a GCR reference field at a particle accelerator. At the NASA Space Radiation Laboratory (NSRL), we have proposed a GCR simulator, which implements a new rapid switching mode and higher energy beam extraction to 1.5 GeV/u, in order to integrate multiple ions into a single simulation within hours or longer for chronic exposures. After considering the GCR environment and energy limitations of NSRL, we performed extensive simulation studies using the stochastic transport code, GERMcode (GCR Event Risk Model) to define a GCR reference field using 9 HZE particle beam-energy combinations each with a unique absorber thickness to provide fragmentation and 10 or more energies of proton and (4)He beams. The reference field is shown to well represent the charge dependence of GCR dose in several energy bins behind shielding compared to a simulated GCR environment. However, a more significant challenge for space radiobiology research is to consider chronic GCR exposure of up to 3 years in relation to simulations with animal models of human risks. We discuss issues in approaches to map important biological time scales in experimental models using ground-based simulation, with extended exposure of up to a few weeks using chronic or fractionation exposures. A kinetics model of HZE particle hit probabilities suggests that experimental simulations of several weeks will be needed to avoid high fluence rate artifacts, which places limitations on the experiments to be performed. Ultimately risk estimates are limited by theoretical understanding, and focus on improving knowledge of mechanisms and development of experimental models to improve this understanding should remain the highest priority for space radiobiology research.

  4. GPU-accelerated phase-field simulation of dendritic solidification in a binary alloy

    NASA Astrophysics Data System (ADS)

    Yamanaka, Akinori; Aoki, Takayuki; Ogawa, Satoi; Takaki, Tomohiro

    2011-03-01

    The phase-field simulation for dendritic solidification of a binary alloy has been accelerated by using a graphic processing unit (GPU). To perform the phase-field simulation of the alloy solidification on GPU, a program code was developed with computer unified device architecture (CUDA). In this paper, the implementation technique of the phase-field model on GPU is presented. Also, we evaluated the acceleration performance of the three-dimensional solidification simulation by using a single NVIDIA TESLA C1060 GPU and the developed program code. The results showed that the GPU calculation for 5763 computational grids achieved the performance of 170 GFLOPS by utilizing the shared memory as a software-managed cache. Furthermore, it can be demonstrated that the computation with the GPU is 100 times faster than that with a single CPU core. From the obtained results, we confirmed the feasibility of realizing a real-time full three-dimensional phase-field simulation of microstructure evolution on a personal desktop computer.

  5. Simulating the effects of timing and energy stability in a laser wakefield accelerator with external injection

    SciTech Connect

    Dijk, W. van; Corstens, J. M.; Stragier, X. F. D.; Brussaard, G. J. H.; Geer, S. B. van der

    2009-01-22

    One of the most compelling reasons to use external injection of electrons into a laser wakefield accelerator is to improve the stability and reproducibility of the accelerated electrons. We have built a simulation tool based on particle tracking to investigate the expected output parameters. Specifically, we are simulating the variations in energy and bunch charge under the influence of variations in laser power and timing jitter. In these simulations a a{sub 0} = 0.32 to a{sub 0} = 1.02 laser pulse with 10% shot-to-shot energy fluctuation is focused into a plasma waveguide with a density of 1.0x10{sup 24} m{sup -3} and a calculated matched spot size of 50.2 {mu}m. The timing of the injected electron bunch with respect to the laser pulse is varied from up to 1 ps from the standard timing (1 ps ahead or behind the laser pulse, depending on the regime). The simulation method and first results will be presented. Shortcomings and possible extensions to the model will be discussed.

  6. GPU-accelerated Monte Carlo simulation of particle coagulation based on the inverse method

    NASA Astrophysics Data System (ADS)

    Wei, J.; Kruis, F. E.

    2013-09-01

    Simulating particle coagulation using Monte Carlo methods is in general a challenging computational task due to its numerical complexity and the computing cost. Currently, the lowest computing costs are obtained when applying a graphic processing unit (GPU) originally developed for speeding up graphic processing in the consumer market. In this article we present an implementation of accelerating a Monte Carlo method based on the Inverse scheme for simulating particle coagulation on the GPU. The abundant data parallelism embedded within the Monte Carlo method is explained as it will allow an efficient parallelization of the MC code on the GPU. Furthermore, the computation accuracy of the MC on GPU was validated with a benchmark, a CPU-based discrete-sectional method. To evaluate the performance gains by using the GPU, the computing time on the GPU against its sequential counterpart on the CPU were compared. The measured speedups show that the GPU can accelerate the execution of the MC code by a factor 10-100, depending on the chosen particle number of simulation particles. The algorithm shows a linear dependence of computing time with the number of simulation particles, which is a remarkable result in view of the n2 dependence of the coagulation.

  7. Accelerated Molecular Dynamics Simulations of Ligand Binding to a Muscarinic G-protein Coupled Receptor

    PubMed Central

    Kappel, Kalli; Miao, Yinglong; McCammon, J. Andrew

    2017-01-01

    Elucidating the detailed process of ligand binding to a receptor is pharmaceutically important for identifying druggable binding sites. With the ability to provide atomistic detail, computational methods are well poised to study these processes. Here, accelerated molecular dynamics (aMD) is proposed to simulate processes of ligand binding to a G-protein coupled receptor (GPCR), in this case the M3 muscarinic receptor, which is a target for treating many human diseases, including cancer, diabetes and obesity. Long-timescale aMD simulations were performed to observe the binding of three chemically diverse ligand molecules: antagonist tiotropium (TTP), partial agonist arecoline (ARc), and full agonist acetylcholine (ACh). In comparison with earlier microsecond-timescale conventional MD simulations, aMD greatly accelerated the binding of ACh to the receptor orthosteric ligand-binding site and the binding of TTP to an extracellular vestibule. Further aMD simulations also captured binding of ARc to the receptor orthosteric site. Additionally, all three ligands were observed to bind in the extracellular vestibule during their binding pathways, suggesting that it is a metastable binding site. This study demonstrates the applicability of aMD to protein-ligand binding, especially the drug recognition of GPCRs. PMID:26537408

  8. Synergy Between Experiments and Simulations in Laser and Beam-Driven Plasma Acceleration and Light Sources

    NASA Astrophysics Data System (ADS)

    Mori, Warren B.

    2015-11-01

    Computer simulations have been an integral part of plasma physics research since the early 1960s. Initially, they provided the ability to confirm and test linear and nonlinear theories in one-dimension. As simulation capabilities and computational power improved, then simulations were also used to test new ideas and applications of plasmas in multi-dimensions. As progress continued, simulations were also used to model experiments. Today computer simulations of plasmas are ubiquitously used to test new theories, understand complicated nonlinear phenomenon, model the full temporal and spatial scale of experiments, simulate parameters beyond the reach of current experiments, and test the performance of new devices before large capital expenditures are made to build them. In this talk I review the progress in simulations in a particular area of plasma physics: plasma based acceleration (PBA). In PBA a short laser pulse or particle beam propagates through long regions of plasma creating plasma wave wakefields on which electrons or positrons surf to high energies. In some cases the wakefields are highly nonlinear, involve three-dimensional effects, and the trajectories of plasma particles cross making it essential that fully kinetic and three-dimensional models are used. I will show how particle-in-cell (PIC) simulations were initially used to propose the basic idea of PBA in one dimension. I will review some of the dramatic progress in the experimental demonstration of PBA and show how this progress was dramatically helped by a synergy between experiments and full-scale multi-dimensional PIC simulations. This will include a review of how the capability of PIC simulation tools has improved. I will also touch on some recent progress on improvements to PIC simulations of PBA and discuss how these improvements may push the synergy further towards real time steering of experiments and start to end modeling of key components of a future linear collider or XFEL based on PBA

  9. Measurement of performance using acceleration control and pulse control in simulated spacecraft docking operations

    NASA Technical Reports Server (NTRS)

    Brody, Adam R.; Ellis, Stephen R.

    1992-01-01

    Nine commercial airline pilots served as test subjects in a study to compare acceleration control with pulse control in simulated spacecraft maneuvers. Simulated remote dockings of an orbital maneuvering vehicle (OMV) to a space station were initiated from 50, 100, and 150 meters along the station's -V-bar (minus velocity vector). All unsuccessful missions were reflown. Five way mixed analysis of variance (ANOVA) with one between factor, first mode, and four within factors (mode, bloch, range, and trial) were performed on the data. Recorded performance measures included mission duration and fuel consumption along each of the three coordinate axes. Mission duration was lower with pulse mode, while delta V (fuel consumption) was lower with acceleration mode. Subjects used more fuel to travel faster with pulse mode than with acceleration mode. Mission duration, delta V, X delta V, Y delta V., and Z delta V all increased with range. Subjects commanded the OMV to 'fly' at faster rates from further distances. These higher average velocities were paid for with increased fuel consumption. Asymmetrical transfer was found in that the mode transitions could not be predicted solely from the mission duration main effect. More testing is advised to understand the manual control aspects of spaceflight maneuvers better.

  10. Accelerated multiscale space-time finite element simulation and application to high cycle fatigue life prediction

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Wen, Lihua; Naboulsi, Sam; Eason, Thomas; Vasudevan, Vijay K.; Qian, Dong

    2016-08-01

    A multiscale space-time finite element method based on time-discontinuous Galerkin and enrichment approach is presented in this work with a focus on improving the computational efficiencies for high cycle fatigue simulations. While the robustness of the TDG-based space-time method has been extensively demonstrated, a critical barrier for the extensive application is the large computational cost due to the additional temporal dimension and enrichment that are introduced. The present implementation focuses on two aspects: firstly, a preconditioned iterative solver is developed along with techniques for optimizing the matrix storage and operations. Secondly, parallel algorithms based on multi-core graphics processing unit are established to accelerate the progressive damage model implementation. It is shown that the computing time and memory from the accelerated space-time implementation scale with the number of degree of freedom N through ˜ O(N^{1.6}) and ˜ O(N), respectively. Finally, we demonstrate the accelerated space-time FEM simulation through benchmark problems.

  11. Simulations of the LEDA RFQ 6.7 MeV Accelerator

    NASA Astrophysics Data System (ADS)

    Young, L. M.

    1997-05-01

    The codes PARMTEQM(K. R. Crandall, et. al. "RFQ Design Codes," Los Alamos National Laboratory report LA-UR-96-1836.) and RFQTRAK(N. J. Diserens "RFTRAK User Guide" AECL Research, May 1993.) simulate the beam transport through the Radio Frequency Quadrupole (RFQ) accelerator(L.M. Young, "An 8-meter-long coupled cavity RFQ Linac", Proc. 1994 Intl. LINAC Conf. (Tsukuba, Japan) 178.) for the Low-Energy Demonstration Accelerator (LEDA). They predict 95% transmission for a matched 110-mA proton beam with a normalized-rms emittance of 0.02 π mm mrad. RFQTRAK simulates the effects of arbitrary vane tip misalignments. This RFQ includes some new features in its design. It consists of four resonantly coupled 2-m-long segments that make up its 8-m length. It has higher vane gap voltages at the high-energy end than the low-energy end. The entrance end of the RFQ has lower transverse focusing strength to facilitate beam matching. The exit of the RFQ has a transition cell and a radial matching section(K. R. Crandall "Ending RFQ Vanetips with Quadrupole Symmetry", Proc. 1994 Intl. LINAC Conf. (Tsukuba, Japan) 227.). The exit radial matching section matches the beam into the following accelerator.

  12. Measurements and simulations of wakefields at the Accelerator Test Facility 2

    NASA Astrophysics Data System (ADS)

    Snuverink, J.; Ainsworth, R.; Boogert, S. T.; Cullinan, F. J.; Lyapin, A.; Kim, Y. I.; Kubo, K.; Kuroda, S.; Okugi, T.; Tauchi, T.; Terunuma, N.; Urakawa, J.; White, G. R.

    2016-09-01

    Wakefields are an important factor in accelerator design, and are a real concern when preserving the low beam emittance in modern machines. Charge dependent beam size growth has been observed at the Accelerator Test Facility (ATF2), a test accelerator for future linear collider beam delivery systems. Part of the explanation of this beam size growth is wakefields. In this paper we present numerical calculations of the wakefields produced by several types of geometrical discontinuities in the beam line as well as tracking simulations to estimate the induced effects. We also discuss precision beam kick measurements performed with the ATF2 cavity beam position monitor system for a test wakefield source in a movable section of the vacuum chamber. Using an improved model independent method we measured a wakefield kick for this movable section of about 0.49 V /pC /mm , which, compared to the calculated value from electromagnetic simulations of 0.41 V /pC /mm , is within the systematic error.

  13. Particle-in-cell simulations of tunneling ionization effects in plasma-based accelerators

    NASA Astrophysics Data System (ADS)

    Bruhwiler, David L.; Dimitrov, D. A.; Cary, John R.; Esarey, Eric; Leemans, Wim; Giacone, Rodolfo E.

    2003-05-01

    Plasma-based accelerators can sustain accelerating gradients on the order of 100 GV/m. If the plasma is not fully ionized, fields of this magnitude will ionize neutral atoms via electron tunneling, which can completely change the dynamics of the plasma wake. Particle-in-cell simulations of a high-field plasma wakefield accelerator, using the OOPIC code [D. L. Bruhwiler et al., Phys. Rev. ST Accel. Beams 4, 101302 (2001)], which includes field-induced tunneling ionization of neutral Li gas, show that the presence of even moderate neutral gas density significantly degrades the quality of the wakefield. The tunneling ionization model in OOPIC has been validated via a detailed comparison with experimental data from the l'OASIS laboratory [W.P. Leemans et al., Phys. Rev. Lett. 89, 174802 (2002)]. The properties of a wake generated directly from a neutral gas are studied, showing that one can recover the peak fields of the fully ionized plasma simulations, if the density of the electron drive bunch is increased such that the bunch rapidly ionizes the gas.

  14. Experimental validation of neutron activation simulation of a varian medical linear accelerator.

    PubMed

    Morato, S; Juste, B; Miro, R; Verdu, G; Diez, S

    2016-08-01

    This work presents a Monte Carlo simulation using the last version of MCNP, v. 6.1.1, of a Varian CLinAc emitting a 15MeV photon beam. The main objective of the work is to estimate the photoneutron production and activated products inside the medical linear accelerator head. To that, the Varian LinAc head was modelled in detail using the manufacturer information, and the model was generated with a CAD software and exported as a mesh to be included in the particle transport simulation. The model includes the transport of photoneutrons generated by primary photons and the (n, γ) reactions which can result in activation products. The validation of this study was done using experimental measures. Activation products have been identified by in situ gamma spectroscopy placed at the jaws exit of the LinAc shortly after termination of a high energy photon beam irradiation. Comparison between experimental and simulation results shows good agreement.

  15. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    SciTech Connect

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  16. SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Le Grand, Scott; Götz, Andreas W.; Walker, Ross C.

    2013-02-01

    A new precision model is proposed for the acceleration of all-atom classical molecular dynamics (MD) simulations on graphics processing units (GPUs). This precision model replaces double precision arithmetic with fixed point integer arithmetic for the accumulation of force components as compared to a previously introduced model that uses mixed single/double precision arithmetic. This significantly boosts performance on modern GPU hardware without sacrificing numerical accuracy. We present an implementation for NVIDIA GPUs of both generalized Born implicit solvent simulations as well as explicit solvent simulations using the particle mesh Ewald (PME) algorithm for long-range electrostatics using this precision model. Tests demonstrate both the performance of this implementation as well as its numerical stability for constant energy and constant temperature biomolecular MD as compared to a double precision CPU implementation and double and mixed single/double precision GPU implementations.

  17. Accelerated simulation of stochastic particle removal processes in particle-resolved aerosol models

    SciTech Connect

    Curtis, J.H.; Michelotti, M.D.; Riemer, N.; Heath, M.T.; West, M.

    2016-10-01

    Stochastic particle-resolved methods have proven useful for simulating multi-dimensional systems such as composition-resolved aerosol size distributions. While particle-resolved methods have substantial benefits for highly detailed simulations, these techniques suffer from high computational cost, motivating efforts to improve their algorithmic efficiency. Here we formulate an algorithm for accelerating particle removal processes by aggregating particles of similar size into bins. We present the Binned Algorithm for particle removal processes and analyze its performance with application to the atmospherically relevant process of aerosol dry deposition. We show that the Binned Algorithm can dramatically improve the efficiency of particle removals, particularly for low removal rates, and that computational cost is reduced without introducing additional error. In simulations of aerosol particle removal by dry deposition in atmospherically relevant conditions, we demonstrate about 50-times increase in algorithm efficiency.

  18. 3-D Simulations of Plasma Wakefield Acceleration with Non-Idealized Plasmas and Beams

    SciTech Connect

    Deng, S.; Katsouleas, T.; Lee, S.; Muggli, P.; Mori, W.B.; Hemker, R.; Ren, C.; Huang, C.; Dodd, E.; Blue, B.E.; Clayton, C.E.; Joshi, C.; Wang, S.; Decker, F.J.; Hogan, M.J.; Iverson, R.H.; O'Connell, C.; Raimondi, P.; Walz, D.; /SLAC

    2005-09-27

    3-D Particle-in-cell OSIRIS simulations of the current E-162 Plasma Wakefield Accelerator Experiment are presented in which a number of non-ideal conditions are modeled simultaneously. These include tilts on the beam in both planes, asymmetric beam emittance, beam energy spread and plasma inhomogeneities both longitudinally and transverse to the beam axis. The relative importance of the non-ideal conditions is discussed and a worst case estimate of the effect of these on energy gain is obtained. The simulation output is then propagated through the downstream optics, drift spaces and apertures leading to the experimental diagnostics to provide insight into the differences between actual beam conditions and what is measured. The work represents a milestone in the level of detail of simulation comparisons to plasma experiments.

  19. Numerical simulation of the process of solid-particle acceleration by gas-jets

    SciTech Connect

    Kasimov, V.Z.; Khomenko, Y.P.

    1985-05-01

    Generalized experimental data on acceleration of spherical solid particles by a high-velocity jet of detonation products from a tubular explosive charge have been presented as has the numerical calculation of the flow in the vicinity of the detonation wave front. Recently, such explosive charges have found wide use in the development of explosive shock tubes which show high efficiency of conversion of explosive energy into gas-jet kinetic energy, and also in other equipment. In designing multistep projectile tubular charge systems, the problem arises of determining the initial particle position within the charge cavity which will ensure maximum final velocity at the permissible level of aerodynamic loading. In order to solve this problem, the authors present a numerical simulation of the process of particle acceleration by a high-velocity detonation-product jet.

  20. Monte Carlo simulation of a medical linear accelerator for radiotherapy use.

    PubMed

    Serrano, B; Hachem, A; Franchisseur, E; Hérault, J; Marcié, S; Costa, A; Bensadoun, R J; Barthe, J; Gérard, J P

    2006-01-01

    A Monte Carlo code MCNPX (Monte Carlo N-particle) was used to model a 25 MV photon beam from a PRIMUS (KD2-Siemens) medical linear electron accelerator at the Centre Antoine Lacassagne in Nice. The entire geometry including the accelerator head and the water phantom was simulated to calculate the dose profile and the relative depth-dose distribution. The measurements were done using an ionisation chamber in water for different square field ranges. The first results show that the mean electron beam energy is not 19 MeV as mentioned by Siemens. The adjustment between the Monte Carlo calculated and measured data is obtained when the mean electron beam energy is approximately 15 MeV. These encouraging results will permit to check calculation data given by the treatment planning system, especially for small fields in high gradient heterogeneous zones, typical for intensity modulated radiation therapy technique.

  1. Numerical simulations of input and output couplers for linear accelerator structures

    SciTech Connect

    Ng, C.K.; Ko, K.

    1993-04-01

    We present the numerical procedures involved in the design of coupler cavities for accelerator sections for linear colliders. The MAFIA code is used to simulate an X-band accelerator section with a symmetrical double-input coupler at each end. The transmission properties of the structure are calculated in the time domain and the dimensions of the coupler cavities are adjusted until the power coupling is optimized and frequency synchronism is obtained. We compare the performance of the symmetrical double-input design with that of the conventional single-input type by evaluating the field amplitude and phase asymmetries. We also evaluate the peak gradient in the coupler and discuss the implication of pulse rise time on dark current generation.

  2. Numerical simulations of input and output couplers for linear accelerator structures

    SciTech Connect

    Ng, C.; Ko, K. )

    1993-12-25

    We present the numerical procedures involved in the design of coupler cavities for accelerator sections for linear colliders. The MAFIA code is used to simulate an X-band accelerator section with a symmetrical double-input coupler at each end. The transmissions properties of the structure are calculated in the time domain and the dimensions of the coupler cavities are adjusted until the power coupling is optimized and frequency synchronism is obtained. We compare the performance of the symmetrical double-input design with that of the conventional single-input type by evaluating the field amplitude and phase asymmetries. We also evaluate the peak gradient in the coupler and discuss the implication of pulse rise time on dark current generation.

  3. Simulation of variation characteristics at thermostabilization of 27 GHz biperiodical accelerating structure

    NASA Astrophysics Data System (ADS)

    Kluchevskaya, Y. D.; Polozov, S. M.

    2016-07-01

    It was proposed to develop the biperiodical accelerating structure with operating frequency of 27 GHz to assess the possibility of design a compact accelerating structure for medical application. It is necessary to do the more careful simulation of variation characteristics this case because of decrease of wavelength 3-10 times in comparison with conventional structures 10 and 3 cm ranges. Results of such study are presented in the article. Also a combination of high electromagnetic fields and long pulses at a high operating frequency leads to the temperature increase in the structure, thermal deformation and significant change of the resonator characteristics, including the frequency of the RF pulse. Development results of three versions of system of temperature stabilization also discuses.

  4. Targeting Atmospheric Simulation Algorithms for Large Distributed Memory GPU Accelerated Computers

    SciTech Connect

    Norman, Matthew R

    2013-01-01

    Computing platforms are increasingly moving to accelerated architectures, and here we deal particularly with GPUs. In [15], a method was developed for atmospheric simulation to improve efficiency on large distributed memory machines by reducing communication demand and increasing the time step. Here, we improve upon this method to further target GPU accelerated platforms by reducing GPU memory accesses, removing a synchronization point, and better clustering computations. The modification ran over two times faster in some cases even though more computations were required, demonstrating the merit of improving memory handling on the GPU. Furthermore, we discover that the modification also has a near 100% hit rate in fast on-chip L1 cache and discuss the reasons for this. In concluding, we remark on further potential improvements to GPU efficiency.

  5. Benchmarking shielding simulations for an accelerator-driven spallation neutron source

    DOE PAGES

    Cherkashyna, Nataliia; Di Julio, Douglas D.; Panzner, Tobias; ...

    2015-08-09

    The shielding at an accelerator-driven spallation neutron facility plays a critical role in the performance of the neutron scattering instruments, the overall safety, and the total cost of the facility. Accurate simulation of shielding components is thus key for the design of upcoming facilities, such as the European Spallation Source (ESS), currently in construction in Lund, Sweden. In this paper, we present a comparative study between the measured and the simulated neutron background at the Swiss Spallation Neutron Source (SINQ), at the Paul Scherrer Institute (PSI), Villigen, Switzerland. The measurements were carried out at several positions along the SINQ monolithmore » wall with the neutron dosimeter WENDI-2, which has a well-characterized response up to 5 GeV. The simulations were performed using the Monte-Carlo radiation transport code Geant4, and include a complete transport from the proton beam to the measurement locations in a single calculation. An agreement between measurements and simulations is about a factor of 2 for the points where the measured radiation dose is above the background level, which is a satisfactory result for such simulations spanning many energy regimes, different physics processes and transport through several meters of shielding materials. The neutrons contributing to the radiation field emanating from the monolith were confirmed to originate from neutrons with energies above 1 MeV in the target region. The current work validates Geant4 as being well suited for deep-shielding calculations at accelerator-based spallation sources. We also extrapolate what the simulated flux levels might imply for short (several tens of meters) instruments at ESS.« less

  6. Accelerating Wright–Fisher Forward Simulations on the Graphics Processing Unit

    PubMed Central

    Lawrie, David S.

    2017-01-01

    Forward Wright–Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright–Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called “embarrassingly parallel,” consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright–Fisher simulation, or “GO Fish” for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. PMID:28768689

  7. Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit.

    PubMed

    Lawrie, David S

    2017-09-07

    Forward Wright-Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright-Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called "embarrassingly parallel," consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright-Fisher simulation, or "GO Fish" for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. Copyright © 2017 Lawrie.

  8. Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU

    NASA Astrophysics Data System (ADS)

    Tian, Zhen; Jiang, Steve B.; Jia, Xun

    2017-04-01

    The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1–197.2.

  9. Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU.

    PubMed

    Tian, Zhen; Jiang, Steve B; Jia, Xun

    2017-04-21

    The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2.

  10. Numerical simulations of Hall-effect plasma accelerators on a magnetic-field-aligned mesh.

    PubMed

    Mikellides, Ioannis G; Katz, Ira

    2012-10-01

    The ionized gas in Hall-effect plasma accelerators spans a wide range of spatial and temporal scales, and exhibits diverse physics some of which remain elusive even after decades of research. Inside the acceleration channel a quasiradial applied magnetic field impedes the current of electrons perpendicular to it in favor of a significant component in the E×B direction. Ions are unmagnetized and, arguably, of wide collisional mean free paths. Collisions between the atomic species are rare. This paper reports on a computational approach that solves numerically the 2D axisymmetric vector form of Ohm's law with no assumptions regarding the resistance to classical electron transport in the parallel relative to the perpendicular direction. The numerical challenges related to the large disparity of the transport coefficients in the two directions are met by solving the equations on a computational mesh that is aligned with the applied magnetic field. This 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 where the lines of force can become nonisothermal. It also allows for the self-consistent solution of the plasma conservation laws near the anode boundary, and for simulations in accelerators with complex magnetic field topologies. Ions are treated as an isothermal, cold (relative to the electrons) fluid, accounting for the ion drag in the momentum equation due to ion-neutral (charge-exchange) and ion-ion collisions. The density of the atomic species is determined using an algorithm that eliminates the statistical noise associated with discrete-particle methods. Numerical simulations are presented that illustrate the impact of the above-mentioned features on our understanding of the plasma in these accelerators.

