Properties of coupled-cluster equations originating in excitation sub-algebras

NASA Astrophysics Data System (ADS)

Kowalski, Karol

2018-03-01

In this paper, we discuss properties of single-reference coupled cluster (CC) equations associated with the existence of sub-algebras of excitations that allow one to represent CC equations in a hybrid fashion where the cluster amplitudes associated with these sub-algebras can be obtained by solving the corresponding eigenvalue problem. For closed-shell formulations analyzed in this paper, the hybrid representation of CC equations provides a natural way for extending active-space and seniority number concepts to provide an accurate description of electron correlation effects. Moreover, a new representation can be utilized to re-define iterative algorithms used to solve CC equations, especially for tough cases defined by the presence of strong static and dynamical correlation effects. We will also explore invariance properties associated with excitation sub-algebras to define a new class of CC approximations referred to in this paper as the sub-algebra-flow-based CC methods. We illustrate the performance of these methods on the example of ground- and excited-state calculations for commonly used small benchmark systems.

Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes

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

Gastegger, Michael; Kauffmann, Clemens; Marquetand, Philipp, E-mail: philipp.marquetand@univie.ac.at

Many approaches, which have been developed to express the potential energy of large systems, exploit the locality of the atomic interactions. A prominent example is the fragmentation methods in which the quantum chemical calculations are carried out for overlapping small fragments of a given molecule that are then combined in a second step to yield the system’s total energy. Here we compare the accuracy of the systematic molecular fragmentation approach with the performance of high-dimensional neural network (HDNN) potentials introduced by Behler and Parrinello. HDNN potentials are similar in spirit to the fragmentation approach in that the total energy ismore » constructed as a sum of environment-dependent atomic energies, which are derived indirectly from electronic structure calculations. As a benchmark set, we use all-trans alkanes containing up to eleven carbon atoms at the coupled cluster level of theory. These molecules have been chosen because they allow to extrapolate reliable reference energies for very long chains, enabling an assessment of the energies obtained by both methods for alkanes including up to 10 000 carbon atoms. We find that both methods predict high-quality energies with the HDNN potentials yielding smaller errors with respect to the coupled cluster reference.« less

Systematic design of active spaces for multi-reference calculations of singlet-triplet gaps of organic diradicals, with benchmarks against doubly electron-attached coupled-cluster data

NASA Astrophysics Data System (ADS)

Stoneburner, Samuel J.; Shen, Jun; Ajala, Adeayo O.; Piecuch, Piotr; Truhlar, Donald G.; Gagliardi, Laura

2017-10-01

Singlet-triplet gaps in diradical organic π-systems are of interest in many applications. In this study, we calculate them in a series of molecules, including cyclobutadiene and its derivatives and cyclopentadienyl cation, by using correlated participating orbitals within the complete active space (CAS) and restricted active space (RAS) self-consistent field frameworks, followed by second-order perturbation theory (CASPT2 and RASPT2). These calculations are evaluated by comparison with the results of doubly electron-attached (DEA) equation-of-motion (EOM) coupled-cluster (CC) calculations with up to 4-particle-2-hole (4p-2h) excitations. We find active spaces that can accurately reproduce the DEA-EOMCC(4p-2h) data while being small enough to be applicable to larger organic diradicals.

Solutions of the two-dimensional Hubbard model: Benchmarks and results from a wide range of numerical algorithms

DOE PAGES

LeBlanc, J. P. F.; Antipov, Andrey E.; Becca, Federico; ...

2015-12-14

Numerical results for ground-state and excited-state properties (energies, double occupancies, and Matsubara-axis self-energies) of the single-orbital Hubbard model on a two-dimensional square lattice are presented, in order to provide an assessment of our ability to compute accurate results in the thermodynamic limit. Many methods are employed, including auxiliary-field quantum Monte Carlo, bare and bold-line diagrammatic Monte Carlo, method of dual fermions, density matrix embedding theory, density matrix renormalization group, dynamical cluster approximation, diffusion Monte Carlo within a fixed-node approximation, unrestricted coupled cluster theory, and multireference projected Hartree-Fock methods. Comparison of results obtained by different methods allows for the identification ofmore » uncertainties and systematic errors. The importance of extrapolation to converged thermodynamic-limit values is emphasized. Furthermore, cases where agreement between different methods is obtained establish benchmark results that may be useful in the validation of new approaches and the improvement of existing methods.« less

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy

NASA Astrophysics Data System (ADS)

Lutz, Jesse J.; Duan, Xiaofeng F.; Ranasinghe, Duminda S.; Jin, Yifan; Margraf, Johannes T.; Perera, Ajith; Burggraf, Larry W.; Bartlett, Rodney J.

2018-05-01

Accurate optical characterization of the closo-Si12C12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si12C12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC2, Si2Cn (n = 1-3), and Si3Cn (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of SinC and Sin-1C7-n (n = 4-6). TD-DFT approaches are then applied to the SinCn (n = 4-12) clusters and unique spectroscopic signatures of closo-Si12C12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si4C4)4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

High-Level Ab Initio Calculations of Intermolecular Interactions: Heavy Main-Group Element π-Interactions.

PubMed

Krasowska, Małgorzata; Schneider, Wolfgang B; Mehring, Michael; Auer, Alexander A

2018-05-02

This work reports high-level ab initio calculations and a detailed analysis on the nature of intermolecular interactions of heavy main-group element compounds and π systems. For this purpose we have chosen a set of benchmark molecules of the form MR 3 , in which M=As, Sb, or Bi, and R=CH 3 , OCH 3 , or Cl. Several methods for the description of weak intermolecular interactions are benchmarked including DFT-D, DFT-SAPT, MP2, and high-level coupled cluster methods in the DLPNO-CCSD(T) approximation. Using local energy decomposition (LED) and an analysis of the electron density, details of the nature of this interaction are unraveled. The results yield insight into the nature of dispersion and donor-acceptor interactions in this type of system, including systematic trends in the periodic table, and also provide a benchmark for dispersion interactions in heavy main-group element compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Performance Evaluation of Supercomputers using HPCC and IMB Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash; Ciotti, Robert; Gunney, Brian T. N.; Spelce, Thomas E.; Koniges, Alice; Dossa, Don; Adamidis, Panagiotis; Rabenseifner, Rolf; Tiyyagura, Sunil R.; Mueller, Matthias;

Customized recommendations for production management clusters of North American automatic milking systems.

PubMed

Tremblay, Marlène; Hess, Justin P; Christenson, Brock M; McIntyre, Kolby K; Smink, Ben; van der Kamp, Arjen J; de Jong, Lisanne G; Döpfer, Dörte

2016-07-01

Automatic milking systems (AMS) are implemented in a variety of situations and environments. Consequently, there is a need to characterize individual farming practices and regional challenges to streamline management advice and objectives for producers. Benchmarking is often used in the dairy industry to compare farms by computing percentile ranks of the production values of groups of farms. Grouping for conventional benchmarking is commonly limited to the use of a few factors such as farms' geographic region or breed of cattle. We hypothesized that herds' production data and management information could be clustered in a meaningful way using cluster analysis and that this clustering approach would yield better peer groups of farms than benchmarking methods based on criteria such as country, region, breed, or breed and region. By applying mixed latent-class model-based cluster analysis to 529 North American AMS dairy farms with respect to 18 significant risk factors, 6 clusters were identified. Each cluster (i.e., peer group) represented unique management styles, challenges, and production patterns. When compared with peer groups based on criteria similar to the conventional benchmarking standards, the 6 clusters better predicted milk produced (kilograms) per robot per day. Each cluster represented a unique management and production pattern that requires specialized advice. For example, cluster 1 farms were those that recently installed AMS robots, whereas cluster 3 farms (the most northern farms) fed high amounts of concentrates through the robot to compensate for low-energy feed in the bunk. In addition to general recommendations for farms within a cluster, individual farms can generate their own specific goals by comparing themselves to farms within their cluster. This is very comparable to benchmarking but adds the specific characteristics of the peer group, resulting in better farm management advice. The improvement that cluster analysis allows for is characterized by the multivariable approach and the fact that comparisons between production units can be accomplished within a cluster and between clusters as a choice. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Two-photon absorption cross sections within equation-of-motion coupled-cluster formalism using resolution-of-the-identity and Cholesky decomposition representations: Theory, implementation, and benchmarks

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

Nanda, Kaushik D.; Krylov, Anna I.

The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increasemore » parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.« less

Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals

NASA Astrophysics Data System (ADS)

Liu, Junzi; Shen, Yue; Asthana, Ayush; Cheng, Lan

2018-01-01

A novel implementation of the two-component spin-orbit (SO) coupled-cluster singles and doubles (CCSD) method and the CCSD augmented with the perturbative inclusion of triple excitations [CCSD(T)] method using mean-field SO integrals is reported. The new formulation of SO-CCSD(T) features an atomic-orbital-based algorithm for the particle-particle ladder term in the CCSD equation, which not only removes the computational bottleneck associated with the large molecular-orbital integral file but also accelerates the evaluation of the particle-particle ladder term by around a factor of 4 by taking advantage of the spin-free nature of the instantaneous electron-electron Coulomb interaction. Benchmark calculations of the SO splittings for the thallium atom and a set of diatomic 2Π radicals as well as of the bond lengths and harmonic frequencies for a set of closed-shell diatomic molecules are presented. The basis-set and core-correlation effects in the calculations of these properties have been carefully analyzed.

Universal state-selective corrections to multireference coupled-cluster theories with single and double excitations

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

Brabec, Jiri; van Dam, Hubertus JJ; Pittner, Jiri

2012-03-28

The recently proposed Universal State-Selective (USS) corrections [K. Kowalski, J. Chem. Phys. 134, 194107 (2011)] to approximate Multi-Reference Coupled Cluster (MRCC) energies can be commonly applied to any type of MRCC theory based on the Jeziorski-Monkhorst [B. Jeziorski, H.J. Monkhorst, Phys. Rev. A 24, 1668 (1981)] exponential Ansatz. In this letter we report on the performance of a simple USS correction to the Brillouin-Wigner MRCC (BW-MRCC) formalism employing single and double excitations (BW-MRCCSD). It is shown that the resulting formalism (USS-BW-MRCCSD), which uses the manifold of single and double excitations to construct the correction, can be related to a posteriorimore » corrections utilized in routine BW-MRCCSD calculations. In several benchmark calculations we compare the results of the USS-BW-MRCCSD method with results of the BW-MRCCSD approach employing a posteriori corrections and with results obtained with the Full Configuration Interaction (FCI) method.« less

Surgeon-Specific Reports in General Surgery: Establishing Benchmarks for Peer Comparison Within a Single Hospital.

PubMed

Hatfield, Mark D; Ashton, Carol M; Bass, Barbara L; Shirkey, Beverly A

2016-02-01

Methods to assess a surgeon's individual performance based on clinically meaningful outcomes have not been fully developed, due to small numbers of adverse outcomes and wide variation in case volumes. The Achievable Benchmark of Care (ABC) method addresses these issues by identifying benchmark-setting surgeons with high levels of performance and greater case volumes. This method was used to help surgeons compare their surgical practice to that of their peers by using merged National Surgical Quality Improvement Program (NSQIP) and Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) data to generate surgeon-specific reports. A retrospective cohort study at a single institution's department of surgery was conducted involving 107 surgeons (8,660 cases) over 5.5 years. Stratification of more than 32,000 CPT codes into 16 CPT clusters served as the risk adjustment. Thirty-day outcomes of interest included surgical site infection (SSI), acute kidney injury (AKI), and mortality. Performance characteristics of the ABC method were explored by examining how many surgeons were identified as benchmark-setters in view of volume and outcome rates within CPT clusters. For the data captured, most surgeons performed cases spanning a median of 5 CPT clusters (range 1 to 15 clusters), with a median of 26 cases (range 1 to 776 cases) and a median of 2.8 years (range 0 to 5.5 years). The highest volume surgeon for that CPT cluster set the benchmark for 6 of 16 CPT clusters for SSIs, 8 of 16 CPT clusters for AKIs, and 9 of 16 CPT clusters for mortality. The ABC method appears to be a sound and useful approach to identifying benchmark-setting surgeons within a single institution. Such surgeons may be able to help their peers improve their performance. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Valence and charge-transfer optical properties for some SinCm (m, n ≤ 12) clusters: Comparing TD-DFT, complete-basis-limit EOMCC, and benchmarks from spectroscopy.

PubMed

Lutz, Jesse J; Duan, Xiaofeng F; Ranasinghe, Duminda S; Jin, Yifan; Margraf, Johannes T; Perera, Ajith; Burggraf, Larry W; Bartlett, Rodney J

2018-05-07

Accurate optical characterization of the closo-Si 12 C 12 molecule is important to guide experimental efforts toward the synthesis of nano-wires, cyclic nano-arrays, and related array structures, which are anticipated to be robust and efficient exciton materials for opto-electronic devices. Working toward calibrated methods for the description of closo-Si 12 C 12 oligomers, various electronic structure approaches are evaluated for their ability to reproduce measured optical transitions of the SiC 2 , Si 2 C n (n = 1-3), and Si 3 C n (n = 1, 2) clusters reported earlier by Steglich and Maier [Astrophys. J. 801, 119 (2015)]. Complete-basis-limit equation-of-motion coupled-cluster (EOMCC) results are presented and a comparison is made between perturbative and renormalized non-iterative triples corrections. The effect of adding a renormalized correction for quadruples is also tested. Benchmark test sets derived from both measurement and high-level EOMCC calculations are then used to evaluate the performance of a variety of density functionals within the time-dependent density functional theory (TD-DFT) framework. The best-performing functionals are subsequently applied to predict valence TD-DFT excitation energies for the lowest-energy isomers of Si n C and Si n-1 C 7-n (n = 4-6). TD-DFT approaches are then applied to the Si n C n (n = 4-12) clusters and unique spectroscopic signatures of closo-Si 12 C 12 are discussed. Finally, various long-range corrected density functionals, including those from the CAM-QTP family, are applied to a charge-transfer excitation in a cyclic (Si 4 C 4 ) 4 oligomer. Approaches for gauging the extent of charge-transfer character are also tested and EOMCC results are used to benchmark functionals and make recommendations.

Fierz Convergence Criterion: A Controlled Approach to Strongly Interacting Systems with Small Embedded Clusters.

PubMed

Ayral, Thomas; Vučičević, Jaksa; Parcollet, Olivier

2017-10-20

We present an embedded-cluster method, based on the triply irreducible local expansion formalism. It turns the Fierz ambiguity, inherent to approaches based on a bosonic decoupling of local fermionic interactions, into a convergence criterion. It is based on the approximation of the three-leg vertex by a coarse-grained vertex computed from a self-consistently determined cluster impurity model. The computed self-energies are, by construction, continuous functions of momentum. We show that, in three interaction and doping regimes of the two-dimensional Hubbard model, self-energies obtained with clusters of size four only are very close to numerically exact benchmark results. We show that the Fierz parameter, which parametrizes the freedom in the Hubbard-Stratonovich decoupling, can be used as a quality control parameter. By contrast, the GW+extended dynamical mean field theory approximation with four cluster sites is shown to yield good results only in the weak-coupling regime and for a particular decoupling. Finally, we show that the vertex has spatially nonlocal components only at low Matsubara frequencies.

Benchmark coupled-cluster g-tensor calculations with full inclusion of the two-particle spin-orbit contributions.

PubMed

Perera, Ajith; Gauss, Jürgen; Verma, Prakash; Morales, Jorge A

2017-04-28

We present a parallel implementation to compute electron spin resonance g-tensors at the coupled-cluster singles and doubles (CCSD) level which employs the ACES III domain-specific software tools for scalable parallel programming, i.e., the super instruction architecture language and processor (SIAL and SIP), respectively. A unique feature of the present implementation is the exact (not approximated) inclusion of the five one- and two-particle contributions to the g-tensor [i.e., the mass correction, one- and two-particle paramagnetic spin-orbit, and one- and two-particle diamagnetic spin-orbit terms]. Like in a previous implementation with effective one-electron operators [J. Gauss et al., J. Phys. Chem. A 113, 11541-11549 (2009)], our implementation utilizes analytic CC second derivatives and, therefore, classifies as a true CC linear-response treatment. Therefore, our implementation can unambiguously appraise the accuracy of less costly effective one-particle schemes and provide a rationale for their widespread use. We have considered a large selection of radicals used previously for benchmarking purposes including those studied in earlier work and conclude that at the CCSD level, the effective one-particle scheme satisfactorily captures the two-particle effects less costly than the rigorous two-particle scheme. With respect to the performance of density functional theory (DFT), we note that results obtained with the B3LYP functional exhibit the best agreement with our CCSD results. However, in general, the CCSD results agree better with the experimental data than the best DFT/B3LYP results, although in most cases within the rather large experimental error bars.

Bond Dissociation Energies for Diatomic Molecules Containing 3d Transition Metals: Benchmark Scalar-Relativistic Coupled-Cluster Calculations for 20 Molecules

DOE PAGES

Cheng, Lan; Gauss, Jürgen; Ruscic, Branko; ...

2017-01-12

Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the 20 diatomic molecules containing 3d transition metals in the 3dMLBE20 database ( J. Chem. Theory Comput. 2015, 11, 2036) are reported in this paper. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of 16 molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol. The discrepancies between theory and experiment remain substantial (more than 20 kJ/mol) for VH, CrH, CoH, and FeH. To explore the source of themore » latter discrepancies, the analysis used to determine the experimental dissociation energies for VH and CrH is revisited. It is shown that, if improved values are used for the heterolytic C–H dissociation energies of di- and trimethylamine involved in the experimental determination, the experimental values for the dissociation energies of VH and CrH are increased by 18 kJ/mol, such that D 0(VH) = 223 ± 7 kJ/mol and D 0(CrH) = 204 ± 7 kJ/mol (or D e(VH) = 233 ± 7 kJ/mol and D e(CrH) = 214 ± 7 kJ/mol). Finally, the new experimental values agree quite well with the calculated values, showing the consistency of the computation and the measured reaction thresholds.« less

An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings

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

Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas

2013-02-07

Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlapmore » matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Angstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.« less

An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings.

PubMed

Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas; Neugebauer, Johannes

2013-02-07

Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Ångstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

DOE PAGES

Sadybekov, Arman; Krylov, Anna I.

2017-07-07

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

Coupled-cluster based approach for core-level states in condensed phase: Theory and application to different protonated forms of aqueous glycine

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

Sadybekov, Arman; Krylov, Anna I.

A theoretical approach for calculating core-level states in condensed phase is presented. The approach is based on equation-of-motion coupled-cluster theory (EOMCC) and effective fragment potential (EFP) method. By introducing an approximate treatment of double excitations in the EOM-CCSD (EOM-CC with single and double substitutions) ansatz, we address poor convergence issues that are encountered for the core-level states and significantly reduce computational costs. While the approximations introduce relatively large errors in the absolute values of transition energies, the errors are systematic. Consequently, chemical shifts, changes in ionization energies relative to reference systems, are reproduced reasonably well. By using different protonation formsmore » of solvated glycine as a benchmark system, we show that our protocol is capable of reproducing the experimental chemical shifts with a quantitative accuracy. The results demonstrate that chemical shifts are very sensitive to the solvent interactions and that explicit treatment of solvent, such as EFP, is essential for achieving quantitative accuracy.« less

Present Status and Extensions of the Monte Carlo Performance Benchmark

NASA Astrophysics Data System (ADS)

Hoogenboom, J. Eduard; Petrovic, Bojan; Martin, William R.

2014-06-01

The NEA Monte Carlo Performance benchmark started in 2011 aiming to monitor over the years the abilities to perform a full-size Monte Carlo reactor core calculation with a detailed power production for each fuel pin with axial distribution. This paper gives an overview of the contributed results thus far. It shows that reaching a statistical accuracy of 1 % for most of the small fuel zones requires about 100 billion neutron histories. The efficiency of parallel execution of Monte Carlo codes on a large number of processor cores shows clear limitations for computer clusters with common type computer nodes. However, using true supercomputers the speedup of parallel calculations is increasing up to large numbers of processor cores. More experience is needed from calculations on true supercomputers using large numbers of processors in order to predict if the requested calculations can be done in a short time. As the specifications of the reactor geometry for this benchmark test are well suited for further investigations of full-core Monte Carlo calculations and a need is felt for testing other issues than its computational performance, proposals are presented for extending the benchmark to a suite of benchmark problems for evaluating fission source convergence for a system with a high dominance ratio, for coupling with thermal-hydraulics calculations to evaluate the use of different temperatures and coolant densities and to study the correctness and effectiveness of burnup calculations. Moreover, other contemporary proposals for a full-core calculation with realistic geometry and material composition will be discussed.