  11. Sustained Accelerated Idioventricular Rhythm in a Centrifuge-Simulated Suborbital Spaceflight.

    PubMed

    Suresh, Rahul; Blue, Rebecca S; Mathers, Charles; Castleberry, Tarah L; Vanderploeg, James M

    2017-08-01

    Hypergravitational exposures during human centrifugation are known to provoke dysrhythmias, including sinus dysrhythmias/tachycardias, premature atrial/ventricular contractions, and even atrial fibrillations or flutter patterns. However, events are generally short-lived and resolve rapidly after cessation of acceleration. This case report describes a prolonged ectopic ventricular rhythm in response to high G exposure. A previously healthy 30-yr-old man voluntarily participated in centrifuge trials as a part of a larger study, experiencing a total of 7 centrifuge runs over 48 h. Day 1 consisted of two +Gz runs (peak +3.5 Gz, run 2) and two +Gx runs (peak +6.0 Gx, run 4). Day 2 consisted of three runs approximating suborbital spaceflight profiles (combined +Gx and +Gz). Hemodynamic data collected included blood pressure, heart rate, and continuous three-lead electrocardiogram. Following the final acceleration exposure of the last Day 2 run (peak +4.5 Gx and +4.0 Gz combined, resultant +6.0 G), during a period of idle resting centrifuge activity (resultant vector +1.4 G), the subject demonstrated a marked change in his three-lead electrocardiogram from normal sinus rhythm to a wide-complex ectopic ventricular rhythm at a rate of 91-95 bpm, consistent with an accelerated idioventricular rhythm (AIVR). This rhythm was sustained for 2 m, 24 s before reversion to normal sinus. The subject reported no adverse symptoms during this time. While prolonged, the dysrhythmia was asymptomatic and self-limited. AIVR is likely a physiological response to acceleration and can be managed conservatively. Vigilance is needed to ensure that AIVR is correctly distinguished from other, malignant rhythms to avoid inappropriate treatment and negative operational impacts.Suresh R, Blue RS, Mathers C, Castleberry TL, Vanderploeg JM. Sustained accelerated idioventricular rhythm in a centrifuge-simulated suborbital spaceflight. Aerosp Med Hum Perform. 2017; 88(8):789-793.

  12. Testing the paradigms of the glass transition in colloids via dynamic simulation

    NASA Astrophysics Data System (ADS)

    Wang, Jialun; Peng, Xiaoguang; Li, Qi; McKenna, Gregory; Zia, Roseanna

    2016-11-01

    Upon cooling, molecular glass-formers undergo a glass transition during which viscosity appears to diverge, and the material transitions from a liquid to an amorphous solid. However, the new state is not an equilibrium phase: material properties such as enthalpy continue to evolve in time. Rather, the material evolves toward an "intransient" state, as measured by the Kovacs signature experiments, e.g. the intrinsic isotherm, which reveals a paradoxical dependence of transition time on quench depth, and suggests that whether the glass transition occurs at the beginning or end of this transition is an open question. Colloidal glass formers provide a natural way to model such behavior, owing to the disparity in time scales that allow tracking of particle dynamics. We interrogate these ideas via dynamic simulation of a hard-sphere colloidal glassy state induced by jumps in volume fraction. We explore three methods to model the jump: evaporation, aspiration, and particle-size jumps. During and following each jump, the positions, velocities, and particle-phase stress are tracked and utilized to characterize relaxation time scales and structural changes. Analogs for the intrinsic isotherms are developed. The results provide insight into the existence of an "ideal" glass transition.

  13. Contact detection acceleration in pebble flow simulation for pebble bed reactor systems

    SciTech Connect

    Li, Y.; Ji, W.

    2013-07-01

    Pebble flow simulation plays an important role in the steady state and transient analysis of thermal-hydraulics and neutronics for Pebble Bed Reactors (PBR). The Discrete Element Method (DEM) and the modified Molecular Dynamics (MD) method are widely used to simulate the pebble motion to obtain the distribution of pebble concentration, velocity, and maximum contact stress. Although DEM and MD present high accuracy in the pebble flow simulation, they are quite computationally expensive due to the large quantity of pebbles to be simulated in a typical PBR and the ubiquitous contacts and collisions between neighboring pebbles that need to be detected frequently in the simulation, which greatly restricted their applicability for large scale PBR designs such as PBMR400. Since the contact detection accounts for more than 60% of the overall CPU time in the pebble flow simulation, the acceleration of the contact detection can greatly enhance the overall efficiency. In the present work, based on the design features of PBRs, two contact detection algorithms, the basic cell search algorithm and the bounding box search algorithm are investigated and applied to pebble contact detection. The influence from the PBR system size, core geometry and the searching cell size on the contact detection efficiency is presented. Our results suggest that for present PBR applications, the bounding box algorithm is less sensitive to the aforementioned effects and has superior performance in pebble contact detection compared with basic cell search algorithm. (authors)

  14. GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method

    NASA Astrophysics Data System (ADS)

    Gong, Chunye; Liu, Jie; Chi, Lihua; Huang, Haowei; Fang, Jingyue; Gong, Zhenghu

    2011-07-01

    Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates ( Sn) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.

  15. GPU accelerated simulations of 3D deterministic particle transport using discrete ordinates method

    SciTech Connect

    Gong Chunye; Liu Jie; Chi Lihua; Huang Haowei; Fang Jingyue; Gong Zhenghu

    2011-07-01

    Graphics Processing Unit (GPU), originally developed for real-time, high-definition 3D graphics in computer games, now provides great faculty in solving scientific applications. The basis of particle transport simulation is the time-dependent, multi-group, inhomogeneous Boltzmann transport equation. The numerical solution to the Boltzmann equation involves the discrete ordinates (S{sub n}) method and the procedure of source iteration. In this paper, we present a GPU accelerated simulation of one energy group time-independent deterministic discrete ordinates particle transport in 3D Cartesian geometry (Sweep3D). The performance of the GPU simulations are reported with the simulations of vacuum boundary condition. The discussion of the relative advantages and disadvantages of the GPU implementation, the simulation on multi GPUs, the programming effort and code portability are also reported. The results show that the overall performance speedup of one NVIDIA Tesla M2050 GPU ranges from 2.56 compared with one Intel Xeon X5670 chip to 8.14 compared with one Intel Core Q6600 chip for no flux fixup. The simulation with flux fixup on one M2050 is 1.23 times faster than on one X5670.

  16. Clouds and Precipitation Simulated by the US DOE Accelerated Climate Modeling for Energy (ACME)

    NASA Astrophysics Data System (ADS)

    Xie, S.; Lin, W.; Yoon, J. H.; Ma, P. L.; Rasch, P. J.; Ghan, S.; Zhang, K.; Zhang, Y.; Zhang, C.; Bogenschutz, P.; Gettelman, A.; Larson, V. E.; Neale, R. B.; Park, S.; Zhang, G. J.

    2015-12-01

    A new US Department of Energy (DOE) climate modeling effort is to develop an Accelerated Climate Model for Energy (ACME) to accelerate the development and application of fully coupled, state-of-the-art Earth system models for scientific and energy application. ACME is a high-resolution climate model with a 0.25 degree in horizontal and more than 60 levels in the vertical. It starts from the Community Earth System Model (CESM) with notable changes to its physical parameterizations and other components. This presentation provides an overview on the ACME model's capability in simulating clouds and precipitation and its sensitivity to convection schemes. Results with using several state-of-the-art cumulus convection schemes, including those unified parameterizations that are being developed in the climate community, will be presented. These convection schemes are evaluated in a multi-scale framework including both short-range hindcasts and free-running climate simulations with both satellite data and ground-based measurements. Running climate model in short-range hindcasts has been proven to be an efficient way to understand model deficiencies. The analysis is focused on those systematic errors in clouds and precipitation simulations that are shared in many climate models. The goal is to understand what model deficiencies might be primarily responsible for these systematic errors.

  17. A grid computing-based approach for the acceleration of simulations in cardiology.

    PubMed

    Alonso, José M; Ferrero, José M; Hernández, Vicente; Moltó, Germán; Saiz, Javier; Trénor, Beatriz

    2008-03-01

    This paper combines high-performance computing and grid computing technologies to accelerate multiple executions of a biomedical application that simulates the action potential propagation on cardiac tissues. First, a parallelization strategy was employed to accelerate the execution of simulations on a cluster of personal computers (PCs). Then, grid computing was employed to concurrently perform the multiple simulations that compose the cardiac case studies on the resources of a grid deployment, by means of a service-oriented approach. This way, biomedical experts are provided with a gateway to easily access a grid infrastructure for the execution of these research studies. Emphasis is stressed on the methodology employed. In order to assess the benefits of the grid, a cardiac case study, which analyzes the effects of premature stimulation on reentry generation during myocardial ischemia, has been carried out. The collaborative usage of a distributed computing infrastructure has reduced the time required for the execution of cardiac case studies, which allows, for example, to take more accurate decisions when evaluating the effects of new antiarrhythmic drugs on the electrical activity of the heart.

  18. Stable boosted-frame simulations of laser-wakefield acceleration using Galilean coordinates

    NASA Astrophysics Data System (ADS)

    Lehe, Remi; Kirchen, Manuel; Godfrey, Brendan; Maier, Andreas; Vay, Jean-Luc

    2016-10-01

    While Particle-In-Cell (PIC) simulations of laser-wakefield acceleration are typically very computationally expensive, it is well-known that representing the system in a well-chosen Lorentz frame can reduce the computational cost by orders of magnitude. One of the limitation of this ``boosted-frame'' technique is the Numerical Cherenkov Instability (NCI) - a numerical instability that rapidly grows in the boosted frame and must be eliminated in order to obtain valid physical results. Several methods have been proposed in order to eliminate the NCI, but they introduce additional numerical corrections (e.g. heavy smoothing, unphysical modification of the dispersion relation, etc.) which could potentially alter the physics. By contrast, here we show that, for boosted-frame simulations of laser-wakefield acceleration, the NCI can be eliminated simply by integrating the PIC equations in Galilean coordinates (a.k.a comoving coordinates), without additional numerical correction. Using this technique, we show excellent agreement between simulations in the laboratory frame and Lorentz-boosted frame, with more than 2 orders of magnitude speedup in the latter case. Work supported by US-DOE Contracts DE-AC02-05CH11231.

  19. The use of computed radiography for routine linear accelerator and simulator quality control.

    PubMed

    Patel, I; Natarajan, T; Hassan, S S; Kirby, M C

    2009-10-01

    Computed radiography (CR) systems were originally developed for the purpose of clinical imaging, and there has been much work published on its effectiveness as a film replacement for this end. However, there has been little published on its use for routine linear accelerator and simulator quality control, and therefore we have evaluated the use of the Kodak 2000RT system with large Agfa CR plates as a replacement for film for this function. A prerequisite for any such use is a detailed understanding of the system behaviour, hence characteristics such as spatial uniformity of response, reproducibility of spatial accuracy, plate signal decay with time and the dose-response of plates were investigated. Finally, a comparison of results obtained using CR for the measurement of radiation field dimensions was made against those from radiographic film, and found to be in agreement within 0.1 mm (mean difference for high-resolution images, 0.3 mm root mean square difference) for megavoltage images and 0.3 mm (maximum difference) for simulator images. In conclusion, the CR system has been shown to be a good alternative to radiographic film for routine quality control of linear accelerators and simulators.

  20. GeNN: a code generation framework for accelerated brain simulations

    NASA Astrophysics Data System (ADS)

    Yavuz, Esin; Turner, James; Nowotny, Thomas

    2016-01-01

    Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

  1. A 3D MPI-Parallel GPU-accelerated framework for simulating ocean wave energy converters

    NASA Astrophysics Data System (ADS)

    Pathak, Ashish; Raessi, Mehdi

    2015-11-01

    We present an MPI-parallel GPU-accelerated computational framework for studying the interaction between ocean waves and wave energy converters (WECs). The computational framework captures the viscous effects, nonlinear fluid-structure interaction (FSI), and breaking of waves around the structure, which cannot be captured in many potential flow solvers commonly used for WEC simulations. The full Navier-Stokes equations are solved using the two-step projection method, which is accelerated by porting the pressure Poisson equation to GPUs. The FSI is captured using the numerically stable fictitious domain method. A novel three-phase interface reconstruction algorithm is used to resolve three phases in a VOF-PLIC context. A consistent mass and momentum transport approach enables simulations at high density ratios. The accuracy of the overall framework is demonstrated via an array of test cases. Numerical simulations of the interaction between ocean waves and WECs are presented. Funding from the National Science Foundation CBET-1236462 grant is gratefully acknowledged.

  2. Hierarchical Acceleration of Multilevel Monte Carlo Methods for Computationally Expensive Simulations in Reservoir Modeling

    NASA Astrophysics Data System (ADS)

    Zhang, G.; Lu, D.; Webster, C.

    2014-12-01

    The rational management of oil and gas reservoir requires an understanding of its response to existing and planned schemes of exploitation and operation. Such understanding requires analyzing and quantifying the influence of the subsurface uncertainties on predictions of oil and gas production. As the subsurface properties are typically heterogeneous causing a large number of model parameters, the dimension independent Monte Carlo (MC) method is usually used for uncertainty quantification (UQ). Recently, multilevel Monte Carlo (MLMC) methods were proposed, as a variance reduction technique, in order to improve computational efficiency of MC methods in UQ. In this effort, we propose a new acceleration approach for MLMC method to further reduce the total computational cost by exploiting model hierarchies. Specifically, for each model simulation on a new added level of MLMC, we take advantage of the approximation of the model outputs constructed based on simulations on previous levels to provide better initial states of new simulations, which will help improve efficiency by, e.g. reducing the number of iterations in linear system solving or the number of needed time-steps. This is achieved by using mesh-free interpolation methods, such as Shepard interpolation and radial basis approximation. Our approach is applied to a highly heterogeneous reservoir model from the tenth SPE project. The results indicate that the accelerated MLMC can achieve the same accuracy as standard MLMC with a significantly reduced cost.

  3. Test Particle Simulation of Acceleration in Cascading Current Sheet Obtained with 2.5D AMR MHD

    NASA Astrophysics Data System (ADS)

    Liu, Siming; Büchner, Jörg; Gan, Weiqun; Bárta, Miroslav; Zhou, Xiaowei

    2016-07-01

    With electro-magnetic field configuration derived from 2.5D AMR MHD simulations, we calculate the orbit of test charged particles with the guiding center approximation and study the particle acceleration by the induction and resistive electric fields. The induction field can lead to gradual acceleration via the drift of the particle guiding center in magnetic field curvature or gradient.The resistive electric field can lead to run away acceleration with particle energy changing drastically in regions with anomalous resistivity. We will discuss the implication of these results on the study of particle acceleration in turbulent reconnection current sheets.

  4. Mixed-field GCR Simulations for Radiobiological Research Using Ground Based Accelerators

    NASA Technical Reports Server (NTRS)

    Kim, Myung-Hee Y.; Rusek, Adam; Cucinotta, Francis A.

    2014-01-01

    Space radiation is comprised of a large number of particle types and energies, which have differential ionization power from high energy protons to high charge and energy (HZE) particles and secondary neutrons produced by galactic cosmic rays (GCR). Ground based accelerators such as the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL) are used to simulate space radiation for radiobiology research and dosimetry, electronics parts, and shielding testing using mono-energetic beams for single ion species. As a tool to support research on new risk assessment models, we have developed a stochastic model of heavy ion beams and space radiation effects, the GCR Event-based Risk Model computer code (GERMcode). For radiobiological research on mixed-field space radiation, a new GCR simulator at NSRL is proposed. The NSRL-GCR simulator, which implements the rapid switching mode and the higher energy beam extraction to 1.5 GeV/u, can integrate multiple ions into a single simulation to create GCR Z-spectrum in major energy bins. After considering the GCR environment and energy limitations of NSRL, a GCR reference field is proposed after extensive simulation studies using the GERMcode. The GCR reference field is shown to reproduce the Z and LET spectra of GCR behind shielding within 20% accuracy compared to simulated full GCR environments behind shielding. A major challenge for space radiobiology research is to consider chronic GCR exposure of up to 3-years in relation to simulations with cell and animal models of human risks. We discuss possible approaches to map important biological time scales in experimental models using ground-based simulation with extended exposure of up to a few weeks and fractionation approaches at a GCR simulator.

  5. Mixed-field GCR Simulations for Radiobiological Research using Ground Based Accelerators

    NASA Astrophysics Data System (ADS)

    Kim, Myung-Hee Y.; Rusek, Adam; Cucinotta, Francis

    Space radiation is comprised of a large number of particle types and energies, which have differential ionization power from high energy protons to high charge and energy (HZE) particles and secondary neutrons produced by galactic cosmic rays (GCR). Ground based accelerators such as the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL) are used to simulate space radiation for radiobiology research and dosimetry, electronics parts, and shielding testing using mono-energetic beams for single ion species. As a tool to support research on new risk assessment models, we have developed a stochastic model of heavy ion beams and space radiation effects, the GCR Event-based Risk Model computer code (GERMcode). For radiobiological research on mixed-field space radiation, a new GCR simulator at NSRL is proposed. The NSRL-GCR simulator, which implements the rapid switching mode and the higher energy beam extraction to 1.5 GeV/u, can integrate multiple ions into a single simulation to create GCR Z-spectrum in major energy bins. After considering the GCR environment and energy limitations of NSRL, a GCR reference field is proposed after extensive simulation studies using the GERMcode. The GCR reference field is shown to reproduce the Z and LET spectra of GCR behind shielding within 20 percents accuracy compared to simulated full GCR environments behind shielding. A major challenge for space radiobiology research is to consider chronic GCR exposure of up to 3-years in relation to simulations with cell and animal models of human risks. We discuss possible approaches to map important biological time scales in experimental models using ground-based simulation with extended exposure of up to a few weeks and fractionation approaches at a GCR simulator.

  6. Particle acceleration with anomalous pitch angle scattering in 2D magnetohydrodynamic reconnection simulations

    NASA Astrophysics Data System (ADS)

    Borissov, A.; Kontar, E. P.; Threlfall, J.; Neukirch, T.

    2017-09-01

    The conversion of magnetic energy into other forms (such as plasma heating, bulk plasma flows, and non-thermal particles) during solar flares is one of the outstanding open problems in solar physics. It is generally accepted that magnetic reconnection plays a crucial role in these conversion processes. In order to achieve the rapid energy release required in solar flares, an anomalous resistivity, which is orders of magnitude higher than the Spitzer resistivity, is often used in magnetohydrodynamic (MHD) simulations of reconnection in the corona. The origin of Spitzer resistivity is based on Coulomb scattering, which becomes negligible at the high energies achieved by accelerated particles. As a result, simulations of particle acceleration in reconnection events are often performed in the absence of any interaction between accelerated particles and any background plasma. This need not be the case for scattering associated with anomalous resistivity caused by turbulence within solar flares, as the higher resistivity implies an elevated scattering rate. We present results of test particle calculations, with and without pitch angle scattering, subject to fields derived from MHD simulations of two-dimensional (2D) X-point reconnection. Scattering rates proportional to the ratio of the anomalous resistivity to the local Spitzer resistivity, as well as at fixed values, are considered. Pitch angle scattering, which is independent of the anomalous resistivity, causes higher maximum energies in comparison to those obtained without scattering. Scattering rates which are dependent on the local anomalous resistivity tend to produce fewer highly energised particles due to weaker scattering in the separatrices, even though scattering in the current sheet may be stronger when compared to resistivity-independent scattering. Strong scattering also causes an increase in the number of particles exiting the computational box in the reconnection outflow region, as opposed to along the

  7. Adaptive accelerated ReaxFF reactive dynamics with validation from simulating hydrogen combustion.

    PubMed

    Cheng, Tao; Jaramillo-Botero, Andrés; Goddard, William A; Sun, Huai

    2014-07-02

    We develop here the methodology for dramatically accelerating the ReaxFF reactive force field based reactive molecular dynamics (RMD) simulations through use of the bond boost concept (BB), which we validate here for describing hydrogen combustion. The bond order, undercoordination, and overcoordination concepts of ReaxFF ensure that the BB correctly adapts to the instantaneous configurations in the reactive system to automatically identify the reactions appropriate to receive the bond boost. We refer to this as adaptive Accelerated ReaxFF Reactive Dynamics or aARRDyn. To validate the aARRDyn methodology, we determined the detailed sequence of reactions for hydrogen combustion with and without the BB. We validate that the kinetics and reaction mechanisms (that is the detailed sequences of reactive intermediates and their subsequent transformation to others) for H2 oxidation obtained from aARRDyn agrees well with the brute force reactive molecular dynamics (BF-RMD) at 2498 K. Using aARRDyn, we then extend our simulations to the whole range of combustion temperatures from ignition (798 K) to flame temperature (2998K), and demonstrate that, over this full temperature range, the reaction rates predicted by aARRDyn agree well with the BF-RMD values, extrapolated to lower temperatures. For the aARRDyn simulation at 798 K we find that the time period for half the H2 to form H2O product is ∼538 s, whereas the computational cost was just 1289 ps, a speed increase of ∼0.42 trillion (10(12)) over BF-RMD. In carrying out these RMD simulations we found that the ReaxFF-COH2008 version of the ReaxFF force field was not accurate for such intermediates as H3O. Consequently we reoptimized the fit to a quantum mechanics (QM) level, leading to the ReaxFF-OH2014 force field that was used in the simulations.

  8. Simulation of Cascaded Longitudinal-Space-Charge Amplifier at the Fermilab Accelerator Science & Technology (Fast) Facility

    SciTech Connect

    Halavanau, A.; Piot, P.

    2015-12-01

    Cascaded Longitudinal Space Charge Amplifiers (LSCA) have been proposed as a mechanism to generate density modulation over a board spectral range. The scheme has been recently demonstrated in the optical regime and has confirmed the production of broadband optical radiation. In this paper we investigate, via numerical simulations, the performance of a cascaded LSCA beamline at the Fermilab Accelerator Science & Technology (FAST) facility to produce broadband ultraviolet radiation. Our studies are carried out using elegant with included tree-based grid-less space charge algorithm.

  9. Simulations of flame acceleration and deflagration-to-detonation transitions in methane-air systems

    SciTech Connect

    Kessler, D.A.; Gamezo, V.N.; Oran, E.S.

    2010-11-15

    Flame acceleration and deflagration-to-detonation transitions (DDT) in large obstructed channels filled with a stoichiometric methane-air mixture are simulated using a single-step reaction mechanism. The reaction parameters are calibrated using known velocities and length scales of laminar flames and detonations. Calculations of the flame dynamics and DDT in channels with obstacles are compared to previously reported experimental data. The results obtained using the simple reaction model qualitatively, and in many cases, quantitatively match the experiments and are found to be largely insensitive to small variations in model parameters. (author)

  10. Accelerating molecular dynamic simulation on the cell processor and Playstation 3.

    PubMed

    Luttmann, Edgar; Ensign, Daniel L; Vaidyanathan, Vishal; Houston, Mike; Rimon, Noam; Øland, Jeppe; Jayachandran, Guha; Friedrichs, Mark; Pande, Vijay S

    2009-01-30

    Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate MD simulations on the Cell processor, a commodity processor found in PlayStation 3 (PS3). In particular, we discuss issues regarding memory access versus computation and the types of calculations which are best suited for streaming processors such as the Cell, focusing on implicit solvation models. We conclude with a comparison of improved performance on the PS3's Cell processor over more traditional processors. (c) 2008 Wiley Periodicals, Inc.

  11. Simulations of a High-Transformer-Ratio Plasma Wakefield Accelerator Using Multiple Electron Bunches

    SciTech Connect

    Kallos, Efthymios; Muggli, Patric; Katsouleas, Thomas; Yakimenko, Vitaly; Park, Jangho

    2009-01-22

    Particle-in-cell simulations of a plasma wakefield accelerator in the linear regime are presented, consisting of four electron bunches that are fed into a high-density plasma. It is found that a high transformer ratio can be maintained over 43 cm of plasma if the charge in each bunch is increased linearly, the bunches are placed 1.5 plasma wavelengths apart and the bunch emmitances are adjusted to compensate for the nonlinear focusing forces. The generated wakefield is sampled by a test witness bunch whose energy gain after the plasma is six times the energy loss of the drive bunches.

  12. High energy gain in three-dimensional simulations of light sail acceleration

    SciTech Connect

    Sgattoni, A.; Sinigardi, S.; Macchi, A.

    2014-08-25

    The dynamics of radiation pressure acceleration in the relativistic light sail regime are analysed by means of large scale, three-dimensional (3D) particle-in-cell simulations. Differently to other mechanisms, the 3D dynamics leads to faster and higher energy gain than in 1D or 2D geometry. This effect is caused by the local decrease of the target density due to transverse expansion leading to a “lighter sail.” However, the rarefaction of the target leads to an earlier transition to transparency limiting the energy gain. A transverse instability leads to a structured and inhomogeneous ion distribution.

  13. Simulation study of accelerator based quasi-mono-energetic epithermal neutron beams for BNCT.

    PubMed

    Adib, M; Habib, N; Bashter, I I; El-Mesiry, M S; Mansy, M S

    2016-01-01

    Filtered neutron techniques were applied to produce quasi-mono-energetic neutron beams in the energy range of 1.5-7.5 keV at the accelerator port using the generated neutron spectrum from a Li (p, n) Be reaction. A simulation study was performed to characterize the filter components and transmitted beam lines. The feature of the filtered beams is detailed in terms of optimal thickness of the primary and additive components. A computer code named "QMNB-AS" was developed to carry out the required calculations. The filtered neutron beams had high purity and intensity with low contamination from the accompanying thermal, fast neutrons and γ-rays.

  14. Neutron activation processes simulation in an Elekta medical linear accelerator head.

    PubMed

    Juste, B; Miró, R; Verdú, G; Díez, S; Campayo, J M

    2014-01-01

    Monte Carlo estimation of the giant-dipole-resonance (GRN) photoneutrons inside the Elekta Precise LINAC head (emitting a 15 MV photon beam) were performed using the MCNP6 (general-purpose Monte Carlo N-Particle code, version 6). Each component of LINAC head geometry and materials were modelled in detail using the given manufacturer information. Primary photons generate photoneutrons and its transport across the treatment head was simulated, including the (n, γ) reactions which undergo activation products. The MCNP6 was used to develop a method for quantifying the activation of accelerator components. The approach described in this paper is useful in quantifying the origin and the amount of nuclear activation.

  15. Atomistic simulations of melting and solidification using temperature accelerated molecular dynamics

    NASA Astrophysics Data System (ADS)

    Yu, Tang-Qing; Samanta, Amit; E, Weinan; Tuckerman, Mark; vanden-Eijnden, Eric

    2013-03-01

    A detailed understanding of melting/solidification mechanisms in metals remains obscure, though over the years many simulations and experiments have been performed for clarifying it. We have applied the enhanced-sampling method, Temperature-Accelerated Molecular Dynamics, to study the melting/solidification of FCC metals like copper, nickel under the constant temperature and pressure conditions. Free energy surfaces along Steinhardt order parameters and local density are obtained and minimum free energy path (MFEP) between the metastable states are calculated. An analysis of the atomic structure along the MFEP, reveals that an interplay between orientation ordering and positional ordering governs this phase transition.

  16. Electron acceleration in the near-Earth magnetotail: test particle calculations in electromagnetic fields from two-dimensional hybrid simulations

    NASA Astrophysics Data System (ADS)

    Guo, Zhifang; Wu, Mingyu; Du, Aimin

    2017-07-01

    Electron acceleration in the near-Earth magnetotail during the substorm period is still an unresolved question. In this paper, by tracing electron trajectories in the dynamically evolving electromagnetic fields obtained from a two-dimensional (2D) global hybrid simulation, we investigate electron acceleration in the near-Earth magnetotail during dipolarization. In our simulation, electrons with energies above several keV can gain energy in the plasma sheet due to the adiabatic acceleration mechanism when these electrons propagate earthward. In the near-Earth magnetotail (about 9-15 RE from the Earth), these electrons can be accelerated by betatron acceleration which is due to the compression of magnetic field associated with dipolarization of magnetotail. Additionally, in the middle and high latitudes of the near-Earth magnetotail, the parallel electric field carrying by kinetic Alfvén waves can also accelerate electrons when these electrons bounce between the mirror points. The combination effects of these three acceleration mechanisms can accelerate electrons from several keV to about one hundred keV. Our results indicate that both the large-scale structure and wave-particle interactions need to be taken into account for electron acceleration in the near-Earth magnetotail.

  17. A Theoretical Analysis of the Perceptual Span based on SWIFT Simulations of the n + 2 Boundary Paradigm

    PubMed Central

    Risse, Sarah; Hohenstein, Sven; Kliegl, Reinhold; Engbert, Ralf

    2014-01-01

    Eye-movement experiments suggest that the perceptual span during reading is larger than the fixated word, asymmetric around the fixation position, and shrinks in size contingent on the foveal processing load. We used the SWIFT model of eye-movement control during reading to test these hypotheses and their implications under the assumption of graded parallel processing of all words inside the perceptual span. Specifically, we simulated reading in the boundary paradigm and analysed the effects of denying the model to have valid preview of a parafoveal word n + 2 two words to the right of fixation. Optimizing the model parameters for the valid preview condition only, we obtained span parameters with remarkably realistic estimates conforming to the empirical findings on the size of the perceptual span. More importantly, the SWIFT model generated parafoveal processing up to word n + 2 without fitting the model to such preview effects. Our results suggest that asymmetry and dynamic modulation are plausible properties of the perceptual span in a parallel word-processing model such as SWIFT. Moreover, they seem to guide the flexible distribution of processing resources during reading between foveal and parafoveal words. PMID:24771996

  18. Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators.

    PubMed

    Sartori, E; Brescaccin, L; Serianni, G

    2016-02-01

    Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production-detrimental for high current negative ion systems such as beam sources for fusion-are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient and energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.

  19. Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators

    NASA Astrophysics Data System (ADS)

    Sartori, E.; Brescaccin, L.; Serianni, G.

    2016-02-01

    Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production—detrimental for high current negative ion systems such as beam sources for fusion—are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient and energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.

  20. Probing particle acceleration in lower hybrid turbulence via synthetic diagnostics produced by PIC simulations

    NASA Astrophysics Data System (ADS)

    Cruz, F.; Fonseca, R. A.; Silva, L. O.; Rigby, A.; Gregori, G.; Bamford, R. A.; Bingham, R.; Koenig, M.

    2016-10-01

    Efficient particle acceleration in astrophysical shocks can only be achieved in the presence of initial high energy particles. A candidate mechanism to provide an initial seed of energetic particles is lower hybrid turbulence (LHT). This type of turbulence is commonly excited in regions where space and astrophysical plasmas interact with large obstacles. Due to the nature of LH waves, energy can be resonantly transferred from ions (travelling perpendicular to the magnetic field) to electrons (travelling parallel to it) and the consequent motion of the latter in turbulent shock electromagnetic fields is believed to be responsible for the observed x-ray fluxes from non-thermal electrons produced in astrophysical shocks. Here we present PIC simulations of plasma flows colliding with magnetized obstacles showing the formation of a bow shock and the consequent development of LHT. The plasma and obstacle parameters are chosen in order to reproduce the results obtained in a recent experiment conducted at the LULI laser facility at Ecole Polytechnique (France) to study accelerated electrons via LHT. The wave and particle spectra are studied and used to produce synthetic diagnostics that show good qualitative agreement with experimental results. Work supported by the European Research Council (Accelerates ERC-2010-AdG 267841).

  1. Simulation of diatomic gas-wall interaction and accommodation coefficients for negative ion sources and accelerators

    SciTech Connect

    Sartori, E. Serianni, G.; Brescaccin, L.

    2016-02-15

    Particle-wall interactions determine in different ways the operating conditions of plasma sources, ion accelerators, and beams operating in vacuum. For instance, a contribution to gas heating is given by ion neutralization at walls; beam losses and stray particle production—detrimental for high current negative ion systems such as beam sources for fusion—are caused by collisional processes with residual gas, with the gas density profile that is determined by the scattering of neutral particles at the walls. This paper shows that Molecular Dynamics (MD) studies at the nano-scale can provide accommodation parameters for gas-wall interactions, such as the momentum accommodation coefficient and energy accommodation coefficient: in non-isothermal flows (such as the neutral gas in the accelerator, coming from the plasma source), these affect the gas density gradients and influence efficiency and losses in particular of negative ion accelerators. For ideal surfaces, the computation also provides the angular distribution of scattered particles. Classical MD method has been applied to the case of diatomic hydrogen molecules. Single collision events, against a frozen wall or a fully thermal lattice, have been simulated by using probe molecules. Different modelling approximations are compared.

  2. The influence of combined alignments on lateral acceleration on mountainous freeways: a driving simulator study.

    PubMed

    Wang, Xuesong; Wang, Ting; Tarko, Andrew; Tremont, Paul J

    2015-03-01

    Combined horizontal and vertical alignments are frequently used in mountainous freeways in China; however, design guidelines that consider the safety impact of combined alignments are not currently available. Past field studies have provided some data on the relationship between road alignment and safety, but the effects of differing combined alignments on either lateral acceleration or safety have not systematically examined. The primary reason for this void in past research is that most of the prior studies used observational methods that did not permit control of the key variables. A controlled parametric study is needed that examines lateral acceleration as drivers adjust their speeds across a range of combined horizontal and vertical alignments. Such a study was conducted in Tongji University's eight-degree-of-freedom driving simulator by replicating the full range of combined alignments used on a mountainous freeway in China. Multiple linear regression models were developed to estimate the effects of the combined alignments on lateral acceleration. Based on these models, domains were calculated to illustrate the results and to assist engineers to design safer mountainous freeways.

  3. Electron Acceleration in the Earth's Magnetotail Using Multi-Scale Simulations

    NASA Astrophysics Data System (ADS)

    Ashour-Abdalla, Maha; Lapenta, Giovanni; El-Alaoui, Mostafa; Walker, Raymond

    2014-05-01

    Magnetic reconnection in magnetized plasma represents a change in the topology of magnetic fields and is associated with a concomitant energization of charged particles that results from a conversion of magnetic energy into particle energy. Using data from the THEMIS and Cluster missions together with global and test particle simulations, we demonstrate that during a substorm on February 15, 2008 electrons are energized in two distinct regions: A low-energy population (up to a few keV) appears to arise in the diffusion region where particles are demagnetized and the magnetic topology changes. In addition a high-energy component that is energized by betatron acceleration arises within dipolarization fronts as they sweep toward the inner magnetosphere far from the diffusion region. This study concluded that particle energization is not associated solely with the conversion of magnetic to kinetic energy but, at least in the magnetosphere, also arises in conjunction with macroscopic flows. In a second substorm study, on March 11, 2008 we found that the test particle results compared favorably with observations only when we added a high-energy tail to the distribution function near the reconnection site. This implies that acceleration near the X-line was substantial and needs to be included. THEMIS and Cluster observations indicate that plasma waves are associated with the dipolarization fronts [1]. The test particle calculations are not self-consistent and do not include plasma waves. Therefore, to fully understand the processes that lead to electron acceleration throughout the near-Earth tail, we need to utilize a self-consistent kinetic approach that includes waves and electron acceleration near the neutral line along with large-scale dynamics. We present results from a model which couples the large scale magnetospheric processes and kinetic processes by developing a simulation approach in which a global MHD simulation is coupled with a particle in cell simulation

  4. Ultra High Resolution Particle-In-Cell Simulations of Transition to Turbulence using GPU acceleration

    NASA Astrophysics Data System (ADS)

    Germaschewski, Kai; Fox, William; Karimabadi, Homa; Roytershteyn, Vadim; Daughton, William

    2012-10-01

    Advances in computing power have enabled kinetic particle-in-cell simulations of plasma transition to turbulence at unprecedent resolutions. Nonlinear Kelvin-Helmholtz and tearing instabilities, driven by an initial shear flow, lead to fully developed turbulence, spanning scales from MHD down to electron kinetic scales. Currently, advances in computational capabilities for some of the largest computers in the world, like DOE's upcoming Titan machine, are driven by the use of graphics processing units (GPUs) to accelerate computationally intensive tasks. We present new modules in the electromagnetic particle-in-cell code PSC that enable effective use of the computational capabilities of massively parallel GPU based computers for kinetic plasma simulations. In particular, we will address (1) efficient algorithms for implementing particle advance, current deposition and sorting, (2) a load balancing scheme based on decomposition into small patches and space-filling curves, and (3) challenges of using both CPU and GPUs simultaneously in order to exploit all available computational resources optimally.

  5. Simulation of direct plasma injection for laser ion beam acceleration with a radio frequency quadrupole

    SciTech Connect

    Jin, Q. Y.; Li, Zh. M.; Liu, W.; Zhao, H. Y. Zhang, J. J.; Sha, Sh.; Zhang, Zh. L.; Zhang, X. Zh.; Sun, L. T.; Zhao, H. W.

    2014-07-15

    The direct plasma injection scheme (DPIS) has been being studied at Institute of Modern Physics since several years ago. A C{sup 6+} beam with peak current of 13 mA, energy of 593 keV/u has been successfully achieved after acceleration with DPIS method. To understand the process of DPIS, some simulations have been done as follows. First, with the total current intensity and the relative yields of different charge states for carbon ions measured at the different distance from the target, the absolute current intensities and time-dependences for different charge states are scaled to the exit of the laser ion source in the DPIS. Then with these derived values as the input parameters, the extraction of carbon beam from the laser ion source to the radio frequency quadrupole with DPIS is simulated, which is well agreed with the experiment results.

  6. Magnetic field simulation of wiggler on LUCX accelerator facility using Radia

    NASA Astrophysics Data System (ADS)

    Sutygina, Y. N.; Harisova, A. E.; Shkitov, D. A.

    2016-11-01

    A flat wiggler consisting of NdFeB permanent magnets was installed on a compact linear electron accelerator LUCX (KEK) in Japan. After installing the wiggler on LUCX, the experiments on the generation of undulator radiation (UR) in the terahertz wavelength range is planned. To perform the detailed calculations and optimization of UR characteristics, it is necessary to know the parameters of the magnetic field generated in the wiggler. In this paper extended simulation results of wiggler magnetic field over the entire volume between the poles are presented. The obtained in the Radia simulation magnetic field is compared with the field calculated by another code, which is based on the finite element method.

  7. Multi-cavity complex controller with vector simulator for TESLA technology linear accelerator

    NASA Astrophysics Data System (ADS)

    Czarski, Tomasz; Pozniak, Krzysztof T.; Romaniuk, Ryszard S.; Szewinski, Jaroslaw

    2008-01-01

    A digital control, as the main part of the Low Level RF system, for superconducting cavities of a linear accelerator is presented. The FPGA based controller, supported by MATLAB system, was developed to investigate a novel firmware implementation. The complex control algorithm based on the non-linear system identification is the proposal verified by the preliminary experimental results. The general idea is implemented as the Multi-Cavity Complex Controller (MCC) and is still under development. The FPGA based controller executes procedure according to the prearranged control tables: Feed-Forward, Set-Point and Corrector unit, to fulfill the required cavity performance: driving in the resonance during filling and field stabilization for the flattop range. Adaptive control algorithm is applied for the feed-forward and feedback modes. The vector Simulator table has been introduced for an efficient verification of the FPGA controller structure. Experimental results of the internal simulation, are presented for a cavity representative condition.

  8. Simulating Electron Effects in Heavy-Ion Accelerators with Solenoid Focusing

    SciTech Connect

    Sharp, W M; Grote, D P; Cohen, R H; Friedman, A; Molvik, A W; Vay, J; Seidl, P; Roy, P K; Coleman, J E; Haber, I

    2007-06-29

    Contamination from electrons is a concern for solenoid-focused ion accelerators being developed for experiments in high-energy-density physics. These electrons, produced directly by beam ions hitting lattice elements or indirectly by ionization of desorbed neutral gas, can potentially alter the beam dynamics, leading to a time-varying focal spot, increased emittance, halo, and possibly electron-ion instabilities. The electrostatic particle-in-cell code WARP is used to simulate electron-cloud studies on the solenoid-transport experiment (STX) at Lawrence Berkeley National Laboratory. We present self-consistent simulations of several STX configurations and compare the results with experimental data in order to calibrate physics parameters in the model.

  9. Simulating Electron Clouds in High-Current Ion Accelerators with Solenoid Focusing

    SciTech Connect

    Sharp, W; Grote, D; Cohen, R; Friedman, A; Vay, J; Seidl, P; Roy, P; Coleman, J; Armijo, J; Haber, I

    2006-08-15

    Contamination from electrons is a concern for the solenoid-focused ion accelerators being developed for experiments in high-energy-density physics (HEDP). These electrons are produced directly by beam ions hitting lattice elements and intercepting diagnostics, or indirectly by ionization of desorbed neutral gas, and they are believed responsible for time dependence of the beam radius, emittance, and focal distance seen on the Solenoid Transport Experiment (STX) at Lawrence Berkeley National Laboratory. The electrostatic particle-in-cell code WARP has been upgraded to included the physics needed to simulate electron-cloud phenomena. We present preliminary self-consistent simulations of STX experiments suggesting that the observed time dependence of the beam stems from a complicated interaction of beam ions, desorbed neutrals, and electrons.

  10. Simulating Electron Clouds in High-Current Ion Accelerators withSolenoid Focusing

    SciTech Connect

    Sharp, W.M.; Grote, D.P.; Cohen, R.H.; Friedman, A.; Vay, J.-L.; Seidl, P.A.; Roy, P.K.; Coleman, J.E.; Armijo, J.; Haber, I.

    2006-09-20

    Contamination from electrons is a concern for the solenoid-focused ion accelerators being developed for experiments in high-energy-density physics (HEDP). These electrons are produced directly by beam ions hitting lattice elements and intercepting diagnostics, or indirectly by ionization of desorbed neutral gas, and they are believed responsible for time dependence of the beam radius, emittance, and focal distance seen on the Solenoid Transport Experiment (STX) at Lawrence Berkeley National Laboratory. The electrostatic particle-in-cell code WARP has been upgraded to included the physics needed to simulate electron-cloud phenomena. We present preliminary self-consistent simulations of STX experiments suggesting that the observed time dependence of the beam stems from a complicated interaction of beam ions, desorbed neutrals, and electrons.

  11. Simulating Electron Effects in Heavy-Ion Accelerators with Solenoid Focusing

    SciTech Connect

    Sharp, W. M.; Grote, D. P.; Cohen, R. H.; Friedman, A.; Molvik, A. W.; Vay, J.-L.; Seidl, P. A.; Roy, P. K.; Coleman, J. E.; Haber, I.

    2007-06-20

    Contamination from electrons is a concern for solenoid-focused ion accelerators being developed for experiments in high-energy-density physics. These electrons, produced directly by beam ions hitting lattice elements or indirectly by ionization of desorbed neutral gas, can potentially alter the beam dynamics, leading to a time-varying focal spot, increased emittance, halo, and possibly electron-ion instabilities. The electrostatic particle-in-cell code WARP is used to simulate electron-cloud studies on the solenoid-transport experiment (STX) at Lawrence Berkeley National Laboratory. We present self-consistent simulations of several STX configurations and compare the results with experimental data in order to calibrate physics parameters in the model.

  12. 3D particle simulations of space-charge-dominated beams in HIF accelerator experiments

    SciTech Connect

    Grote, D.P.; Friedman, A.; Lund, S.M.; Haber, I.

    1997-05-01

    The development of a high current, heavy-ion beam for inertial confinement fusion requires a detailed understanding of the behavior of the beam, including effects of the large self-fields. This necessity makes particle-in-cell (PIC) simulation the appropriate tool, and for this reason, the three-dimensional PIC/accelerator code WARP3d is being developed. WARP3d has been used extensively to study the creation and propagation of ion beams both to support experiments and for the understanding of basic beam physics. An overview of the structure of the code is presented along with a discussion of features that make the code an effective tool in the understanding of space-charge dominated beam behavior. A number of applications where WARP3d has played an important role is discussed, emphasizing the need of three-dimensional, first principles simulations. Results and comparisons with experiment are presented.

  13. GPU accelerated Monte Carlo simulation of pulsed-field gradient NMR experiments.

    PubMed

    Waudby, Christopher A; Christodoulou, John

    2011-07-01

    The simulation of diffusion by Monte Carlo methods is often essential to describing NMR measurements of diffusion in porous media. However, simulation timescales must often span hundreds of milliseconds, with large numbers of trajectories required to ensure statistical convergence. Here we demonstrate that by parallelising code to run on graphics processing units (GPUs), these calculations may be accelerated by over three orders of magnitude, opening new frontiers in experimental design and analysis. As such cards are commonly installed on most desktop computers, we expect that this will prove useful in many cases where simple analytical descriptions are not available or appropriate, e.g. in complex geometries or where short gradient pulse approximations do not hold, or for the analysis of diffusion-weighted MRI in complex tissues such as the lungs and brain. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. R-leaping: accelerating the stochastic simulation algorithm by reaction leaps.

    PubMed

    Auger, Anne; Chatelain, Philippe; Koumoutsakos, Petros

    2006-08-28

    A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

  15. R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps

    NASA Astrophysics Data System (ADS)

    Auger, Anne; Chatelain, Philippe; Koumoutsakos, Petros

    2006-08-01

    A novel algorithm is proposed for the acceleration of the exact stochastic simulation algorithm by a predefined number of reaction firings (R-leaping) that may occur across several reaction channels. In the present approach, the numbers of reaction firings are correlated binomial distributions and the sampling procedure is independent of any permutation of the reaction channels. This enables the algorithm to efficiently handle large systems with disparate rates, providing substantial computational savings in certain cases. Several mechanisms for controlling the accuracy and the appearance of negative species are described. The advantages and drawbacks of R-leaping are assessed by simulations on a number of benchmark problems and the results are discussed in comparison with established methods.

  16. Simulation of direct plasma injection for laser ion beam acceleration with a radio frequency quadrupole.

    PubMed

    Jin, Q Y; Zhao, H Y; Zhang, J J; Sha, Sh; Zhang, Zh L; Li, Zh M; Liu, W; Zhang, X Zh; Sun, L T; Zhao, H W

    2014-07-01

    The direct plasma injection scheme (DPIS) has been being studied at Institute of Modern Physics since several years ago. A C(6+) beam with peak current of 13 mA, energy of 593 keV/u has been successfully achieved after acceleration with DPIS method. To understand the process of DPIS, some simulations have been done as follows. First, with the total current intensity and the relative yields of different charge states for carbon ions measured at the different distance from the target, the absolute current intensities and time-dependences for different charge states are scaled to the exit of the laser ion source in the DPIS. Then with these derived values as the input parameters, the extraction of carbon beam from the laser ion source to the radio frequency quadrupole with DPIS is simulated, which is well agreed with the experiment results.

  17. High-resolution, Antarctic Ice Sheet simulations forced by submarine melting simulated by the Accelerated Climate Model for Energy (ACME)

    NASA Astrophysics Data System (ADS)

    Price, S. F.; Asay-Davis, X.; Fyke, J. G.; Hoffman, M. J.; Jacobson, D.; Petersen, M. R.; Tezaur, I.; Perego, M.; Salinger, A.; Turner, A. K.; Wolfe, J.

    2016-12-01

    The capability for simulating sub-ice shelf circulation and submarine melting and freezing has recently been added to the U.S. Department of Energy's Accelerated Climate Model for Energy (ACME). With this new capability, we use an eddy permitting ocean model to conduct two sets of simulations in the spirit of Spence et al. (GRL, 41, 2014), who demonstrate increased warm water upwelling along the Antarctic coast in response to poleward shifting and strengthening of Southern Ocean westerly winds. These characteristics, symptomatic of a positive Southern Annual Model (SAM), are projected to continue into the 21st century under anthropogenic climate change (Fyfe et al., J. Clim., 20, 2007). In our first simulation, we force our climate model using repeat cycles of the standard CORE interannual forcing dataset (Large and Yeager; Clim. Dyn., 33, 2009). These melt rates are used to force our high-resolution (30-to-1 km) ice sheet model, MPAS-Land Ice, offline and to derive a quasi-steady state ice sheet model initial condition. In our second simulation, we force our climate model using an altered version of CORE interannual forcing, based on the latter half of the full time series, which we take as a proxy for a future climate state biased towards a positive SAM. Melt rate anomalies from this second simulation are then used to force our ice sheet model offline out to year 2100. We compare ocean model states and sub-ice shelf melt rates with observations and present estimates for Antarctic Ice Sheet mass loss from our simulations.

  18. Vertical accelerator device to apply loads simulating blast environments in the military to human surrogates.

    PubMed

    Yoganandan, Narayan; Pintar, Frank A; Schlick, Michael; Humm, John R; Voo, Liming; Merkle, Andrew; Kleinberger, Michael

    2015-09-18

    The objective of the study was to develop a simple device, Vertical accelerator (Vertac), to apply vertical impact loads to Post Mortem Human Subject (PMHS) or dummy surrogates because injuries sustained in military conflicts are associated with this vector; example, under-body blasts from explosive devices/events. The two-part mechanically controlled device consisted of load-application and load-receiving sections connected by a lever arm. The former section incorporated a falling weight to impact one end of the lever arm inducing a reaction at the other/load-receiving end. The "launch-plate" on this end of the arm applied the vertical impact load/acceleration pulse under different initial conditions to biological/physical surrogates, attached to second section. It is possible to induce different acceleration pulses by using varying energy absorbing materials and controlling drop height and weight. The second section of Vertac had the flexibility to accommodate different body regions for vertical loading experiments. The device is simple and inexpensive. It has the ability to control pulses and flexibility to accommodate different sub-systems/components of human surrogates. It has the capability to incorporate preloads and military personal protective equipment (e.g., combat helmet). It can simulate vehicle roofs. The device allows for intermittent specimen evaluations (x-ray and palpation, without changing specimen alignment). The two free but interconnected sections can be used to advance safety to military personnel. Examples demonstrating feasibilities of the Vertac device to apply vertical impact accelerations using PMHS head-neck preparations with helmet and booted Hybrid III dummy lower leg preparations under in-contact and launch-type impact experiments are presented.

  19. High-resolution simulations of downslope gravity currents in the acceleration phase

    NASA Astrophysics Data System (ADS)

    Dai, Albert

    2015-07-01

    Gravity currents generated from an instantaneous buoyancy source propagating down a slope in the range of 0∘ ≤ θ < 90∘ have been investigated in the acceleration phase by means of high-resolution two-dimensional simulations of the incompressible Navier-Stokes equations with the Boussinesq approximation. Front velocity history shows that, after the heavy fluid is released from rest, the flow goes through the acceleration phase, reaching a maximum front velocity Uf,max, and followed by the deceleration phase. The existence of a maximum of Uf,max is found near θ = 40∘, which is supported by the improved theory. It is identified for the first time that the time of acceleration decreases as the slope angle increases, when the slope angle is approximately greater than 10∘, and the time of acceleration increases as the slope angle increases for gravity currents on lower slope angles. A fundamental difference in flow patterns, which helps explain the distinct characteristics of gravity currents on high and low slope angles using scaling arguments, is revealed. Energy budgets further show that, as the slope angle increases, the ambient fluid is more easily engaged in the gravitational convection and the potential energy loss is more efficiently converted into the kinetic energy associated with ambient fluid. The propagation of gravity currents on a slope is found to be qualitatively modified as the depth ratio, i.e., the lock height to channel height ratio, approaches unity. As the depth ratio increases, the conversion of potential energy loss into the kinetic energy associated with heavy fluid is inhibited and the conversion into the kinetic energy associated with ambient fluid is enhanced by the confinement of the top wall.

  20. BrainFrame: A node-level heterogeneous accelerator platform for neuron simulations.

    PubMed

    Smaragdos, Georgios; Chatzikonstantis, Georgios; Kukreja, Rahul; Sidiropoulos, Harry; Rodopoulos, Dimitrios; Sourdis, Ioannis; Al-Ars, Zaid; Kachris, Christoforos; Soudris, Dimitrios; de Zeeuw, Chris; Strydis, Christos

    2017-07-14

    Objective: The advent of High-Performance Computing (HPC) in recent years has led to its increasing use in brain study through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the vast diversity of the modeling field does not permit for a homogeneous acceleration platform to effectively address the complete array of modeling requirements. Approach: In this paper we propose and build BrainFrame, a heterogeneous acceleration platform that incorporates three distinct acceleration technologies, an Intel Xeon-Phi CPU, a NVidia GP-GPU and a Maxeler Dataflow Engine. The PyNN software framework is also integrated into the platform. As a challenging proof of concept, we analyze the performance of BrainFrame on different experiment instances of a state-of-the-art neuron model, representing the Inferior-Olivary Nucleus using a biophysically-meaningful, extended Hodgkin-Huxley representation. The model instances take into account not only the neuronal-network dimensions but also different network-connectivity densities, which can drastically affect the workload's performance characteristics. Main results: The combined use of different HPC fabrics demonstrated that BrainFrame is better able to cope with the modeling diversity encountered in realistic experiments. Our performance analysis shows clearly that the model directly affects performance and all three technologies are required to cope with all the model use cases. Significance: The BrainFrame framework is designed to transparently configure and select the appropriate back-end accelerator technology for use per simulation run. The PyNN integration provides a familiar bridge to the vast number of models already available. Additionally, it gives a clear roadmap for extending the platform support beyond the proof of concept, with improved usability and directly

  1. Monte Carlo Simulation of Siemens ONCOR Linear Accelerator with BEAMnrc and DOSXYZnrc Code.

    PubMed

    Jabbari, Keyvan; Anvar, Hossein Saberi; Tavakoli, Mohammad Bagher; Amouheidari, Alireza

    2013-07-01

    The Monte Carlo method is the most accurate method for simulation of radiation therapy equipment. The linear accelerators (linac) are currently the most widely used machines in radiation therapy centers. In this work, a Monte Carlo modeling of the Siemens ONCOR linear accelerator in 6 MV and 18 MV beams was performed. The results of simulation were validated by measurements in water by ionization chamber and extended dose range (EDR2) film in solid water. The linac's X-ray particular are so sensitive to the properties of primary electron beam. Square field size of 10 cm × 10 cm produced by the jaws was compared with ionization chamber and film measurements. Head simulation was performed with BEAMnrc and dose calculation with DOSXYZnrc for film measurements and 3ddose file produced by DOSXYZnrc analyzed used homemade MATLAB program. At 6 MV, the agreement between dose calculated by Monte Carlo modeling and direct measurement was obtained to the least restrictive of 1%, even in the build-up region. At 18 MV, the agreement was obtained 1%, except for in the build-up region. In the build-up region, the difference was 1% at 6 MV and 2% at 18 MV. The mean difference between measurements and Monte Carlo simulation is very small in both of ONCOR X-ray energy. The results are highly accurate and can be used for many applications such as patient dose calculation in treatment planning and in studies that model this linac with small field size like intensity-modulated radiation therapy technique.