Time-dependent density functional theory description of total photoabsorption cross sections

NASA Astrophysics Data System (ADS)

Tenorio, Bruno Nunes Cabral; Nascimento, Marco Antonio Chaer; Rocha, Alexandre Braga

2018-02-01

The time-dependent version of the density functional theory (TDDFT) has been used to calculate the total photoabsorption cross section of a number of molecules, namely, benzene, pyridine, furan, pyrrole, thiophene, phenol, naphthalene, and anthracene. The discrete electronic pseudo-spectra, obtained in a L2 basis set calculation were used in an analytic continuation procedure to obtain the photoabsorption cross sections. The ammonia molecule was chosen as a model system to compare the results obtained with TDDFT to those obtained with the linear response coupled cluster approach in order to make a link with our previous work and establish benchmarks.

First principles electron-correlated calculations of optical absorption in magnesium clusters★

NASA Astrophysics Data System (ADS)

Shinde, Ravindra; Shukla, Alok

2017-11-01

In this paper, we report large-scale configuration interaction (CI) calculations of linear optical absorption spectra of various isomers of magnesium clusters Mgn (n = 2-5), corresponding to valence transitions. Geometry optimization of several low-lying isomers of each cluster was carried out using coupled-cluster singles doubles (CCSD) approach, and these geometries were subsequently employed to perform ground and excited state calculations using either the full-CI (FCI) or the multi-reference singles-doubles configuration interaction (MRSDCI) approach, within the frozen-core approximation. Our calculated photoabsorption spectrum of magnesium dimer (Mg2) is in excellent agreement with the experiments both for peak positions, and intensities. Owing to the sufficiently inclusive electron-correlation effects, these results can serve as benchmarks against which future experiments, as well as calculations performed using other theoretical approaches, can be tested. Supplementary material in the form of one pdf fille available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80356-6.

Cbench

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

Ogden, Jeffry B.

2005-09-26

Cbench is intended to be a relatively straightforward collection of tests, benchmarks, applications, utilities, and framework with the goal of facilitating scalable testing and benchmarking of a Linus cluster.

Acidity in DMSO from the embedded cluster integral equation quantum solvation model.

PubMed

Heil, Jochen; Tomazic, Daniel; Egbers, Simon; Kast, Stefan M

2014-04-01

The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pK(a) shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment.

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations.

PubMed

Peng, Bo; Kowalski, Karol

2017-09-12

The representation and storage of two-electron integral tensors are vital in large-scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this work, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition of the two-electron integral tensor in our implementation. For the size of the atomic basis set, N b , ranging from ∼100 up to ∼2,000, the observed numerical scaling of our implementation shows [Formula: see text] versus [Formula: see text] cost of performing single CD on the two-electron integral tensor in most of the other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic orbital (AO) two-electron integral tensor from [Formula: see text] to [Formula: see text] with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled cluster formalism employing single and double excitations (CCSD) on several benchmark systems including the C 60 molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10 -4 to 10 -3 to give acceptable compromise between efficiency and accuracy.

Evaluation of B3LYP, X3LYP, and M06-Class Density Functionals for Predicting the Binding Energies of Neutral, Protonated, and Deprotonated Water Clusters.

PubMed

Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

2009-04-14

In this paper we assess the accuracy of the B3LYP, X3LYP, and newly developed M06-L, M06-2X, and M06 functionals to predict the binding energies of neutral and charged water clusters including (H2O)n, n = 2-8, 20), H3O(+)(H2O)n, n = 1-6, and OH(-)(H2O)n, n = 1-6. We also compare the predicted energies of two ion hydration and neutralization reactions on the basis of the calculated binding energies. In all cases, we use as benchmarks calculated binding energies of water clusters extrapolated to the complete basis set limit of the second-order Møller-Plesset perturbation theory with the effects of higher order correlation estimated at the coupled-cluster theory with single, double, and perturbative triple excitations in the aug-cc-pVDZ basis set. We rank the accuracy of the functionals on the basis of the mean unsigned error (MUE) between calculated benchmark and density functional theory energies. The corresponding MUE (kcal/mol) for each functional is listed in parentheses. We find that M06-L (0.73) and M06 (0.84) give the most accurate binding energies using very extended basis sets such as aug-cc-pV5Z. For more affordable basis sets, the best methods for predicting the binding energies of water clusters are M06-L/aug-cc-pVTZ (1.24), B3LYP/6-311++G(2d,2p) (1.29), and M06/aug-cc-PVTZ (1.33). M06-L/aug-cc-pVTZ also gives more accurate energies for the neutralization reactions (1.38), whereas B3LYP/6-311++G(2d,2p) gives more accurate energies for the ion hydration reactions (1.69).

The X40×10 Halogen Bonding Benchmark Revisited: Surprising Importance of (n-1)d Subvalence Correlation.

PubMed

Kesharwani, Manoj K; Manna, Debashree; Sylvetsky, Nitai; Martin, Jan M L

2018-03-01

We have re-evaluated the X40×10 benchmark for halogen bonding using conventional and explicitly correlated coupled cluster methods. For the aromatic dimers at small separation, improved CCSD(T)-MP2 "high-level corrections" (HLCs) cause substantial reductions in the dissociation energy. For the bromine and iodine species, (n-1)d subvalence correlation increases dissociation energies and turns out to be more important for noncovalent interactions than is generally realized; (n-1)sp subvalence correlation is much less important. The (n-1)d subvalence term is dominated by core-valence correlation; with the smaller cc-pVDZ-F12-PP and cc-pVTZ-F12-PP basis sets, basis set convergence for the core-core contribution becomes sufficiently erratic that it may compromise results overall. The two factors conspire to generate discrepancies of up to 0.9 kcal/mol (0.16 kcal/mol RMS) between the original X40×10 data and the present revision.

SeSBench - An initiative to benchmark reactive transport models for environmental subsurface processes

NASA Astrophysics Data System (ADS)

Jacques, Diederik

2017-04-01

As soil functions are governed by a multitude of interacting hydrological, geochemical and biological processes, simulation tools coupling mathematical models for interacting processes are needed. Coupled reactive transport models are a typical example of such coupled tools mainly focusing on hydrological and geochemical coupling (see e.g. Steefel et al., 2015). Mathematical and numerical complexity for both the tool itself or of the specific conceptual model can increase rapidly. Therefore, numerical verification of such type of models is a prerequisite for guaranteeing reliability and confidence and qualifying simulation tools and approaches for any further model application. In 2011, a first SeSBench -Subsurface Environmental Simulation Benchmarking- workshop was held in Berkeley (USA) followed by four other ones. The objective is to benchmark subsurface environmental simulation models and methods with a current focus on reactive transport processes. The final outcome was a special issue in Computational Geosciences (2015, issue 3 - Reactive transport benchmarks for subsurface environmental simulation) with a collection of 11 benchmarks. Benchmarks, proposed by the participants of the workshops, should be relevant for environmental or geo-engineering applications; the latter were mostly related to radioactive waste disposal issues - excluding benchmarks defined for pure mathematical reasons. Another important feature is the tiered approach within a benchmark with the definition of a single principle problem and different sub problems. The latter typically benchmarked individual or simplified processes (e.g. inert solute transport, simplified geochemical conceptual model) or geometries (e.g. batch or one-dimensional, homogeneous). Finally, three codes should be involved into a benchmark. The SeSBench initiative contributes to confidence building for applying reactive transport codes. Furthermore, it illustrates the use of those type of models for different environmental and geo-engineering applications. SeSBench will organize new workshops to add new benchmarks in a new special issue. Steefel, C. I., et al. (2015). "Reactive transport codes for subsurface environmental simulation." Computational Geosciences 19: 445-478.

Calculations of Helium Bubble Evolution in the PISCES Experiments with Cluster Dynamics

NASA Astrophysics Data System (ADS)

Blondel, Sophie; Younkin, Timothy; Wirth, Brian; Lasa, Ane; Green, David; Canik, John; Drobny, Jon; Curreli, Davide

2017-10-01

Plasma surface interactions in fusion tokamak reactors involve an inherently multiscale, highly non-equilibrium set of phenomena, for which current models are inadequate to predict the divertor response to and feedback on the plasma. In this presentation, we describe the latest code developments of Xolotl, a spatially-dependent reaction diffusion cluster dynamics code to simulate the divertor surface response to fusion-relevant plasma exposure. Xolotl is part of a code-coupling effort to model both plasma and material simultaneously; the first benchmark for this effort is the series of PISCES linear device experiments. We will discuss the processes leading to surface morphology changes, which further affect erosion, as well as how Xolotl has been updated in order to communicate with other codes. Furthermore, we will show results of the sub-surface evolution of helium bubbles in tungsten as well as the material surface displacement under these conditions.

A benchmark study of electronic excitation energies, transition moments, and excited-state energy gradients on the nicotine molecule

NASA Astrophysics Data System (ADS)

Egidi, Franco; Segado, Mireia; Koch, Henrik; Cappelli, Chiara; Barone, Vincenzo

2014-12-01

In this work, we report a comparative study of computed excitation energies, oscillator strengths, and excited-state energy gradients of (S)-nicotine, chosen as a test case, using multireference methods, coupled cluster singles and doubles, and methods based on time-dependent density functional theory. This system was chosen because its apparent simplicity hides a complex electronic structure, as several different types of valence excitations are possible, including n-π*, π-π*, and charge-transfer states, and in order to simulate its spectrum it is necessary to describe all of them consistently well by the chosen method.

A benchmark study of electronic excitation energies, transition moments, and excited-state energy gradients on the nicotine molecule

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

Egidi, Franco, E-mail: franco.egidi@sns.it; Segado, Mireia; Barone, Vincenzo, E-mail: vincenzo.barone@sns.it

In this work, we report a comparative study of computed excitation energies, oscillator strengths, and excited-state energy gradients of (S)-nicotine, chosen as a test case, using multireference methods, coupled cluster singles and doubles, and methods based on time-dependent density functional theory. This system was chosen because its apparent simplicity hides a complex electronic structure, as several different types of valence excitations are possible, including n-π{sup *}, π-π{sup *}, and charge-transfer states, and in order to simulate its spectrum it is necessary to describe all of them consistently well by the chosen method.

Benchmark quality total atomization energies of small polyatomic molecules

NASA Astrophysics Data System (ADS)

Martin, Jan M. L.; Taylor, Peter R.

1997-05-01

Successive coupled-cluster [CCSD(T)] calculations in basis sets of spdf, spdfg, and spdfgh quality, combined with separate Schwartz-type extrapolations A+B/(l+1/2)α of the self-consistent field (SCF) and correlation energies, permit the calculations of molecular total atomization energies (TAEs) with a mean absolute error of as low as 0.12 kcal/mol. For the largest molecule treated, C2H4, we find ∑D0=532.0 kcal/mol, in perfect agreement with experiment. The aug-cc-pV5Z basis set recovers on average about 99% of the valence correlation contribution to the TAE, and essentially the entire SCF contribution.

Combinations of coupled cluster, density functionals, and the random phase approximation for describing static and dynamic correlation, and van der Waals interactions

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.; Bulik, Ireneusz W.; Alencar, Ana G. Sousa; Sun, Jianwei; Perdew, John P.; Scuseria, Gustavo E.

2016-04-01

Contrary to standard coupled cluster doubles (CCD) and Brueckner doubles (BD), singlet-paired analogues of CCD and BD (denoted here as CCD0 and BD0) do not break down when static correlation is present, but neglect substantial amounts of dynamic correlation. In fact, CCD0 and BD0 do not account for any contributions from multielectron excitations involving only same-spin electrons at all. We exploit this feature to add - without introducing double counting, self-interaction, or increase in cost - the missing correlation to these methods via meta-GGA (generalised gradient approximation) density functionals (Tao-Perdew-Staroverov-Scuseria and strongly constrained and appropriately normed). Furthermore, we improve upon these CCD0+DFT blends by invoking range separation: the short- and long-range correlations absent in CCD0/BD0 are evaluated with density functional theory and the direct random phase approximation, respectively. This corrects the description of long-range van der Waals forces. Comprehensive benchmarking shows that the combinations presented here are very accurate for weakly correlated systems, while also providing a reasonable description of strongly correlated problems without resorting to symmetry breaking.

Comparing the OpenMP, MPI, and Hybrid Programming Paradigm on an SMP Cluster

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Haoqiang; anMey, Dieter; Hatay, Ferhat F.

2003-01-01

With the advent of parallel hardware and software technologies users are faced with the challenge to choose a programming paradigm best suited for the underlying computer architecture. With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors (SMP), parallel programming techniques have evolved to support parallelism beyond a single level. Which programming paradigm is the best will depend on the nature of the given problem, the hardware architecture, and the available software. In this study we will compare different programming paradigms for the parallelization of a selected benchmark application on a cluster of SMP nodes. We compare the timings of different implementations of the same CFD benchmark application employing the same numerical algorithm on a cluster of Sun Fire SMP nodes. The rest of the paper is structured as follows: In section 2 we briefly discuss the programming models under consideration. We describe our compute platform in section 3. The different implementations of our benchmark code are described in section 4 and the performance results are presented in section 5. We conclude our study in section 6.

The Star Schema Benchmark and Augmented Fact Table Indexing

NASA Astrophysics Data System (ADS)

O'Neil, Patrick; O'Neil, Elizabeth; Chen, Xuedong; Revilak, Stephen

We provide a benchmark measuring star schema queries retrieving data from a fact table with Where clause column restrictions on dimension tables. Clustering is crucial to performance with modern disk technology, since retrievals with filter factors down to 0.0005 are now performed most efficiently by sequential table search rather than by indexed access. DB2’s Multi-Dimensional Clustering (MDC) provides methods to "dice" the fact table along a number of orthogonal "dimensions", but only when these dimensions are columns in the fact table. The diced cells cluster fact rows on several of these "dimensions" at once so queries restricting several such columns can access crucially localized data, with much faster query response. Unfortunately, columns of dimension tables of a star schema are not usually represented in the fact table. In this paper, we show a simple way to adjoin physical copies of dimension columns to the fact table, dicing data to effectively cluster query retrieval, and explain how such dicing can be achieved on database products other than DB2. We provide benchmark measurements to show successful use of this methodology on three commercial database products.

On the accuracy of explicitly correlated methods to generate potential energy surfaces for scattering calculations and clustering: application to the HCl-He complex.

PubMed

Ajili, Yosra; Hammami, Kamel; Jaidane, Nejm Eddine; Lanza, Mathieu; Kalugina, Yulia N; Lique, François; Hochlaf, Majdi

2013-07-07

We closely compare the accuracy of multidimensional potential energy surfaces (PESs) generated by the recently developed explicitly correlated coupled cluster (CCSD(T)-F12) methods in connection with the cc-pVXZ-F12 (X = D, T) and aug-cc-pVTZ basis sets and those deduced using the well-established orbital-based coupled cluster techniques employing correlation consistent atomic basis sets (aug-cc-pVXZ, X = T, Q, 5) and extrapolated to the complete basis set (CBS) limit. This work is performed on the benchmark rare gas-hydrogen halide interaction (HCl-He) system. These PESs are then incorporated into quantum close-coupling scattering dynamical calculations in order to check the impact of the accuracy of the PES on the scattering calculations. For this system, we deduced inelastic collisional data including (de-)excitation collisional and pressure broadening cross sections. Our work shows that the CCSD(T)-F12/aug-cc-pVTZ PES describes correctly the repulsive wall, the van der Waals minimum and long range internuclear distances whereas cc-pVXZ-F12 (X = D,T) basis sets are not diffuse enough for that purposes. Interestingly, the collision cross sections deduced from the CCSD(T)-F12/aug-cc-pVTZ PES are in excellent agreement with those obtained with CCSD(T)/CBS methodology. The position of the resonances and the general shape of these cross sections almost coincide. Since the cost of the electronic structure computations is reduced by several orders of magnitude when using CCSD(T)-F12/aug-cc-pVTZ compared to CCSD(T)/CBS methodology, this approach can be recommended as an alternative for generation of PESs of molecular clusters and for the interpretation of accurate scattering experiments as well as for a wide production of collisional data to be included in astrophysical and atmospherical models.

An introduction to mass cytometry: fundamentals and applications.

PubMed

Tanner, Scott D; Baranov, Vladimir I; Ornatsky, Olga I; Bandura, Dmitry R; George, Thaddeus C

2013-05-01

Mass cytometry addresses the analytical challenges of polychromatic flow cytometry by using metal atoms as tags rather than fluorophores and atomic mass spectrometry as the detector rather than photon optics. The many available enriched stable isotopes of the transition elements can provide up to 100 distinguishable reporting tags, which can be measured simultaneously because of the essential independence of detection provided by the mass spectrometer. We discuss the adaptation of traditional inductively coupled plasma mass spectrometry to cytometry applications. We focus on the generation of cytometry-compatible data and on approaches to unsupervised multivariate clustering analysis. Finally, we provide a high-level review of some recent benchmark reports that highlight the potential for massively multi-parameter mass cytometry.

Characteristic and factors of competitive maritime industry clusters in Indonesia

NASA Astrophysics Data System (ADS)

Marlyana, N.; Tontowi, A. E.; Yuniarto, H. A.

2017-12-01

Indonesia is situated in the strategic position between two oceans therefore is identified as a maritime state. The fact opens big opportunity to build a competitive maritime industry. However, potential factors to boost the competitive maritime industry still need to be explored. The objective of this paper is then to determine the main characteristics and potential factors of competitive maritime industry cluster. Qualitative analysis based on literature review has been carried out in two aspects. First, benchmarking analysis conducted to distinguish the most relevant factors of maritime clusters in several countries in Europe (Norway, Spain, South West of England) and Asia (China, South Korea, Malaysia). Seven key dimensions are used for this benchmarking. Secondly, the competitiveness of maritime clusters in Indonesia was diagnosed through a reconceptualization of Porter’s Diamond model. There were four interlinked of advanced factors in and between companies within clusters, which can be influenced in a proactive way by government.

Clustering Millions of Faces by Identity.

PubMed

Otto, Charles; Wang, Dayong; Jain, Anil K

2018-02-01

Given a large collection of unlabeled face images, we address the problem of clustering faces into an unknown number of identities. This problem is of interest in social media, law enforcement, and other applications, where the number of faces can be of the order of hundreds of million, while the number of identities (clusters) can range from a few thousand to millions. To address the challenges of run-time complexity and cluster quality, we present an approximate Rank-Order clustering algorithm that performs better than popular clustering algorithms (k-Means and Spectral). Our experiments include clustering up to 123 million face images into over 10 million clusters. Clustering results are analyzed in terms of external (known face labels) and internal (unknown face labels) quality measures, and run-time. Our algorithm achieves an F-measure of 0.87 on the LFW benchmark (13 K faces of 5,749 individuals), which drops to 0.27 on the largest dataset considered (13 K faces in LFW + 123M distractor images). Additionally, we show that frames in the YouTube benchmark can be clustered with an F-measure of 0.71. An internal per-cluster quality measure is developed to rank individual clusters for manual exploration of high quality clusters that are compact and isolated.

Tensor-decomposed vibrational coupled-cluster theory: Enabling large-scale, highly accurate vibrational-structure calculations

NASA Astrophysics Data System (ADS)

Madsen, Niels Kristian; Godtliebsen, Ian H.; Losilla, Sergio A.; Christiansen, Ove

2018-01-01

A new implementation of vibrational coupled-cluster (VCC) theory is presented, where all amplitude tensors are represented in the canonical polyadic (CP) format. The CP-VCC algorithm solves the non-linear VCC equations without ever constructing the amplitudes or error vectors in full dimension but still formally includes the full parameter space of the VCC[n] model in question resulting in the same vibrational energies as the conventional method. In a previous publication, we have described the non-linear-equation solver for CP-VCC calculations. In this work, we discuss the general algorithm for evaluating VCC error vectors in CP format including the rank-reduction methods used during the summation of the many terms in the VCC amplitude equations. Benchmark calculations for studying the computational scaling and memory usage of the CP-VCC algorithm are performed on a set of molecules including thiadiazole and an array of polycyclic aromatic hydrocarbons. The results show that the reduced scaling and memory requirements of the CP-VCC algorithm allows for performing high-order VCC calculations on systems with up to 66 vibrational modes (anthracene), which indeed are not possible using the conventional VCC method. This paves the way for obtaining highly accurate vibrational spectra and properties of larger molecules.