  2. Accelerated fatigue behavior and mechano-physical characterizations of in vitro physiological simulation of nitinol stents.

    PubMed

    Saidane, K; Polizu, S; Yahia, L'h

    2007-01-01

    In this study, we have provided an experimental evaluation of the fatigue behavior of the nitinol (NiTi) endovascular device (peripheral stent). The accelerated fatigue tests were performed using arterial conditions, which mimicked actual physiological conditions. Natural, rubber latex-tubing materials were used to simulate human arteries. The equipment design and the test parameters used allowed for the simulation of a compliant artery and the application of circumferential forces to the device.The stent compliance values were good indicators for tracking the time evolution of fatigue behavior. Moreover, the analyses of changes on the surface morphology and on the chemical composition were used to establish a relationship between surface characteristics and peripheral stent response during 400 million cycles, which is equivalent to 10 yrs of human life. In order to determine the influence of the accelerated fatigue, an evaluation of both mechanical and surface characteristics was carried out before and after testing using the following tests and methods, respectively: radial hoop testing (RH), scanning electron microscope analysis (SEM), auger electron spectroscopy (AES), atomic absorption spectroscopy (AAS), and X-ray photoelectron spectroscopy (XPS). Under these experimental conditions, the studies have shown that after 400 million cycles, the tested stents did not demonstrate any mechanical failure. Moreover, the surface did not undergo any changes in its chemical composition. However, we did observe an increase in roughness and signs of pitting corrosion.

  3. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    PubMed

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

  4. Warp simulations for capture and control of laser-accelerated proton beams

    SciTech Connect

    Nurnberg, F; Friedman, A; Grote, D P; Harres, K; Logan, B G; Schollmeier, M; Roth, M

    2009-10-22

    The capture of laser-accelerated proton beams accompanied by co-moving electrons via a solenoid field has been studied with particle-in-cell simulations. The main advantages of the Warp simulation suite that was used, relative to envelope or tracking codes, are the possibility of including all source parameters energy resolved, adding electrons as second species and considering the non-negligible space-charge forces and electrostatic self-fields. It was observed that the influence of the electrons is of vital importance. The magnetic effect on the electrons out balances the space-charge force. Hence, the electrons are forced onto the beam axis and attract protons. Besides the energy dependent proton density increase on axis, the change in the particle spectrum is also important for future applications. Protons are accelerated/decelerated slightly, electrons highly. 2/3 of all electrons get lost directly at the source and 27% of all protons hit the inner wall of the solenoid.

  5. Accelerated rescaling of single Monte Carlo simulation runs with the Graphics Processing Unit (GPU).

    PubMed

    Yang, Owen; Choi, Bernard

    2013-01-01

    To interpret fiber-based and camera-based measurements of remitted light from biological tissues, researchers typically use analytical models, such as the diffusion approximation to light transport theory, or stochastic models, such as Monte Carlo modeling. To achieve rapid (ideally real-time) measurement of tissue optical properties, especially in clinical situations, there is a critical need to accelerate Monte Carlo simulation runs. In this manuscript, we report on our approach using the Graphics Processing Unit (GPU) to accelerate rescaling of single Monte Carlo runs to calculate rapidly diffuse reflectance values for different sets of tissue optical properties. We selected MATLAB to enable non-specialists in C and CUDA-based programming to use the generated open-source code. We developed a software package with four abstraction layers. To calculate a set of diffuse reflectance values from a simulated tissue with homogeneous optical properties, our rescaling GPU-based approach achieves a reduction in computation time of several orders of magnitude as compared to other GPU-based approaches. Specifically, our GPU-based approach generated a diffuse reflectance value in 0.08ms. The transfer time from CPU to GPU memory currently is a limiting factor with GPU-based calculations. However, for calculation of multiple diffuse reflectance values, our GPU-based approach still can lead to processing that is ~3400 times faster than other GPU-based approaches.

  6. MCNP Neutron Simulations: The Effectiveness of the University of Kentucky Accelerator Laboratory Pit

    NASA Astrophysics Data System (ADS)

    Jackson, Daniel; Nguyen, Thien An; Hicks, S. F.; Rice, Ben; Vanhoy, J. R.

    2015-10-01

    The design of the Van de Graaff Particle Accelerator complex at the University of Kentucky is marked by the unique addition of a pit in the main neutron scattering room underneath the neutron source and detection shielding assembly. This pit was constructed as a neutron trap in order to decrease the amount of neutron flux within the laboratory. Such a decrease of background neutron flux effectively reduces as much noise as possible in detection of neutrons scattering off of desired samples to be studied. This project uses the Monte-Carlo N-Particle Transport Code (MCNP) to model the structure of the accelerator complex, gas cell, and the detector's collimator and shielding apparatus to calculate the neutron flux in various sections of the laboratory. Simulations were completed with baseline runs of 107 neutrons of energies 4 MeV and 17 MeV, produced respectively by 3H(p,n)3He and 3H(d,n)4He source reactions. In addition, a comparison model of the complex with simply a floor and no pit was designed, and the respective neutron fluxes of both models were calculated and compared. The results of the simulations seem to affirm the validity of the pit design in significantly reducing the overall neutron flux throughout the accelerator complex, which could be used in future designs to increase the precision and reliability of data. This project was supported in part by the DOE NEUP Grant NU-12-KY-UK-0201-05 and the Donald A. Cowan Physics Institute at the University of Dallas.

  7. Simulations of ion acceleration from ultrathin targets with the VEGA petawatt laser

    NASA Astrophysics Data System (ADS)

    Stockhausen, Luca C.; Torres, Ricardo; Conejero Jarque, Enrique

    2015-05-01

    The Spanish Pulsed Laser Centre (CLPU) is a new high-power laser facility for users. Its main system, VEGA, is a CPA Ti:Sapphire laser which, in its final phase, will be able to reach petawatt peak powers in pulses of 30 fs with a pulse contrast of 1 : 1010 at 1 ps. The extremely low level of pre-pulse intensity makes this system ideally suited for studying the laser interaction with ultrathin targets. We have used the particle-in-cell (PIC) code OSIRIS to carry out 2D simulations of the acceleration of ions from ultrathin solid targets under the unique conditions provided by VEGA, with laser intensities up to 1022Wcm-2 impinging normally on 5 - 40 nm thick overdense plasmas, with different polarizations and pre-plasma scale lengths. We show how signatures of the radiation pressure dominated regime, such as layer compression and bunch formation, are only present with circular polarization. By passively shaping the density gradient of the plasma, we demonstrate an enhancement in peak energy up to tens of MeV and monoenergetic features. On the contrary linear polarization at the same intensity level causes the target to blow up, resulting in much lower energies and broader spectra. One limiting factor of Radiation Pressure Acceleration is the development of Rayleigh-Taylor like instabilities at the interface of the plasma and photon fluid. This results in the formation of bubbles in the spatial profile of laser-accelerated proton beams. These structures were previously evidenced both experimentally and theoretically. We have performed 2D simulations to characterize this bubble-like structure and report on the dependency on laser and target parameters.

  8. Simulations of radiation pressure ion acceleration with the VEGA Petawatt laser

    NASA Astrophysics Data System (ADS)

    Stockhausen, Luca C.; Torres, Ricardo; Conejero Jarque, Enrique

    2016-09-01

    The Spanish Pulsed Laser Centre (CLPU) is a new high-power laser facility for users. Its main system, VEGA, is a CPA Ti:Sapphire laser which, in its final phase, will be able to reach Petawatt peak powers in pulses of 30 fs with a pulse contrast of 1 :1010 at 1 ps. The extremely low level of pre-pulse intensity makes this system ideally suited for studying the laser interaction with ultrathin targets. We have used the particle-in-cell (PIC) code OSIRIS to carry out 2D simulations of the acceleration of ions from ultrathin solid targets under the unique conditions provided by VEGA, with laser intensities up to 1022 W cm-2 impinging normally on 20 - 60 nm thick overdense plasmas, with different polarizations and pre-plasma scale lengths. We show how signatures of the radiation pressure-dominated regime, such as layer compression and bunch formation, are only present with circular polarization. By passively shaping the density gradient of the plasma, we demonstrate an enhancement in peak energy up to tens of MeV and monoenergetic features. On the contrary linear polarization at the same intensity level causes the target to blow up, resulting in much lower energies and broader spectra. One limiting factor of Radiation Pressure Acceleration is the development of Rayleigh-Taylor like instabilities at the interface of the plasma and photon fluid. This results in the formation of bubbles in the spatial profile of laser-accelerated proton beams. These structures were previously evidenced both experimentally and theoretically. We have performed 2D simulations to characterize this bubble-like structure and report on the dependency on laser and target parameters.

  9. Self-consistent core-pedestal transport simulations with neural network accelerated models

    DOE PAGES

    Meneghini, Orso; Smith, Sterling P.; Snyder, Philip B.; ...

    2017-07-12

    Fusion whole device modeling simulations require comprehensive models that are simultaneously physically accurate, fast, robust, and predictive. In this paper we describe the development of two neural-network (NN) based models as a means to perform a snon-linear multivariate regression of theory-based models for the core turbulent transport fluxes, and the pedestal structure. Specifically, we find that a NN-based approach can be used to consistently reproduce the results of the TGLF and EPED1 theory-based models over a broad range of plasma regimes, and with a computational speedup of several orders of magnitudes. These models are then integrated into a predictive workflowmore » that allows prediction with self-consistent core-pedestal coupling of the kinetic profiles within the last closed flux surface of the plasma. Finally, the NN paradigm is capable of breaking the speed-accuracy trade-off that is expected of traditional numerical physics models, and can provide the missing link towards self-consistent coupled core-pedestal whole device modeling simulations that are physically accurate and yet take only seconds to run.« less

  10. Self-consistent core-pedestal transport simulations with neural network accelerated models

    NASA Astrophysics Data System (ADS)

    Meneghini, O.; Smith, S. P.; Snyder, P. B.; Staebler, G. M.; Candy, J.; Belli, E.; Lao, L.; Kostuk, M.; Luce, T.; Luda, T.; Park, J. M.; Poli, F.

    2017-08-01

    Fusion whole device modeling simulations require comprehensive models that are simultaneously physically accurate, fast, robust, and predictive. In this paper we describe the development of two neural-network (NN) based models as a means to perform a snon-linear multivariate regression of theory-based models for the core turbulent transport fluxes, and the pedestal structure. Specifically, we find that a NN-based approach can be used to consistently reproduce the results of the TGLF and EPED1 theory-based models over a broad range of plasma regimes, and with a computational speedup of several orders of magnitudes. These models are then integrated into a predictive workflow that allows prediction with self-consistent core-pedestal coupling of the kinetic profiles within the last closed flux surface of the plasma. The NN paradigm is capable of breaking the speed-accuracy trade-off that is expected of traditional numerical physics models, and can provide the missing link towards self-consistent coupled core-pedestal whole device modeling simulations that are physically accurate and yet take only seconds to run.

  11. Multi-core/GPU accelerated multi-resolution simulations of compressible flows

    NASA Astrophysics Data System (ADS)

    Hejazialhosseini, Babak; Rossinelli, Diego; Koumoutsakos, Petros

    2010-11-01

    We develop a multi-resolution solver for single and multi-phase compressible flow simulations by coupling average interpolating wavelets and local time stepping schemes with high order finite volume schemes. Wavelets allow for high compression rates and explicit control over the error in adaptive representation of the flow field, but their efficient parallel implementation is hindered by the use of traditional data parallel models. In this work we demonstrate that this methodology can be implemented so that it can benefit from the processing power of emerging hybrid multicore and multi-GPU architectures. This is achieved by exploiting task-based parallelism paradigm and the concept of wavelet blocks combined with OpenCL and Intel Threading Building Blocks. The solver is able to handle high resolution jumps and benefits from adaptive time integration using local time stepping schemes as implemented on heterogeneous multi-core/GPU architectures. We demonstrate the accuracy of our method and the performance of our solver on different architectures for 2D simulations of shock-bubble interaction and Richtmeyer-Meshkov instability.

  12. Acceleration of a Particle-in-Cell Code for Space Plasma Simulations with OpenACC

    NASA Astrophysics Data System (ADS)

    Peng, Ivy Bo; Markidis, Stefano; Vaivads, Andris; Vencels, Juris; Deca, Jan; Lapenta, Giovanni; Hart, Alistair; Laure, Erwin

    2015-04-01

    We simulate space plasmas with the Particle-in-cell (PIC) method that uses computational particles to mimic electrons and protons in solar wind and in Earth magnetosphere. The magnetic and electric fields are computed by solving the Maxwell's equations on a computational grid. In each PIC simulation step, there are four major phases: interpolation of fields to particles, updating the location and velocity of each particle, interpolation of particles to grids and solving the Maxwell's equations on the grid. We use the iPIC3D code, which was implemented in C++, using both MPI and OpenMP, for our case study. By November 2014, heterogeneous systems using hardware accelerators such as Graphics Processing Unit (GPUs) and the Many Integrated Core (MIC) coprocessors for high performance computing continue growth in the top 500 most powerful supercomputers world wide. Scientific applications for numerical simulations need to adapt to using accelerators to achieve portability and scalability in the coming exascale systems. In our work, we conduct a case study of using OpenACC to offload the computation intensive parts: particle mover and interpolation of particles to grids, in a massively parallel Particle-in-Cell simulation code, iPIC3D, to multi-GPU systems. We use MPI for inter-node communication for halo exchange and communicating particles. We identify the most promising parts suitable for GPUs accelerator by profiling using CrayPAT. We implemented manual deep copy to address the challenges of porting C++ classes to GPU. We document the necessary changes in the exiting algorithms to adapt for GPU computation. We present the challenges and findings as well as our methodology for porting a Particle-in-Cell code to multi-GPU systems using OpenACC. In this work, we will present the challenges, findings and our methodology of porting a Particle-in-Cell code for space applications as follows: We profile the iPIC3D code by Cray Performance Analysis Tool (CrayPAT) and identify

  13. Man-systems evaluation of moving base vehicle simulation motion cues. [human acceleration perception involving visual feedback

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, M.; Brye, R. G.

    1974-01-01

    A motion cue investigation program is reported that deals with human factor aspects of high fidelity vehicle simulation. General data on non-visual motion thresholds and specific threshold values are established for use as washout parameters in vehicle simulation. A general purpose similator is used to test the contradictory cue hypothesis that acceleration sensitivity is reduced during a vehicle control task involving visual feedback. The simulator provides varying acceleration levels. The method of forced choice is based on the theory of signal detect ability.

  14. 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.

  15. GPU-accelerated red blood cells simulations with transport dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Blumers, Ansel L.; Tang, Yu-Hang; Li, Zhen; Li, Xuejin; Karniadakis, George E.

    2017-08-01

    Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particle Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterize scalability. We observe a speedup of 10 . 1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

  16. Tabulated square-shaped source model for linear accelerator electron beam simulation.

    PubMed

    Khaledi, Navid; Aghamiri, Mahmood Reza; Aslian, Hossein; Ameri, Ahmad

    2017-01-01

    Using this source model, the Monte Carlo (MC) computation becomes much faster for electron beams. The aim of this study was to present a source model that makes linear accelerator (LINAC) electron beam geometry simulation less complex. In this study, a tabulated square-shaped source with transversal and axial distribution biasing and semi-Gaussian spectrum was investigated. A low energy photon spectrum was added to the semi-Gaussian beam to correct the bremsstrahlung X-ray contamination. After running the MC code multiple times and optimizing all spectrums for four electron energies in three different medical LINACs (Elekta, Siemens, and Varian), the characteristics of a beam passing through a 10 cm × 10 cm applicator were obtained. The percentage depth dose and dose profiles at two different depths were measured and simulated. The maximum difference between simulated and measured percentage of depth doses and dose profiles was 1.8% and 4%, respectively. The low energy electron and photon spectrum and the Gaussian spectrum peak energy and associated full width at half of maximum and transversal distribution weightings were obtained for each electron beam. The proposed method yielded a maximum computation time 702 times faster than a complete head simulation. Our study demonstrates that there was an excellent agreement between the results of our proposed model and measured data; furthermore, an optimum calculation speed was achieved because there was no need to define geometry and materials in the LINAC head.

  17. Fourier analysis of Solar atmospheric numerical simulations accelerated with GPUs (CUDA).

    NASA Astrophysics Data System (ADS)

    Marur, A.

    2015-12-01

    Solar dynamics from the convection zone creates a variety of waves that may propagate through the solar atmosphere. These waves are important in facilitating the energy transfer between the sun's surface and the corona as well as propagating energy throughout the solar system. How and where these waves are dissipated remains an open question. Advanced 3D numerical simulations have furthered our understanding of the processes involved. Fourier transforms to understand the nature of the waves by finding the frequency and wavelength of these waves through the simulated atmosphere, as well as the nature of their propagation and where they get dissipated. In order to analyze the different waves produced by the aforementioned simulations and models, Fast Fourier Transform algorithms will be applied. Since the processing of the multitude of different layers of the simulations (of the order of several 100^3 grid points) would be time intensive and inefficient on a CPU, CUDA, a computing architecture that harnesses the power of the GPU, will be used to accelerate the calculations.

  18. Statistical comparison between experiments and numerical simulations of shock-accelerated gas cylinders

    SciTech Connect

    Rider, William; Kamm, J. R.; Zoldi, C. A.; Tomkins, C. D.

    2002-01-01

    We present detailed spatial analysis comparing experimental data and numerical simulation results for Richtmyer-Meshkov instability experiments of Prestridge et al. and Tomkins et al. These experiments consist, respectively, of one and two diffuse cylinders of sulphur hexafluoride (SF{sub 6}) impulsively accelerated by a Mach 1.2 shockwave in air. The subsequent fluid evolution and mixing is driven by the deposition of baroclinic vorticity at the interface between the two fluids. Numerical simulations of these experiments are performed with three different versions of high resolution finite volume Godunov methods, including a new weighted adaptive Runge-Kutta (WARK) scheme. We quantify the nature of the mixing using using integral measures as well as fractal analysis and continuous wavelet transforms. Our investigation of the gas cylinder configurations follows the path of our earlier studies of the geometrically and dynamically more complex gas 'curtain' experiment. In those studies, we found significant discrepancies in the details of the experimentally measured mixing and the details of the numerical simulations. Here we evaluate the effects of these hydrodynamic integration techniques on the diffuse gas cylinder simulations, which we quantitatively compare with experimental data.

  19. Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

    PubMed Central

    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. PMID:23152751

  20. 3D simulations of young core-collapse supernova remnants undergoing efficient particle acceleration

    NASA Astrophysics Data System (ADS)

    Ferrand, Gilles; Safi-Harb, Samar

    2016-06-01

    Within our Galaxy, supernova remnants are believed to be the major sources of cosmic rays up to the 'knee'. However important questions remain regarding the share of the hadronic and leptonic components, and the fraction of the supernova energy channelled into these components. We address such question by the means of numerical simulations that combine a hydrodynamic treatment of the shock wave with a kinetic treatment of particle acceleration. Performing 3D simulations allows us to produce synthetic projected maps and spectra of the thermal and non-thermal emission, that can be compared with multi-wavelength observations (in radio, X-rays, and γ-rays). Supernovae come in different types, and although their energy budget is of the same order, their remnants have different properties, and so may contribute in different ways to the pool of Galactic cosmic-rays. Our first simulations were focused on thermonuclear supernovae, like Tycho's SNR, that usually occur in a mostly undisturbed medium. Here we present our 3D simulations of core-collapse supernovae, like the Cas A SNR, that occur in a more complex medium bearing the imprint of the wind of the progenitor star.

  1. GPU accelerated simulations of bluff body flows using vortex particle methods

    NASA Astrophysics Data System (ADS)

    Rossinelli, Diego; Bergdorf, Michael; Cottet, Georges-Henri; Koumoutsakos, Petros

    2010-05-01

    We present a GPU accelerated solver for simulations of bluff body flows in 2D using a remeshed vortex particle method and the vorticity formulation of the Brinkman penalization technique to enforce boundary conditions. The efficiency of the method relies on fast and accurate particle-grid interpolations on GPUs for the remeshing of the particles and the computation of the field operators. The GPU implementation uses OpenGL so as to perform efficient particle-grid operations and a CUFFT-based solver for the Poisson equation with unbounded boundary conditions. The accuracy and performance of the GPU simulations and their relative advantages/drawbacks over CPU based computations are reported in simulations of flows past an impulsively started circular cylinder from Reynolds numbers between 40 and 9500. The results indicate up to two orders of magnitude speed up of the GPU implementation over the respective CPU implementations. The accuracy of the GPU computations depends on the Re number of the flow. For Re up to 1000 there is little difference between GPU and CPU calculations but this agreement deteriorates (albeit remaining to within 5% in drag calculations) for higher Re numbers as the single precision of the GPU adversely affects the accuracy of the simulations.

  2. Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability.

    PubMed

    Thanh, Vo Hong; Priami, Corrado; Zunino, Roberto

    2016-06-14

    Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions.

  3. Accelerating the FE-Simulation of Roll Forming Processes with the Aid of specific Process's Properties

    NASA Astrophysics Data System (ADS)

    Abrass, Ahmad; Özel, Mahmut; Groche, Peter

    2011-08-01

    Roll forming is an effective and economical sheet forming process that is well-established in industry for the manufacturing of large quantities of profile-shaped products. In cold-roll forming, a metal sheet is fed through successive pairs of forming rolls until it is formed into the desired cross-sectional profile. The deformation of the sheet is complex. For this reason, the theoretical analysis is very difficult, especially, if the strain distribution and the occurring forces are to be determined [1]. The design of roll forming processes depends upon a large number of variables, which mainly relies upon experience based knowledge [2]. In order to overcome the challenges and to optimize these processes, FE-simulations are used. The simulation of these processes is time-consuming. The main objective of this work is to accelerate the simulation of roll forming processes by taking advantage of their steady state properties. These properties allow the transformation of points on the sheet metal according to a mathematical function. This transformation function is determined with the help of the finite element method and then the next forming steps are computed, based on the generated function. With the aid of this developed method, the computational time can be reduced effectively. The details of the FE-model and new numerical algorithms will be described. Furthermore, the results of numerical simulations with and without the application of the developed method will be compared regarding computational time and numerical results.

  4. Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.

    PubMed

    Jung, Jaewoon; Naurse, Akira; Kobayashi, Chigusa; Sugita, Yuji

    2016-10-11

    The graphics processing unit (GPU) has become a popular computational platform for molecular dynamics (MD) simulations of biomolecules. A significant speedup in the simulations of small- or medium-size systems using only a few computer nodes with a single or multiple GPUs has been reported. Because of GPU memory limitation and slow communication between GPUs on different computer nodes, it is not straightforward to accelerate MD simulations of large biological systems that contain a few million or more atoms on massively parallel supercomputers with GPUs. In this study, we develop a new scheme in our MD software, GENESIS, to reduce the total computational time on such computers. Computationally intensive real-space nonbonded interactions are computed mainly on GPUs in the scheme, while less intensive bonded interactions and communication-intensive reciprocal-space interactions are performed on CPUs. On the basis of the midpoint cell method as a domain decomposition scheme, we invent the single particle interaction list for reducing the GPU memory usage. Since total computational time is limited by the reciprocal-space computation, we utilize the RESPA multiple time-step integration and reduce the CPU resting time by assigning a subset of nonbonded interactions on CPUs as well as on GPUs when the reciprocal-space computation is skipped. We validated our GPU implementations in GENESIS on BPTI and a membrane protein, porin, by MD simulations and an alanine-tripeptide by REMD simulations. Benchmark calculations on TSUBAME supercomputer showed that an MD simulation of a million atoms system was scalable up to 256 computer nodes with GPUs.

  5. On-X Heart Valve Prosthesis: Numerical Simulation of Hemodynamic Performance in Accelerating Systole.

    PubMed

    Mirkhani, Nima; Davoudi, Mohammad Reza; Hanafizadeh, Pedram; Javidi, Daryoosh; Saffarian, Niloofar

    2016-09-01

    Numerical simulation of the bileaflet mechanical heart valves (BMHVs) has been of interest for many researchers due to its capability of predicting hemodynamic performance. A lot of studies have tried to simulate this three-dimensional complex flow in order to analyze the effect of different valve designs on the blood flow pattern. However, simplified models and prescribed motion for the leaflets were utilized. In this paper, transient complex blood flow in the location of ascending aorta has been investigated in a realistic model by fully coupled simulation. Geometry model for the aorta and the replaced valve is constructed based on the medical images and extracted point clouds. A 23-mm On-X Medical BMHV as the new generation design has been selected for the flow field analysis. The two-way coupling simulation is conducted throughout the accelerating phase in order to obtain valve dynamics in the opening process. The complex flow field in the hinge recess is captured precisely for all leaflet positions and recirculating zones and elevated shear stress areas have been observed. Results indicate that On-X valve yields relatively less transvalvular pressure gradient which would lower cardiac external work. Furthermore, converging inlet leads to a more uniform flow and consequently less turbulent eddies. However, the leaflets cannot open fully due to middle diffuser-shaped orifice. In addition, asymmetric butterfly-shaped hinge design and converging orifice leads to better hemodynamic performance. With the help of two-way fluid solid interaction simulation, leaflet angle follows the experimental trends more precisely rather than the prescribed motion in previous 3D simulations.

  6. Magnetohydrodynamic simulation study of plasma jets and plasma-surface contact in coaxial plasma accelerators

    NASA Astrophysics Data System (ADS)

    Subramaniam, Vivek; Raja, Laxminarayan L.

    2017-06-01

    Recent experiments by Loebner et al. [IEEE Trans. Plasma Sci. 44, 1534 (2016)] studied the effect of a hypervelocity jet emanating from a coaxial plasma accelerator incident on target surfaces in an effort to mimic the transient loading created during edge localized mode disruption events in fusion plasmas. In this paper, we present a magnetohydrodynamic (MHD) numerical model to simulate plasma jet formation and plasma-surface contact in this coaxial plasma accelerator experiment. The MHD system of equations is spatially discretized using a cell-centered finite volume formulation. The temporal discretization is performed using a fully implicit backward Euler scheme and the resultant stiff system of nonlinear equations is solved using the Newton method. The numerical model is employed to obtain some key insights into the physical processes responsible for the generation of extreme stagnation conditions on the target surfaces. Simulations of the plume (without the target plate) are performed to isolate and study phenomena such as the magnetic pinch effect that is responsible for launching pressure pulses into the jet free stream. The simulations also yield insights into the incipient conditions responsible for producing the pinch, such as the formation of conductive channels. The jet-target impact studies indicate the existence of two distinct stages involved in the plasma-surface interaction. A fast transient stage characterized by a thin normal shock transitions into a pseudo-steady stage that exhibits an extended oblique shock structure. A quadratic scaling of the pinch and stagnation conditions with the total current discharged between the electrodes is in qualitative agreement with the results obtained in the experiments. This also illustrates the dominant contribution of the magnetic pressure term in determining the magnitude of the quantities of interest.

  7. Convergence acceleration for partitioned simulations of the fluid-structure interaction in arteries

    NASA Astrophysics Data System (ADS)

    Radtke, Lars; Larena-Avellaneda, Axel; Debus, Eike Sebastian; Düster, Alexander

    2016-06-01

    We present a partitioned approach to fluid-structure interaction problems arising in analyses of blood flow in arteries. Several strategies to accelerate the convergence of the fixed-point iteration resulting from the coupling of the fluid and the structural sub-problem are investigated. The Aitken relaxation and variants of the interface quasi-Newton -least-squares method are applied to different test cases. A hybrid variant of two well-known variants of the interface quasi-Newton-least-squares method is found to perform best. The test cases cover the typical boundary value problem faced when simulating the fluid-structure interaction in arteries, including a strong added mass effect and a wet surface which accounts for a large part of the overall surface of each sub-problem. A rubber-like Neo Hookean material model and a soft-tissue-like Holzapfel-Gasser-Ogden material model are used to describe the artery wall and are compared in terms of stability and computational expenses. To avoid any kind of locking, high-order finite elements are used to discretize the structural sub-problem. The finite volume method is employed to discretize the fluid sub-problem. We investigate the influence of mass-proportional damping and the material model chosen for the artery on the performance and stability of the acceleration strategies as well as on the simulation results. To show the applicability of the partitioned approach to clinical relevant studies, the hemodynamics in a pathologically deformed artery are investigated, taking the findings of the test case simulations into account.

  8. Magnetohydrodynamic simulation study of plasma jets and plasma-surface contact in coaxial plasma accelerators

    DOE PAGES

    Subramaniam, Vivek; Raja, Laxminarayan L.

    2017-06-13

    Recent experiments by Loebner et al. [IEEE Trans. Plasma Sci. 44, 1534 (2016)] studied the effect of a hypervelocity jet emanating from a coaxial plasma accelerator incident on target surfaces in an effort to mimic the transient loading created during edge localized mode disruption events in fusion plasmas. In this study, we present a magnetohydrodynamic (MHD) numerical model to simulate plasma jet formation and plasma-surface contact in this coaxial plasma accelerator experiment. The MHD system of equations is spatially discretized using a cell-centered finite volume formulation. The temporal discretization is performed using a fully implicit backward Euler scheme and themore » resultant stiff system of nonlinear equations is solved using the Newton method. The numerical model is employed to obtain some key insights into the physical processes responsible for the generation of extreme stagnation conditions on the target surfaces. Simulations of the plume (without the target plate) are performed to isolate and study phenomena such as the magnetic pinch effect that is responsible for launching pressure pulses into the jet free stream. The simulations also yield insights into the incipient conditions responsible for producing the pinch, such as the formation of conductive channels. The jet-target impact studies indicate the existence of two distinct stages involved in the plasma-surface interaction. A fast transient stage characterized by a thin normal shock transitions into a pseudo-steady stage that exhibits an extended oblique shock structure. A quadratic scaling of the pinch and stagnation conditions with the total current discharged between the electrodes is in qualitative agreement with the results obtained in the experiments. Finally, this also illustrates the dominant contribution of the magnetic pressure term in determining the magnitude of the quantities of interest.« less

  9. A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators.

    PubMed

    Nguyen, Trung Dac; Carrillo, Jan-Michael Y; Dobrynin, Andrey V; Brown, W Michael

    2013-01-08

    Numerous issues have disrupted the trend for increasing computational performance with faster CPU clock frequencies. In order to exploit the potential performance of new computers, it is becoming increasingly desirable to re-evaluate computational physics methods and models with an eye toward approaches that allow for increased concurrency and data locality. The evaluation of long-range Coulombic interactions is a common bottleneck for molecular dynamics simulations. Enhanced truncation approaches have been proposed as an alternative method and are particularly well-suited for many-core architectures and GPUs due to the inherent fine-grain parallelism that can be exploited. In this paper, we compare efficient truncation-based approximations to evaluation of electrostatic forces with the more traditional particle-particle particle-mesh (P(3)M) method for the molecular dynamics simulation of polyelectrolyte brush layers. We show that with the use of GPU accelerators, large parallel simulations using P(3)M can be greater than 3 times faster due to a reduction in the mesh-size required. Alternatively, using a truncation-based scheme can improve performance even further. This approach can be up to 3.9 times faster than GPU-accelerated P(3)M for many polymer systems and results in accurate calculation of shear velocities and disjoining pressures for brush layers. For configurations with highly nonuniform charge distributions, however, we find that it is more efficient to use P(3)M; for these systems, computationally efficient parametrizations of the truncation-based approach do not produce accurate counterion density profiles or brush morphologies.

  10. Particle in Cell Simulations of the Pulsar Y-Point -- Nature of the Accelerating Electric Field

    NASA Astrophysics Data System (ADS)

    Belyaev, Mikhail

    2016-06-01

    Over the last decade, satellite observations have yielded a wealth of data on pulsed high-energy emission from pulsars. Several different models have been advanced to fit this data, all of which “paint” the emitting region onto a different portion of the magnetosphere.In the last few years, particle in cell simulations of pulsar magnetospheres have reached the point where they are able to self-consistently model particle acceleration and dissipation. One of the key findings of these simulations is that the region of the current sheet in and around the Y-point provides the highest rate of dissipation of Poynting flux (Belyaev 2015a). On the basis of this physical evidence, it is quite plausible that this region should be associated with the pulsed high energy emission from pulsars. We present high resolution PIC simulations of an axisymmetric pulsar magnetosphere, which are run using PICsar (Belyaev 2015b). These simulations focus on the particle dynamics and electric fields in and around the Y-point region. We run two types of simulations -- first, a force-free magnetosphere and second, a magnetosphere with a gap between the return current layer and the outflowing plasma in the polar wind zone. The latter setup is motivated by studies of pair production with general relativity (Philippov et al. 2015, Belyaev & Parfrey (in preparation)). In both cases, we find that the Y-point and the current sheet in its direct vicinity act like an “electric particle filter” outwardly accelerating particles of one sign of charge while returning the other sign of charge back to the pulsar. We argue that this is a natural behavior of the plasma as it tries to adjust to a solution that is as close to force-free as possible. As a consequence, a large E dot J develops in the vicinity of the Y-point leading to dissipation of Poynting flux. Our work is relevant for explaining the plasma physical mechanisms underlying pulsed high energy emission from pulsars.

  11. Start-to-end beam dynamics simulation of double triangular current profile generation in Argonne Wakefield Accelerator

    SciTech Connect

    Ha, G.; Power, J.; Kim, S. H.; Gai, W.; Kim, K.-J.; Cho, M. H.; Namkung, W.

    2012-12-21

    Double triangular current profile (DT) gives a high transformer ratio which is the determining factor of the performance of collinear wakefield accelerator. This current profile can be generated using the emittance exchange (EEX) beam line. Argonne Wakefield Accelerator (AWA) facility plans to generate DT using the EEX beam line. We conducted start-to-end simulation for the AWA beam line using PARMELA code. Also, we discuss requirements of beam parameters for the generation of DT.

  12. PARTICLE ACCELERATION AND WAVE EXCITATION IN QUASI-PARALLEL HIGH-MACH-NUMBER COLLISIONLESS SHOCKS: PARTICLE-IN-CELL SIMULATION

    SciTech Connect

    Kato, Tsunehiko N.

    2015-04-01

    We herein investigate shock formation and particle acceleration processes for both protons and electrons in a quasi-parallel high-Mach-number collisionless shock through a long-term, large-scale, particle-in-cell simulation. We show that both protons and electrons are accelerated in the shock and that these accelerated particles generate large-amplitude Alfvénic waves in the upstream region of the shock. After the upstream waves have grown sufficiently, the local structure of the collisionless shock becomes substantially similar to that of a quasi-perpendicular shock due to the large transverse magnetic field of the waves. A fraction of protons are accelerated in the shock with a power-law-like energy distribution. The rate of proton injection to the acceleration process is approximately constant, and in the injection process, the phase-trapping mechanism for the protons by the upstream waves can play an important role. The dominant acceleration process is a Fermi-like process through repeated shock crossings of the protons. This process is a “fast” process in the sense that the time required for most of the accelerated protons to complete one cycle of the acceleration process is much shorter than the diffusion time. A fraction of the electrons are also accelerated by the same mechanism, and have a power-law-like energy distribution. However, the injection does not enter a steady state during the simulation, which may be related to the intermittent activity of the upstream waves. Upstream of the shock, a fraction of the electrons are pre-accelerated before reaching the shock, which may contribute to steady electron injection at a later time.

  13. Particle Acceleration and Wave Excitation in Quasi-parallel High-Mach-number Collisionless Shocks: Particle-in-cell Simulation

    NASA Astrophysics Data System (ADS)

    Kato, Tsunehiko N.

    2015-04-01

    We herein investigate shock formation and particle acceleration processes for both protons and electrons in a quasi-parallel high-Mach-number collisionless shock through a long-term, large-scale, particle-in-cell simulation. We show that both protons and electrons are accelerated in the shock and that these accelerated particles generate large-amplitude Alfvénic waves in the upstream region of the shock. After the upstream waves have grown sufficiently, the local structure of the collisionless shock becomes substantially similar to that of a quasi-perpendicular shock due to the large transverse magnetic field of the waves. A fraction of protons are accelerated in the shock with a power-law-like energy distribution. The rate of proton injection to the acceleration process is approximately constant, and in the injection process, the phase-trapping mechanism for the protons by the upstream waves can play an important role. The dominant acceleration process is a Fermi-like process through repeated shock crossings of the protons. This process is a “fast” process in the sense that the time required for most of the accelerated protons to complete one cycle of the acceleration process is much shorter than the diffusion time. A fraction of the electrons are also accelerated by the same mechanism, and have a power-law-like energy distribution. However, the injection does not enter a steady state during the simulation, which may be related to the intermittent activity of the upstream waves. Upstream of the shock, a fraction of the electrons are pre-accelerated before reaching the shock, which may contribute to steady electron injection at a later time.

  14. Simulations of ion acceleration at non-relativistic shocks. III. Particle diffusion

    SciTech Connect

    Caprioli, D.; Spitkovsky, A.

    2014-10-10

    We use large hybrid (kinetic-protons-fluid-electrons) simulations to investigate the transport of energetic particles in self-consistent electromagnetic configurations of collisionless shocks. In previous papers of this series, we showed that ion acceleration may be very efficient (up to 10%-20% in energy), and outlined how the streaming of energetic particles amplifies the upstream magnetic field. Here, we measure particle diffusion around shocks with different strengths, finding that the mean free path for pitch-angle scattering of energetic ions is comparable with their gyroradii calculated in the self-generated turbulence. For moderately strong shocks, magnetic field amplification proceeds in the quasi-linear regime, and particles diffuse according to the self-generated diffusion coefficient, i.e., the scattering rate depends only on the amount of energy in modes with wavelengths comparable with the particle gyroradius. For very strong shocks, instead, the magnetic field is amplified up to non-linear levels, with most of the energy in modes with wavelengths comparable to the gyroradii of highest-energy ions, and energetic particles experience Bohm-like diffusion in the amplified field. We also show how enhanced diffusion facilitates the return of energetic particles to the shock, thereby determining the maximum energy that can be achieved in a given time via diffusive shock acceleration. The parameterization of the diffusion coefficient that we derive can be used to introduce self-consistent microphysics into large-scale models of cosmic ray acceleration in astrophysical sources, such as supernova remnants and clusters of galaxies.

  15. A Coupled Multiphysics Approach for Simulating Induced Seismicity, Ground Acceleration and Structural Damage

    NASA Astrophysics Data System (ADS)

    Podgorney, Robert; Coleman, Justin; Wilkins, Amdrew; Huang, Hai; Veeraraghavan, Swetha; Xia, Yidong; Permann, Cody

    2017-04-01

    Numerical modeling has played an important role in understanding the behavior of coupled subsurface thermal-hydro-mechanical (THM) processes associated with a number of energy and environmental applications since as early as the 1970s. While the ability to rigorously describe all key tightly coupled controlling physics still remains a challenge, there have been significant advances in recent decades. These advances are related primarily to the exponential growth of computational power, the development of more accurate equations of state, improvements in the ability to represent heterogeneity and reservoir geometry, and more robust nonlinear solution schemes. The work described in this paper documents the development and linkage of several fully-coupled and fully-implicit modeling tools. These tools simulate: (1) the dynamics of fluid flow, heat transport, and quasi-static rock mechanics; (2) seismic wave propagation from the sources of energy release through heterogeneous material; and (3) the soil-structural damage resulting from ground acceleration. These tools are developed in Idaho National Laboratory's parallel Multiphysics Object Oriented Simulation Environment, and are integrated together using a global implicit approach. The governing equations are presented, the numerical approach for simultaneously solving and coupling the three coupling physics tools is discussed, and the data input and output methodology is outlined. An example is presented to demonstrate the capabilities of the coupled multiphysics approach. The example involves simulating a system conceptually similar to the geothermal development in Basel Switzerland, and the resultant induced seismicity, ground motion and structural damage is predicted.

  16. Shock experiments and numerical simulations on low energy portable electrically exploding foil accelerators

    SciTech Connect

    Saxena, A. K.; Kaushik, T. C.; Gupta, Satish C.

    2010-03-15

    Two low energy (1.6 and 8 kJ) portable electrically exploding foil accelerators are developed for moderately high pressure shock studies at small laboratory scale. Projectile velocities up to 4.0 km/s have been measured on Kapton flyers of thickness 125 {mu}m and diameter 8 mm, using an in-house developed Fabry-Perot velocimeter. An asymmetric tilt of typically few milliradians has been measured in flyers using fiber optic technique. High pressure impact experiments have been carried out on tantalum, and aluminum targets up to pressures of 27 and 18 GPa, respectively. Peak particle velocities at the target-glass interface as measured by Fabry-Perot velocimeter have been found in good agreement with the reported equation of state data. A one-dimensional hydrodynamic code based on realistic models of equation of state and electrical resistivity has been developed to numerically simulate the flyer velocity profiles. The developed numerical scheme is validated against experimental and simulation data reported in literature on such systems. Numerically computed flyer velocity profiles and final flyer velocities have been found in close agreement with the previously reported experimental results with a significant improvement over reported magnetohydrodynamic simulations. Numerical modeling of low energy systems reported here predicts flyer velocity profiles higher than experimental values, indicating possibility of further improvement to achieve higher shock pressures.

  17. Accelerating atomistic simulations through self-learning bond-boost hyperdynamics

    SciTech Connect

    Perez, Danny; Voter, Arthur F

    2008-01-01

    By altering the potential energy landscape on which molecular dynamics are carried out, the hyperdynamics method of Voter enables one to significantly accelerate the simulation state-to-state dynamics of physical systems. While very powerful, successful application of the method entails solving the subtle problem of the parametrization of the so-called bias potential. In this study, we first clarify the constraints that must be obeyed by the bias potential and demonstrate that fast sampling of the biased landscape is key to the obtention of proper kinetics. We then propose an approach by which the bond boost potential of Miron and Fichthorn can be safely parametrized based on data acquired in the course of a molecular dynamics simulation. Finally, we introduce a procedure, the Self-Learning Bond Boost method, in which the parametrization is step efficiently carried out on-the-fly for each new state that is visited during the simulation by safely ramping up the strength of the bias potential up to its optimal value. The stability and accuracy of the method are demonstrated.

  18. DOE accelerated strategic computing initiative: challenges and opportunities for predictive materials simulation capabilities

    SciTech Connect

    Mailhiot, C.

    1997-10-01

    In response to the unprecedented national security challenges derived from the end of nuclear testing, the Defense Programs of the Department of Energy has developed a long-term strategic plan based on a vigorous Science-Based Stockpile Stewardship (SBSS) program. The main objective of the SBSS program is to ensure confidence in the performance, safety, and reliability of the stockpile on the basis of a fundamental science-based approach. A central element of this approach is the development of predictive, full-physics, full-scale computer simulation tools. As a critical component of the SBSS program, the Accelerated Strategic Computing Initiative (ASCI) was established to provide the required advances in computer platforms and to enable predictive, physics-based simulation technologies. Foremost among the key elements needed to develop predictive simulation capabilities, the development of improved physics-based materials models has been universally identified as one of the highest-priority, highest-leverage activity. We indicate some of the materials modeling issues of relevance to stockpile materials and illustrate how the ASCI program will enable the tools necessary to advance the state-of-the-art in the field of computational condensed matter and materials physics.

  19. Merging metadynamics into hyperdynamics: accelerated molecular simulations reaching time scales from microseconds to seconds.

    PubMed

    Bal, Kristof M; Neyts, Erik C

    2015-10-13

    The hyperdynamics method is a powerful tool to simulate slow processes at the atomic level. However, the construction of an optimal hyperdynamics potential is a task that is far from trivial. Here, we propose a generally applicable implementation of the hyperdynamics algorithm, borrowing two concepts from metadynamics. First, the use of a collective variable (CV) to represent the accelerated dynamics gives the method a very large flexibility and simplicity. Second, a metadynamics procedure can be used to construct a suitable history-dependent bias potential on-the-fly, effectively turning the algorithm into a self-learning accelerated molecular dynamics method. This collective variable-driven hyperdynamics (CVHD) method has a modular design: both the local system properties on which the bias is based, as well as the characteristics of the biasing method itself, can be chosen to match the needs of the considered system. As a result, system-specific details are abstracted from the biasing algorithm itself, making it extremely versatile and transparent. The method is tested on three model systems: diffusion on the Cu(001) surface and nickel-catalyzed methane decomposition, as examples of “reactive” processes with a bond-length-based CV, and the folding of a long polymer-like chain, using a set of dihedral angles as a CV. Boost factors up to 109, corresponding to a time scale of seconds, could be obtained while still accurately reproducing correct dynamics.

  20. Experimental Characterization of a Plasma Deflagration Accelerator for Simulating Fusion Wall Response to Disruption Events

    NASA Astrophysics Data System (ADS)

    Underwood, Thomas; Loebner, Keith; Cappelli, Mark

    2016-10-01

    In this work, the suitability of a pulsed deflagration accelerator to simulate the interaction of edge-localized modes with plasma first wall materials is investigated. Experimental measurements derived from a suite of diagnostics are presented that focus on the both the properties of the plasma jet and the manner in which such jets couple with material interfaces. Detailed measurements of the thermodynamic plasma state variables within the jet are presented using a quadruple Langmuir probe operating in current-saturation mode. This data in conjunction with spectroscopic measurements of H α Stark broadening via a fast-framing, intensified CCD camera provide spatial and temporal measurements of how the plasma density and temperature scale as a function of input energy. Using these measurements, estimates for the energy flux associated with the deflagration accelerator are found to be completely tunable over a range spanning 150 MW m-2 - 30 GW m-2. The plasma-material interface is investigated using tungsten tokens exposed to the plasma plume under variable conditions. Visualizations of resulting shock structures are achieved through Schlieren cinematography and energy transfer dynamics are discussed by presenting temperature measurements of exposed materials. This work is supported by the U.S. Department of Energy Stewardship Science Academic Program in addition to the National Defense Science Engineering Graduate Fellowship.

  1. OpenMP-accelerated SWAT simulation using Intel C and FORTRAN compilers: Development and benchmark

    NASA Astrophysics Data System (ADS)

    Ki, Seo Jin; Sugimura, Tak; Kim, Albert S.

    2015-02-01

    We developed a practical method to accelerate execution of Soil and Water Assessment Tool (SWAT) using open (free) computational resources. The SWAT source code (rev 622) was recompiled using a non-commercial Intel FORTRAN compiler in Ubuntu 12.04 LTS Linux platform, and newly named iOMP-SWAT in this study. GNU utilities of make, gprof, and diff were used to develop the iOMP-SWAT package, profile memory usage, and check identicalness of parallel and serial simulations. Among 302 SWAT subroutines, the slowest routines were identified using GNU gprof, and later modified using Open Multiple Processing (OpenMP) library in an 8-core shared memory system. In addition, a C wrapping function was used to rapidly set large arrays to zero by cross compiling with the original SWAT FORTRAN package. A universal speedup ratio of 2.3 was achieved using input data sets of a large number of hydrological response units. As we specifically focus on acceleration of a single SWAT run, the use of iOMP-SWAT for parameter calibrations will significantly improve the performance of SWAT optimization.

  2. Benchmarked Simulations of Slow Capillary Discharges for Laser-Plasma Accelerators

    NASA Astrophysics Data System (ADS)

    Johnson, Jeffrey; Colella, Phillip; Geddes, Cameron; Mittelberger, Daniel; Bulanov, Stepan; Esarey, Eric; Leemans, Wim; Applied Numerical Algorithms Group (Lbl) Team; Loasis Laboratory (Lbl) Team

    2011-10-01

    We report our progress on a non-equilibrium, 2-temperature plasma model used for slow capillary discharges pertinent to laser-plasma accelerators. In these experiments, energy transport plays a major role in the formation of a plasma channel, which is used to guide the laser and enhance acceleration. We describe a series of simulations used to study the effects of electrical and thermal conduction, diffusion, and externally-applied magnetic fields in present and ongoing experiments with relevant geometries and densities. Scylla, a 1D cylindrical plasma/hydro code, was used to explore transport models and to resolve the radial profile of the plasma within the capillary. It has also been benchmarked against existing codes and experimental data. Since the capillary has 3D features such as gas feed slots, we have begun implementing a multi-dimensional AMR plasma model that solves the governing equations on irregular domains. Application to the BELLA Project at LBNL will be discussed. This work was supported by the Department of En- ergy under contract number DE-AC02-05-CH11231.

  3. Accidental beam loss in superconducting accelerators: Simulations, consequences of accidents and protective measures

    SciTech Connect

    Drozhdin, A.; Mokhov, N.; Parker, B.

    1994-02-01

    The consequences of an accidental beam loss in superconducting accelerators and colliders of the next generation range from the mundane to rather dramatic, i.e., from superconducting magnet quench, to overheating of critical components, to a total destruction of some units via explosion. Specific measures are required to minimize and eliminate such events as much as practical. In this paper we study such accidents taking the Superconducting Supercollider complex as an example. Particle tracking, beam loss and energy deposition calculations were done using the realistic machine simulation with the Monte-Carlo codes MARS 12 and STRUCT. Protective measures for minimizing the damaging effects of prefire and misfire of injection and extraction kicker magnets are proposed here.

  4. Current status of MCNP6 as a simulation tool useful for space and accelerator applications

    SciTech Connect

    Mashnik, Stepan G; Bull, Jeffrey S; Hughes, H. Grady; Prael, Richard E; Sierk, Arnold J

    2012-07-20

    For the past several years, a major effort has been undertaken at Los Alamos National Laboratory (LANL) to develop the transport code MCNP6, the latest LANL Monte-Carlo transport code representing a merger and improvement of MCNP5 and MCNPX. We emphasize a description of the latest developments of MCNP6 at higher energies to improve its reliability in calculating rare-isotope production, high-energy cumulative particle production, and a gamut of reactions important for space-radiation shielding, cosmic-ray propagation, and accelerator applications. We present several examples of validation and verification of MCNP6 compared to a wide variety of intermediate- and high-energy experimental data on reactions induced by photons, mesons, nucleons, and nuclei at energies from tens of MeV to about 1 TeV/nucleon, and compare to results from other modern simulation tools.

  5. Jupiter entry simulation with the ANAA shock tube. [ANnular Arc Accelerator

    NASA Technical Reports Server (NTRS)

    Leibowitz, L. P.

    1974-01-01

    An annular arc accelerator (ANAA) shock tube has been built which produces shock velocities and pressures that simulate entry into the atmosphere of Jupiter. The ANAA driver deposits the energy of an arc discharge into a flowing gas, which then expands and cools without any delay for the opening of a diaphragm. A flow transducer, trigger system, and spark gap switches have been developed to coordinate the flow from a high-pressure helium driver with the discharge from a 300-kJ capacitor bank. Shock velocities up to 47 km/sec have been produced in 1.0 torr of hydrogen with the ANAA shock tube, compared with 35 km/sec velocity produced in a conical arc driver with three times the available energy. Attenuation with the ANAA shock tube is comparable to that of a conical arc driver shock tube, and initial spectroscopic measurements indicate that an impurity-free test slug is formed behind the shock wave.

  6. Vlasov Simulations of Ladder Climbing and Autoresonant Acceleration of Langmuir Waves

    NASA Astrophysics Data System (ADS)

    Hara, Kentaro; Barth, Ido; Kaminski, Erez; Dodin, Ilya; Fisch, Nathaniel

    2016-10-01

    The energy of plasma waves can be moved up and down the spectrum using chirped modulations of plasma parameters, which can be driven by external fields. Depending on the discreteness of the wave spectrum, this phenomenon is called ladder climbing (LC) or autroresonant acceleration (AR) of plasmons, and was first proposed by Barth et al. based on a linear fluid model. Here, we report a demonstration of LC/AR from first principles using fully nonlinear Vlasov simulations of collisionless bounded plasma. We show that, in agreement to the basic theory, plasmons survive substantial transformations of the spectrum and are destroyed only when their wave numbers become large enough to trigger Landau damping. The work was supported by the NNSA SSAA Program through DOE Research Grant No. DE-NA0002948 and the DTRA Grant No. HDTRA1-11-1-0037.

  7. Losses in a multi-cell accelerating cavity:. measurement against simulation

    NASA Astrophysics Data System (ADS)

    Balleyguier, Pascal

    In the Trispal CCL accelerating cavities, the coupling slots between contiguous cells had been optimized with MAFIA, in a way to maximize the shunt impedance. The result was a set of "4-petal" slots that were supposed to yield almost no shunt impedance drop, compared to a single cell cavity [P. Balleyguier, Linac conf. Geneva, 1996, p. 414]. In order to check this out, a cold model has been constructed. The goal was to accurately measure the Q-drop caused by coupling slots, and to compare it to predicted values. We achieved a good experimental precision on the Q-drop, and we can state that the predictions were definitely wrong: the actual Q-drop is (-22.5±0.5) %, about four times more than simulated. We conclude that the "4-petal" slots should be abandoned, and that 3D-code estimations of local power loss may be very inaccurate in some cases.

  8. GPU accelerated Monte Carlo simulation of Brownian motors dynamics with CUDA

    NASA Astrophysics Data System (ADS)

    Spiechowicz, J.; Kostur, M.; Machura, L.

    2015-06-01

    This work presents an updated and extended guide on methods of a proper acceleration of the Monte Carlo integration of stochastic differential equations with the commonly available NVIDIA Graphics Processing Units using the CUDA programming environment. We outline the general aspects of the scientific computing on graphics cards and demonstrate them with two models of a well known phenomenon of the noise induced transport of Brownian motors in periodic structures. As a source of fluctuations in the considered systems we selected the three most commonly occurring noises: the Gaussian white noise, the white Poissonian noise and the dichotomous process also known as a random telegraph signal. The detailed discussion on various aspects of the applied numerical schemes is also presented. The measured speedup can be of the astonishing order of about 3000 when compared to a typical CPU. This number significantly expands the range of problems solvable by use of stochastic simulations, allowing even an interactive research in some cases.