New algorithm for tensor contractions on multi-core CPUs, GPUs, and accelerators enables CCSD and EOM-CCSD calculations with over 1000 basis functions on a single compute node.

PubMed

Kaliman, Ilya A; Krylov, Anna I

2017-04-30

A new hardware-agnostic contraction algorithm for tensors of arbitrary symmetry and sparsity is presented. The algorithm is implemented as a stand-alone open-source code libxm. This code is also integrated with general tensor library libtensor and with the Q-Chem quantum-chemistry package. An overview of the algorithm, its implementation, and benchmarks are presented. Similarly to other tensor software, the algorithm exploits efficient matrix multiplication libraries and assumes that tensors are stored in a block-tensor form. The distinguishing features of the algorithm are: (i) efficient repackaging of the individual blocks into large matrices and back, which affords efficient graphics processing unit (GPU)-enabled calculations without modifications of higher-level codes; (ii) fully asynchronous data transfer between disk storage and fast memory. The algorithm enables canonical all-electron coupled-cluster and equation-of-motion coupled-cluster calculations with single and double substitutions (CCSD and EOM-CCSD) with over 1000 basis functions on a single quad-GPU machine. We show that the algorithm exhibits predicted theoretical scaling for canonical CCSD calculations, O(N 6 ), irrespective of the data size on disk. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Benchmarking the Fundamental Electronic Properties of small TiO 2 Nanoclusters by GW and Coupled Cluster Theory Calculations

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

Berardo, Enrico; Kaplan, Ferdinand; Bhaskaran-Nair, Kiran

We study the vertical ionisation potential, electron affinity, fundamental gap and exciton binding energy values of small bare and hydroxylated TiO 2 nanoclusters to understand how the excited state properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G 0 W 0, qs GW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare (i.e. non-hydroxylated) clusters all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow themore » same trends as the electron affinity and ionisation potentials predicted by the many-body methods but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend on the functional used and do not necessarily follow trends based on the many-body methods. The effect of hydroxylation of the clusters is to open up both the optical and fundamental gap. In conclusion, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the Madelung onsite potential.« less

Benchmarking the Fundamental Electronic Properties of small TiO 2 Nanoclusters by GW and Coupled Cluster Theory Calculations

DOE PAGES

Berardo, Enrico; Kaplan, Ferdinand; Bhaskaran-Nair, Kiran; ...

2017-06-19

We study the vertical ionisation potential, electron affinity, fundamental gap and exciton binding energy values of small bare and hydroxylated TiO 2 nanoclusters to understand how the excited state properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G 0 W 0, qs GW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare (i.e. non-hydroxylated) clusters all many-body methods predict the same trend with cluster size. The highest occupied and lowest unoccupied DFT orbitals follow themore » same trends as the electron affinity and ionisation potentials predicted by the many-body methods but are generally far too shallow and deep respectively in absolute terms. In contrast, the ΔDFT method is found to yield values in the correct energy window. However, its predictions depend on the functional used and do not necessarily follow trends based on the many-body methods. The effect of hydroxylation of the clusters is to open up both the optical and fundamental gap. In conclusion, a simple microscopic explanation for the observed trends with cluster size and upon hydroxylation is proposed in terms of the Madelung onsite potential.« less

Benchmark of Dynamic Electron Correlation Models for Seniority-Zero Wave Functions and Their Application to Thermochemistry.

PubMed

Boguslawski, Katharina; Tecmer, Paweł

2017-12-12

Wave functions restricted to electron-pair states are promising models to describe static/nondynamic electron correlation effects encountered, for instance, in bond-dissociation processes and transition-metal and actinide chemistry. To reach spectroscopic accuracy, however, the missing dynamic electron correlation effects that cannot be described by electron-pair states need to be included a posteriori. In this Article, we extend the previously presented perturbation theory models with an Antisymmetric Product of 1-reference orbital Geminal (AP1roG) reference function that allows us to describe both static/nondynamic and dynamic electron correlation effects. Specifically, our perturbation theory models combine a diagonal and off-diagonal zero-order Hamiltonian, a single-reference and multireference dual state, and different excitation operators used to construct the projection manifold. We benchmark all proposed models as well as an a posteriori Linearized Coupled Cluster correction on top of AP1roG against CR-CC(2,3) reference data for reaction energies of several closed-shell molecules that are extrapolated to the basis set limit. Moreover, we test the performance of our new methods for multiple bond breaking processes in the homonuclear N 2 , C 2 , and F 2 dimers as well as the heteronuclear BN, CO, and CN + dimers against MRCI-SD, MRCI-SD+Q, and CR-CC(2,3) reference data. Our numerical results indicate that the best performance is obtained from a Linearized Coupled Cluster correction as well as second-order perturbation theory corrections employing a diagonal and off-diagonal zero-order Hamiltonian and a single-determinant dual state. These dynamic corrections on top of AP1roG provide substantial improvements for binding energies and spectroscopic properties obtained with the AP1roG approach, while allowing us to approach chemical accuracy for reaction energies involving closed-shell species.

Performance Analysis of the ARL Linux Networx Cluster

DTIC Science & Technology

2004-06-01

OVERFLOW, used processors selected by SGE. All benchmarks on the GAMESS, COBALT, LSDYNA and FLUENT. Each code Origin 3800 were executed using IRIX cpusets...scheduler. for these benchmarks defines a missile with grid fins consisting of seventeen million cells [31. 4. Application Performance Results and

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

Computational Nuclear Physics and Post Hartree-Fock Methods

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

Lietz, Justin; Sam, Novario; Hjorth-Jensen, M.

We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions onmore » strategies for porting the code to present and planned high-performance computing facilities.« less

Relativistic all-order many-body calculation of energies, wavelengths, and M 1 and E 2 transition rates for the 3 dn configurations in tungsten ions

NASA Astrophysics Data System (ADS)

Safronova, M. S.; Safronova, U. I.; Porsev, S. G.; Kozlov, M. G.; Ralchenko, Yu.

2018-01-01

Energy levels, wavelengths, magnetic-dipole and electric-quadrupole transition rates between the low-lying states are evaluated for W51 + to W54 + ions with 3 dn (n =2 to 5) electronic configurations by using an approach combining configuration interaction with the linearized coupled-cluster single-double method. The QED corrections are directly incorporated into the calculations and their effect is studied in detail. Uncertainties of the calculations are discussed. This study of such highly charged ions with the present method opens the way for future applications allowing an accurate prediction of properties for a very wide range of highly charged ions aimed at providing precision benchmarks for various applications.

Quasi-Particle Self-Consistent GW for Molecules.

PubMed

Kaplan, F; Harding, M E; Seiler, C; Weigend, F; Evers, F; van Setten, M J

2016-06-14

We present the formalism and implementation of quasi-particle self-consistent GW (qsGW) and eigenvalue only quasi-particle self-consistent GW (evGW) adapted to standard quantum chemistry packages. Our implementation is benchmarked against high-level quantum chemistry computations (coupled-cluster theory) and experimental results using a representative set of molecules. Furthermore, we compare the qsGW approach for five molecules relevant for organic photovoltaics to self-consistent GW results (scGW) and analyze the effects of the self-consistency on the ground state density by comparing calculated dipole moments to their experimental values. We show that qsGW makes a significant improvement over conventional G0W0 and that partially self-consistent flavors (in particular evGW) can be excellent alternatives.

Determining Distance, Age, and Activity in a New Benchmark Cluster: Ruprecht 147

NASA Astrophysics Data System (ADS)

Wright, Jason T.

2009-08-01

This proposal seeks 0.7 night of time on Hectochelle to observe the F, G, and K dwarfs of Ruprecht 147, recently identified as the closest old stellar cluster. At only ~ 200 pc and at an age of ~ 1-2 Gyr, this will be an important benchmark in stellar astrophysics, providing the only sample of spectroscopically accessible old, late-type stars of determinable age. Hectochelle is the ideal instrument to study this cluster, with a FOV, fiber count, and telescope aperture well matched to the cluster's diameter (~ 1°), richness (~ 100 identified members), and distance modulus (6.5-7 mag., putting the G and K dwarfs at B=11-15). Hectochelle will measure the Ca II line strengths of members to establish, for the first time, the chromospheric activity levels of a statistically significant sample of single, G and K dwarfs of this modest age. Hectochelle will also vet background stars for suitability as astrometric reference stars for a forthcoming HST FGS proposal to robustly measure the cluster's distance.

A heuristic approach to handle capacitated facility location problem evaluated using clustering internal evaluation

NASA Astrophysics Data System (ADS)

Sutanto, G. R.; Kim, S.; Kim, D.; Sutanto, H.

2018-03-01

One of the problems in dealing with capacitated facility location problem (CFLP) is occurred because of the difference between the capacity numbers of facilities and the number of customers that needs to be served. A facility with small capacity may result in uncovered customers. These customers need to be re-allocated to another facility that still has available capacity. Therefore, an approach is proposed to handle CFLP by using k-means clustering algorithm to handle customers’ allocation. And then, if customers’ re-allocation is needed, is decided by the overall average distance between customers and the facilities. This new approach is benchmarked to the existing approach by Liao and Guo which also use k-means clustering algorithm as a base idea to decide the facilities location and customers’ allocation. Both of these approaches are benchmarked by using three clustering evaluation methods with connectedness, compactness, and separations factors.

Strömgren survey for asteroseismology and galactic archaeology: Let the saga begin

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

Casagrande, L.; Dotter, A.; Milone, A. P.

2014-06-01

Asteroseismology has the capability of precisely determining stellar properties that would otherwise be inaccessible, such as radii, masses, and thus ages of stars. When coupling this information with classical determinations of stellar parameters, such as metallicities, effective temperatures, and angular diameters, powerful new diagnostics for Galactic studies can be obtained. The ongoing Strömgren survey for Asteroseismology and Galactic Archaeology has the goal of transforming the Kepler field into a new benchmark for Galactic studies, similar to the solar neighborhood. Here we present the first results from a stripe centered at a Galactic longitude of 74° and covering latitude from aboutmore » 8° to 20°, which includes almost 1000 K giants with seismic information and the benchmark open cluster NGC 6819. We describe the coupling of classical and seismic parameters, the accuracy as well as the caveats of the derived effective temperatures, metallicities, distances, surface gravities, masses, and radii. Confidence in the achieved precision is corroborated by the detection of the first and secondary clumps in a population of field stars with a ratio of 2 to 1 and by the negligible scatter in the seismic distances among NGC 6819 member stars. An assessment of the reliability of stellar parameters in the Kepler Input Catalog is also performed, and the impact of our results for population studies in the Milky Way is discussed, along with the importance of an all-sky Strömgren survey.« less

New Multi-group Transport Neutronics (PHISICS) Capabilities for RELAP5-3D and its Application to Phase I of the OECD/NEA MHTGR-350 MW Benchmark

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

Gerhard Strydom; Cristian Rabiti; Andrea Alfonsi

2012-10-01

PHISICS is a neutronics code system currently under development at the Idaho National Laboratory (INL). Its goal is to provide state of the art simulation capability to reactor designers. The different modules for PHISICS currently under development are a nodal and semi-structured transport core solver (INSTANT), a depletion module (MRTAU) and a cross section interpolation (MIXER) module. The INSTANT module is the most developed of the mentioned above. Basic functionalities are ready to use, but the code is still in continuous development to extend its capabilities. This paper reports on the effort of coupling the nodal kinetics code package PHISICSmore » (INSTANT/MRTAU/MIXER) to the thermal hydraulics system code RELAP5-3D, to enable full core and system modeling. This will enable the possibility to model coupled (thermal-hydraulics and neutronics) problems with more options for 3D neutron kinetics, compared to the existing diffusion theory neutron kinetics module in RELAP5-3D (NESTLE). In the second part of the paper, an overview of the OECD/NEA MHTGR-350 MW benchmark is given. This benchmark has been approved by the OECD, and is based on the General Atomics 350 MW Modular High Temperature Gas Reactor (MHTGR) design. The benchmark includes coupled neutronics thermal hydraulics exercises that require more capabilities than RELAP5-3D with NESTLE offers. Therefore, the MHTGR benchmark makes extensive use of the new PHISICS/RELAP5-3D coupling capabilities. The paper presents the preliminary results of the three steady state exercises specified in Phase I of the benchmark using PHISICS/RELAP5-3D.« less

MARC calculations for the second WIPP structural benchmark problem

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

Morgan, H.S.

1981-05-01

This report describes calculations made with the MARC structural finite element code for the second WIPP structural benchmark problem. Specific aspects of problem implementation such as element choice, slip line modeling, creep law implementation, and thermal-mechanical coupling are discussed in detail. Also included are the computational results specified in the benchmark problem formulation.

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

NASA Astrophysics Data System (ADS)

Garza, Alejandro J.

Perhaps the most important approximations to the electronic structure problem in quantum chemistry are those based on coupled cluster and density functional theories. Coupled cluster theory has been called the ``gold standard'' of quantum chemistry due to the high accuracy that it achieves for weakly correlated systems. Kohn-Sham density functionals based on semilocal approximations are, without a doubt, the most widely used methods in chemistry and material science because of their high accuracy/cost ratio. The root of the success of coupled cluster and density functionals is their ability to efficiently describe the dynamic part of the electron correlation. However, both traditional coupled cluster and density functional approximations may fail catastrophically when substantial static correlation is present. This severely limits the applicability of these methods to a plethora of important chemical and physical problems such as, e.g., the description of bond breaking, transition states, transition metal-, lanthanide- and actinide-containing compounds, and superconductivity. In an attempt to tackle this problem, nonstandard (single-reference) coupled cluster-based techniques that aim to describe static correlation have been recently developed: pair coupled cluster doubles (pCCD) and singlet-paired coupled cluster doubles (CCD0). The ability to describe static correlation in pCCD and CCD0 comes, however, at the expense of important amounts of dynamic correlation so that the high accuracy of standard coupled cluster becomes unattainable. Thus, the reliable and efficient description of static and dynamic correlation in a simultaneous manner remains an open problem for quantum chemistry and many-body theory in general. In this thesis, different ways to combine pCCD and CCD0 with density functionals in order to describe static and dynamic correlation simultaneously (and efficiently) are explored. The combination of wavefunction and density functional methods has a long history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

Full dimensional (15-dimensional) quantum-dynamical simulation of the protonated water-dimer III: Mixed Jacobi-valence parametrization and benchmark results for the zero point energy, vibrationally excited states, and infrared spectrum.

PubMed

Vendrell, Oriol; Brill, Michael; Gatti, Fabien; Lauvergnat, David; Meyer, Hans-Dieter

2009-06-21

Quantum dynamical calculations are reported for the zero point energy, several low-lying vibrational states, and the infrared spectrum of the H(5)O(2)(+) cation. The calculations are performed by the multiconfiguration time-dependent Hartree (MCTDH) method. A new vector parametrization based on a mixed Jacobi-valence description of the system is presented. With this parametrization the potential energy surface coupling is reduced with respect to a full Jacobi description, providing a better convergence of the n-mode representation of the potential. However, new coupling terms appear in the kinetic energy operator. These terms are derived and discussed. A mode-combination scheme based on six combined coordinates is used, and the representation of the 15-dimensional potential in terms of a six-combined mode cluster expansion including up to some 7-dimensional grids is discussed. A statistical analysis of the accuracy of the n-mode representation of the potential at all orders is performed. Benchmark, fully converged results are reported for the zero point energy, which lie within the statistical uncertainty of the reference diffusion Monte Carlo result for this system. Some low-lying vibrationally excited eigenstates are computed by block improved relaxation, illustrating the applicability of the approach to large systems. Benchmark calculations of the linear infrared spectrum are provided, and convergence with increasing size of the time-dependent basis and as a function of the order of the n-mode representation is studied. The calculations presented here make use of recent developments in the parallel version of the MCTDH code, which are briefly discussed. We also show that the infrared spectrum can be computed, to a very good approximation, within D(2d) symmetry, instead of the G(16) symmetry used before, in which the complete rotation of one water molecule with respect to the other is allowed, thus simplifying the dynamical problem.

On coupling fluid plasma and kinetic neutral physics models

DOE PAGES

Joseph, I.; Rensink, M. E.; Stotler, D. P.; ...

2017-03-01

The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that theymore » scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.« less

First-principles energetics of water clusters and ice: A many-body analysis

NASA Astrophysics Data System (ADS)

Gillan, M. J.; Alfè, D.; Bartók, A. P.; Csányi, G.

2013-12-01

Standard forms of density-functional theory (DFT) have good predictive power for many materials, but are not yet fully satisfactory for cluster, solid, and liquid forms of water. Recent work has stressed the importance of DFT errors in describing dispersion, but we note that errors in other parts of the energy may also contribute. We obtain information about the nature of DFT errors by using a many-body separation of the total energy into its 1-body, 2-body, and beyond-2-body components to analyze the deficiencies of the popular PBE and BLYP approximations for the energetics of water clusters and ice structures. The errors of these approximations are computed by using accurate benchmark energies from the coupled-cluster technique of molecular quantum chemistry and from quantum Monte Carlo calculations. The systems studied are isomers of the water hexamer cluster, the crystal structures Ih, II, XV, and VIII of ice, and two clusters extracted from ice VIII. For the binding energies of these systems, we use the machine-learning technique of Gaussian Approximation Potentials to correct successively for 1-body and 2-body errors of the DFT approximations. We find that even after correction for these errors, substantial beyond-2-body errors remain. The characteristics of the 2-body and beyond-2-body errors of PBE are completely different from those of BLYP, but the errors of both approximations disfavor the close approach of non-hydrogen-bonded monomers. We note the possible relevance of our findings to the understanding of liquid water.

Developing effective electronic-only coupled-cluster and Møller-Plesset perturbation theories for the muonic molecules.

PubMed

Goli, Mohammad; Shahbazian, Shant

2018-06-20

Recently we have proposed an effective Hartree-Fock (EHF) theory for the electrons of the muonic molecules that is formally equivalent to the HF theory within the context of the nuclear-electronic orbital theory [Phys. Chem. Chem. Phys., 2018, 20, 4466]. In the present report we extend the muon-specific effective electronic structure theory beyond the EHF level by introducing the effective second order Møller-Plesset perturbation theory (EMP2) and the effective coupled-cluster theory at single and double excitation levels (ECCSD) as well as an improved version including perturbative triple excitations (ECCSD(T)). These theories incorporate electron-electron correlation into the effective paradigm and through their computational implementation, a diverse set of small muonic species is considered as a benchmark at these post-EHF levels. A comparative computational study on this set demonstrates that the muonic bond length is in general non-negligibly longer than corresponding hydrogenic analogs. Next, the developed post-EHF theories are applied for the muoniated N-heterocyclic carbene/silylene/germylene and the muoniated triazolium cation revealing the relative stability of the sticking sites of the muon in each species. The computational results, in line with previously reported experimental data demonstrate that the muon generally prefers to attach to the divalent atom with carbeneic nature. A detailed comparison of these muonic adducts with the corresponding hydrogenic adducts reveals subtle differences that have already been overlooked.

Stochastic multi-reference perturbation theory with application to the linearized coupled cluster method

NASA Astrophysics Data System (ADS)

Jeanmairet, Guillaume; Sharma, Sandeep; Alavi, Ali

2017-01-01

In this article we report a stochastic evaluation of the recently proposed multireference linearized coupled cluster theory [S. Sharma and A. Alavi, J. Chem. Phys. 143, 102815 (2015)]. In this method, both the zeroth-order and first-order wavefunctions are sampled stochastically by propagating simultaneously two populations of signed walkers. The sampling of the zeroth-order wavefunction follows a set of stochastic processes identical to the one used in the full configuration interaction quantum Monte Carlo (FCIQMC) method. To sample the first-order wavefunction, the usual FCIQMC algorithm is augmented with a source term that spawns walkers in the sampled first-order wavefunction from the zeroth-order wavefunction. The second-order energy is also computed stochastically but requires no additional overhead outside of the added cost of sampling the first-order wavefunction. This fully stochastic method opens up the possibility of simultaneously treating large active spaces to account for static correlation and recovering the dynamical correlation using perturbation theory. The method is used to study a few benchmark systems including the carbon dimer and aromatic molecules. We have computed the singlet-triplet gaps of benzene and m-xylylene. For m-xylylene, which has proved difficult for standard complete active space self consistent field theory with perturbative correction, we find the singlet-triplet gap to be in good agreement with the experimental values.