  9. Particle-in-Cell Simulations of THz Coherent Transition Radiation from Laser-Plasma Accelerators

    NASA Astrophysics Data System (ADS)

    Bruhwiler, D.; Messmer, P.; Cary, J. R.; Leemans, W. P.; Esarey, E.; Schroeder, C.; Geddes, C.; van Tilborg, J.; Shadwick, B.

    2004-11-01

    Laser wakefield accelerator (LWFA) concepts are characterized by ultra-high gradients and ultra-short (tens of fs) bunch lengths. Non-invasive bunch-length diagnostics, at or very near the plasma exit, are key to continuing the rapid advances in LWFA technology. These short bunches can radiate strongly at THz frequencies via coherent transition radiation (CTR) as they exit the plasma [1]. Careful measurements of the THz spectrum will provide the necessary bunch-length diagnostic [2], once the effects of various secondary complications have been quantified. Particle-in-cell simulations, using the VORPAL code [3] are being used to characterize CTR emitted from a self-modulated LWFA. The status of this on-going work will be presented. [1] Wim Leemans et al., Phys. Rev. Lett. 91, 074802-1 (2003). [2] C. Schroeder et al., Phys. Rev. E 69, 016501 (2004). [3] C. Nieter and J. Cary, J. Comp. Phys. 196, 488 (2004).

  10. Simulation of high-average power windows for accelerator production of tritium

    SciTech Connect

    Cummings, K A; Daily, L D; Mayhall, D J; Nelson, S D; Salem, J; Shang, C C

    1998-08-20

    Development of a robust, high-average-power (210 kW, CW) microwave transmission line system for the Accelerator Production of Tritium (APT) facility is a stringent engineering and operational requirement. One key component in this RF transmission system is the vacuum barrier window. The requirement of high-power handling capability coupled to the desirability of good mean time to failure characteristics can be treated substantially with a set of microwave, thermal-structural, and Weibull analysis codes. In this paper, we examine realistic 3-D engineering models of the ceramic windows. We model the detailed cooling circuit and make use of accurate heat deposition models for the RF. This input and simulation detail is used to analyze the thermal- structural induced stresses in baseline coaxial window configurations. We also use a Weibull-distribution failure.

  11. Accelerated equilibrium core composition search using a new MCNP-based simulator

    NASA Astrophysics Data System (ADS)

    Seifried, Jeffrey E.; Gorman, Phillip M.; Vujic, Jasmina L.; Greenspan, Ehud

    2014-06-01

    MocDown is a new Monte Carlo depletion and recycling simulator which couples neutron transport with MCNP and transmutation with ORIGEN. This modular approach to depletion allows for flexible operation by incorporating the accelerated progression of a complex fuel processing scheme towards equilibrium and by allowing for the online coupling of thermo-fluids feedback. MocDown also accounts for the variation of decay heat with fuel isotopics evolution. In typical cases, MocDown requires just over a day to find the equilibrium core composition for a multi-recycling fuel cycle, with a self-consistent thermo-fluids solution-a task that required between one and two weeks using previous Monte Carlo-based approaches.

  12. PIC Simulations of direct laser accelerated electron from underdense plasmas using the OMEGA EP Laser

    NASA Astrophysics Data System (ADS)

    Hussein, Amina; Batson, Thomas; Krushelnick, Karl; Willingale, Louise; Arefiev, Alex; Wang, Tao; Nilson, Phil; Froula, Dustin; Haberberger, Dan; Davies, Andrew; Theobald, Wolfgang; Williams, Jackson; Chen, Hui

    2016-10-01

    The OMEGA EP laser system is used to study channeling phenomena and direct laser acceleration (DLA) through an underdense plasma. The interaction of a ps laser pulse with a subcritical density CH plasma plume results in the expulsion of electron along the laser axis, forming a positively charged channel. Electrons confined within this channel are subject to the action of the laser field as well as the transverse electric field of the channel, resulting the DLA of these electrons and the formation of a high energy electron beam. We have performed 2D simulations of ultra-intense laser radiation with underdense plasma using the PIC code EPOCH to investigate electron densities and self-consistently generated electric fields, as well as electron trajectories. This work was supported by the National Laser Users' Facility (NLUF), DOE.

  13. Full-scale accelerated pavement testing of Texas Mobile Load Simulator

    SciTech Connect

    Chen, D.H.; Hugo, F.

    1998-09-01

    This paper presents the test results from full-scale accelerated pavement testing with the Texas Mobile Load Simulator. Data from in-situ instrumentation and nondestructive testing were collected and analyzed at different loading stages to assess material property changes under accelerated loading. Forensic studies were made to study material characteristics in the longitudinal and transverse directions. It was found that at the early stage of trafficking the test pad responded to falling weight deflectometer (FWD) load linearly, not only over the whole pavement system but also within individual layers. Before mobile load simulator testing, FWD data indicated the weakest area exists at the left wheel path (LWP) of 7.5-m line (7.5L). Later, this weak area was confirmed to have the highest rutting and the most intensive cracking. The dynamic cone penetration results showed that the base at this location was at its weakest. Also, at 7.5L the dry density was lowest, {approximately}7% lower with a moisture content {approximately}8% higher than the adjacent area. The LWP had higher FWD deflections than the right wheel path (RWP), and consequently the LWP manifested more rutting. This proved to be primarily due to differences in moisture content. This was probably because more water infiltrated in the area during rain due to manifestation of more extensive cracking during early phases of trafficking. The maximum surface deflection values increased as trafficking increased in the left and right wheel paths due to pavement deterioration, while deflection for the center remained constant because of the lack of traffic loading. The LWP had more rutting than the RWP and this correlated with the measured FWL deflections prior to trafficking. The WI values increased as trafficking increased for the LWP and RWP due to pavement deterioration. The majority (>60%) of rutting was from the 300-mm uncrushed river gravel base.

  14. Acceleration of Monte Carlo simulation of photon migration in complex heterogeneous media using Intel many-integrated core architecture.

    PubMed

    Gorshkov, Anton V; Kirillin, Mikhail Yu

    2015-08-01

    Over two decades, the Monte Carlo technique has become a gold standard in simulation of light propagation in turbid media, including biotissues. Technological solutions provide further advances of this technique. The Intel Xeon Phi coprocessor is a new type of accelerator for highly parallel general purpose computing, which allows execution of a wide range of applications without substantial code modification. We present a technical approach of porting our previously developed Monte Carlo (MC) code for simulation of light transport in tissues to the Intel Xeon Phi coprocessor. We show that employing the accelerator allows reducing computational time of MC simulation and obtaining simulation speed-up comparable to GPU. We demonstrate the performance of the developed code for simulation of light transport in the human head and determination of the measurement volume in near-infrared spectroscopy brain sensing.

  15. Nonlinear Site Response Due to Large Ground Acceleration: Observation and Computer Simulation

    NASA Astrophysics Data System (ADS)

    Noguchi, S.; Furumura, T.; Sasatani, T.

    2009-12-01

    We studied nonlinear site response due to large ground acceleration during the 2003 off-Miyagi Earthquake (Mw7.0) in Japan by means of horizontal-to-vertical spectral ratio analysis of S-wave motion. The results were then confirmed by finite-difference method (FDM) simulation of nonlinear seismic wave propagation. A nonlinear site response is often observed at soft sediment sites, and even at hard bedrock sites which are covered by thin soil layers. Nonlinear site response can be induced by strong ground motion whose peak ground acceleration (PGA) exceeds about 100 cm/s/s, and seriously affects the amplification of high frequency ground motion and PGA. Noguchi and Sasatani (2008) developed an efficient technique for quantitative evaluation of nonlinear site response using the horizontal-to-vertical spectral ratio of S-wave (S-H/V) derived from strong ground motion records, based on Wen et al. (2006). We applied this technique to perform a detailed analysis of the properties of nonlinear site response based on a large amount of data recorded at 132 K-NET and KiK-net strong motion stations in Northern Japan during the off-Miyagi Earthquake. We succeeded in demonstrating a relationship between ground motion level, nonlinear site response and surface soil characteristics. For example, the seismic data recorded at KiK-net IWTH26 showed obvious characteristics of nonlinear site response when the PGA exceeded 100 cm/s/s. As the ground motion level increased, the dominant peak of S-H/V shifted to lower frequency, the high frequency level of S-H/V dropped, and PGA amplification decreased. On the other hand, the records at MYGH03 seemed not to be affected by nonlinear site response even for high ground motion levels in which PGA exceeds 800 cm/s/s. The characteristics of such nonlinear site amplification can be modeled by evaluating Murnaghan constants (e.g. McCall, 1994), which are the third-order elastic constants. In order to explain the observed characteristics of

  16. Accelerating Simulation of Seismic Wave Propagation by Multi-GPUs (Invited)

    NASA Astrophysics Data System (ADS)

    Okamoto, T.; Takenaka, H.; Nakamura, T.; Aoki, T.

    2010-12-01

    Simulation of seismic wave propagation is essential in modern seismology: the effects of irregular topography of the surface, internal discontinuities and heterogeneity on the seismic waveforms must be precisely modeled in order to probe the Earth's and other planets' interiors, to study the earthquake sources, and to evaluate the strong ground motions due to earthquakes. Devices with high computing performance are necessary because in large scale simulations more than one billion of grid points are required. GPU (Graphics Processing Unit) is a remarkable device for its many core architecture with more-than-one-hundred processing units, and its high memory bandwidth. Now GPU delivers extremely high computing performance (more than one tera-flops in single-precision arithmetic) at a reduced power and cost compared to conventional CPUs. The simulation of seismic wave propagation is a memory intensive problem which involves large amount of data transfer between the memory and the arithmetic units while the number of arithmetic calculations is relatively small. Therefore the simulation should benefit from the high memory bandwidth of the GPU. Thus several approaches to adopt GPU to the simulation of seismic wave propagation have been emerging (e.g., Komatitsch et al., 2009; Micikevicius, 2009; Michea and Komatitsch, 2010; Aoi et al., SSJ 2009, JPGU 2010; Okamoto et al., SSJ 2009, SACSIS 2010). In this paper we describe our approach to accelerate the simulation of seismic wave propagation based on the finite-difference method (FDM) by adopting multi-GPU computing. The finite-difference scheme we use is the three-dimensional, velocity-stress staggered grid scheme (e.g., Grave 1996; Moczo et al., 2007) for heterogeneous medium with perfect elasticity (incorporation of an-elasticity is underway). We use the GPUs (NVIDIA S1070, 1.44 GHz) installed in the TSUBAME grid cluster in the Global Scientific Information and Computing Center, Tokyo Institute of Technology and NVIDIA

  17. Distribution of absorbed doses in the materials irradiated by ''RHODOTRON'' electron accelerator: Experiment and Monte Carlo simulations

    SciTech Connect

    Oleg E. Krivosheev et al.

    2001-07-02

    This paper describes the experimental setup and presents studies of absorbed doses in different metals and dielectrics along with corresponding Monte Carlo energy deposition simulations. Experiments were conducted using a 5 MeV electron accelerator. We used several Monte Carlo code systems, namely MARS, MCNP, and GEANT to simulate the absorbed doses under the same conditions as in experiment. We compare calculated and measured high and low absorbed doses (from few kGy to hundreds kGy) and discuss the applicability of these computer codes for applied accelerator dosimetry.

  18. A Comparison Between GATE and MCNPX Monte Carlo Codes in Simulation of Medical Linear Accelerator.

    PubMed

    Sadoughi, Hamid-Reza; Nasseri, Shahrokh; Momennezhad, Mahdi; Sadeghi, Hamid-Reza; Bahreyni-Toosi, Mohammad-Hossein

    2014-01-01

    Radiotherapy dose calculations can be evaluated by Monte Carlo (MC) simulations with acceptable accuracy for dose prediction in complicated treatment plans. In this work, Standard, Livermore and Penelope electromagnetic (EM) physics packages of GEANT4 application for tomographic emission (GATE) 6.1 were compared versus Monte Carlo N-Particle eXtended (MCNPX) 2.6 in simulation of 6 MV photon Linac. To do this, similar geometry was used for the two codes. The reference values of percentage depth dose (PDD) and beam profiles were obtained using a 6 MV Elekta Compact linear accelerator, Scanditronix water phantom and diode detectors. No significant deviations were found in PDD, dose profile, energy spectrum, radial mean energy and photon radial distribution, which were calculated by Standard and Livermore EM models and MCNPX, respectively. Nevertheless, the Penelope model showed an extreme difference. Statistical uncertainty in all the simulations was <1%, namely 0.51%, 0.27%, 0.27% and 0.29% for PDDs of 10 cm(2)× 10 cm(2) filed size, for MCNPX, Standard, Livermore and Penelope models, respectively. Differences between spectra in various regions, in radial mean energy and in photon radial distribution were due to different cross section and stopping power data and not the same simulation of physics processes of MCNPX and three EM models. For example, in the Standard model, the photoelectron direction was sampled from the Gavrila-Sauter distribution, but the photoelectron moved in the same direction of the incident photons in the photoelectric process of Livermore and Penelope models. Using the same primary electron beam, the Standard and Livermore EM models of GATE and MCNPX showed similar output, but re-tuning of primary electron beam is needed for the Penelope model.

  19. A Comparison Between GATE and MCNPX Monte Carlo Codes in Simulation of Medical Linear Accelerator

    PubMed Central

    Sadoughi, Hamid-Reza; Nasseri, Shahrokh; Momennezhad, Mahdi; Sadeghi, Hamid-Reza; Bahreyni-Toosi, Mohammad-Hossein

    2014-01-01

    Radiotherapy dose calculations can be evaluated by Monte Carlo (MC) simulations with acceptable accuracy for dose prediction in complicated treatment plans. In this work, Standard, Livermore and Penelope electromagnetic (EM) physics packages of GEANT4 application for tomographic emission (GATE) 6.1 were compared versus Monte Carlo N-Particle eXtended (MCNPX) 2.6 in simulation of 6 MV photon Linac. To do this, similar geometry was used for the two codes. The reference values of percentage depth dose (PDD) and beam profiles were obtained using a 6 MV Elekta Compact linear accelerator, Scanditronix water phantom and diode detectors. No significant deviations were found in PDD, dose profile, energy spectrum, radial mean energy and photon radial distribution, which were calculated by Standard and Livermore EM models and MCNPX, respectively. Nevertheless, the Penelope model showed an extreme difference. Statistical uncertainty in all the simulations was <1%, namely 0.51%, 0.27%, 0.27% and 0.29% for PDDs of 10 cm2× 10 cm2 filed size, for MCNPX, Standard, Livermore and Penelope models, respectively. Differences between spectra in various regions, in radial mean energy and in photon radial distribution were due to different cross section and stopping power data and not the same simulation of physics processes of MCNPX and three EM models. For example, in the Standard model, the photoelectron direction was sampled from the Gavrila-Sauter distribution, but the photoelectron moved in the same direction of the incident photons in the photoelectric process of Livermore and Penelope models. Using the same primary electron beam, the Standard and Livermore EM models of GATE and MCNPX showed similar output, but re-tuning of primary electron beam is needed for the Penelope model. PMID:24696804

  20. Progress towards the development of transient ram accelerator simulation as part of the U.S. Air Force Armament Directorate Research Program

    NASA Astrophysics Data System (ADS)

    Sinha, N.; York, B. J.; Dash, S. M.; Drabczuk, R.; Rolader, G. E.

    1992-07-01

    This paper describes the development of an advanced CFD simulation capability in support of the U.S. Air Force Armament Directorate's ram accelerator research initiative. The state-of-the-art CRAFT computer code has been specialized for high fidelity, transient ram accelerator simulations via inclusion of generalized dynamic gridding, solution adaptive grid clustering, high pressure thermochemistry, etc. Selected ram accelerator simulations are presented which serve to exhibit the CRAFT code's capabilities and identify some of the principal research/design issues.

  1. Accelerating the design of solar thermal fuel materials through high throughput simulations.

    PubMed

    Liu, Yun; Grossman, Jeffrey C

    2014-12-10

    Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.

  2. GPU accelerated flow solver for direct numerical simulation of turbulent flows

    SciTech Connect

    Salvadore, Francesco; Botti, Michela

    2013-02-15

    Graphical processing units (GPUs), characterized by significant computing performance, are nowadays very appealing for the solution of computationally demanding tasks in a wide variety of scientific applications. However, to run on GPUs, existing codes need to be ported and optimized, a procedure which is not yet standardized and may require non trivial efforts, even to high-performance computing specialists. In the present paper we accurately describe the porting to CUDA (Compute Unified Device Architecture) of a finite-difference compressible Navier–Stokes solver, suitable for direct numerical simulation (DNS) of turbulent flows. Porting and validation processes are illustrated in detail, with emphasis on computational strategies and techniques that can be applied to overcome typical bottlenecks arising from the porting of common computational fluid dynamics solvers. We demonstrate that a careful optimization work is crucial to get the highest performance from GPU accelerators. The results show that the overall speedup of one NVIDIA Tesla S2070 GPU is approximately 22 compared with one AMD Opteron 2352 Barcelona chip and 11 compared with one Intel Xeon X5650 Westmere core. The potential of GPU devices in the simulation of unsteady three-dimensional turbulent flows is proved by performing a DNS of a spatially evolving compressible mixing layer.

  3. Multi-GPU accelerated multi-spin Monte Carlo simulations of the 2D Ising model

    NASA Astrophysics Data System (ADS)

    Block, Benjamin; Virnau, Peter; Preis, Tobias

    2010-09-01

    A Modern Graphics Processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two-dimensional Ising model [T. Preis et al., Journal of Chemical Physics 228 (2009) 4468-4477] in order to overcome the memory limitations of a single GPU which enables us to simulate significantly larger systems. Using multi-spin coding techniques, we are able to accelerate simulations on a single GPU by factors up to 35 compared to an optimized single Central Processor Unit (CPU) core implementation which employs multi-spin coding. By combining the Compute Unified Device Architecture (CUDA) with the Message Parsing Interface (MPI) on the CPU level, a single Ising lattice can be updated by a cluster of GPUs in parallel. For large systems, the computation time scales nearly linearly with the number of GPUs used. As proof of concept we reproduce the critical temperature of the 2D Ising model using finite size scaling techniques.

  4. Lorentz boosted frame simulation of Laser wakefield acceleration in quasi-3D geometry

    NASA Astrophysics Data System (ADS)

    Yu, Peicheng; Xu, Xinlu; Davidson, Asher; Tableman, Adam; Meyers, Michael; Dalichaouch, Thamine; Tsung, Frank; Decyk, Viktor; Fiuza, Frederico; Vieira, Jorge; Fonseca, Ricardo; Lu, Wei; Silva, Luis; Mori, Warren

    2015-11-01

    We present results on a systematic study of Particle-In-Cell simulation of Laser Wakefield Acceleration (LWFA) by combining the Lorentz boosted frame technique with the quasi-3D algorithm, in which fields are expanded into azimuthal harmonics and solved on an r - z PIC grid keeping only a few harmonics. The studies emphasize on LWFA in the nonlinear blowout regime, which is more challenging from a computational standpoint. We first discuss strategies for eliminating the numerical Cerenkov instability (NCI) that inevitably arises due to the presence of plasma drifting across the grid with relativistic speeds in quasi-3D geometry. These strategies work for FFT based Maxwell solvers. We have incorporated these mitigation strategies into our PIC code OSIRIS by adding a new hybrid Yee-FFT Maxwell solver. With these strategies, OSIRIS can now be used to combine the quasi-3D algorithm and Lorentz boosted frame technique, and carry out high fidelity LWFA boosted frame simulation with no evidence of the NCI in the quasi-3D geometry, leading to unprecedented speedups. Work supported by NSF and DOE.

  5. GPU accelerated flow solver for direct numerical simulation of turbulent flows

    NASA Astrophysics Data System (ADS)

    Salvadore, Francesco; Bernardini, Matteo; Botti, Michela

    2013-02-01

    Graphical processing units (GPUs), characterized by significant computing performance, are nowadays very appealing for the solution of computationally demanding tasks in a wide variety of scientific applications. However, to run on GPUs, existing codes need to be ported and optimized, a procedure which is not yet standardized and may require non trivial efforts, even to high-performance computing specialists. In the present paper we accurately describe the porting to CUDA (Compute Unified Device Architecture) of a finite-difference compressible Navier-Stokes solver, suitable for direct numerical simulation (DNS) of turbulent flows. Porting and validation processes are illustrated in detail, with emphasis on computational strategies and techniques that can be applied to overcome typical bottlenecks arising from the porting of common computational fluid dynamics solvers. We demonstrate that a careful optimization work is crucial to get the highest performance from GPU accelerators. The results show that the overall speedup of one NVIDIA Tesla S2070 GPU is approximately 22 compared with one AMD Opteron 2352 Barcelona chip and 11 compared with one Intel Xeon X5650 Westmere core. The potential of GPU devices in the simulation of unsteady three-dimensional turbulent flows is proved by performing a DNS of a spatially evolving compressible mixing layer.

  6. Accelerating the Design of Solar Thermal Fuel Materials through High Throughput Simulations

    SciTech Connect

    Liu, Y; Grossman, JC

    2014-12-01

    Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.

  7. Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach.

    PubMed

    Kadam, Shantanu; Vanka, Kumar

    2013-02-15

    Methods based on the stochastic formulation of chemical kinetics have the potential to accurately reproduce the dynamical behavior of various biochemical systems of interest. However, the computational expense makes them impractical for the study of real systems. Attempts to render these methods practical have led to the development of accelerated methods, where the reaction numbers are modeled by Poisson random numbers. However, for certain systems, such methods give rise to physically unrealistic negative numbers for species populations. The methods which make use of binomial variables, in place of Poisson random numbers, have since become popular, and have been partially successful in addressing this problem. In this manuscript, the development of two new computational methods, based on the representative reaction approach (RRA), has been discussed. The new methods endeavor to solve the problem of negative numbers, by making use of tools like the stochastic simulation algorithm and the binomial method, in conjunction with the RRA. It is found that these newly developed methods perform better than other binomial methods used for stochastic simulations, in resolving the problem of negative populations.

  8. Accelerated path integral methods for atomistic simulations at ultra-low temperatures

    NASA Astrophysics Data System (ADS)

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-01

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5+. We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.

  9. Accelerated path integral methods for atomistic simulations at ultra-low temperatures.

    PubMed

    Uhl, Felix; Marx, Dominik; Ceriotti, Michele

    2016-08-07

    Path integral methods provide a rigorous and systematically convergent framework to include the quantum mechanical nature of atomic nuclei in the evaluation of the equilibrium properties of molecules, liquids, or solids at finite temperature. Such nuclear quantum effects are often significant for light nuclei already at room temperature, but become crucial at cryogenic temperatures such as those provided by superfluid helium as a solvent. Unfortunately, the cost of converged path integral simulations increases significantly upon lowering the temperature so that the computational burden of simulating matter at the typical superfluid helium temperatures becomes prohibitive. Here we investigate how accelerated path integral techniques based on colored noise generalized Langevin equations, in particular the so-called path integral generalized Langevin equation thermostat (PIGLET) variant, perform in this extreme quantum regime using as an example the quasi-rigid methane molecule and its highly fluxional protonated cousin, CH5 (+). We show that the PIGLET technique gives a speedup of two orders of magnitude in the evaluation of structural observables and quantum kinetic energy at ultralow temperatures. Moreover, we computed the spatial spread of the quantum nuclei in CH4 to illustrate the limits of using such colored noise thermostats close to the many body quantum ground state.

  10. Evaluation of the physical annealing strategy for simulated annealing: a function-based analysis in the landscape paradigm.

    PubMed

    Hasegawa, M

    2012-05-01

    The effectiveness of the actual annealing strategy in finite-time optimization by simulated annealing (SA) is analyzed by focusing on the search function of the relaxation dynamics observed in the multimodal landscape of the cost function. The rate-cycling experiment, which was introduced in the previous study [M. Hasegawa, Phys. Rev. E 83, 036708 (2011)] to examine the role of the relaxation dynamics in optimization, and the temperature-cycling experiment, which was developed for a laboratory experiment on relaxation-related phenomena, are conducted on two types of random traveling salesman problems (TSPs). In each experiment, the SA search starting from a quenched solution is performed systematically under a nonmonotonic temperature control used in the actual heat treatment of metals and glasses. The results show that, as in the previous monotonic cooling from a random solution, the optimizing ability is enhanced by allocating a lot of time to the search performed near an effective intermediate temperature irrespective of the annealing technique. In this productive phase, the relaxation dynamics successfully function as an optimizer and the relevant characteristics analogous to the stabilization phenomenon and the acceleration of relaxation, which are observed in glass-forming materials, play favorable roles in the present optimization. This nonmonotonic approach also has the advantage of a wider operation range of the effective relaxation dynamics, and in conclusion, the actual annealing strategy is useful and more workable than the conventional slow-cooling strategy, at least for the present TSPs. Further discussion is given of an illuminating aspect of computational physics analysis in the optimization algorithm research.

  11. Evaluation of the physical annealing strategy for simulated annealing: A function-based analysis in the landscape paradigm

    NASA Astrophysics Data System (ADS)

    Hasegawa, M.

    2012-05-01

    The effectiveness of the actual annealing strategy in finite-time optimization by simulated annealing (SA) is analyzed by focusing on the search function of the relaxation dynamics observed in the multimodal landscape of the cost function. The rate-cycling experiment, which was introduced in the previous study [M. Hasegawa, Phys. Rev. EPLEEE81063-651X 10.1103/PhysRevE.83.036708 83, 036708 (2011)] to examine the role of the relaxation dynamics in optimization, and the temperature-cycling experiment, which was developed for a laboratory experiment on relaxation-related phenomena, are conducted on two types of random traveling salesman problems (TSPs). In each experiment, the SA search starting from a quenched solution is performed systematically under a nonmonotonic temperature control used in the actual heat treatment of metals and glasses. The results show that, as in the previous monotonic cooling from a random solution, the optimizing ability is enhanced by allocating a lot of time to the search performed near an effective intermediate temperature irrespective of the annealing technique. In this productive phase, the relaxation dynamics successfully function as an optimizer and the relevant characteristics analogous to the stabilization phenomenon and the acceleration of relaxation, which are observed in glass-forming materials, play favorable roles in the present optimization. This nonmonotonic approach also has the advantage of a wider operation range of the effective relaxation dynamics, and in conclusion, the actual annealing strategy is useful and more workable than the conventional slow-cooling strategy, at least for the present TSPs. Further discussion is given of an illuminating aspect of computational physics analysis in the optimization algorithm research.

  12. Combining rigorous diffraction calculation and GPU accelerated nonsequential raytracing for high precision simulation of a linear grating spectrometer

    NASA Astrophysics Data System (ADS)

    Mauch, Florian; Fleischle, David; Lyda, Wolfram; Osten, Wolfgang; Krug, Torsten; Häring, Reto

    2011-05-01

    Simulation of grating spectrometers constitutes the problem of propagating a spectrally broad light field through a macroscopic optical system that contains a nanostructured grating surface. The interest of the simulation is to quantify and optimize the stray light behaviour, which is the limiting factor in modern high end spectrometers. In order to accomplish this we present a simulation scheme that combines a RCWA (rigorous coupled wave analysis) simulation of the grating surface with a selfmade GPU (graphics processor unit) accelerated nonsequential raytracer. Using this, we are able to represent the broad spectrum of the light field as a superposition of many monochromatic raysets and handle the huge raynumber in reasonable time.