An ab initio benchmark study of the H + CO --> HCO reaction

NASA Technical Reports Server (NTRS)

Woon, D. E.

1996-01-01

The H + CO --> HCO reaction has been characterized with correlation consistent basis sets at five levels of theory in order to benchmark the sensitivities of the barrier height and reaction ergicity to the one-electron and n-electron expansions of the electronic wave function. Single and multireference methods are compared and contrasted. The coupled cluster method RCCSD(T) was found to be in very good agreement with Davidson-corrected internally-contracted multireference configuration interaction (MRCI+Q). Second-order Moller-Plesset perturbation theory (MP2) was also employed. The estimated complete basis set (CBS) limits for the barrier height (in kcal/mol) for the five methods, including harmonic zero-point energy corrections, are MP2, 4.66; RCCSD, 4.78; RCCSD(T), 4.15; MRCI, 5.10; and MRCI+Q, 4.07. Similarly, the estimated CBS limits for the ergicity of the reaction are: MP2, -17.99; RCCSD, -13.34; RCCSD(T), -13.79; MRCI, -11.46; and MRCI+Q, -13.70. Additional basis set explorations for the RCCSD(T) method demonstrate that aug-cc-pVTZ sets, even with some functions removed, are sufficient to reproduce the CBS limits to within 0.1-0.3 kcal/mol.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

An explicitly spin-free compact open-shell coupled cluster theory using a multireference combinatoric exponential ansatz: formal development and pilot applications.

PubMed

Datta, Dipayan; Mukherjee, Debashis

2009-07-28

In this paper, we present a comprehensive account of an explicitly spin-free compact state-universal multireference coupled cluster (CC) formalism for computing the state energies of simple open-shell systems, e.g., doublets and biradicals, where the target open-shell states can be described by a few configuration state functions spanning a model space. The cluster operators in this formalism are defined in terms of the spin-free unitary generators with respect to the common closed-shell component of all model functions (core) as vacuum. The spin-free cluster operators are either closed-shell-like n hole-n particle excitations (denoted by T(mu)) or involve excitations from the doubly occupied (nonvalence) orbitals to the singly occupied (valence) orbitals (denoted by S(e)(mu)). In addition, there are cluster operators with exchange spectator scatterings involving the valence orbitals (denoted by S(re)(mu)). We propose a new multireference cluster expansion ansatz for the wave operator with the above generally noncommuting cluster operators which essentially has the same physical content as the Jeziorski-Monkhorst ansatz with the commuting cluster operators defined in the spin-orbital basis. The T(mu) operators in our ansatz are taken to commute with all other operators, while the S(e)(mu) and S(re)(mu) operators are allowed to contract among themselves through the spectator valence orbitals. An important innovation of this ansatz is the choice of an appropriate automorphic factor accompanying each contracted composite of cluster operators in order to ensure that each distinct excitation generated by this composite appears only once in the wave operator. The resulting CC equations consist of two types of terms: a "direct" term and a "normalization" term containing the effective Hamiltonian operator. It is emphasized that the direct term is almost quartic in the cluster amplitudes, barring only a handful of terms and termination of the normalization term depends on the valence rank of the effective Hamiltonian operator and the excitation rank of the cluster operators at which the theory is truncated. Illustrative applications are presented by computing the state energies of neutral doublet radicals and doublet molecular cations and ionization energies of neutral molecules and comparing our results with the other open-shell CC theories, benchmark full CI results (when available) in the same basis, and the experimental results. Highly encouraging results show the efficacy of the method.

Relativistic many-body calculation of energies, multipole transition rates, and lifetimes in tungsten ions

NASA Astrophysics Data System (ADS)

Safronova, U. I.; Safronova, M. S.; Nakamura, N.

2017-04-01

Atomic properties of Cd-like W26 +, In-like W25 +, and Sn-like W24 + ions are evaluated by using a relativistic CI+all -order approach that combines configuration-interaction and the coupled-cluster methods. The energies, transition rates, and lifetimes of low-lying levels are calculated and compared with available theoretical and experimental values. The magnetic-dipole transition rates are calculated to determine the branching ratios and lifetimes for the 4 f3 states in W25 + and for the 4 f4 states in W24 + ions. Excellent agreement of the CI+all -order values provided a benchmark test of this method for the 4 fn configurations validating the recommended values of tungsten ion properties calculated in this work.

Cancer Detection in Microarray Data Using a Modified Cat Swarm Optimization Clustering Approach

PubMed

M, Pandi; R, Balamurugan; N, Sadhasivam

2017-12-29

Objective: A better understanding of functional genomics can be obtained by extracting patterns hidden in gene expression data. This could have paramount implications for cancer diagnosis, gene treatments and other domains. Clustering may reveal natural structures and identify interesting patterns in underlying data. The main objective of this research was to derive a heuristic approach to detection of highly co-expressed genes related to cancer from gene expression data with minimum Mean Squared Error (MSE). Methods: A modified CSO algorithm using Harmony Search (MCSO-HS) for clustering cancer gene expression data was applied. Experiment results are analyzed using two cancer gene expression benchmark datasets, namely for leukaemia and for breast cancer. Result: The results indicated MCSO-HS to be better than HS and CSO, 13% and 9% with the leukaemia dataset. For breast cancer dataset improvement was by 22% and 17%, respectively, in terms of MSE. Conclusion: The results showed MCSO-HS to outperform HS and CSO with both benchmark datasets. To validate the clustering results, this work was tested with internal and external cluster validation indices. Also this work points to biological validation of clusters with gene ontology in terms of function, process and component. Creative Commons Attribution License

Theoretical investigation of the He4Br2 conformers.

PubMed

Valdés, Álvaro; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

2012-07-05

Full dimensional quantum dynamics calculations of the three lowest isomers of the He(4)Br(2) van der Waals molecule in its ground electronic state are reported. The calculations are performed using the multiconfiguration time-dependent Hartree (MCTDH) method and a realistic potential form that includes the sum of three body ab initio coupled-cluster single double triple [CCSD(T)] He-Br(2) interactions plus the He-He and Br-Br interactions. This potential exhibits several multiple minima, with the three lowest ones lying very close in energy, just within 2 cm(-1). Such small differences are also found in the calculated binding energies of the three most stable conformers, indicating the floppiness of the system and, thus, the need of accurate potential forms and quantum full dynamics methods to treat this kind of complexes. The 12 dimensional results reported in this work present benchmark data and, thus, can serve to evaluate approximate methods aiming to describe higher order rare gas-dihalogen (N > 4) complexes. A comparison with previous studies using different potential forms and approaches to the energetics for the He(4)Br(2) cluster is also presented.

Results of the GABLS3 diurnal-cycle benchmark for wind energy applications

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

Rodrigo, J. Sanz; Allaerts, D.; Avila, M.

We present results of the GABLS3 model intercomparison benchmark revisited for wind energy applications. The case consists of a diurnal cycle, measured at the 200-m tall Cabauw tower in the Netherlands, including a nocturnal low-level jet. The benchmark includes a sensitivity analysis of WRF simulations using two input meteorological databases and five planetary boundary-layer schemes. A reference set of mesoscale tendencies is used to drive microscale simulations using RANS k-ϵ and LES turbulence models. The validation is based on rotor-based quantities of interest. Cycle-integrated mean absolute errors are used to quantify model performance. The results of the benchmark are usedmore » to discuss input uncertainties from mesoscale modelling, different meso-micro coupling strategies (online vs offline) and consistency between RANS and LES codes when dealing with boundary-layer mean flow quantities. Altogether, all the microscale simulations produce a consistent coupling with mesoscale forcings.« less

Results of the GABLS3 diurnal-cycle benchmark for wind energy applications

DOE PAGES

Rodrigo, J. Sanz; Allaerts, D.; Avila, M.; ...

2017-06-13

We present results of the GABLS3 model intercomparison benchmark revisited for wind energy applications. The case consists of a diurnal cycle, measured at the 200-m tall Cabauw tower in the Netherlands, including a nocturnal low-level jet. The benchmark includes a sensitivity analysis of WRF simulations using two input meteorological databases and five planetary boundary-layer schemes. A reference set of mesoscale tendencies is used to drive microscale simulations using RANS k-ϵ and LES turbulence models. The validation is based on rotor-based quantities of interest. Cycle-integrated mean absolute errors are used to quantify model performance. The results of the benchmark are usedmore » to discuss input uncertainties from mesoscale modelling, different meso-micro coupling strategies (online vs offline) and consistency between RANS and LES codes when dealing with boundary-layer mean flow quantities. Altogether, all the microscale simulations produce a consistent coupling with mesoscale forcings.« less

Singlet-paired coupled cluster theory for open shells

NASA Astrophysics Data System (ADS)

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

2016-06-01

Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior for strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.

Radiation Coupling with the FUN3D Unstructured-Grid CFD Code

NASA Technical Reports Server (NTRS)

Wood, William A.

2012-01-01

The HARA radiation code is fully-coupled to the FUN3D unstructured-grid CFD code for the purpose of simulating high-energy hypersonic flows. The radiation energy source terms and surface heat transfer, under the tangent slab approximation, are included within the fluid dynamic ow solver. The Fire II flight test, at the Mach-31 1643-second trajectory point, is used as a demonstration case. Comparisons are made with an existing structured-grid capability, the LAURA/HARA coupling. The radiative surface heat transfer rates from the present approach match the benchmark values within 6%. Although radiation coupling is the focus of the present work, convective surface heat transfer rates are also reported, and are seen to vary depending upon the choice of mesh connectivity and FUN3D ux reconstruction algorithm. On a tetrahedral-element mesh the convective heating matches the benchmark at the stagnation point, but under-predicts by 15% on the Fire II shoulder. Conversely, on a mixed-element mesh the convective heating over-predicts at the stagnation point by 20%, but matches the benchmark away from the stagnation region.

Descriptor Fingerprints and Their Application to WhiteWine Clustering and Discrimination.

NASA Astrophysics Data System (ADS)

Bangov, I. P.; Moskovkina, M.; Stojanov, B. P.

2018-03-01

This study continues the attempt to use the statistical process for a large-scale analytical data. A group of 3898 white wines, each with 11 analytical laboratory benchmarks was analyzed by a fingerprint similarity search in order to be grouped into separate clusters. A characterization of the wine's quality in each individual cluster was carried out according to individual laboratory parameters.

Identifying Peer Institutions Using Cluster Analysis

ERIC Educational Resources Information Center

Boronico, Jess; Choksi, Shail S.

2012-01-01

The New York Institute of Technology's (NYIT) School of Management (SOM) wishes to develop a list of peer institutions for the purpose of benchmarking and monitoring/improving performance against other business schools. The procedure utilizes relevant criteria for the purpose of establishing this peer group by way of a cluster analysis. The…

Numerical Analysis of Base Flowfield for a Four-Engine Clustered Nozzle Configuration

NASA Technical Reports Server (NTRS)

Wang, Ten-See

1995-01-01

Excessive base heating has been a problem for many launch vehicles. For certain designs such as the direct dump of turbine exhaust inside and at the lip of the nozzle, the potential burning of the turbine exhaust in the base region can be of great concern. Accurate prediction of the base environment at altitudes is therefore very important during the vehicle design phase. Otherwise, undesirable consequences may occur. In this study, the turbulent base flowfield of a cold flow experimental investigation for a four-engine clustered nozzle was numerically benchmarked using a pressure-based computational fluid dynamics (CFD) method. This is a necessary step before the benchmarking of hot flow and combustion flow tests can be considered. Since the medium was unheated air, reasonable prediction of the base pressure distribution at high altitude was the main goal. Several physical phenomena pertaining to the multiengine clustered nozzle base flow physics were deduced from the analysis.

Cluster synchronization induced by one-node clusters in networks with asymmetric negative couplings

NASA Astrophysics Data System (ADS)

Zhang, Jianbao; Ma, Zhongjun; Zhang, Gang

2013-12-01

This paper deals with the problem of cluster synchronization in networks with asymmetric negative couplings. By decomposing the coupling matrix into three matrices, and employing Lyapunov function method, sufficient conditions are derived for cluster synchronization. The conditions show that the couplings of multi-node clusters from one-node clusters have beneficial effects on cluster synchronization. Based on the effects of the one-node clusters, an effective and universal control scheme is put forward for the first time. The obtained results may help us better understand the relation between cluster synchronization and cluster structures of the networks. The validity of the control scheme is confirmed through two numerical simulations, in a network with no cluster structure and in a scale-free network.

Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

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

Huang, Yuanhang; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu

2015-07-28

Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simplemore » model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.« less

Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking

PubMed Central

2012-01-01

A key metric to assess molecular docking remains ligand enrichment against challenging decoys. Whereas the directory of useful decoys (DUD) has been widely used, clear areas for optimization have emerged. Here we describe an improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC. To ensure chemotype diversity, we cluster each target’s ligands by their Bemis–Murcko atomic frameworks. We add net charge to the matched physicochemical properties and include only the most dissimilar decoys, by topology, from the ligands. An online automated tool (http://decoys.docking.org) generates these improved matched decoys for user-supplied ligands. We test this data set by docking all 102 targets, using the results to improve the balance between ligand desolvation and electrostatics in DOCK 3.6. The complete DUD-E benchmarking set is freely available at http://dude.docking.org. PMID:22716043

PMLB: a large benchmark suite for machine learning evaluation and comparison.

PubMed

Olson, Randal S; La Cava, William; Orzechowski, Patryk; Urbanowicz, Ryan J; Moore, Jason H

2017-01-01

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. From this study, we find that existing benchmarks lack the diversity to properly benchmark machine learning algorithms, and there are several gaps in benchmarking problems that still need to be considered. This work represents another important step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.

CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys.

PubMed

Omori, Satoshi; Kitao, Akio

2013-06-01

We propose a fast clustering and reranking method, CyClus, for protein-protein docking decoys. This method enables comprehensive clustering of whole decoys generated by rigid-body docking using cylindrical approximation of the protein-proteininterface and hierarchical clustering procedures. We demonstrate the clustering and reranking of 54,000 decoy structures generated by ZDOCK for each complex within a few minutes. After parameter tuning for the test set in ZDOCK benchmark 2.0 with the ZDOCK and ZRANK scoring functions, blind tests for the incremental data in ZDOCK benchmark 3.0 and 4.0 were conducted. CyClus successfully generated smaller subsets of decoys containing near-native decoys. For example, the number of decoys required to create subsets containing near-native decoys with 80% probability was reduced from 22% to 50% of the number required in the original ZDOCK. Although specific ZDOCK and ZRANK results were demonstrated, the CyClus algorithm was designed to be more general and can be applied to a wide range of decoys and scoring functions by adjusting just two parameters, p and T. CyClus results were also compared to those from ClusPro. Copyright © 2013 Wiley Periodicals, Inc.

Shift Verification and Validation

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

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

Automatic Clustering Using FSDE-Forced Strategy Differential Evolution

NASA Astrophysics Data System (ADS)

Yasid, A.

2018-01-01

Clustering analysis is important in datamining for unsupervised data, cause no adequate prior knowledge. One of the important tasks is defining the number of clusters without user involvement that is known as automatic clustering. This study intends on acquiring cluster number automatically utilizing forced strategy differential evolution (AC-FSDE). Two mutation parameters, namely: constant parameter and variable parameter are employed to boost differential evolution performance. Four well-known benchmark datasets were used to evaluate the algorithm. Moreover, the result is compared with other state of the art automatic clustering methods. The experiment results evidence that AC-FSDE is better or competitive with other existing automatic clustering algorithm.

Cluster synchronization induced by one-node clusters in networks with asymmetric negative couplings

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

Zhang, Jianbao; Ma, Zhongjun, E-mail: mzj1234402@163.com; Zhang, Gang

2013-12-15

This paper deals with the problem of cluster synchronization in networks with asymmetric negative couplings. By decomposing the coupling matrix into three matrices, and employing Lyapunov function method, sufficient conditions are derived for cluster synchronization. The conditions show that the couplings of multi-node clusters from one-node clusters have beneficial effects on cluster synchronization. Based on the effects of the one-node clusters, an effective and universal control scheme is put forward for the first time. The obtained results may help us better understand the relation between cluster synchronization and cluster structures of the networks. The validity of the control scheme ismore » confirmed through two numerical simulations, in a network with no cluster structure and in a scale-free network.« less

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method.

PubMed

Sinha, Debalina; Pavanello, Michele

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.

Modeling dioxygen reduction at multicopper oxidase cathodes.

PubMed

Agbo, Peter; Heath, James R; Gray, Harry B

2014-10-01

We report a general kinetics model for catalytic dioxygen reduction on multicopper oxidase (MCO) cathodes. Our rate equation combines Butler-Volmer (BV) electrode kinetics and the Michaelis-Menten (MM) formalism for enzymatic catalysis, with the BV model accounting for interfacial electron transfer (ET) between the electrode surface and the MCO type 1 copper site. Extending the principles of MM kinetics to this system produced an analytical expression incorporating the effects of subsequent intramolecular ET and dioxygen binding to the trinuclear copper cluster into the cumulative model. We employed experimental electrochemical data on Thermus thermophilus laccase as benchmarks to validate our model, which we suggest will aid in the design of more efficient MCO cathodes. In addition, we demonstrate the model's utility in determining estimates for both the electronic coupling and average distance between the laccase type-1 active site and the cathode substrate.

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method

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

Sinha, Debalina; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term themore » Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.« less

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

NASA Astrophysics Data System (ADS)

Kubas, Adam; Hoffmann, Felix; Heck, Alexander; Oberhofer, Harald; Elstner, Marcus; Blumberger, Jochen

2014-03-01

We introduce a database (HAB11) of electronic coupling matrix elements (Hab) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute Hab values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

CHIMERA: Top-down model for hierarchical, overlapping and directed cluster structures in directed and weighted complex networks

NASA Astrophysics Data System (ADS)

Franke, R.

2016-11-01

In many networks discovered in biology, medicine, neuroscience and other disciplines special properties like a certain degree distribution and hierarchical cluster structure (also called communities) can be observed as general organizing principles. Detecting the cluster structure of an unknown network promises to identify functional subdivisions, hierarchy and interactions on a mesoscale. It is not trivial choosing an appropriate detection algorithm because there are multiple network, cluster and algorithmic properties to be considered. Edges can be weighted and/or directed, clusters overlap or build a hierarchy in several ways. Algorithms differ not only in runtime, memory requirements but also in allowed network and cluster properties. They are based on a specific definition of what a cluster is, too. On the one hand, a comprehensive network creation model is needed to build a large variety of benchmark networks with different reasonable structures to compare algorithms. On the other hand, if a cluster structure is already known, it is desirable to separate effects of this structure from other network properties. This can be done with null model networks that mimic an observed cluster structure to improve statistics on other network features. A third important application is the general study of properties in networks with different cluster structures, possibly evolving over time. Currently there are good benchmark and creation models available. But what is left is a precise sandbox model to build hierarchical, overlapping and directed clusters for undirected or directed, binary or weighted complex random networks on basis of a sophisticated blueprint. This gap shall be closed by the model CHIMERA (Cluster Hierarchy Interconnection Model for Evaluation, Research and Analysis) which will be introduced and described here for the first time.

Communication: A simplified coupled-cluster Lagrangian for polarizable embedding.

PubMed

Krause, Katharina; Klopper, Wim

2016-01-28

A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

Communication: A simplified coupled-cluster Lagrangian for polarizable embedding

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

Krause, Katharina; Klopper, Wim, E-mail: klopper@kit.edu

A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.

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

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior formore » strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.« less

TRACE/PARCS analysis of the OECD/NEA Oskarshamn-2 BWR stability benchmark

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

Kozlowski, T.; Downar, T.; Xu, Y.

2012-07-01

On February 25, 1999, the Oskarshamn-2 NPP experienced a stability event which culminated in diverging power oscillations with a decay ratio of about 1.4. The event was successfully modeled by the TRACE/PARCS coupled code system, and further analysis of the event is described in this paper. The results show very good agreement with the plant data, capturing the entire behavior of the transient including the onset of instability, growth of the oscillations (decay ratio) and oscillation frequency. This provides confidence in the prediction of other parameters which are not available from the plant records. The event provides coupled code validationmore » for a challenging BWR stability event, which involves the accurate simulation of neutron kinetics (NK), thermal-hydraulics (TH), and TH/NK. coupling. The success of this work has demonstrated the ability of the 3-D coupled systems code TRACE/PARCS to capture the complex behavior of BWR stability events. The problem was released as an international OECD/NEA benchmark, and it is the first benchmark based on measured plant data for a stability event with a DR greater than one. Interested participants are invited to contact authors for more information. (authors)« less

Statistical Analysis of NAS Parallel Benchmarks and LINPACK Results

NASA Technical Reports Server (NTRS)

Meuer, Hans-Werner; Simon, Horst D.; Strohmeier, Erich; Lasinski, T. A. (Technical Monitor)

1994-01-01

In the last three years extensive performance data have been reported for parallel machines both based on the NAS Parallel Benchmarks, and on LINPACK. In this study we have used the reported benchmark results and performed a number of statistical experiments using factor, cluster, and regression analyses. In addition to the performance results of LINPACK and the eight NAS parallel benchmarks, we have also included peak performance of the machine, and the LINPACK n and n(sub 1/2) values. Some of the results and observations can be summarized as follows: 1) All benchmarks are strongly correlated with peak performance. 2) LINPACK and EP have each a unique signature. 3) The remaining NPB can grouped into three groups as follows: (CG and IS), (LU and SP), and (MG, FT, and BT). Hence three (or four with EP) benchmarks are sufficient to characterize the overall NPB performance. Our poster presentation will follow a standard poster format, and will present the data of our statistical analysis in detail.

Benchmark solutions for the galactic heavy-ion transport equations with energy and spatial coupling

NASA Technical Reports Server (NTRS)

Ganapol, Barry D.; Townsend, Lawrence W.; Lamkin, Stanley L.; Wilson, John W.

1991-01-01

Nontrivial benchmark solutions are developed for the galactic heavy ion transport equations in the straightahead approximation with energy and spatial coupling. Analytical representations of the ion fluxes are obtained for a variety of sources with the assumption that the nuclear interaction parameters are energy independent. The method utilizes an analytical LaPlace transform inversion to yield a closed form representation that is computationally efficient. The flux profiles are then used to predict ion dose profiles, which are important for shield design studies.

Time-dependent risks of cancer clustering among couples: a nationwide population-based cohort study in Taiwan.

PubMed

Wang, Jong-Yi; Liang, Yia-Wen; Yeh, Chun-Chen; Liu, Chiu-Shong; Wang, Chen-Yu

2018-02-21

Spousal clustering of cancer warrants attention. Whether the common environment or high-age vulnerability determines cancer clustering is unclear. The risk of clustering in couples versus non-couples is undetermined. The time to cancer clustering after the first cancer diagnosis is yet to be reported. This study investigated cancer clustering over time among couples by using nationwide data. A cohort of 5643 married couples in the 2002-2013 Taiwan National Health Insurance Research Database was identified and randomly matched with 5643 non-couple pairs through dual propensity score matching. Factors associated with clustering (both spouses with tumours) were analysed by using the Cox proportional hazard model. Propensity-matched analysis revealed that the risk of clustering of all tumours among couples (13.70%) was significantly higher than that among non-couples (11.84%) (OR=1.182, 95% CI 1.058 to 1.321, P=0.0031). The median time to clustering of all tumours and of malignant tumours was 2.92 and 2.32 years, respectively. Risk characteristics associated with clustering included high age and comorbidity. Shared environmental factors among spouses might be linked to a high incidence of cancer clustering. Cancer incidence in one spouse may signal cancer vulnerability in the other spouse. Promoting family-oriented cancer care in vulnerable families and preventing shared lifestyle risk factors for cancer are suggested. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

PubMed

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Stochastic coupled cluster theory: Efficient sampling of the coupled cluster expansion

NASA Astrophysics Data System (ADS)

Scott, Charles J. C.; Thom, Alex J. W.

2017-09-01

We consider the sampling of the coupled cluster expansion within stochastic coupled cluster theory. Observing the limitations of previous approaches due to the inherently non-linear behavior of a coupled cluster wavefunction representation, we propose new approaches based on an intuitive, well-defined condition for sampling weights and on sampling the expansion in cluster operators of different excitation levels. We term these modifications even and truncated selections, respectively. Utilising both approaches demonstrates dramatically improved calculation stability as well as reduced computational and memory costs. These modifications are particularly effective at higher truncation levels owing to the large number of terms within the cluster expansion that can be neglected, as demonstrated by the reduction of the number of terms to be sampled when truncating at triple excitations by 77% and hextuple excitations by 98%.

Benchmarking Ada tasking on tightly coupled multiprocessor architectures

NASA Technical Reports Server (NTRS)

Collard, Philippe; Goforth, Andre; Marquardt, Matthew

1989-01-01

The development of benchmarks and performance measures for parallel Ada tasking is reported with emphasis on the macroscopic behavior of the benchmark across a set of load parameters. The application chosen for the study was the NASREM model for telerobot control, relevant to many NASA missions. The results of the study demonstrate the potential of parallel Ada in accomplishing the task of developing a control system for a system such as the Flight Telerobotic Servicer using the NASREM framework.

Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

NASA Astrophysics Data System (ADS)

Datta, Dipayan; Kossmann, Simone; Neese, Frank

2016-09-01

The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the threshold for the natural orbital occupation number cutoff by an order of magnitude compared to the DLPNO-CCSD energy calculations.

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

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

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Cherry-picking functionally relevant substates from long md trajectories using a stratified sampling approach.

PubMed

Chandramouli, Balasubramanian; Mancini, Giordano

2016-01-01

Classical Molecular Dynamics (MD) simulations can provide insights at the nanoscopic scale into protein dynamics. Currently, simulations of large proteins and complexes can be routinely carried out in the ns-μs time regime. Clustering of MD trajectories is often performed to identify selective conformations and to compare simulation and experimental data coming from different sources on closely related systems. However, clustering techniques are usually applied without a careful validation of results and benchmark studies involving the application of different algorithms to MD data often deal with relatively small peptides instead of average or large proteins; finally clustering is often applied as a means to analyze refined data and also as a way to simplify further analysis of trajectories. Herein, we propose a strategy to classify MD data while carefully benchmarking the performance of clustering algorithms and internal validation criteria for such methods. We demonstrate the method on two showcase systems with different features, and compare the classification of trajectories in real and PCA space. We posit that the prototype procedure adopted here could be highly fruitful in clustering large trajectories of multiple systems or that resulting especially from enhanced sampling techniques like replica exchange simulations. Copyright: © 2016 by Fabrizio Serra editore, Pisa · Roma.

Diary Data Subjected to Cluster Analysis of Intake/Output/Void Habits with Resulting Clusters Compared by Continence Status, Age, Race

PubMed Central

Miller, Janis M; Guo, Ying; Rodseth, Sarah Becker

2011-01-01

Background Data that incorporate the full complexity of healthy beverage intake and voiding frequency do not exist; therefore, clinicians reviewing bladder habits or voiding diaries for continence care must rely on expert opinion recommendations. Objective To use data-driven cluster analyses to reduce complex voiding diary variables into discrete patterns or data cluster profiles, descriptively name the clusters, and perform validity testing. Method Participants were 352 community women who filled out a 3-day voiding diary. Six variables (void frequency during daytime hours, void frequency during nighttime hours, modal output, total output, total intake, and body mass index) were entered into cluster analyses. The clusters were analyzed for differences by continence status, age, race (Black women, n = 196 White women, n = 156), and for those who were incontinent, by leakage episode severity. Results Three clusters emerged, labeled descriptively as Conventional, Benchmark, and Superplus. The Conventional cluster (68% of the sample) demonstrated mean daily intake of 45 ±13 ounces; mean daily output of 37 ± 15 ounces, mean daily voids 5 ± 2 times, mean modal daytime output 10±0.5 ounces, and mean nighttime voids 1±1 times. The Superplus cluster (7% of the sample) showed double or triple these values across the 5 variables, and the Benchmark cluster (25%) showed values consistent with current popular recommendations on intake and output (e.g., meeting or exceeding the 8 × 8 fluid intake rule of thumb). The clusters differed significantly (p < .05) by age, race, amount of irritating beverages consumed, and incontinence status. Discussion Identification of three discrete clusters provides for a potential parsimonious but data-driven means of classifying individuals for additional epidemiological or clinical study. The clinical utility rests with potential for intervening to move an individual from a high risk to low risk cluster with regards to incontinence. PMID:21317828

Benchmarking and tuning the MILC code on clusters and supercomputers

NASA Astrophysics Data System (ADS)

Gottlieb, Steven

2002-03-01

Recently, we have benchmarked and tuned the MILC code on a number of architectures including Intel Itanium and Pentium IV (PIV), dual-CPU Athlon, and the latest Compaq Alpha nodes. Results will be presented for many of these, and we shall discuss some simple code changes that can result in a very dramatic speedup of the KS conjugate gradient on processors with more advanced memory systems such as PIV, IBM SP and Alpha.

Benchmarking and tuning the MILC code on clusters and supercomputers

NASA Astrophysics Data System (ADS)

Gottlieb, Steven

Recently, we have benchmarked and tuned the MILC code on a number of architectures including Intel Itanium and Pentium IV (PIV), dual-CPU Athlon, and the latest Compaq Alpha nodes. Results will be presented for many of these, and we shall discuss some simple code changes that can result in a very dramatic speedup of the KS conjugate gradient on processors with more advanced memory systems such as PIV, IBM SP and Alpha.

More than one way to be happy: a typology of marital happiness.

PubMed

Rauer, Amy; Volling, Brenda

2013-09-01

This study utilized observational and self-report data from 57 happily married couples to explore assumptions regarding marital happiness. Suggesting that happily married couples are not a homogeneous group, cluster analyses revealed the existence of three types of couples based on their observed behaviors in a problem-solving task: (1) mutually engaged couples (characterized by both spouses' higher negative and positive problem-solving); (2) mutually supportive couples (characterized by both spouses' higher positivity and support); and (3) wife compensation couples (characterized by high wife positivity). Although couples in all three clusters were equally happy with and committed to their marriages, these clusters were differentially associated with spouses' evaluations of their marriage. Spouses in the mutually supportive cluster reported greater intimacy and maintenance and less conflict and ambivalence, although this was more consistently the case in comparison to the wife compensation cluster, as opposed to the mutually engaged cluster. The implications of these typologies are discussed as they pertain to efforts on the part of both practitioners to promote marital happiness and repair marital relations when couples are faced with difficulties. © FPI, Inc.

Modification and benchmarking of MCNP for low-energy tungsten spectra.

PubMed

Mercier, J R; Kopp, D T; McDavid, W D; Dove, S B; Lancaster, J L; Tucker, D M

2000-12-01

The MCNP Monte Carlo radiation transport code was modified for diagnostic medical physics applications. In particular, the modified code was thoroughly benchmarked for the production of polychromatic tungsten x-ray spectra in the 30-150 kV range. Validating the modified code for coupled electron-photon transport with benchmark spectra was supplemented with independent electron-only and photon-only transport benchmarks. Major revisions to the code included the proper treatment of characteristic K x-ray production and scoring, new impact ionization cross sections, and new bremsstrahlung cross sections. Minor revisions included updated photon cross sections, electron-electron bremsstrahlung production, and K x-ray yield. The modified MCNP code is benchmarked to electron backscatter factors, x-ray spectra production, and primary and scatter photon transport.

Validation of tsunami inundation model TUNA-RP using OAR-PMEL-135 benchmark problem set

NASA Astrophysics Data System (ADS)

Koh, H. L.; Teh, S. Y.; Tan, W. K.; Kh'ng, X. Y.

2017-05-01

A standard set of benchmark problems, known as OAR-PMEL-135, is developed by the US National Tsunami Hazard Mitigation Program for tsunami inundation model validation. Any tsunami inundation model must be tested for its accuracy and capability using this standard set of benchmark problems before it can be gainfully used for inundation simulation. The authors have previously developed an in-house tsunami inundation model known as TUNA-RP. This inundation model solves the two-dimensional nonlinear shallow water equations coupled with a wet-dry moving boundary algorithm. This paper presents the validation of TUNA-RP against the solutions provided in the OAR-PMEL-135 benchmark problem set. This benchmark validation testing shows that TUNA-RP can indeed perform inundation simulation with accuracy consistent with that in the tested benchmark problem set.

Complex absorbing potentials within EOM-CC family of methods: Theory, implementation, and benchmarks

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

Zuev, Dmitry; Jagau, Thomas-C.; Krylov, Anna I.

2014-07-14

A production-level implementation of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) for electron attachment and excitation energies augmented by a complex absorbing potential (CAP) is presented. The new method enables the treatment of metastable states within the EOM-CC formalism in a similar manner as bound states. The numeric performance of the method and the sensitivity of resonance positions and lifetimes to the CAP parameters and the choice of one-electron basis set are investigated. A protocol for studying molecular shape resonances based on the use of standard basis sets and a universal criterion for choosing the CAP parameters are presented. Our resultsmore » for a variety of π{sup *} shape resonances of small to medium-size molecules demonstrate that CAP-augmented EOM-CCSD is competitive relative to other theoretical approaches for the treatment of resonances and is often able to reproduce experimental results.« less

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

Cheng, Lan, E-mail: chenglanster@gmail.com; Stopkowicz, Stella, E-mail: stella.stopkowicz@kjemi.uio.no; Gauss, Jürgen, E-mail: gauss@uni-mainz.de

A perturbative approach to compute second-order spin-orbit (SO) corrections to a spin-free Dirac-Coulomb Hartree-Fock (SFDC-HF) calculation is suggested. The proposed scheme treats the difference between the DC and SFDC Hamiltonian as perturbation and exploits analytic second-derivative techniques. In addition, a cost-effective scheme for incorporating relativistic effects in high-accuracy calculations is suggested consisting of a SFDC coupled-cluster treatment augmented by perturbative SO corrections obtained at the HF level. Benchmark calculations for the hydrogen halides HX, X = F-At as well as the coinage-metal fluorides CuF, AgF, and AuF demonstrate the accuracy of the proposed perturbative treatment of SO effects on energiesmore » and electrical properties in comparison with the more rigorous full DC treatment. Furthermore, we present, as an application of our scheme, results for the electrical properties of AuF and XeAuF.« less

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

Wang, Weizhou, E-mail: wzw@lynu.edu.cn, E-mail: ybw@gzu.edu.cn; Zhang, Yu; Sun, Tao

High-level coupled cluster singles, doubles, and perturbative triples [CCSD(T)] computations with up to the aug-cc-pVQZ basis set (1924 basis functions) and various extrapolations toward the complete basis set (CBS) limit are presented for the sandwich, T-shaped, and parallel-displaced benzene⋯naphthalene complex. Using the CCSD(T)/CBS interaction energies as a benchmark, the performance of some newly developed wave function and density functional theory methods has been evaluated. The best performing methods were found to be the dispersion-corrected PBE0 functional (PBE0-D3) and spin-component scaled zeroth-order symmetry-adapted perturbation theory (SCS-SAPT0). The success of SCS-SAPT0 is very encouraging because it provides one method for energy componentmore » analysis of π-stacked complexes with 200 atoms or more. Most newly developed methods do, however, overestimate the interaction energies. The results of energy component analysis show that interaction energies are overestimated mainly due to the overestimation of dispersion energy.« less

Experimental benchmark of kinetic simulations of capacitively coupled plasmas in molecular gases

NASA Astrophysics Data System (ADS)

Donkó, Z.; Derzsi, A.; Korolov, I.; Hartmann, P.; Brandt, S.; Schulze, J.; Berger, B.; Koepke, M.; Bruneau, B.; Johnson, E.; Lafleur, T.; Booth, J.-P.; Gibson, A. R.; O'Connell, D.; Gans, T.

2018-01-01

We discuss the origin of uncertainties in the results of numerical simulations of low-temperature plasma sources, focusing on capacitively coupled plasmas. These sources can be operated in various gases/gas mixtures, over a wide domain of excitation frequency, voltage, and gas pressure. At low pressures, the non-equilibrium character of the charged particle transport prevails and particle-based simulations become the primary tools for their numerical description. The particle-in-cell method, complemented with Monte Carlo type description of collision processes, is a well-established approach for this purpose. Codes based on this technique have been developed by several authors/groups, and have been benchmarked with each other in some cases. Such benchmarking demonstrates the correctness of the codes, but the underlying physical model remains unvalidated. This is a key point, as this model should ideally account for all important plasma chemical reactions as well as for the plasma-surface interaction via including specific surface reaction coefficients (electron yields, sticking coefficients, etc). In order to test the models rigorously, comparison with experimental ‘benchmark data’ is necessary. Examples will be given regarding the studies of electron power absorption modes in O2, and CF4-Ar discharges, as well as on the effect of modifications of the parameters of certain elementary processes on the computed discharge characteristics in O2 capacitively coupled plasmas.

Elastic K-means using posterior probability.

PubMed

Zheng, Aihua; Jiang, Bo; Li, Yan; Zhang, Xuehan; Ding, Chris

2017-01-01

The widely used K-means clustering is a hard clustering algorithm. Here we propose a Elastic K-means clustering model (EKM) using posterior probability with soft capability where each data point can belong to multiple clusters fractionally and show the benefit of proposed Elastic K-means. Furthermore, in many applications, besides vector attributes information, pairwise relations (graph information) are also available. Thus we integrate EKM with Normalized Cut graph clustering into a single clustering formulation. Finally, we provide several useful matrix inequalities which are useful for matrix formulations of learning models. Based on these results, we prove the correctness and the convergence of EKM algorithms. Experimental results on six benchmark datasets demonstrate the effectiveness of proposed EKM and its integrated model.

Computing Cluster for Large Scale Turbulence Simulations and Applications in Computational Aeroacoustics

NASA Astrophysics Data System (ADS)

Lele, Sanjiva K.

2002-08-01

Funds were received in April 2001 under the Department of Defense DURIP program for construction of a 48 processor high performance computing cluster. This report details the hardware which was purchased and how it has been used to enable and enhance research activities directly supported by, and of interest to, the Air Force Office of Scientific Research and the Department of Defense. The report is divided into two major sections. The first section after this summary describes the computer cluster, its setup, and some cluster performance benchmark results. The second section explains ongoing research efforts which have benefited from the cluster hardware, and presents highlights of those efforts since installation of the cluster.

Evaluation of a demand-creation intervention for couples' HIV testing services among married or cohabiting individuals in Rakai, Uganda: a cluster-randomized intervention trial.

PubMed

Matovu, Joseph K B; Todd, Jim; Wanyenze, Rhoda K; Kairania, Robert; Serwadda, David; Wabwire-Mangen, Fred

2016-08-08

Uptake of couples' HIV counseling and testing (couples' HCT) services remains largely low in most settings. We report the effect of a demand-creation intervention trial on couples' HCT uptake among married or cohabiting individuals who had never received couples' HCT. This was a cluster-randomized intervention trial implemented in three study regions with differing HIV prevalence levels (range: 9-43 %) in Rakai district, southwestern Uganda, between February and September 2014. We randomly assigned six clusters (1:1) to receive the intervention or serve as the comparison arm using computer-generated random numbers. In the intervention clusters, individuals attended small group, couple and male-focused interactive sessions, reinforced with testimonies from 'expert couples', and received invitation coupons to test together with their partners at designated health facilities. In the comparison clusters, participants attended general adult health education sessions but received no invitation coupons. The primary outcome was couples' HCT uptake, measured 12 months post-baseline. Baseline data were collected between November 2013 and February 2014 while follow-up data were collected between March and April 2015. We conducted intention-to-treat analysis using a mixed effects Poisson regression model to assess for differences in couples' HCT uptake between the intervention and comparison clusters. Data analysis was conducted using STATA statistical software, version 14.1. Of 2135 married or cohabiting individuals interviewed at baseline, 42 % (n = 846) had ever received couples' HCT. Of those who had never received couples' HCT (n = 1,174), 697 were interviewed in the intervention clusters while 477 were interviewed in the comparison clusters. 73.6 % (n = 513) of those interviewed in the intervention and 82.6 % (n = 394) of those interviewed in the comparison cluster were interviewed at follow-up. Of those interviewed, 72.3 % (n = 371) in the intervention and 65.2 % (n = 257) in the comparison clusters received HCT. Couples' HCT uptake was higher in the intervention than in the comparison clusters (20.3 % versus 13.7 %; adjusted prevalence ratio (aPR) = 1.43, 95 % CI: 1.02, 2.01, P = 0.04). Our findings show that a small group, couple and male-focused, demand-creation intervention reinforced with testimonies from 'expert couples', improved uptake of couples' HCT in this rural setting. ClinicalTrials.gov, NCT02492061 . Date of registration: June 14, 2015.