  13. Advanced Simulation and Optimization Tools for Dynamic Aperture of Non-scaling FFAGs and Accelerators including Modern User Interfaces

    SciTech Connect

    Mills, F.; Makino, Kyoko; Berz, Martin; Johnstone, C.

    2010-09-01

    With the U.S. experimental effort in HEP largely located at laboratories supporting the operations of large, highly specialized accelerators, colliding beam facilities, and detector facilities, the understanding and prediction of high energy particle accelerators becomes critical to the success, overall, of the DOE HEP program. One area in which small businesses can contribute to the ongoing success of the U.S. program in HEP is through innovations in computer techniques and sophistication in the modeling of high-energy accelerators. Accelerator modeling at these facilities is performed by experts with the product generally highly specific and representative only of in-house accelerators or special-interest accelerator problems. Development of new types of accelerators like FFAGs with their wide choices of parameter modifications, complicated fields, and the simultaneous need to efficiently handle very large emittance beams requires the availability of new simulation environments to assure predictability in operation. In this, ease of use and interfaces are critical to realizing a successful model, or optimization of a new design or working parameters of machines. In Phase I, various core modules for the design and analysis of FFAGs were developed and Graphical User Interfaces (GUI) have been investigated instead of the more general yet less easily manageable console-type output COSY provides.

  14. The design of a simulated in-line side-coupled 6 MV linear accelerator waveguide.

    PubMed

    St Aubin, Joel; Steciw, Stephen; Fallone, B G

    2010-02-01

    The design of a 3D in-line side-coupled 6 MV linac waveguide for medical use is given, and the effect of the side-coupling and port irises on the radio frequency (RF), beam dynamics, and dosimetric solutions is examined. This work was motivated by our research on a linac-MR hybrid system, where accurate electron trajectory information for a clinical medical waveguide in the presence of an external magnetic field was needed. For this work, the design of the linac waveguide was generated using the finite element method. The design outlined here incorporates the necessary geometric changes needed to incorporate a full-end accelerating cavity with a single-coupling iris, a waveguide-cavity coupling port iris that allows power transfer into the waveguide from the magnetron, as well as a method to control the RF field magnitude within the first half accelerating cavity into which the electrons from the gun are injected. With the full waveguide designed to resonate at 2998.5 +/- 0.1 MHz, a full 3D RF field solution was obtained. The accuracy of the 3D RF field solution was estimated through a comparison of important linac parameters (Q factor, shunt impedance, transit time factor, and resonant frequency) calculated for one accelerating cavity with the benchmarked program SUPERFISH. It was found that the maximum difference between the 3D solution and SUPERFISH was less than 0.03%. The eigenvalue solver, which determines the resonant frequencies of the 3D side-coupled waveguide simulation, was shown to be highly accurate through a comparison with lumped circuit theory. Two different waveguide geometries were examined, one incorporating a 0.5 mm first side cavity shift and another with a 1.5 mm first side cavity shift. The asymmetrically placed side-coupling irises and the port iris for both models were shown to introduce asymmetries in the RF field large enough to cause a peak shift and skewing (center of gravity minus peak shift) of an initially cylindrically uniform

  15. Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.

    PubMed

    Miao, Yinglong; Sinko, William; Pierce, Levi; Bucher, Denis; Walker, Ross C; McCammon, J Andrew

    2014-07-08

    Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. In this work, we systematically compare the accuracy of different reweighting algorithms including the exponential average, Maclaurin series, and cumulant expansion on three model systems: alanine dipeptide, chignolin, and Trp-cage. Exponential average reweighting can recover the original free energy profiles easily only when the distribution of the boost potential is narrow (e.g., the range ≤20kBT) as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, exponential average generally leads to high energetic fluctuations, largely due to the fact that the Boltzmann reweighting factors are dominated by a very few high boost potential frames. In comparison, reweighting based on Maclaurin series expansion (equivalent to cumulant expansion on the first order) greatly suppresses the energetic noise but often gives incorrect energy minimum positions and significant errors at the energy barriers (∼2-3kBT). Finally, reweighting using cumulant expansion to the second order is able to recover the most accurate free energy profiles within statistical errors of ∼kBT, particularly when the distribution of the boost potential exhibits low anharmonicity (i.e., near-Gaussian distribution), and should be of wide applicability. A toolkit of Python scripts for aMD reweighting "PyReweighting" is distributed free of charge at http://mccammon.ucsd.edu/computing/amdReweighting/.

  16. Accelerating groundwater flow simulation in MODFLOW using JASMIN-based parallel computing.

    PubMed

    Cheng, Tangpei; Mo, Zeyao; Shao, Jingli

    2014-01-01

    To accelerate the groundwater flow simulation process, this paper reports our work on developing an efficient parallel simulator through rebuilding the well-known software MODFLOW on JASMIN (J Adaptive Structured Meshes applications Infrastructure). The rebuilding process is achieved by designing patch-based data structure and parallel algorithms as well as adding slight modifications to the compute flow and subroutines in MODFLOW. Both the memory requirements and computing efforts are distributed among all processors; and to reduce communication cost, data transfers are batched and conveniently handled by adding ghost nodes to each patch. To further improve performance, constant-head/inactive cells are tagged and neglected during the linear solving process and an efficient load balancing strategy is presented. The accuracy and efficiency are demonstrated through modeling three scenarios: The first application is a field flow problem located at Yanming Lake in China to help design reasonable quantity of groundwater exploitation. Desirable numerical accuracy and significant performance enhancement are obtained. Typically, the tagged program with load balancing strategy running on 40 cores is six times faster than the fastest MICCG-based MODFLOW program. The second test is simulating flow in a highly heterogeneous aquifer. The AMG-based JASMIN program running on 40 cores is nine times faster than the GMG-based MODFLOW program. The third test is a simplified transient flow problem with the order of tens of millions of cells to examine the scalability. Compared to 32 cores, parallel efficiency of 77 and 68% are obtained on 512 and 1024 cores, respectively, which indicates impressive scalability.

  17. Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer.

    PubMed

    Mukherjee, Shruti; Kar, Rajiv K; Nanga, Ravi Prakash Reddy; Mroue, Kamal H; Ramamoorthy, Ayyalusamy; Bhunia, Anirban

    2017-07-26

    Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7 : 3), POPC/POPS (7 : 3), and POPG/POPE (1 : 3 and 3 : 1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.

  18. Generalized Temporal Acceleration Scheme for Kinetic Monte Carlo Simulations of Surface Catalytic Processes by Scaling the Rates of Fast Reactions.

    PubMed

    Dybeck, Eric Christopher; Plaisance, Craig Patrick; Neurock, Matthew

    2017-02-14

    A novel algorithm has been developed to achieve temporal acceleration during kinetic Monte Carlo (KMC) simulations of surface catalytic processes. This algorithm allows for the direct simulation of reaction networks containing kinetic processes occurring on vastly disparate timescales which computationally overburden standard KMC methods. Previously developed methods for temporal acceleration in KMC have been designed for specific systems and often require a priori information from the user such as identifying the fast and slow processes. In the approach presented herein, quasi-equilibrated processes are identified automatically based on previous executions of the forward and reverse reactions. Temporal acceleration is achieved by automatically scaling the intrinsic rate constants of the quasi-equilibrated processes, bringing their rates closer to the timescales of the slow kinetically relevant non-equilibrated processes. All reactions are still simulated directly, although with modified rate constants. Abrupt changes in the underlying dynamics of the reaction network are identified during the simulation and the reaction rate constants are rescaled accordingly. The algorithm has been utilized here to model the Fischer-Tropsch synthesis reaction over ruthenium nanoparticles. This reaction network has multiple timescale-disparate processes which would be intractable to simulate without the aid of temporal acceleration. The accelerated simulations are found to give reaction rates and selectivities indistinguishable from those calculated by an equivalent mean-field kinetic model. The computational savings of the algorithm can span many orders of magnitude in realistic systems and the computational cost is not limited by the magnitude of the timescale disparity in the system processes. Furthermore, the algorithm has been designed in a generic fashion and can easily be applied to other surface catalytic processes of interest.

  19. IEC accelerator beam coordinate transformations for clinical Monte Carlo simulation from a phase space or full BEAMnrc particle source.

    PubMed

    Bush, Karl K; Zavgorodni, Sergei F

    2010-12-01

    Monte Carlo simulation of clinical treatment plans require, in general, a coordinate transformation to describe the incident radiation field orientation on a patient phantom coordinate system. The International Electrotechnical Commission (IEC) has defined an accelerator coordinate system along with positive directions for gantry, couch and collimator rotations. In order to describe the incident beam's orientation with respect to the patient's coordinate system, DOSXYZnrc simulations often require transformation of the accelerator's gantry, couch and collimator angles to describe the incident beam. Similarly, versions of the voxelized Monte Carlo code (VMC(++)) require non-trivial transformation of the accelerator's gantry, couch and collimator angles to standard Euler angles α, β, γ, to describe an incident phase space source orientation with respect to the patient's coordinate system. The transformations, required by each of these Monte Carlo codes to transport phase spaces through a phantom, have been derived with a rotation operator approach. The transformations have been tested and verified against the Eclipse treatment planning system.

  20. Experimental and Simulated Characterization of a Beam Shaping Assembly for Accelerator- Based Boron Neutron Capture Therapy (AB-BNCT)

    SciTech Connect

    Burlon, Alejandro A.; Valda, Alejandro A.; Girola, Santiago; Minsky, Daniel M.; Kreiner, Andres J.

    2010-08-04

    In the frame of the construction of a Tandem Electrostatic Quadrupole Accelerator facility devoted to the Accelerator-Based Boron Neutron Capture Therapy, a Beam Shaping Assembly has been characterized by means of Monte-Carlo simulations and measurements. The neutrons were generated via the {sup 7}Li(p, n){sup 7}Be reaction by irradiating a thick LiF target with a 2.3 MeV proton beam delivered by the TANDAR accelerator at CNEA. The emerging neutron flux was measured by means of activation foils while the beam quality and directionality was evaluated by means of Monte Carlo simulations. The parameters show compliance with those suggested by IAEA. Finally, an improvement adding a beam collimator has been evaluated.

  1. Simulation of launch and re-entry acceleration profiles for testing of shuttle and unmanned microgravity research payloads

    NASA Astrophysics Data System (ADS)

    Cassanto, J. M.; Ziserman, H. I.; Chapman, D. K.; Korszun, Z. R.; Todd, P.

    Microgravity experiments designed for execution in Get-Away Special canisters, Hitchhiker modules, and Reusable Re-entry Satellites will be subjected to launch and re-entry accelerations. Crew-dependent provisions for preventing acceleration damage to equipment or products will not be available for these payloads during flight; therefore, the effects of launch and re-entry accelerations on all aspects of such payloads must be evaluated prior to flight. A procedure was developed for conveniently simulating the launch and re-entry acceleration profiles of the Space Shuttle (3.3 and 1.7 × g maximum, respectively) and of two versions of NASA's proposed materials research Re-usable Re-entry Satellite (8 × g maximum in one case and 4 × g in the other). By using the 7 m centrifuge of the Gravitational Plant Physiology Laboratory in Philadelphia it was found possible to simulate the time dependence of these 5 different acceleration episodes for payload masses up to 59 kg. A commercial low-cost payload device, the “Materials Dispersion Apparatus” of Instrumentation Technology Associates was tested for (1) integrity of mechanical function, (2) retention of fluid in its compartments, and (3) integrity of products under simulated re-entry g-loads. In particular, the sharp rise from 1 g to maximum g-loading that occurs during re-entry in various unmanned vehicles was successfully simulated, conditions were established for reliable functioning of the MDA, and crystals of 5 proteins suspended in compartments filled with mother liquor were subjected to this acceleration load.

  2. Simulation of launch and re-entry acceleration profiles for testing of shuttle and unmanned microgravity research payloads.

    PubMed

    Cassanto, J M; Ziserman, H I; Chapman, D K; Korszun, Z R; Todd, P

    1988-01-01

    Microgravity experiments designed for execution in Get-Away Special canisters, Hitchhiker modules, and Reusable Re-entry Satellites will be subjected to launch and re-entry accelerations. Crew-dependent provisions for preventing acceleration damage to equipment or products will not be available for these payloads during flight; therefore, the effects of launch and re-entry accelerations on all aspects of such payloads must be evaluated prior to flight. A procedure was developed for conveniently simulating the launch and re-entry acceleration profiles of the Space Shuttle (3.3 and 1.7 x g maximum, respectively) and of two versions of NASA's proposed materials research Re-usable Re-entry Satellite (8 x g maximum in one case and 4 x g in the other). By using the 7 m centrifuge of the Gravitational Plant Physiology Laboratory in Philadelphia it was found possible to simulate the time dependence of these 5 different acceleration episodes for payload masses up to 59 kg. A commercial low-cost payload device, the "Materials Dispersion Apparatus" of Instrumentation Technology Associates was tested for (1) integrity of mechanical function, (2) retention of fluid in its compartments, and (3) integrity of products under simulated re-entry g-loads. In particular, the sharp rise from 1 g to maximum g-loading that occurs during re-entry in various unmanned vehicles was successfully simulated, conditions were established for reliable functioning of the MDA, and crystals of 5 proteins suspended in compartments filled with mother liquor were subjected to this acceleration load.

  3. A Theoretical Analysis of Anderson Acceleration and Its Application in Multiphysics Simulation for Light-Water Reactors

    NASA Astrophysics Data System (ADS)

    Toth, Alexander Raymond

    In this work, we are concerned with both contributing to the theoretical foundation for Anderson acceleration, a method for accelerating the convergence rate of Picard iteration, and evaluating its performance in the context of coupled multiphysics problems in nuclear reactor simulation. Anderson acceleration proceeds by maintaining a depth of previous iterate information in order to compute a new iterate as a linear combination of previous evaluations of the fixed-point map, where the linear combination coefficients are obtained by solving a linear leastsquares problem. Prior to this work, theory for this method was fairly sparse, dealing mainly with showing its relation to quasi-Newton multisecant updating and, when applied to linear problems, GMRES iteration. The analysis presented in this work significantly expands upon the theory for this method. As this method is intended as an acceleration method for Picard iteration, our analysis concerns problems for which Picard iteration is convergent, namely when the fixed-point mapping is contractive. We present analysis which represent the first convergence results for limited-memory variations of Anderson acceleration and for nonlinear problems. Additionally, we present analysis for several variations on the standard Anderson acceleration method. In particular, we consider a variation which adjusts the memory utilization in order to maintain good conditioning of the least-squares problem, and we present local improvement results for the case in which the fixed-point map can only be evaluated approximately. With respect to coupled multiphysics problems, we examine Anderson acceleration as an alternative to Picard iteration in the context of black-box code coupling in nuclear reactor simulation. Picard iteration comes with several drawbacks in this context, namely relatively slow convergence and poor robustness. To test the potential for Anderson acceleration to improve upon the weaknesses of Picard iteration, we first

  4. Particle acceleration in regions of magnetic flux emergence: a statistical approach using test-particle- and MHD-simulations

    NASA Astrophysics Data System (ADS)

    Vlahos, Loukas; Archontis, Vasilis; Isliker, Heinz

    We consider 3D nonlinear MHD simulations of an emerging flux tube, from the convection zone into the corona, focusing on the coronal part of the simulations. We first analyze the statistical nature and spatial structure of the electric field, calculating histograms and making use of iso-contour visualizations. Then test-particle simulations are performed for electrons, in order to study heating and acceleration phenomena, as well as to determine HXR emission. This study is done by comparatively exploring quiet, turbulent explosive, and mildly explosive phases of the MHD simulations. Also, the importance of collisional and relativistic effects is assessed, and the role of the integration time is investigated. Particular aim of this project is to verify the quasi- linear assumptions made in standard transport models, and to identify possible transport effects that cannot be captured with the latter. In order to determine the relation of our results to Fermi acceleration and Fokker-Planck modeling, we determine the standard transport coefficients. After all, we find that the electric field of the MHD simulations must be downscaled in order to prevent an un-physically high degree of acceleration, and the value chosen for the scale factor strongly affects the results. In different MHD time-instances we find heating to take place, and acceleration that depends on the level of MHD turbulence. Also, acceleration appears to be a transient phenomenon, there is a kind of saturation effect, and the parallel dynamics clearly dominate the energetics. The HXR spectra are not yet really compatible with observations, we have though to further explore the scaling of the electric field and the integration times used.

  5. ELECTRON ACCELERATIONS AT HIGH MACH NUMBER SHOCKS: TWO-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS IN VARIOUS PARAMETER REGIMES

    SciTech Connect

    Matsumoto, Yosuke; Amano, Takanobu; Hoshino, Masahiro

    2012-08-20

    Electron accelerations at high Mach number collisionless shocks are investigated by means of two-dimensional electromagnetic particle-in-cell simulations with various Alfven Mach numbers, ion-to-electron mass ratios, and the upstream electron {beta}{sub e} (the ratio of the thermal pressure to the magnetic pressure). We find electrons are effectively accelerated at a super-high Mach number shock (M{sub A} {approx} 30) with a mass ratio of M/m = 100 and {beta}{sub e} = 0.5. The electron shock surfing acceleration is an effective mechanism for accelerating the particles toward the relativistic regime even in two dimensions with a large mass ratio. Buneman instability excited at the leading edge of the foot in the super-high Mach number shock results in a coherent electrostatic potential structure. While multi-dimensionality allows the electrons to escape from the trapping region, they can interact with the strong electrostatic field several times. Simulation runs in various parameter regimes indicate that the electron shock surfing acceleration is an effective mechanism for producing relativistic particles in extremely high Mach number shocks in supernova remnants, provided that the upstream electron temperature is reasonably low.

  6. Electron Accelerations at High Mach Number Shocks: Two-dimensional Particle-in-cell Simulations in Various Parameter Regimes

    NASA Astrophysics Data System (ADS)

    Matsumoto, Yosuke; Amano, Takanobu; Hoshino, Masahiro

    2012-08-01

    Electron accelerations at high Mach number collisionless shocks are investigated by means of two-dimensional electromagnetic particle-in-cell simulations with various Alfvén Mach numbers, ion-to-electron mass ratios, and the upstream electron β e (the ratio of the thermal pressure to the magnetic pressure). We find electrons are effectively accelerated at a super-high Mach number shock (MA ~ 30) with a mass ratio of M/m = 100 and β e = 0.5. The electron shock surfing acceleration is an effective mechanism for accelerating the particles toward the relativistic regime even in two dimensions with a large mass ratio. Buneman instability excited at the leading edge of the foot in the super-high Mach number shock results in a coherent electrostatic potential structure. While multi-dimensionality allows the electrons to escape from the trapping region, they can interact with the strong electrostatic field several times. Simulation runs in various parameter regimes indicate that the electron shock surfing acceleration is an effective mechanism for producing relativistic particles in extremely high Mach number shocks in supernova remnants, provided that the upstream electron temperature is reasonably low.

  7. Electron Accelerations at High Mach Number Shocks: Two-Dimensional Particle-in-Cell Simulations in Various Parameter Regimes

    NASA Astrophysics Data System (ADS)

    Matsumoto, Y.; Amano, T.; Hoshino, M.

    2012-12-01

    Electron accelerations at high Mach number collision-less shocks are investigated by means of two-dimensional electromagnetic Particle-in-Cell simulations with various Alfven Mach numbers, ion-to-electron mass ratios, and the upstream electron βe (the ratio of the thermal pressure to the magnetic pressure). We found electrons are effectively accelerated at a super-high Mach number shock (MA ~ 30) with a mass ratio of M/m=100 and βe=0.5. The electron shock surfing acceleration is an effective mechanism for accelerating the particles toward the relativistic regime even in two dimensions with the large mass ratio. Buneman instability excited at the leading edge of the foot in the super-high Mach number shock results in a coherent electrostatic potential structure. While multi-dimensionality allows the electrons to escape from the trapping region, they can interact with the strong electrostatic field several times. Simulation runs in various parameter regimes indicate that the electron shock surfing acceleration is an effective mechanism for producing relativistic particles in extremely-high Mach number shocks in supernova remnants, provided that the upstream electron temperature is reasonably low. Matsumoto et al., Astrophys. J., 755, 109, 2012.

  8. MO-F-CAMPUS-I-03: GPU Accelerated Monte Carlo Technique for Fast Concurrent Image and Dose Simulation

    SciTech Connect

    Becchetti, M; Tian, X; Segars, P; Samei, E

    2015-06-15

    Purpose: To develop an accurate and fast Monte Carlo (MC) method of simulating CT that is capable of correlating dose with image quality using voxelized phantoms. Methods: A realistic voxelized phantom based on patient CT data, XCAT, was used with a GPU accelerated MC code for helical MDCT. Simulations were done with both uniform density organs and with textured organs. The organ doses were validated using previous experimentally validated simulations of the same phantom under the same conditions. Images acquired by tracking photons through the phantom with MC require lengthy computation times due to the large number of photon histories necessary for accurate representation of noise. A substantial speed up of the process was attained by using a low number of photon histories with kernel denoising of the projections from the scattered photons. These FBP reconstructed images were validated against those that were acquired in simulations using many photon histories by ensuring a minimal normalized root mean square error. Results: Organ doses simulated in the XCAT phantom are within 10% of the reference values. Corresponding images attained using projection kernel smoothing were attained with 3 orders of magnitude less computation time compared to a reference simulation using many photon histories. Conclusion: Combining GPU acceleration with kernel denoising of scattered photon projections in MC simulations allows organ dose and corresponding image quality to be attained with reasonable accuracy and substantially reduced computation time than is possible with standard simulation approaches.

  9. Accelerated 20-year sunlight exposure simulation of a photochromic foldable intraocular lens in a rabbit model

    PubMed Central

    Werner, Liliana; Abdel-Aziz, Salwa; Peck, Carolee Cutler; Monson, Bryan; Espandar, Ladan; Zaugg, Brian; Stringham, Jack; Wilcox, Chris; Mamalis, Nick

    2011-01-01

    PURPOSE To assess the long-term biocompatibility and photochromic stability of a new photochromic hydrophobic acrylic intraocular lens (IOL) under extended ultraviolet (UV) light exposure. SETTING John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, USA. DESIGN Experimental study. METHODS A Matrix Aurium photochromic IOL was implanted in right eyes and a Matrix Acrylic IOL without photochromic properties (n = 6) or a single-piece AcrySof Natural SN60AT (N = 5) IOL in left eyes of 11 New Zealand rabbits. The rabbits were exposed to a UV light source of 5 mW/cm2 for 3 hours during every 8-hour period, equivalent to 9 hours a day, and followed for up to 12 months. The photochromic changes were evaluated during slitlamp examination by shining a penlight UV source in the right eye. After the rabbits were humanely killed and the eyes enucleated, study and control IOLs were explanted and evaluated in vitro on UV exposure and studied histopathologically. RESULTS The photochromic IOL was as biocompatible as the control IOLs after 12 months under conditions simulating at least 20 years of UV exposure. In vitro evaluation confirmed the retained optical properties, with photochromic changes observed within 7 seconds of UV exposure. The rabbit eyes had clinical and histopathological changes expected in this model with a 12-month follow-up. CONCLUSIONS The new photochromic IOL turned yellow only on exposure to UV light. The photochromic changes were reversible, reproducible, and stable over time. The IOL was biocompatible with up to 12 months of accelerated UV exposure simulation. PMID:21241924

  10. Accelerated 20-year sunlight exposure simulation of a photochromic foldable intraocular lens in a rabbit model.

    PubMed

    Werner, Liliana; Abdel-Aziz, Salwa; Cutler Peck, Carolee; Monson, Bryan; Espandar, Ladan; Zaugg, Brian; Stringham, Jack; Wilcox, Chris; Mamalis, Nick

    2011-02-01

    To assess the long-term biocompatibility and photochromic stability of a new photochromic hydrophobic acrylic intraocular lens (IOL) under extended ultraviolet (UV) light exposure. John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, USA. Experimental study. A Matrix Aurium photochromic IOL was implanted in right eyes and a Matrix Acrylic IOL without photochromic properties (n = 6) or a single-piece AcrySof Natural SN60AT IOL (n = 5) in left eyes of 11 New Zealand rabbits. The rabbits were exposed to a UV light source of 5 mW/cm(2) for 3 hours during every 8-hour period, equivalent to 9 hours a day, and followed for up to 12 months. The photochromic changes were evaluated during slitlamp examination by shining a penlight UV source in the right eye. After the rabbits were humanely killed and the eyes enucleated, study and control IOLs were explanted and evaluated in vitro on UV exposure and studied histopathologically. The photochromic IOL was as biocompatible as the control IOLs after 12 months under conditions simulating at least 20 years of UV exposure. In vitro evaluation confirmed the retained optical properties, with photochromic changes observed within 7 seconds of UV exposure. The rabbit eyes had clinical and histopathological changes expected in this model with a 12-month follow-up. The new photochromic IOL turned yellow only on exposure to UV light. The photochromic changes were reversible, reproducible, and stable over time. The IOL was biocompatible with up to 12 months of accelerated UV exposure simulation. Copyright © 2011 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  11. Monte Carlo simulations for 20 MV X-ray spectrum reconstruction of a linear induction accelerator

    NASA Astrophysics Data System (ADS)

    Wang, Yi; Li, Qin; Jiang, Xiao-Guo

    2012-09-01

    To study the spectrum reconstruction of the 20 MV X-ray generated by the Dragon-I linear induction accelerator, the Monte Carlo method is applied to simulate the attenuations of the X-ray in the attenuators of different thicknesses and thus provide the transmission data. As is known, the spectrum estimation from transmission data is an ill-conditioned problem. The method based on iterative perturbations is employed to derive the X-ray spectra, where initial guesses are used to start the process. This algorithm takes into account not only the minimization of the differences between the measured and the calculated transmissions but also the smoothness feature of the spectrum function. In this work, various filter materials are put to use as the attenuator, and the condition for an accurate and robust solution of the X-ray spectrum calculation is demonstrated. The influences of the scattering photons within different intervals of emergence angle on the X-ray spectrum reconstruction are also analyzed.

  12. The GENGA code: gravitational encounters in N-body simulations with GPU acceleration

    SciTech Connect

    Grimm, Simon L.; Stadel, Joachim G.

    2014-11-20

    We describe an open source GPU implementation of a hybrid symplectic N-body integrator, GENGA (Gravitational ENcounters with Gpu Acceleration), designed to integrate planet and planetesimal dynamics in the late stage of planet formation and stability analyses of planetary systems. GENGA uses a hybrid symplectic integrator to handle close encounters with very good energy conservation, which is essential in long-term planetary system integration. We extended the second-order hybrid integration scheme to higher orders. The GENGA code supports three simulation modes: integration of up to 2048 massive bodies, integration with up to a million test particles, or parallel integration of a large number of individual planetary systems. We compare the results of GENGA to Mercury and pkdgrav2 in terms of energy conservation and performance and find that the energy conservation of GENGA is comparable to Mercury and around two orders of magnitude better than pkdgrav2. GENGA runs up to 30 times faster than Mercury and up to 8 times faster than pkdgrav2. GENGA is written in CUDA C and runs on all NVIDIA GPUs with a computing capability of at least 2.0.