Distinct collective states due to trade-off between attractive and repulsive couplings

NASA Astrophysics Data System (ADS)

Sathiyadevi, K.; Chandrasekar, V. K.; Senthilkumar, D. V.; Lakshmanan, M.

2018-03-01

We investigate the effect of repulsive coupling together with an attractive coupling in a network of nonlocally coupled oscillators. To understand the complex interaction between these two couplings we introduce a control parameter in the repulsive coupling which plays a crucial role in inducing distinct complex collective patterns. In particular, we show the emergence of various cluster chimera death states through a dynamically distinct transition route, namely the oscillatory cluster state and coherent oscillation death state as a function of the repulsive coupling in the presence of the attractive coupling. In the oscillatory cluster state, the oscillators in the network are grouped into two distinct dynamical states of homogeneous and inhomogeneous oscillatory states. Further, the network of coupled oscillators follow the same transition route in the entire coupling range. Depending upon distinct coupling ranges, the system displays different number of clusters in the death state and oscillatory state. We also observe that the number of coherent domains in the oscillatory cluster state exponentially decreases with increase in coupling range and obeys a power-law decay. Additionally, we show analytical stability for observed solitary state, synchronized state, and incoherent oscillation death state.

Corepressive interaction and clustering of degrade-and-fire oscillators

PubMed Central

Fernandez, Bastien; Tsimring, Lev S.

2016-01-01

Strongly nonlinear degrade-and-fire (DF) oscillations may emerge in genetic circuits having a delayed negative feedback loop as their core element. Here we study the synchronization of DF oscillators coupled through a common repressor field. For weak coupling, initially distinct oscillators remain desynchronized. For stronger coupling, oscillators can be forced to wait in the repressed state until the global repressor field is sufficiently degraded, and then they fire simultaneously forming a synchronized cluster. Our analytical theory provides necessary and sufficient conditions for clustering and specifies the maximum number of clusters that can be formed in the asymptotic regime. We find that in the thermodynamic limit a phase transition occurs at a certain coupling strength from the weakly clustered regime with only microscopic clusters to a strongly clustered regime where at least one giant cluster has to be present. PMID:22181453

Query by example video based on fuzzy c-means initialized by fixed clustering center

NASA Astrophysics Data System (ADS)

Hou, Sujuan; Zhou, Shangbo; Siddique, Muhammad Abubakar

2012-04-01

Currently, the high complexity of video contents has posed the following major challenges for fast retrieval: (1) efficient similarity measurements, and (2) efficient indexing on the compact representations. A video-retrieval strategy based on fuzzy c-means (FCM) is presented for querying by example. Initially, the query video is segmented and represented by a set of shots, each shot can be represented by a key frame, and then we used video processing techniques to find visual cues to represent the key frame. Next, because the FCM algorithm is sensitive to the initializations, here we initialized the cluster center by the shots of query video so that users could achieve appropriate convergence. After an FCM cluster was initialized by the query video, each shot of query video was considered a benchmark point in the aforesaid cluster, and each shot in the database possessed a class label. The similarity between the shots in the database with the same class label and benchmark point can be transformed into the distance between them. Finally, the similarity between the query video and the video in database was transformed into the number of similar shots. Our experimental results demonstrated the performance of this proposed approach.

M-Isomap: Orthogonal Constrained Marginal Isomap for Nonlinear Dimensionality Reduction.

PubMed

Zhang, Zhao; Chow, Tommy W S; Zhao, Mingbo

2013-02-01

Isomap is a well-known nonlinear dimensionality reduction (DR) method, aiming at preserving geodesic distances of all similarity pairs for delivering highly nonlinear manifolds. Isomap is efficient in visualizing synthetic data sets, but it usually delivers unsatisfactory results in benchmark cases. This paper incorporates the pairwise constraints into Isomap and proposes a marginal Isomap (M-Isomap) for manifold learning. The pairwise Cannot-Link and Must-Link constraints are used to specify the types of neighborhoods. M-Isomap computes the shortest path distances over constrained neighborhood graphs and guides the nonlinear DR through separating the interclass neighbors. As a result, large margins between both interand intraclass clusters are delivered and enhanced compactness of intracluster points is achieved at the same time. The validity of M-Isomap is examined by extensive simulations over synthetic, University of California, Irvine, and benchmark real Olivetti Research Library, YALE, and CMU Pose, Illumination, and Expression databases. The data visualization and clustering power of M-Isomap are compared with those of six related DR methods. The visualization results show that M-Isomap is able to deliver more separate clusters. Clustering evaluations also demonstrate that M-Isomap delivers comparable or even better results than some state-of-the-art DR algorithms.

Development of a Computing Cluster At the University of Richmond

NASA Astrophysics Data System (ADS)

Carbonneau, J.; Gilfoyle, G. P.; Bunn, E. F.

2010-11-01

The University of Richmond has developed a computing cluster to support the massive simulation and data analysis requirements for programs in intermediate-energy nuclear physics, and cosmology. It is a 20-node, 240-core system running Red Hat Enterprise Linux 5. We have built and installed the physics software packages (Geant4, gemc, MADmap...) and developed shell and Perl scripts for running those programs on the remote nodes. The system has a theoretical processing peak of about 2500 GFLOPS. Testing with the High Performance Linpack (HPL) benchmarking program (one of the standard benchmarks used by the TOP500 list of fastest supercomputers) resulted in speeds of over 900 GFLOPS. The difference between the maximum and measured speeds is due to limitations in the communication speed among the nodes; creating a bottleneck for large memory problems. As HPL sends data between nodes, the gigabit Ethernet connection cannot keep up with the processing power. We will show how both the theoretical and actual performance of the cluster compares with other current and past clusters, as well as the cost per GFLOP. We will also examine the scaling of the performance when distributed to increasing numbers of nodes.

A coupled-cluster study of photodetachment cross sections of closed-shell anions

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Decleva, Piero; Coriani, Sonia

2014-11-01

We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H-, Li-, Na-, F-, Cl-, and OH-. The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

A coupled-cluster study of photodetachment cross sections of closed-shell anions.

PubMed

Cukras, Janusz; Decleva, Piero; Coriani, Sonia

2014-11-07

We investigate the performance of Stieltjes Imaging applied to Lanczos pseudo-spectra generated at the coupled cluster singles and doubles, coupled cluster singles and approximate iterative doubles and coupled cluster singles levels of theory in modeling the photodetachment cross sections of the closed shell anions H(-), Li(-), Na(-), F(-), Cl(-), and OH(-). The accurate description of double excitations is found to play a much more important role than in the case of photoionization of neutral species.

Efficient calculation of nuclear spin-rotation constants from auxiliary density functional theory.

PubMed

Zuniga-Gutierrez, Bernardo; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso; Simon-Bastida, Patricia; Calaminici, Patrizia; Köster, Andreas M

2015-09-14

The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-cluster level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H(12)C-(12)CH-DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.

A new numerical benchmark of a freshwater lens

NASA Astrophysics Data System (ADS)

Stoeckl, L.; Walther, M.; Graf, T.

2016-04-01

A numerical benchmark for 2-D variable-density flow and solute transport in a freshwater lens is presented. The benchmark is based on results of laboratory experiments conducted by Stoeckl and Houben (2012) using a sand tank on the meter scale. This benchmark describes the formation and degradation of a freshwater lens over time as it can be found under real-world islands. An error analysis gave the appropriate spatial and temporal discretization of 1 mm and 8.64 s, respectively. The calibrated parameter set was obtained using the parameter estimation tool PEST. Comparing density-coupled and density-uncoupled results showed that the freshwater-saltwater interface position is strongly dependent on density differences. A benchmark that adequately represents saltwater intrusion and that includes realistic features of coastal aquifers or freshwater lenses was lacking. This new benchmark was thus developed and is demonstrated to be suitable to test variable-density groundwater models applied to saltwater intrusion investigations.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

PubMed

Fox, Naomi; Streinu, Ileana

2013-01-01

Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

PubMed Central

2013-01-01

Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu. PMID:24564209

A benchmark theoretical study of the electronic ground state and of the singlet-triplet split of benzene and linear acenes

NASA Astrophysics Data System (ADS)

Hajgató, B.; Szieberth, D.; Geerlings, P.; De Proft, F.; Deleuze, M. S.

2009-12-01

A benchmark theoretical study of the electronic ground state and of the vertical and adiabatic singlet-triplet (ST) excitation energies of benzene (n =1) and n-acenes (C4n+2H2n+4) ranging from naphthalene (n =2) to heptacene (n =7) is presented, on the ground of single- and multireference calculations based on restricted or unrestricted zero-order wave functions. High-level and large scale treatments of electronic correlation in the ground state are found to be necessary for compensating giant but unphysical symmetry-breaking effects in unrestricted single-reference treatments. The composition of multiconfigurational wave functions, the topologies of natural orbitals in symmetry-unrestricted CASSCF calculations, the T1 diagnostics of coupled cluster theory, and further energy-based criteria demonstrate that all investigated systems exhibit a A1g singlet closed-shell electronic ground state. Singlet-triplet (S0-T1) energy gaps can therefore be very accurately determined by applying the principles of a focal point analysis onto the results of a series of single-point and symmetry-restricted calculations employing correlation consistent cc-pVXZ basis sets (X=D, T, Q, 5) and single-reference methods [HF, MP2, MP3, MP4SDQ, CCSD, CCSD(T)] of improving quality. According to our best estimates, which amount to a dual extrapolation of energy differences to the level of coupled cluster theory including single, double, and perturbative estimates of connected triple excitations [CCSD(T)] in the limit of an asymptotically complete basis set (cc-pV∞Z), the S0-T1 vertical excitation energies of benzene (n =1) and n-acenes (n =2-7) amount to 100.79, 76.28, 56.97, 40.69, 31.51, 22.96, and 18.16 kcal/mol, respectively. Values of 87.02, 62.87, 46.22, 32.23, 24.19, 16.79, and 12.56 kcal/mol are correspondingly obtained at the CCSD(T)/cc-pV∞Z level for the S0-T1 adiabatic excitation energies, upon including B3LYP/cc-PVTZ corrections for zero-point vibrational energies. In line with the absence of Peierls distortions, extrapolations of results indicate a vanishingly small S0-T1 energy gap of 0 to ˜4 kcal/mol (˜0.17 eV) in the limit of an infinitely large polyacene.

Benchmarking CRISPR on-target sgRNA design.

PubMed

Yan, Jifang; Chuai, Guohui; Zhou, Chi; Zhu, Chenyu; Yang, Jing; Zhang, Chao; Gu, Feng; Xu, Han; Wei, Jia; Liu, Qi

2017-02-15

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based gene editing has been widely implemented in various cell types and organisms. A major challenge in the effective application of the CRISPR system is the need to design highly efficient single-guide RNA (sgRNA) with minimal off-target cleavage. Several tools are available for sgRNA design, while limited tools were compared. In our opinion, benchmarking the performance of the available tools and indicating their applicable scenarios are important issues. Moreover, whether the reported sgRNA design rules are reproducible across different sgRNA libraries, cell types and organisms remains unclear. In our study, a systematic and unbiased benchmark of the sgRNA predicting efficacy was performed on nine representative on-target design tools, based on six benchmark data sets covering five different cell types. The benchmark study presented here provides novel quantitative insights into the available CRISPR tools. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-01

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra.

PubMed

Cukras, Janusz; Coriani, Sonia; Decleva, Piero; Christiansen, Ove; Norman, Patrick

2013-09-07

A recently implemented asymmetric Lanczos algorithm for computing (complex) linear response functions within the coupled cluster singles (CCS), coupled cluster singles and iterative approximate doubles (CC2), and coupled cluster singles and doubles (CCSD) is coupled to a Stieltjes imaging technique in order to describe the photoionization cross section of atoms and molecules, in the spirit of a similar procedure recently proposed by Averbukh and co-workers within the Algebraic Diagrammatic Construction approach. Pilot results are reported for the atoms He, Ne, and Ar and for the molecules H2, H2O, NH3, HF, CO, and CO2.

Four-body extension of the continuum-discretized coupled-channels method

NASA Astrophysics Data System (ADS)

Descouvemont, P.

2018-06-01

I develop an extension of the continuum-discretized coupled-channels (CDCC) method to reactions where both nuclei present a low breakup threshold. This leads to a four-body model, where the only inputs are the interactions describing the colliding nuclei, and the four optical potentials between the fragments. Once these potentials are chosen, the model does not contain any additional parameter. First I briefly discuss the general formalism, and emphasize the need for dealing with large coupled-channel systems. The method is tested with existing benchmarks on 4 α bound states with the Ali-Bodmer potential. Then I apply the four-body CDCC to the 11Be+d system, where I consider the 10Be(0+,2+)+n configuration for 11Be. I show that breakup channels are crucial to reproduce the elastic cross section, but that core excitation plays a weak role. The 7Li+d system is investigated with an α +t cluster model for 7Li. I show that breakup channels significantly improve the agreement with the experimental cross section, but an additional imaginary term, simulating missing transfer channels, is necessary. The full CDCC results can be interpreted by equivalent potentials. For both systems, the real part is weakly affected by breakup channels, but the imaginary part is strongly modified. I suggest that the present wave functions could be used in future DWBA calculations.

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

RISC Processors and High Performance Computing

NASA Technical Reports Server (NTRS)

Saini, Subhash; Bailey, David H.; Lasinski, T. A. (Technical Monitor)

1995-01-01

In this tutorial, we will discuss top five current RISC microprocessors: The IBM Power2, which is used in the IBM RS6000/590 workstation and in the IBM SP2 parallel supercomputer, the DEC Alpha, which is in the DEC Alpha workstation and in the Cray T3D; the MIPS R8000, which is used in the SGI Power Challenge; the HP PA-RISC 7100, which is used in the HP 700 series workstations and in the Convex Exemplar; and the Cray proprietary processor, which is used in the new Cray J916. The architecture of these microprocessors will first be presented. The effective performance of these processors will then be compared, both by citing standard benchmarks and also in the context of implementing a real applications. In the process, different programming models such as data parallel (CM Fortran and HPF) and message passing (PVM and MPI) will be introduced and compared. The latest NAS Parallel Benchmark (NPB) absolute performance and performance per dollar figures will be presented. The next generation of the NP13 will also be described. The tutorial will conclude with a discussion of general trends in the field of high performance computing, including likely future developments in hardware and software technology, and the relative roles of vector supercomputers tightly coupled parallel computers, and clusters of workstations. This tutorial will provide a unique cross-machine comparison not available elsewhere.

Elastic K-means using posterior probability

PubMed Central

Zheng, Aihua; Jiang, Bo; Li, Yan; Zhang, Xuehan; Ding, Chris

2017-01-01

The widely used K-means clustering is a hard clustering algorithm. Here we propose a Elastic K-means clustering model (EKM) using posterior probability with soft capability where each data point can belong to multiple clusters fractionally and show the benefit of proposed Elastic K-means. Furthermore, in many applications, besides vector attributes information, pairwise relations (graph information) are also available. Thus we integrate EKM with Normalized Cut graph clustering into a single clustering formulation. Finally, we provide several useful matrix inequalities which are useful for matrix formulations of learning models. Based on these results, we prove the correctness and the convergence of EKM algorithms. Experimental results on six benchmark datasets demonstrate the effectiveness of proposed EKM and its integrated model. PMID:29240756

Improved Ant Colony Clustering Algorithm and Its Performance Study

PubMed Central

Gao, Wei

2016-01-01

Clustering analysis is used in many disciplines and applications; it is an important tool that descriptively identifies homogeneous groups of objects based on attribute values. The ant colony clustering algorithm is a swarm-intelligent method used for clustering problems that is inspired by the behavior of ant colonies that cluster their corpses and sort their larvae. A new abstraction ant colony clustering algorithm using a data combination mechanism is proposed to improve the computational efficiency and accuracy of the ant colony clustering algorithm. The abstraction ant colony clustering algorithm is used to cluster benchmark problems, and its performance is compared with the ant colony clustering algorithm and other methods used in existing literature. Based on similar computational difficulties and complexities, the results show that the abstraction ant colony clustering algorithm produces results that are not only more accurate but also more efficiently determined than the ant colony clustering algorithm and the other methods. Thus, the abstraction ant colony clustering algorithm can be used for efficient multivariate data clustering. PMID:26839533

Fuzzy Kernel k-Medoids algorithm for anomaly detection problems

NASA Astrophysics Data System (ADS)

Rustam, Z.; Talita, A. S.

2017-07-01

Intrusion Detection System (IDS) is an essential part of security systems to strengthen the security of information systems. IDS can be used to detect the abuse by intruders who try to get into the network system in order to access and utilize the available data sources in the system. There are two approaches of IDS, Misuse Detection and Anomaly Detection (behavior-based intrusion detection). Fuzzy clustering-based methods have been widely used to solve Anomaly Detection problems. Other than using fuzzy membership concept to determine the object to a cluster, other approaches as in combining fuzzy and possibilistic membership or feature-weighted based methods are also used. We propose Fuzzy Kernel k-Medoids that combining fuzzy and possibilistic membership as a powerful method to solve anomaly detection problem since on numerical experiment it is able to classify IDS benchmark data into five different classes simultaneously. We classify IDS benchmark data KDDCup'99 data set into five different classes simultaneously with the best performance was achieved by using 30 % of training data with clustering accuracy reached 90.28 percent.

Summary of comparison and analysis of results from exercises 1 and 2 of the OECD PBMR coupled neutronics/thermal hydraulics transient benchmark

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

Mkhabela, P.; Han, J.; Tyobeka, B.

2006-07-01

The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has accepted, through the Nuclear Science Committee (NSC), the inclusion of the Pebble-Bed Modular Reactor 400 MW design (PBMR-400) coupled neutronics/thermal hydraulics transient benchmark problem as part of their official activities. The scope of the benchmark is to establish a well-defined problem, based on a common given library of cross sections, to compare methods and tools in core simulation and thermal hydraulics analysis with a specific focus on transient events through a set of multi-dimensional computational test problems. The benchmark includes three steady state exercises andmore » six transient exercises. This paper describes the first two steady state exercises, their objectives and the international participation in terms of organization, country and computer code utilized. This description is followed by a comparison and analysis of the participants' results submitted for these two exercises. The comparison of results from different codes allows for an assessment of the sensitivity of a result to the method employed and can thus help to focus the development efforts on the most critical areas. The two first exercises also allow for removing of user-related modeling errors and prepare core neutronics and thermal-hydraulics models of the different codes for the rest of the exercises in the benchmark. (authors)« less

Implementation, capabilities, and benchmarking of Shift, a massively parallel Monte Carlo radiation transport code

DOE PAGES

Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; ...

2015-12-21

This paper discusses the implementation, capabilities, and validation of Shift, a massively parallel Monte Carlo radiation transport package developed and maintained at Oak Ridge National Laboratory. It has been developed to scale well from laptop to small computing clusters to advanced supercomputers. Special features of Shift include hybrid capabilities for variance reduction such as CADIS and FW-CADIS, and advanced parallel decomposition and tally methods optimized for scalability on supercomputing architectures. Shift has been validated and verified against various reactor physics benchmarks and compares well to other state-of-the-art Monte Carlo radiation transport codes such as MCNP5, CE KENO-VI, and OpenMC. Somemore » specific benchmarks used for verification and validation include the CASL VERA criticality test suite and several Westinghouse AP1000 ® problems. These benchmark and scaling studies show promising results.« less

Numerically Exact Calculation of Rovibrational Levels of Cl^-H_2O

NASA Astrophysics Data System (ADS)

Wang, Xiao-Gang; Carrington, Tucker

2014-06-01

Large amplitude vibrations of Van der Waals clusters are important because they reveal large regions of a potential energy surface (PES). To calculate spectra of Van der Waals clusters it is common to use an adiabatic approximation. When coupling between intra- and inter-molecular coordinates is important non-adiabatic coupling cannot be neglected and it is therefore critical to develop and test theoretical methods that couple both types of coordinates. We have developed new product basis and contracted basis Lanczos methods for Van der Waals complexes and tested them by computing rovibrational energy levels of Cl^-H_2O. The new product basis is made of functions of the inter-monomer distance, Wigner functions that depend on Euler angles specifying the orientation of H_2O with respect to a frame attached to the inter-monomer Jacobi vector, basis functions for H_2O vibration, and Wigner functions that depend on Euler angles specifying the orientation of the inter-monomer Jacobi vector with respect to a space-fixed frame. An advantage of this product basis is that it can be used to make an efficient contracted basis by replacing the vibrational basis functions for the monomer with monomer vibrational wavefunctions. Due to weak coupling between intra- and inter-molecular coordinates, only a few tens of monomer vibrational wavefunctions are necessary. The validity of the two new methods is established by comparing energy levels with benchmark rovibrational levels obtained with polyspherical coordinates and spherical harmonic type basis functions. For all bases, product structure is exploited to calculate eigenvalues with the Lanczos algorithm. For Cl^-H_2O, we are able, for the first time, to compute accurate splittings due to tunnelling between the two equivalent C_s minima. We use the PES of Rheinecker and Bowman (RB). Our results are in good agreement with experiment for the five fundamental bands observed. J. Rheinecker and J. M. Bowman, J. Chem. Phys. 124 131102 (2006) J. Rheinecker and J. M. Bowman, J. Chem. Phys. 125 133206 (2006)} S. Horvath, A. B. McCoy, B. M. Elliott, G. H. Weddle, J. R. Roscioli, and M. A. Johnson J. Phys. Chem. A 114 1556 (2010)

Investing in innovation: trade-offs in the costs and cost-efficiency of school feeding using community-based kitchens in Bangladesh.

PubMed

Gelli, Aulo; Suwa, Yuko

2014-09-01

School feeding programs have been a key response to the recent food and economic crises and function to some degree in nearly every country in the world. However, school feeding programs are complex and exhibit different, context-specific models or configurations. To examine the trade-offs, including the costs and cost-efficiency, of an innovative cluster kitchen implementation model in Bangladesh using a standardized framework. A supply chain framework based on international standards was used to provide benchmarks for meaningful comparisons across models. Implementation processes specific to the program in Bangladesh were mapped against this reference to provide a basis for standardized performance measures. Qualitative and quantitative data on key metrics were collected retrospectively using semistructured questionnaires following an ingredients approach, including both financial and economic costs. Costs were standardized to a 200-feeding-day year and 700 kcal daily. The cluster kitchen model had similarities with the semidecentralized model and outsourced models in the literature, the main differences involving implementation scale, scale of purchasing volumes, and frequency of purchasing. Two important features stand out in terms of implementation: the nutritional quality of meals and the level of community involvement. The standardized full cost per child per year was US$110. Despite the nutritious content of the meals, the overall cost-efficiency in cost per nutrient output was lower than the benchmark for centralized programs, due mainly to support and start-up costs. Cluster kitchens provide an example of an innovative implementation model, combining an emphasis on quality meal delivery with strong community engagement. However, the standardized costs-per child were above the average benchmarks for both low-and middle-income countries. In contrast to the existing benchmark data from mature, centralized models, the main cost drivers of the program were associated with support and start-up activities. Further research is required to better understand changes in cost drivers as programs mature.

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

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

Liu, Peiyuan; Brown, Timothy; Fullmer, William D.

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling ofmore » the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.« less

A large-scale benchmark of gene prioritization methods.

PubMed

Guala, Dimitri; Sonnhammer, Erik L L

2017-04-21

In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.

Performance Characteristics of the Multi-Zone NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; VanderWijngaart, Rob F.

2003-01-01

We describe a new suite of computational benchmarks that models applications featuring multiple levels of parallelism. Such parallelism is often available in realistic flow computations on systems of grids, but had not previously been captured in bench-marks. The new suite, named NPB Multi-Zone, is extended from the NAS Parallel Benchmarks suite, and involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy provides relatively easily exploitable coarse-grain parallelism between meshes. Three reference implementations are available: one serial, one hybrid using the Message Passing Interface (MPI) and OpenMP, and another hybrid using a shared memory multi-level programming model (SMP+OpenMP). We examine the effectiveness of hybrid parallelization paradigms in these implementations on three different parallel computers. We also use an empirical formula to investigate the performance characteristics of the multi-zone benchmarks.

Structure and decays of nuclear three-body systems: The Gamow coupled-channel method in Jacobi coordinates

NASA Astrophysics Data System (ADS)

Wang, S. M.; Michel, N.; Nazarewicz, W.; Xu, F. R.

2017-10-01

Background: Weakly bound and unbound nuclear states appearing around particle thresholds are prototypical open quantum systems. Theories of such states must take into account configuration mixing effects in the presence of strong coupling to the particle continuum space. Purpose: To describe structure and decays of three-body systems, we developed a Gamow coupled-channel (GCC) approach in Jacobi coordinates by employing the complex-momentum formalism. We benchmarked the complex-energy Gamow shell model (GSM) against the new framework. Methods: The GCC formalism is expressed in Jacobi coordinates, so that the center-of-mass motion is automatically eliminated. To solve the coupled-channel equations, we use hyperspherical harmonics to describe the angular wave functions while the radial wave functions are expanded in the Berggren ensemble, which includes bound, scattering, and Gamow states. Results: We show that the GCC method is both accurate and robust. Its results for energies, decay widths, and nucleon-nucleon angular correlations are in good agreement with the GSM results. Conclusions: We have demonstrated that a three-body GSM formalism explicitly constructed in the cluster-orbital shell model coordinates provides results similar to those with a GCC framework expressed in Jacobi coordinates, provided that a large configuration space is employed. Our calculations for A =6 systems and 26O show that nucleon-nucleon angular correlations are sensitive to the valence-neutron interaction. The new GCC technique has many attractive features when applied to bound and unbound states of three-body systems: it is precise, is efficient, and can be extended by introducing a microscopic model of the core.

A Weight-Adaptive Laplacian Embedding for Graph-Based Clustering.

PubMed

Cheng, De; Nie, Feiping; Sun, Jiande; Gong, Yihong

2017-07-01

Graph-based clustering methods perform clustering on a fixed input data graph. Thus such clustering results are sensitive to the particular graph construction. If this initial construction is of low quality, the resulting clustering may also be of low quality. We address this drawback by allowing the data graph itself to be adaptively adjusted in the clustering procedure. In particular, our proposed weight adaptive Laplacian (WAL) method learns a new data similarity matrix that can adaptively adjust the initial graph according to the similarity weight in the input data graph. We develop three versions of these methods based on the L2-norm, fuzzy entropy regularizer, and another exponential-based weight strategy, that yield three new graph-based clustering objectives. We derive optimization algorithms to solve these objectives. Experimental results on synthetic data sets and real-world benchmark data sets exhibit the effectiveness of these new graph-based clustering methods.

Highly Efficient and Scalable Compound Decomposition of Two-Electron Integral Tensor and Its Application in Coupled Cluster Calculations

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

Peng, Bo; Kowalski, Karol

The representation and storage of two-electron integral tensors are vital in large- scale applications of accurate electronic structure methods. Low-rank representation and efficient storage strategy of integral tensors can significantly reduce the numerical overhead and consequently time-to-solution of these methods. In this paper, by combining pivoted incomplete Cholesky decomposition (CD) with a follow-up truncated singular vector decomposition (SVD), we develop a decomposition strategy to approximately represent the two-electron integral tensor in terms of low-rank vectors. A systematic benchmark test on a series of 1-D, 2-D, and 3-D carbon-hydrogen systems demonstrates high efficiency and scalability of the compound two-step decomposition ofmore » the two-electron integral tensor in our implementation. For the size of atomic basis set N_b ranging from ~ 100 up to ~ 2, 000, the observed numerical scaling of our implementation shows O(N_b^{2.5~3}) versus O(N_b^{3~4}) of single CD in most of other implementations. More importantly, this decomposition strategy can significantly reduce the storage requirement of the atomic-orbital (AO) two-electron integral tensor from O(N_b^4) to O(N_b^2 log_{10}(N_b)) with moderate decomposition thresholds. The accuracy tests have been performed using ground- and excited-state formulations of coupled- cluster formalism employing single and double excitations (CCSD) on several bench- mark systems including the C_{60} molecule described by nearly 1,400 basis functions. The results show that the decomposition thresholds can be generally set to 10^{-4} to 10^{-3} to give acceptable compromise between efficiency and accuracy.« less

Delay-induced cluster patterns in coupled Cayley tree networks

NASA Astrophysics Data System (ADS)

Singh, A.; Jalan, S.

2013-07-01

We study effects of delay in diffusively coupled logistic maps on the Cayley tree networks. We find that smaller coupling values exhibit sensitiveness to value of delay, and lead to different cluster patterns of self-organized and driven types. Whereas larger coupling strengths exhibit robustness against change in delay values, and lead to stable driven clusters comprising nodes from last generation of the Cayley tree. Furthermore, introduction of delay exhibits suppression as well as enhancement of synchronization depending upon coupling strength values. To the end we discuss the importance of results to understand conflicts and cooperations observed in family business.

Core Collapse: The Race Between Stellar Evolution and Binary Heating

NASA Astrophysics Data System (ADS)

Converse, Joseph M.; Chandar, R.

2012-01-01

The dynamical formation of binary stars can dramatically affect the evolution of their host star clusters. In relatively small clusters (M < 6000 Msun) the most massive stars rapidly form binaries, heating the cluster and preventing any significant contraction of the core. The situation in much larger globular clusters (M 105 Msun) is quite different, with many showing collapsed cores, implying that binary formation did not affect them as severely as lower mass clusters. More massive clusters, however, should take longer to form their binaries, allowing stellar evolution more time to prevent the heating by causing the larger stars to die off. Here, we simulate the evolution of clusters between those of open and globular clusters in order to find at what size a star cluster is able to experience true core collapse. Our simulations make use of a new GPU-based computing cluster recently purchased at the University of Toledo. We also present some benchmarks of this new computational resource.

A Benchmarking Initiative for Reactive Transport Modeling Applied to Subsurface Environmental Applications

NASA Astrophysics Data System (ADS)

Steefel, C. I.

2015-12-01

Over the last 20 years, we have seen the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface environmental applications it is being used to address. Reactive transport modeling is being asked to provide accurate assessments of engineering performance and risk for important issues with far-reaching consequences. As a result, the complexity and detail of subsurface processes, properties, and conditions that can be simulated have significantly expanded. Closed form solutions are necessary and useful, but limited to situations that are far simpler than typical applications that combine many physical and chemical processes, in many cases in coupled form. In the absence of closed form and yet realistic solutions for complex applications, numerical benchmark problems with an accepted set of results will be indispensable to qualifying codes for various environmental applications. The intent of this benchmarking exercise, now underway for more than five years, is to develop and publish a set of well-described benchmark problems that can be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. The objective is not to verify this or that specific code--the reactive transport codes play a supporting role in this regard—but rather to use the codes to verify that a common solution of the problem can be achieved. Thus, the objective of each of the manuscripts is to present an environmentally-relevant benchmark problem that tests the conceptual model capabilities, numerical implementation, process coupling, and accuracy. The benchmark problems developed to date include 1) microbially-mediated reactions, 2) isotopes, 3) multi-component diffusion, 4) uranium fate and transport, 5) metal mobility in mining affected systems, and 6) waste repositories and related aspects.

Modeling Blast Loading on Buried Reinforced Concrete Structures with Zapotec

DOE PAGES

Bessette, Greg C.

2008-01-01

A coupled Euler-Lagrange solution approach is used to model the response of a buried reinforced concrete structure subjected to a close-in detonation of a high explosive charge. The coupling algorithm is discussed along with a set of benchmark calculations involving detonations in clay and sand.

Comparing the OpenMP, MPI, and Hybrid Programming Paradigm on an SMP Cluster

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Hao-Qiang; anMey, Dieter; Hatay, Ferhat F.

2003-01-01

Clusters of SMP (Symmetric Multi-Processors) nodes provide support for a wide range of parallel programming paradigms. The shared address space within each node is suitable for OpenMP parallelization. Message passing can be employed within and across the nodes of a cluster. Multiple levels of parallelism can be achieved by combining message passing and OpenMP parallelization. Which programming paradigm is the best will depend on the nature of the given problem, the hardware components of the cluster, the network, and the available software. In this study we compare the performance of different implementations of the same CFD benchmark application, using the same numerical algorithm but employing different programming paradigms.

Antiferromagnetic exchange coupling measurements on single Co clusters

NASA Astrophysics Data System (ADS)

Wernsdorfer, W.; Leroy, D.; Portemont, C.; Brenac, A.; Morel, R.; Notin, L.; Mailly, D.

2009-03-01

We report on single-cluster measurements of the angular dependence of the low-temperature ferromagnetic core magnetization switching field in exchange-coupled Co/CoO core-shell clusters (4 nm) using a micro-bridge DC superconducting quantum interference device (μ-SQUID). It is observed that the coupling with the antiferromagnetic shell induces modification in the switching field for clusters with intrinsic uniaxial anisotropy depending on the direction of the magnetic field applied during the cooling. Using a modified Stoner-Wohlfarth model, it is shown that the core interacts with two weakly coupled and asymmetrical antiferromagnetic sublattices. Ref.: C. Portemont, R. Morel, W. Wernsdorfer, D. Mailly, A. Brenac, and L. Notin, Phys. Rev. B 78, 144415 (2008)

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

Kung, Y. F.; Bazin, C.; Wohlfeld, K.

Using determinant quantum Monte Carlo (DQMC) simulations, we systematically study the doping dependence of the crossover from one to two dimensions and its impact on the magnetic properties of the Hubbard model. A square lattice of chains is used, in which the dimensionality can be tuned by varying the interchain coupling t ⊥. The dynamical spin structure factor and static quantities, such as the static spin susceptibility and nearest-neighbor spin correlation function, are characterized in the one- and two-dimensional limits as a benchmark. When the dimensionality is tuned between these limits, the magnetic properties, while evolving smoothly from one tomore » two dimensions, drastically change regardless of the doping level. This suggests that the spin excitations in the two-dimensional Hubbard model, even in the heavily doped case, cannot be explained using the spinon picture known from one dimension. In conclusion, the DQMC calculations are complemented by cluster perturbation theory studies to form a more complete picture of how the crossover occurs as a function of doping and how doped holes impact magnetic order.« less

Towards black-box calculations of tunneling splittings obtained from vibrational structure methods based on normal coordinates.

PubMed

Neff, Michael; Rauhut, Guntram

2014-02-05

Multidimensional potential energy surfaces obtained from explicitly correlated coupled-cluster calculations and further corrections for high-order correlation contributions, scalar relativistic effects and core-correlation energy contributions were generated in a fully automated fashion for the double-minimum benchmark systems OH3(+) and NH3. The black-box generation of the potentials is based on normal coordinates, which were used in the underlying multimode expansions of the potentials and the μ-tensor within the Watson operator. Normal coordinates are not the optimal choice for describing double-minimum potentials and the question remains if they can be used for accurate calculations at all. However, their unique definition is an appealing feature, which removes remaining errors in truncated potential expansions arising from different choices of curvilinear coordinate systems. Fully automated calculations are presented, which demonstrate, that the proposed scheme allows for the determination of energy levels and tunneling splittings as a routine application. Copyright © 2013 Elsevier B.V. All rights reserved.

An integral-factorized implementation of the driven similarity renormalization group second-order multireference perturbation theory

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

Hannon, Kevin P.; Li, Chenyang; Evangelista, Francesco A., E-mail: francesco.evangelista@emory.edu

2016-05-28

We report an efficient implementation of a second-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT2) [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)]. Our implementation employs factorized two-electron integrals to avoid storage of large four-index intermediates. It also exploits the block structure of the reference density matrices to reduce the computational cost to that of second-order Møller–Plesset perturbation theory. Our new DSRG-MRPT2 implementation is benchmarked on ten naphthyne isomers using basis sets up to quintuple-ζ quality. We find that the singlet-triplet splittings (Δ{sub ST}) of the naphthyne isomers strongly depend onmore » the equilibrium structures. For a consistent set of geometries, the Δ{sub ST} values predicted by the DSRG-MRPT2 are in good agreements with those computed by the reduced multireference coupled cluster theory with singles, doubles, and perturbative triples.« less

Benchmark studies on the building blocks of DNA. 3. Watson-Crick and stacked base pairs.

PubMed

Szalay, Péter G; Watson, Thomas; Perera, Ajith; Lotrich, Victor; Bartlett, Rodney J

2013-04-18

Excited states of stacked adenine-thymine and guanine-cytosine pairs as well as the Watson-Crick pair of guanine-thymine have been investigated using the equation of motion coupled-cluster (EOM-CC) method with single and double as well as approximate triple excitations. Transitions have been assigned, and the form of the excitations has been analyzed. The majority of the excitations could be classified as localized on the nucleobases, but for all three studied systems, charge-transfer (CT) transitions could also be identified. The main aim of this study was to compare the performance of lower-level methods (ADC(2) and TDDFT) to the high-level EOM-CC ones. It was shown that both ADC(2) and TDDFT with long-range correction have nonsystematic error in excitation energies, causing alternation of the energetic ordering of the excitations. Considering the high costs of the EOM-CC calculations, there is a need for reliable new approximate methods.

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

Zhou, Chong-Wen; Simmie, John M.; Pitz, William J.

Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. We present calculated thermodynamic and kinetic data for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. Furthermore, these radicals can be formed via H atom abstraction reactions by H and Ö atoms and OH, HO 2, and CH 3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when OH is involved, but the reverse holds truemore » for HO 2 radicals. We also determined the subsequent β-scission of the radicals formed, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit.« less

A low-cost approach to electronic excitation energies based on the driven similarity renormalization group

NASA Astrophysics Data System (ADS)

Li, Chenyang; Verma, Prakash; Hannon, Kevin P.; Evangelista, Francesco A.

2017-08-01

We propose an economical state-specific approach to evaluate electronic excitation energies based on the driven similarity renormalization group truncated to second order (DSRG-PT2). Starting from a closed-shell Hartree-Fock wave function, a model space is constructed that includes all single or single and double excitations within a given set of active orbitals. The resulting VCIS-DSRG-PT2 and VCISD-DSRG-PT2 methods are introduced and benchmarked on a set of 28 organic molecules [M. Schreiber et al., J. Chem. Phys. 128, 134110 (2008)]. Taking CC3 results as reference values, mean absolute deviations of 0.32 and 0.22 eV are observed for VCIS-DSRG-PT2 and VCISD-DSRG-PT2 excitation energies, respectively. Overall, VCIS-DSRG-PT2 yields results with accuracy comparable to those from time-dependent density functional theory using the B3LYP functional, while VCISD-DSRG-PT2 gives excitation energies comparable to those from equation-of-motion coupled cluster with singles and doubles.

A theoretical study of the adiabatic and vertical ionization potentials of water.

PubMed

Feller, David; Davidson, Ernest R

2018-06-21

Theoretical predictions of the three lowest adiabatic and vertical ionization potentials of water were obtained from the Feller-Peterson-Dixon approach. This approach combines multiple levels of coupled cluster theory with basis sets as large as aug-cc-pV8Z in some cases and various corrections up to and including full configuration interaction theory. While agreement with experiment for the adiabatic ionization potential of the lowest energy 2 B 1 state was excellent, differences for other states were much larger, sometimes exceeding 10 kcal/mol (0.43 eV). Errors of this magnitude are inconsistent with previous benchmark work on 52 adiabatic ionization potentials, where a root mean square of 0.20 kcal/mol (0.009 eV) was found. Difficulties in direct comparisons between theory and experiment for vertical ionization potentials are discussed. With regard to the differences found for the 2 A 1 / 2 Π u and 2 B 2 adiabatic ionization potentials, a reinterpretation of the experimental spectrum appears justified.