  13. Neural-network accelerated fusion simulation with self-consistent core-pedestal coupling

    NASA Astrophysics Data System (ADS)

    Meneghini, O.; Candy, J.; Snyder, P. B.; Staebler, G.; Belli, E.

    2016-10-01

    Practical fusion Whole Device Modeling (WDM) simulations require the ability to perform predictions that are fast, but yet account for the sensitivity of the fusion performance to the boundary constraint that is imposed by the pedestal structure of H-mode plasmas due to the stiff core transport models. This poster presents the development of a set of neural-network (NN) models for the pedestal structure (as predicted by the EPED model), and the neoclassical and turbulent transport fluxes (as predicted by the NEO and TGLF codes, respectively), and their self-consistent coupling within the TGYRO transport code. The results are benchmarked with the ones obtained via the coupling scheme described in [Meneghini PoP 2016]. By substituting the most demanding codes with their NN-accelerated versions, the solution can be found at a fraction of the computation cost of the original coupling scheme, thereby combining the accuracy of a high-fidelity model with the fast turnaround time of a reduced model. Work supported by U.S. DOE DE-FC02-04ER54698 and DE-FG02-95ER54309.

  14. Numerical simulations of recent proton acceleration experiments with sub-100 TW laser systems

    NASA Astrophysics Data System (ADS)

    Sinigardi, Stefano

    2016-09-01

    Recent experiments carried out at the Italian National Research Center, National Optics Institute Department in Pisa, are showing interesting results regarding maximum proton energies achievable with sub-100 TW laser systems. While laser systems are being continuously upgraded in laboratories around the world, at the same time a new trend on stabilizing and making ion acceleration results reproducible is growing in importance. Almost all applications require a beam with fixed performance, so that the energy spectrum and the total charge exhibit moderate shot to shot variations. This result is surely far from being achieved, but many paths are being explored in order to reach it. Some of the reasons for this variability come from fluctuations in laser intensity and focusing, due to optics instability. Other variation sources come from small differences in the target structure. The target structure can vary substantially, when it is impacted by the main pulse, due to the prepulse duration and intensity, the shape of the main pulse and the total energy deposited. In order to qualitatively describe the prepulse effect, we will present a two dimensional parametric scan of its relevant parameters. A single case is also analyzed with a full three dimensional simulation, obtaining reasonable agreement between the numerical and the experimental energy spectrum.

  15. Acceleration of the matrix multiplication of Radiance three phase daylighting simulations with parallel computing on heterogeneous hardware of personal computer

    SciTech Connect

    Zuo, Wangda; McNeil, Andrew; Wetter, Michael; Lee, Eleanor S.

    2013-05-23

    Building designers are increasingly relying on complex fenestration systems to reduce energy consumed for lighting and HVAC in low energy buildings. Radiance, a lighting simulation program, has been used to conduct daylighting simulations for complex fenestration systems. Depending on the configurations, the simulation can take hours or even days using a personal computer. This paper describes how to accelerate the matrix multiplication portion of a Radiance three-phase daylight simulation by conducting parallel computing on heterogeneous hardware of a personal computer. The algorithm was optimized and the computational part was implemented in parallel using OpenCL. The speed of new approach was evaluated using various daylighting simulation cases on a multicore central processing unit and a graphics processing unit. Based on the measurements and analysis of the time usage for the Radiance daylighting simulation, further speedups can be achieved by using fast I/O devices and storing the data in a binary format.

  16. Application of the Reduction of Scale Range in a Lorentz Boosted Frame to the Numerical Simulation of Particle Acceleration Devices

    SciTech Connect

    Vay, J.-L.; Fawley, W.M.; Geddes, C.G.R.; Cormier-Michel, E.; Grote, D.P.

    2009-05-01

    It has been shown [1] that it may be computationally advantageous to perform computer simulations in a boosted frame for a certain class of systems: particle beams interacting with electron clouds, free electron lasers, and laser-plasma accelerators. However, even if the computer model relies on a covariant set of equations, it was also pointed out that algorithmic difficulties related to discretization errors may have to be overcome in order to take full advantage of the potential speedup [2] . In this paper, we focus on the analysis of the complication of data input and output in a Lorentz boosted frame simulation, and describe the procedures that were implemented in the simulation code Warp[3]. We present our most recent progress in the modeling of laser wakefield acceleration in a boosted frame, and describe briefly the potential benefits of calculating in a boosted frame for the modeling of coherent synchrotron radiation.

  17. Reaching extended length scales and time scales in atomistic simulations via spatially parallel temperature-accelerated dynamics

    NASA Astrophysics Data System (ADS)

    Shim, Yunsic; Amar, Jacques G.; Uberuaga, B. P.; Voter, A. F.

    2007-11-01

    We present a method for performing parallel temperature-accelerated dynamics (TAD) simulations over extended length scales. In our method, a two-dimensional spatial decomposition is used along with the recently proposed semirigorous synchronous sublattice algorithm of Shim and Amar [Phys. Rev. B 71, 125432 (2005)]. The scaling behavior of the simulation time as a function of system size is studied and compared with serial TAD in simulations of the early stages of Cu/Cu(100) growth as well as for a simple case of surface relaxation. In contrast to the corresponding serial TAD simulations, for which the simulation time tser increases as a power of the system size N (tser˜Nx) with an exponent x that can be as large as three, in our parallel simulations the simulation time increases only logarithmically with system size. As a result, even for relatively small system sizes our parallel TAD simulations are significantly faster than the corresponding serial TAD simulations. The significantly improved scaling behavior of our parallel TAD simulations over the corresponding serial simulations indicates that our parallel TAD method may be useful in performing simulations over significantly larger length scales than serial TAD, while preserving all the atomistic details provided by the TAD method.

  18. Community Project for Accelerator Science and Simulation (ComPASS) Final Report

    SciTech Connect

    Cary, John R.; Cowan, Benjamin M.; Veitzer, S. A.

    2016-03-04

    Tech-X participated across the full range of ComPASS activities, with efforts in the Energy Frontier primarily through modeling of laser plasma accelerators and dielectric laser acceleration, in the Intensity Frontier primarily through electron cloud modeling, and in Uncertainty Quantification being applied to dielectric laser acceleration. In the following we present the progress and status of our activities for the entire period of the ComPASS project for the different areas of Energy Frontier, Intensity Frontier and Uncertainty Quantification.

  19. Design and Simulation of IOTA - a Novel Concept of Integrable Optics Test Accelerator

    SciTech Connect

    Nagaitsev, S.; Valishev, A.; Danilov, V.V.; Shatilov, D.N.; /Novosibirsk, IYF

    2012-05-01

    The use of nonlinear lattices with large betatron tune spreads can increase instability and space charge thresholds due to improved Landau damping. Unfortunately, the majority of nonlinear accelerator lattices turn out to be nonintegrable, producing chaotic motion and a complex network of stable and unstable resonances. Recent advances in finding the integrable nonlinear accelerator lattices have led to a proposal to construct at Fermilab a test accelerator with strong nonlinear focusing which avoids resonances and chaotic particle motion. This presentation will outline the main challenges, theoretical design solutions and construction status of the Integrable Optics Test Accelerator (IOTA) underway at Fermilab.

  20. Magnetogasdynamic compression of a coaxial plasma accelerator flow for micrometeoroid simulation

    NASA Technical Reports Server (NTRS)

    Igenbergs, E. B.; Shriver, E. L.

    1974-01-01

    A new configuration of a coaxial plasma accelerator with self-energized magnetic compressor coil attached is described. It is shown that the circuit may be treated theoretically by analyzing an equivalent circuit mesh. The results obtained from the theoretical analysis compare favorably with the results measured experimentally. Using this accelerator configuration, glass beads of 125 micron diameter were accelerated to velocities as high as 11 kilometers per second, while 700 micron diameter glass beads were accelerated to velocities as high as 5 kilometers per second. The velocities are within the hypervelocity regime of meteoroids.

  1. Magnetogasdynamic compression of a coaxial plasma accelerator flow for micrometeoroid simulation.

    NASA Technical Reports Server (NTRS)

    Igenbergs, E. B.; Shriver, E. L.

    1973-01-01

    A new configuration of a coaxial plasma accelerator with self-energized magnetic compressor coil attached is described. It is shown that the circuit may be treated theoretically by analyzing an equivalent circuit mesh. The results obtained from the theoretical analysis are shown to compare favorably with the results measured experimentally. Using this accelerator configuration, glass beads of 125-micron diameter were accelerated to velocities as high as 11 km/sec, while 700-micron-diam glass beads were accelerated to velocities as high as 5 km/sec. The velocities are within the hypervelocity regime of meteroids.

  2. The aortic reservoir-wave as a paradigm for arterial haemodynamics: insights from three-dimensional fluid-structure interaction simulations in a model of aortic coarctation.

    PubMed

    Segers, Patrick; Taelman, Liesbeth; Degroote, Joris; Bols, Joris; Vierendeels, Jan

    2015-03-01

    The reservoir-wave paradigm considers aortic pressure as the superposition of a 'reservoir pressure', directly related to changes in reservoir volume, and an 'excess' component ascribed to wave dynamics. The change in reservoir pressure is assumed to be proportional to the difference between aortic inflow and outflow (i.e. aortic volume changes), an assumption that is virtually impossible to validate in vivo. The aim of this study is therefore to apply the reservoir-wave paradigm to aortic pressure and flow waves obtained from three-dimensional fluid-structure interaction simulations in a model of a normal aorta, aortic coarctation (narrowed descending aorta) and stented coarctation (stiff segment in descending aorta). We found no unequivocal relation between the intraaortic volume and the reservoir pressure for any of the simulated cases. When plotted in a pressure-volume diagram, hysteresis loops are found that are looped in a clockwise way indicating that the reservoir pressure is lower than the pressure associated with the change in volume. The reservoir-wave analysis leads to very high excess pressures, especially for the coarctation models, but to surprisingly little changes of the reservoir component despite the impediment of the buffer capacity of the aorta. With the observation that reservoir pressure is not related to the volume in the aortic reservoir in systole, an intrinsic assumption in the wave-reservoir concept is invalidated and, consequently, also the assumption that the excess pressure is the component of pressure that can be attributed to wave travel and reflection.

  3. Simulation of 1 GeV laser wakefield accelerator experiments and scaling to 10 GeV

    NASA Astrophysics Data System (ADS)

    Cormier-Michel, Estelle; Geddes, C. G. R.; Isaacs, W. A.; Stinus, N.; Esarey, E.; Schroeder, C. B.; Leemans, W. P.; Bruhwiler, D. L.; Cary, J. R.

    2007-11-01

    Recent laser-plasma accelerator experiments at LBNL have demonstrated the production of high quality 0.5 and 1.0 GeV electron beams.ootnotetextW.P. Leemans et al., Nature Physics 2, 696 (2006) In these experiments, the 10-40 TW laser pulse was guided in a 3 cm long capillary discharge plasma channel. Particle-In-Cell (PIC) simulations provide information not accessible from experiments on the nonlinear laser-plasma interaction that governs the accelerator internal dynamics. Simulations show that high quality electron bunches are formed by self-trapping of electrons in the wake, followed by loading of the wake by the trapped bunch, creating a bunch of electrons isolated in phase space. A narrow energy spread beam is then obtained by extracting the bunch as it outran the accelerating phase of the wake. Simulations in 2D and 3D showing details on the electron bunch, wakefield, and laser evolution are presented and compared to experimental results. Simulations on scaling these experiments to the 10 GeV level are also presented.

  4. Identification of key factors in Accelerated Low Water Corrosion through experimental simulation of tidal conditions: influence of stimulated indigenous microbiota.

    PubMed

    Marty, Florence; Gueuné, Hervé; Malard, Emilie; Sánchez-Amaya, José M; Sjögren, Lena; Abbas, Ben; Quillet, Laurent; van Loosdrecht, Mark C M; Muyzer, Gerard

    2014-01-01

    Biotic and abiotic factors favoring Accelerated Low Water Corrosion (ALWC) on harbor steel structures remain unclear warranting their study under controlled experimental tidal conditions. Initial stimulation of marine microbial consortia by a pulse of organic matter resulted in localized corrosion and the highest corrosion rates (up to 12-times higher than non-stimulated conditions) in the low water zone, persisting after nine months exposure to natural seawater. Correlations between corrosion severity and the abundance and composition of metabolically active sulfate-reducing bacteria (SRB) indicated the importance and persistence of specific bacterial populations in accelerated corrosion. One phylotype related to the electrogenic SRB Desulfopila corrodens appeared as the major causative agent of the accelerated corrosion. The similarity of bacterial populations related to sulfur and iron cycles, mineral and tuberculation with those identified in ALWC support the relevance of experimental simulation of tidal conditions in the management of steel corrosion exposed to harbor environments.

  5. Accelerating moderately stiff chemical kinetics in reactive-flow simulations using GPUs

    NASA Astrophysics Data System (ADS)

    Niemeyer, Kyle E.; Sung, Chih-Jen

    2014-01-01

    The chemical kinetics ODEs arising from operator-split reactive-flow simulations were solved on GPUs using explicit integration algorithms. Nonstiff chemical kinetics of a hydrogen oxidation mechanism (9 species and 38 irreversible reactions) were computed using the explicit fifth-order Runge-Kutta-Cash-Karp method, and the GPU-accelerated version performed faster than single- and six-core CPU versions by factors of 126 and 25, respectively, for 524,288 ODEs. Moderately stiff kinetics, represented with mechanisms for hydrogen/carbon-monoxide (13 species and 54 irreversible reactions) and methane (53 species and 634 irreversible reactions) oxidation, were computed using the stabilized explicit second-order Runge-Kutta-Chebyshev (RKC) algorithm. The GPU-based RKC implementation demonstrated an increase in performance of nearly 59 and 10 times, for problem sizes consisting of 262,144 ODEs and larger, than the single- and six-core CPU-based RKC algorithms using the hydrogen/carbon-monoxide mechanism. With the methane mechanism, RKC-GPU performed more than 65 and 11 times faster, for problem sizes consisting of 131,072 ODEs and larger, than the single- and six-core RKC-CPU versions, and up to 57 times faster than the six-core CPU-based implicit VODE algorithm on 65,536 ODEs. In the presence of more severe stiffness, such as ethylene oxidation (111 species and 1566 irreversible reactions), RKC-GPU performed more than 17 times faster than RKC-CPU on six cores for 32,768 ODEs and larger, and at best 4.5 times faster than VODE on six CPU cores for 65,536 ODEs. With a larger time step size, RKC-GPU performed at best 2.5 times slower than six-core VODE for 8192 ODEs and larger. Therefore, the need for developing new strategies for integrating stiff chemistry on GPUs was discussed.

  6. Exploring inhibitor release pathways in histone deacetylases using random acceleration molecular dynamics simulations.

    PubMed

    Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe

    2012-02-27

    Molecular channel exploration perseveres to be the prominent solution for eliciting structure and accessibility of active site and other internal spaces of macromolecules. The volume and silhouette characterization of these channels provides answers for the issues of substrate access and ligand swapping between the obscured active site and the exterior of the protein. Histone deacetylases (HDACs) are metal-dependent enzymes that are involved in the cell growth, cell cycle regulation, and progression, and their deregulations have been linked with different types of cancers. Hence HDACs, especially the class I family, are widely recognized as the important cancer targets, and the characterizations of their structures and functions have been of special interest in cancer drug discovery. The class I HDACs are known to possess two different protein channels, an 11 Å and a 14 Å (named channels A and B1, respectively), of which the former is a ligand or substrate occupying tunnel that leads to the buried active site zinc ion and the latter is speculated to be involved in product release. In this work, we have carried out random acceleration molecular dynamics (RAMD) simulations coupled with the classical molecular dynamics to explore the release of the ligand, N-(2-aminophenyl) benzamide (LLX) from the active sites of the recently solved X-ray crystal structure of HDAC2 and the computationally modeled HDAC1 proteins. The RAMD simulations identified significant structural and dynamic features of the HDAC channels, especially the key 'gate-keeping' amino acid residues that control these channels and the ligand release events. Further, this study identified a novel and unique channel B2, a subchannel from channel B1, in the HDAC1 protein structure. The roles of water molecules in the LLX release from the HDAC1 and HDAC2 enzymes are also discussed. Such structural and dynamic properties of the HDAC protein channels that govern the ligand escape reactions will provide

  7. Wavelet and Multiresolution Analysis for Finite Element Networking Paradigms

    NASA Technical Reports Server (NTRS)

    Kurdila, Andrew J.; Sharpley, Robert C.

    1999-01-01

    This paper presents a final report on Wavelet and Multiresolution Analysis for Finite Element Networking Paradigms. The focus of this research is to derive and implement: 1) Wavelet based methodologies for the compression, transmission, decoding, and visualization of three dimensional finite element geometry and simulation data in a network environment; 2) methodologies for interactive algorithm monitoring and tracking in computational mechanics; and 3) Methodologies for interactive algorithm steering for the acceleration of large scale finite element simulations. Also included in this report are appendices describing the derivation of wavelet based Particle Image Velocity algorithms and reduced order input-output models for nonlinear systems by utilizing wavelet approximations.

  8. The role of the electron convection term for the parallel electric field and electron acceleration in MHD simulations

    SciTech Connect

    Matsuda, K.; Terada, N.; Katoh, Y.; Misawa, H.

    2011-08-15

    There has been a great concern about the origin of the parallel electric field in the frame of fluid equations in the auroral acceleration region. This paper proposes a new method to simulate magnetohydrodynamic (MHD) equations that include the electron convection term and shows its efficiency with simulation results in one dimension. We apply a third-order semi-discrete central scheme to investigate the characteristics of the electron convection term including its nonlinearity. At a steady state discontinuity, the sum of the ion and electron convection terms balances with the ion pressure gradient. We find that the electron convection term works like the gradient of the negative pressure and reduces the ion sound speed or amplifies the sound mode when parallel current flows. The electron convection term enables us to describe a situation in which a parallel electric field and parallel electron acceleration coexist, which is impossible for ideal or resistive MHD.

  9. EFFECTS OF LASER RADIATION ON MATTER: Simulation of photon acceleration upon irradiation of a mylar target by femtosecond laser pulses

    NASA Astrophysics Data System (ADS)

    Andreev, Stepan N.; Rukhadze, Anri A.; Tarakanov, V. P.; Yakutov, B. P.

    2010-01-01

    Acceleration of protons is simulated by the particle-in-cell (PIC) method upon irradiation of mylar targets of different thicknesses by femtosecond plane-polarised pulsed laser radiation and at different angles of radiation incidence on the target. The comparison of the results of calculations with the experimental data obtained in recent experiments shows their good agreement. The optimal angle of incidence (458) at which the proton energy achieves its absolute maximum is obtained.

  10. [The acceleration of ultrastructure changes of synapses in somatosensory cortex of the rats at repeated simulation of weightlessness effects].

    PubMed

    Krasnov, I B; D'iachkova, L N

    2006-01-01

    The electronmicroscopica/study of brain somatosensory cortex in the rats, exposed to postponed for a long time repeated lack of support load on hindlimbs by means of tail-suspension, has been revealed in hindlimb area of cortex the changes of ultrastructure of axodendritic synapses and neurons pointing out the acceleration of decrease in functional activity of synapses and neurons in 3-4 layers at postponed for a long time repeated simulation of weightlessness effects.

  11. Simulation of high-frequency modes and their effect on insulator breakdown in the pulse line ion accelerator

    NASA Astrophysics Data System (ADS)

    Ling, C. Y.; Yu, S. S.; Henestroza, E.

    2009-07-01

    The pulse line ion accelerator (PLIA) produces a traveling electromagnetic (EM) wave by applying a voltage pulse to one end of a helix that accelerates and axially confines a heavy-ion beam pulse. An anomalous flashover phenomenon has been observed on the vacuum-insulator surface that limits the amplitude of the accelerating field. It has been suspected that a small component of high-frequency modes in the input pulse may be the cause of the breakdown. Simulation using MAFIA (MAxwell's equations by Finite Integration Algorithm) was conducted to investigate the fields on the insulator surface. A scaling law was proposed to reduce substantially the computational time in simulation. It is based on the hypothesis that the pattern of EM field for a given wavelength is independent of the wire spacing as long as the wavelength is much longer than the inter-wire spacing and the termination resistors are adjusted to maintain impedance matching. On the basis of these numerical simulations, we conclude that high-frequency modes, even at very low amplitudes, may indeed lead to the observed insulator flashover.

  12. Accelerating solidification process simulation for large-sized system of liquid metal atoms using GPU with CUDA

    SciTech Connect

    Jie, Liang; Li, KenLi; Shi, Lin; Liu, RangSu; Mei, Jing

    2014-01-15

    Molecular dynamics simulation is a powerful tool to simulate and analyze complex physical processes and phenomena at atomic characteristic for predicting the natural time-evolution of a system of atoms. Precise simulation of physical processes has strong requirements both in the simulation size and computing timescale. Therefore, finding available computing resources is crucial to accelerate computation. However, a tremendous computational resource (GPGPU) are recently being utilized for general purpose computing due to its high performance of floating-point arithmetic operation, wide memory bandwidth and enhanced programmability. As for the most time-consuming component in MD simulation calculation during the case of studying liquid metal solidification processes, this paper presents a fine-grained spatial decomposition method to accelerate the computation of update of neighbor lists and interaction force calculation by take advantage of modern graphics processors units (GPU), enlarging the scale of the simulation system to a simulation system involving 10 000 000 atoms. In addition, a number of evaluations and tests, ranging from executions on different precision enabled-CUDA versions, over various types of GPU (NVIDIA 480GTX, 580GTX and M2050) to CPU clusters with different number of CPU cores are discussed. The experimental results demonstrate that GPU-based calculations are typically 9∼11 times faster than the corresponding sequential execution and approximately 1.5∼2 times faster than 16 CPU cores clusters implementations. On the basis of the simulated results, the comparisons between the theoretical results and the experimental ones are executed, and the good agreement between the two and more complete and larger cluster structures in the actual macroscopic materials are observed. Moreover, different nucleation and evolution mechanism of nano-clusters and nano-crystals formed in the processes of metal solidification is observed with large

  13. Accelerating solidification process simulation for large-sized system of liquid metal atoms using GPU with CUDA

    NASA Astrophysics Data System (ADS)

    Jie, Liang; Li, KenLi; Shi, Lin; Liu, RangSu; Mei, Jing

    2014-01-01

    Molecular dynamics simulation is a powerful tool to simulate and analyze complex physical processes and phenomena at atomic characteristic for predicting the natural time-evolution of a system of atoms. Precise simulation of physical processes has strong requirements both in the simulation size and computing timescale. Therefore, finding available computing resources is crucial to accelerate computation. However, a tremendous computational resource (GPGPU) are recently being utilized for general purpose computing due to its high performance of floating-point arithmetic operation, wide memory bandwidth and enhanced programmability. As for the most time-consuming component in MD simulation calculation during the case of studying liquid metal solidification processes, this paper presents a fine-grained spatial decomposition method to accelerate the computation of update of neighbor lists and interaction force calculation by take advantage of modern graphics processors units (GPU), enlarging the scale of the simulation system to a simulation system involving 10 000 000 atoms. In addition, a number of evaluations and tests, ranging from executions on different precision enabled-CUDA versions, over various types of GPU (NVIDIA 480GTX, 580GTX and M2050) to CPU clusters with different number of CPU cores are discussed. The experimental results demonstrate that GPU-based calculations are typically 9∼11 times faster than the corresponding sequential execution and approximately 1.5∼2 times faster than 16 CPU cores clusters implementations. On the basis of the simulated results, the comparisons between the theoretical results and the experimental ones are executed, and the good agreement between the two and more complete and larger cluster structures in the actual macroscopic materials are observed. Moreover, different nucleation and evolution mechanism of nano-clusters and nano-crystals formed in the processes of metal solidification is observed with large-sized system.

  14. SU-E-T-498: A Preliminary Monte Carlo Simulation Study of the Varian TrueBeam Linear Accelerator.

    PubMed

    Johnson, D; Chen, Y; Schnell, E; Ahmad, S

    2012-06-01

    To benchmark the quality of Monte Carlo simulation results with the commissioning data for a Varian TrueBeam accelerator. IAEA phase space files of a 6MV TrueBeam accelerator provided by Varian were implemented using GEANT4 Monte Carlo code. The present application consisted of upper and lower jaws and a cubic water phantom of 0.125 cubic meters in volume. Both radial and transverse dose profiles (in 5 different depths) and a central axis percentage depth dose (PDD) curve were recorded in the phantom. Field sizes of as small as 4×4 cm(2) and as large as 30×30 cm(2) were simulated with 2.0E9 incident particles each. The results were then compared with our commissioning data performed in a Wellhoffer Blue Phantom with a 0.13cc ion-chamber and a 0.8×0.8mm diode. The GEANT4 simulated PDD curve compared favorably within ∼2% against the measured ion-chamber PDD for all field sizes and against the measured diode PDD for all fields less then 20×20cm(2) . The simulated in-plane and cross-plane profiles compared well within 2 mm at the 50% level against the measured profiles for all field sizes. These results demonstrate the feasibility of utilizing Monte-Carlo simulated beam data in the commissioning of a linear accelerator. The increasing speed and capability of the desktop computer will Result in the adoption of Monte- Carlo techniques for dosimetric calculations. © 2012 American Association of Physicists in Medicine.

  15. Bacterial cells enhance laser driven ion acceleration

    PubMed Central

    Dalui, Malay; Kundu, M.; Trivikram, T. Madhu; Rajeev, R.; Ray, Krishanu; Krishnamurthy, M.

    2014-01-01

    Intense laser produced plasmas generate hot electrons which in turn leads to ion acceleration. Ability to generate faster ions or hotter electrons using the same laser parameters is one of the main outstanding paradigms in the intense laser-plasma physics. Here, we present a simple, albeit, unconventional target that succeeds in generating 700 keV carbon ions where conventional targets for the same laser parameters generate at most 40 keV. A few layers of micron sized bacteria coating on a polished surface increases the laser energy coupling and generates a hotter plasma which is more effective for the ion acceleration compared to the conventional polished targets. Particle-in-cell simulations show that micro-particle coated target are much more effective in ion acceleration as seen in the experiment. We envisage that the accelerated, high-energy carbon ions can be used as a source for multiple applications. PMID:25102948

  16. Bacterial cells enhance laser driven ion acceleration.

    PubMed

    Dalui, Malay; Kundu, M; Trivikram, T Madhu; Rajeev, R; Ray, Krishanu; Krishnamurthy, M

    2014-08-08

    Intense laser produced plasmas generate hot electrons which in turn leads to ion acceleration. Ability to generate faster ions or hotter electrons using the same laser parameters is one of the main outstanding paradigms in the intense laser-plasma physics. Here, we present a simple, albeit, unconventional target that