An atomic mean-field spin-orbit approach within exact two-component theory for a non-perturbative treatment of spin-orbit coupling

NASA Astrophysics Data System (ADS)

Liu, Junzi; Cheng, Lan

2018-04-01

An atomic mean-field (AMF) spin-orbit (SO) approach within exact two-component theory (X2C) is reported, thereby exploiting the exact decoupling scheme of X2C, the one-electron approximation for the scalar-relativistic contributions, the mean-field approximation for the treatment of the two-electron SO contribution, and the local nature of the SO interactions. The Hamiltonian of the proposed SOX2CAMF scheme comprises the one-electron X2C Hamiltonian, the instantaneous two-electron Coulomb interaction, and an AMF SO term derived from spherically averaged Dirac-Coulomb Hartree-Fock calculations of atoms; no molecular relativistic two-electron integrals are required. Benchmark calculations for bond lengths, harmonic frequencies, dipole moments, and electric-field gradients for a set of diatomic molecules containing elements across the periodic table show that the SOX2CAMF scheme offers a balanced treatment for SO and scalar-relativistic effects and appears to be a promising candidate for applications to heavy-element containing systems. SOX2CAMF coupled-cluster calculations of molecular properties for bismuth compounds (BiN, BiP, BiF, BiCl, and BiI) are also presented and compared with experimental results to further demonstrate the accuracy and applicability of the SOX2CAMF scheme.

Spectral biclustering of microarray data: coclustering genes and conditions.

PubMed

Kluger, Yuval; Basri, Ronen; Chang, Joseph T; Gerstein, Mark

2003-04-01

Global analyses of RNA expression levels are useful for classifying genes and overall phenotypes. Often these classification problems are linked, and one wants to find "marker genes" that are differentially expressed in particular sets of "conditions." We have developed a method that simultaneously clusters genes and conditions, finding distinctive "checkerboard" patterns in matrices of gene expression data, if they exist. In a cancer context, these checkerboards correspond to genes that are markedly up- or downregulated in patients with particular types of tumors. Our method, spectral biclustering, is based on the observation that checkerboard structures in matrices of expression data can be found in eigenvectors corresponding to characteristic expression patterns across genes or conditions. In addition, these eigenvectors can be readily identified by commonly used linear algebra approaches, in particular the singular value decomposition (SVD), coupled with closely integrated normalization steps. We present a number of variants of the approach, depending on whether the normalization over genes and conditions is done independently or in a coupled fashion. We then apply spectral biclustering to a selection of publicly available cancer expression data sets, and examine the degree to which the approach is able to identify checkerboard structures. Furthermore, we compare the performance of our biclustering methods against a number of reasonable benchmarks (e.g., direct application of SVD or normalized cuts to raw data).

Hybrid Correlation Energy (HyCE): An Approach Based on Separate Evaluations of Internal and External Components.

PubMed

Ivanic, Joseph; Schmidt, Michael W

2018-06-04

A novel hybrid correlation energy (HyCE) approach is proposed that determines the total correlation energy via distinct computation of its internal and external components. This approach evolved from two related studies. First, rigorous assessment of the accuracies and size extensivities of a number of electron correlation methods, that include perturbation theory (PT2), coupled-cluster (CC), configuration interaction (CI), and coupled electron pair approximation (CEPA), shows that the CEPA(0) variant of the latter and triples-corrected CC methods consistently perform very similarly. These findings were obtained by comparison to near full CI results for four small molecules and by charting recovered correlation energies for six steadily growing chain systems. Second, by generating valence virtual orbitals (VVOs) and utilizing the CEPA(0) method, we were able to partition total correlation energies into internal (or nondynamic) and external (or dynamic) parts for the aforementioned six chain systems and a benchmark test bed of 36 molecules. When using triple-ζ basis sets it was found that per orbital internal correlation energies were appreciably larger than per orbital external energies and that the former showed far more chemical variation than the latter. Additionally, accumulations of external correlation energies were seen to proceed smoothly, and somewhat linearly, as the virtual space is gradually increased. Combination of these two studies led to development of the HyCE approach, whereby the internal and external correlation energies are determined separately by CEPA(0)/VVO and PT2/external calculations, respectively. When applied to the six chain systems and the 36-molecule benchmark test set it was found that HyCE energies followed closely those of triples-corrected CC and CEPA(0) while easily outperforming MP2 and CCSD. The success of the HyCE approach is more notable when considering that its cost is only slightly more than MP2 and significantly cheaper than the CC approaches.

Correlation consistent basis sets for lanthanides: The atoms La–Lu

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

Lu, Qing; Peterson, Kirk A., E-mail: kipeters@wsu.edu

Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples,more » CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd{sub 2}, GdF, and GdF{sub 3}. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd{sub 2}, 151.7 (−36.6) for GdF, and 447.1 (−295.2) for GdF{sub 3}.« less

Analysis of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Pedretti, Kevin T.; Kutler, Paul (Technical Monitor)

1997-01-01

We evaluate the performance of a Fast Ethernet network configured with a single large switch, a single hub, and a 4x4 2D torus topology in a testbed cluster of "commodity" Pentium Pro PCs. We also evaluated a mixed network composed of ethernet hubs and switches. An MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2) show that the torus network performs best for all sizes that we were able to test (up to 16 nodes). For larger networks the ethernet switch outperforms the hub, though its performance is far less than peak. The hub/switch combination tests indicate that the NAS parallel benchmarks are relatively insensitive to hub densities of less than 7 nodes per hub.

Dynamics of a network of phase oscillators with plastic couplings

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

Nekorkin, V. I.; Kasatkin, D. V.; Moscow Institute of Physics and Technology

The processes of synchronization and phase cluster formation are investigated in a complex network of dynamically coupled phase oscillators. Coupling weights evolve dynamically depending on the phase relations between the oscillators. It is shown that the network exhibits several types of behavior: the globally synchronized state, two-cluster and multi-cluster states, different synchronous states with a fixed phase relationship between the oscillators and chaotic desynchronized state.

Benchmarking of calculation schemes in APOLLO2 and COBAYA3 for WER lattices

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

Zheleva, N.; Ivanov, P.; Todorova, G.

This paper presents solutions of the NURISP WER lattice benchmark using APOLLO2, TRIPOLI4 and COBAYA3 pin-by-pin. The main objective is to validate MOC based calculation schemes for pin-by-pin cross-section generation with APOLLO2 against TRIPOLI4 reference results. A specific objective is to test the APOLLO2 generated cross-sections and interface discontinuity factors in COBAYA3 pin-by-pin calculations with unstructured mesh. The VVER-1000 core consists of large hexagonal assemblies with 2 mm inter-assembly water gaps which require the use of unstructured meshes in the pin-by-pin core simulators. The considered 2D benchmark problems include 19-pin clusters, fuel assemblies and 7-assembly clusters. APOLLO2 calculation schemes withmore » the step characteristic method (MOC) and the higher-order Linear Surface MOC have been tested. The comparison of APOLLO2 vs. TRIPOLI4 results shows a very close agreement. The 3D lattice solver in COBAYA3 uses transport corrected multi-group diffusion approximation with interface discontinuity factors of Generalized Equivalence Theory (GET) or Black Box Homogenization (BBH) type. The COBAYA3 pin-by-pin results in 2, 4 and 8 energy groups are close to the reference solutions when using side-dependent interface discontinuity factors. (authors)« less

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

Witte, Jonathon; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Neaton, Jeffrey B., E-mail: jbneaton@lbl.gov

Adsorption of gas molecules in metal-organic frameworks is governed by many factors, the most dominant of which are the interaction of the gas with open metal sites, and the interaction of the gas with the ligands. Herein, we examine the latter class of interaction in the context of CO{sub 2} binding to benzene. We begin by clarifying the geometry of the CO{sub 2}–benzene complex. We then generate a benchmark binding curve using a coupled-cluster approach with single, double, and perturbative triple excitations [CCSD(T)] at the complete basis set (CBS) limit. Against this ΔCCSD(T)/CBS standard, we evaluate a plethora of electronicmore » structure approximations: Hartree-Fock, second-order Møller-Plesset perturbation theory (MP2) with the resolution-of-the-identity approximation, attenuated MP2, and a number of density functionals with and without different empirical and nonempirical van der Waals corrections. We find that finite-basis MP2 significantly overbinds the complex. On the other hand, even the simplest empirical correction to standard density functionals is sufficient to bring the binding energies to well within 1 kJ/mol of the benchmark, corresponding to an error of less than 10%; PBE-D in particular performs well. Methods that explicitly include nonlocal correlation kernels, such as VV10, vdW-DF2, and ωB97X-V, perform with similar accuracy for this system, as do ωB97X and M06-L.« less

Experiences using OpenMP based on Computer Directed Software DSM on a PC Cluster

NASA Technical Reports Server (NTRS)

Hess, Matthias; Jost, Gabriele; Mueller, Matthias; Ruehle, Roland

2003-01-01

In this work we report on our experiences running OpenMP programs on a commodity cluster of PCs running a software distributed shared memory (DSM) system. We describe our test environment and report on the performance of a subset of the NAS Parallel Benchmarks that have been automaticaly parallelized for OpenMP. We compare the performance of the OpenMP implementations with that of their message passing counterparts and discuss performance differences.

Assessing the capability of continuum and discrete particle methods to simulate gas-solids flow using DNS predictions as a benchmark

DOE PAGES

Lu, Liqiang; Liu, Xiaowen; Li, Tingwen; ...

2017-08-12

For this study, gas–solids flow in a three-dimension periodic domain was numerically investigated by direct numerical simulation (DNS), computational fluid dynamic-discrete element method (CFD-DEM) and two-fluid model (TFM). DNS data obtained by finely resolving the flow around every particle are used as a benchmark to assess the validity of coarser DEM and TFM approaches. The CFD-DEM predicts the correct cluster size distribution and under-predicts the macro-scale slip velocity even with a grid size as small as twice the particle diameter. The TFM approach predicts larger cluster size and lower slip velocity with a homogeneous drag correlation. Although the slip velocitymore » can be matched by a simple modification to the drag model, the predicted voidage distribution is still different from DNS: Both CFD-DEM and TFM over-predict the fraction of particles in dense regions and under-predict the fraction of particles in regions of intermediate void fractions. Also, the cluster aspect ratio of DNS is smaller than CFD-DEM and TFM. Since a simple correction to the drag model can predict a correct slip velocity, it is hopeful that drag corrections based on more elaborate theories that consider voidage gradient and particle fluctuations may be able to improve the current predictions of cluster distribution.« less

Assessing the capability of continuum and discrete particle methods to simulate gas-solids flow using DNS predictions as a benchmark

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

Lu, Liqiang; Liu, Xiaowen; Li, Tingwen

For this study, gas–solids flow in a three-dimension periodic domain was numerically investigated by direct numerical simulation (DNS), computational fluid dynamic-discrete element method (CFD-DEM) and two-fluid model (TFM). DNS data obtained by finely resolving the flow around every particle are used as a benchmark to assess the validity of coarser DEM and TFM approaches. The CFD-DEM predicts the correct cluster size distribution and under-predicts the macro-scale slip velocity even with a grid size as small as twice the particle diameter. The TFM approach predicts larger cluster size and lower slip velocity with a homogeneous drag correlation. Although the slip velocitymore » can be matched by a simple modification to the drag model, the predicted voidage distribution is still different from DNS: Both CFD-DEM and TFM over-predict the fraction of particles in dense regions and under-predict the fraction of particles in regions of intermediate void fractions. Also, the cluster aspect ratio of DNS is smaller than CFD-DEM and TFM. Since a simple correction to the drag model can predict a correct slip velocity, it is hopeful that drag corrections based on more elaborate theories that consider voidage gradient and particle fluctuations may be able to improve the current predictions of cluster distribution.« less

A New Soft Computing Method for K-Harmonic Means Clustering.

PubMed

Yeh, Wei-Chang; Jiang, Yunzhi; Chen, Yee-Fen; Chen, Zhe

2016-01-01

The K-harmonic means clustering algorithm (KHM) is a new clustering method used to group data such that the sum of the harmonic averages of the distances between each entity and all cluster centroids is minimized. Because it is less sensitive to initialization than K-means (KM), many researchers have recently been attracted to studying KHM. In this study, the proposed iSSO-KHM is based on an improved simplified swarm optimization (iSSO) and integrates a variable neighborhood search (VNS) for KHM clustering. As evidence of the utility of the proposed iSSO-KHM, we present extensive computational results on eight benchmark problems. From the computational results, the comparison appears to support the superiority of the proposed iSSO-KHM over previously developed algorithms for all experiments in the literature.

A new collaborative recommendation approach based on users clustering using artificial bee colony algorithm.

PubMed

Ju, Chunhua; Xu, Chonghuan

2013-01-01

Although there are many good collaborative recommendation methods, it is still a challenge to increase the accuracy and diversity of these methods to fulfill users' preferences. In this paper, we propose a novel collaborative filtering recommendation approach based on K-means clustering algorithm. In the process of clustering, we use artificial bee colony (ABC) algorithm to overcome the local optimal problem caused by K-means. After that we adopt the modified cosine similarity to compute the similarity between users in the same clusters. Finally, we generate recommendation results for the corresponding target users. Detailed numerical analysis on a benchmark dataset MovieLens and a real-world dataset indicates that our new collaborative filtering approach based on users clustering algorithm outperforms many other recommendation methods.

A New Collaborative Recommendation Approach Based on Users Clustering Using Artificial Bee Colony Algorithm

PubMed Central

Ju, Chunhua

2013-01-01

Although there are many good collaborative recommendation methods, it is still a challenge to increase the accuracy and diversity of these methods to fulfill users' preferences. In this paper, we propose a novel collaborative filtering recommendation approach based on K-means clustering algorithm. In the process of clustering, we use artificial bee colony (ABC) algorithm to overcome the local optimal problem caused by K-means. After that we adopt the modified cosine similarity to compute the similarity between users in the same clusters. Finally, we generate recommendation results for the corresponding target users. Detailed numerical analysis on a benchmark dataset MovieLens and a real-world dataset indicates that our new collaborative filtering approach based on users clustering algorithm outperforms many other recommendation methods. PMID:24381525

Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

NASA Astrophysics Data System (ADS)

Yen, Chi-Fu; Sivasankar, Sanjeevi

2018-03-01

Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

A photocatalyst-enzyme coupled artificial photosynthesis system for solar energy in production of formic acid from CO2.

PubMed

Yadav, Rajesh K; Baeg, Jin-Ook; Oh, Gyu Hwan; Park, No-Joong; Kong, Ki-jeong; Kim, Jinheung; Hwang, Dong Won; Biswas, Soumya K

2012-07-18

The photocatalyst-enzyme coupled system for artificial photosynthesis process is one of the most promising methods of solar energy conversion for the synthesis of organic chemicals or fuel. Here we report the synthesis of a novel graphene-based visible light active photocatalyst which covalently bonded the chromophore, such as multianthraquinone substituted porphyrin with the chemically converted graphene as a photocatalyst of the artificial photosynthesis system for an efficient photosynthetic production of formic acid from CO(2). The results not only show a benchmark example of the graphene-based material used as a photocatalyst in general artificial photosynthesis but also the benchmark example of the selective production system of solar chemicals/solar fuel directly from CO(2).

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Roux, Nicolas; Anbergen, Hauke; Collier, Nathaniel; Costard, Francois; Ferrry, Michel; Frampton, Andrew; Frederick, Jennifer; Holmen, Johan; Jost, Anne; Kokh, Samuel; Kurylyk, Barret; McKenzie, Jeffrey; Molson, John; Orgogozo, Laurent; Rivière, Agnès; Rühaak, Wolfram; Selroos, Jan-Olof; Therrien, René; Vidstrand, Patrik

2015-04-01

The impacts of climate change in boreal regions has received considerable attention recently due to the warming trends that have been experienced in recent decades and are expected to intensify in the future. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) that interact with the surrounding permafrost. For example, the thermal state of the surrounding soil influences the energy and water budget of the surface water bodies. Also, these water bodies generate taliks (unfrozen zones below) that disturb the thermal regimes of permafrost and may play a key role in the context of climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model the past and future evolution of landscapes, rivers, lakes and associated groundwater systems in a changing climate. However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, and the lack of study can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. Numerical approaches can only be validated against analytical solutions for a purely thermic 1D equation with phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare the results from different codes to provided test cases and/or to have controlled experiments for validation. Such inter-code comparisons can propel discussions to try to improve code performances. A benchmark exercise was initialized in 2014 with a kick-off meeting in Paris in November. Participants from USA, Canada, Germany, Sweden and France convened, representing altogether 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones. They range from simpler, purely thermal cases (benchmark T1) to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test cases database at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases (TH1, TH2 & TH3). Further perspectives of the exercise will also be presented. Extensions to more complex physical conditions (e.g. unsaturated conditions and geometrical deformations) are contemplated. In addition, 1D vertical cases of interest to the Climate Modeling community will be proposed. Keywords: Permafrost; Numerical modeling; River-soil interaction; Arctic systems; soil freeze-thaw

Approximate solution of coupled cluster equations: application to the coupled cluster doubles method and non-covalent interacting systems.

PubMed

Smiga, Szymon; Fabiano, Eduardo

2017-11-15

We have developed a simplified coupled cluster (SCC) methodology, using the basic idea of scaled MP2 methods. The scheme has been applied to the coupled cluster double equations and implemented in three different non-iterative variants. This new method (especially the SCCD[3] variant, which utilizes a spin-resolved formalism) has been found to be very efficient and to yield an accurate approximation of the reference CCD results for both total and interaction energies of different atoms and molecules. Furthermore, we demonstrate that the equations determining the scaling coefficients for the SCCD[3] approach can generate non-empirical SCS-MP2 scaling coefficients which are in good agreement with previous theoretical investigations.

Comparison of discrete ordinate and Monte Carlo simulations of polarized radiative transfer in two coupled slabs with different refractive indices.

PubMed

Cohen, D; Stamnes, S; Tanikawa, T; Sommersten, E R; Stamnes, J J; Lotsberg, J K; Stamnes, K

2013-04-22

A comparison is presented of two different methods for polarized radiative transfer in coupled media consisting of two adjacent slabs with different refractive indices, each slab being a stratified medium with no change in optical properties except in the direction of stratification. One of the methods is based on solving the integro-differential radiative transfer equation for the two coupled slabs using the discrete ordinate approximation. The other method is based on probabilistic and statistical concepts and simulates the propagation of polarized light using the Monte Carlo approach. The emphasis is on non-Rayleigh scattering for particles in the Mie regime. Comparisons with benchmark results available for a slab with constant refractive index show that both methods reproduce these benchmark results when the refractive index is set to be the same in the two slabs. Computed results for test cases with coupling (different refractive indices in the two slabs) show that the two methods produce essentially identical results for identical input in terms of absorption and scattering coefficients and scattering phase matrices.

Effects of cluster-shell competition and BCS-like pairing in 12C

NASA Astrophysics Data System (ADS)

Matsuno, H.; Itagaki, N.

2017-12-01

The antisymmetrized quasi-cluster model (AQCM) was proposed to describe α-cluster and jj-coupling shell models on the same footing. In this model, the cluster-shell transition is characterized by two parameters, R representing the distance between α clusters and Λ describing the breaking of α clusters, and the contribution of the spin-orbit interaction, very important in the jj-coupling shell model, can be taken into account starting with the α-cluster model wave function. Not only the closure configurations of the major shells but also the subclosure configurations of the jj-coupling shell model can be described starting with the α-cluster model wave functions; however, the particle-hole excitations of single particles have not been fully established yet. In this study we show that the framework of AQCM can be extended even to the states with the character of single-particle excitations. For ^{12}C, two-particle-two-hole (2p2h) excitations from the subclosure configuration of 0p_{3/2} corresponding to a BCS-like pairing are described, and these shell model states are coupled with the three α-cluster model wave functions. The correlation energy from the optimal configuration can be estimated not only in the cluster part but also in the shell model part. We try to pave the way to establish a generalized description of the nuclear structure.

On the Coupling Time of the Heat-Bath Process for the Fortuin-Kasteleyn Random-Cluster Model

NASA Astrophysics Data System (ADS)

Collevecchio, Andrea; Elçi, Eren Metin; Garoni, Timothy M.; Weigel, Martin

2018-01-01

We consider the coupling from the past implementation of the random-cluster heat-bath process, and study its random running time, or coupling time. We focus on hypercubic lattices embedded on tori, in dimensions one to three, with cluster fugacity at least one. We make a number of conjectures regarding the asymptotic behaviour of the coupling time, motivated by rigorous results in one dimension and Monte Carlo simulations in dimensions two and three. Amongst our findings, we observe that, for generic parameter values, the distribution of the appropriately standardized coupling time converges to a Gumbel distribution, and that the standard deviation of the coupling time is asymptotic to an explicit universal constant multiple of the relaxation time. Perhaps surprisingly, we observe these results to hold both off criticality, where the coupling time closely mimics the coupon collector's problem, and also at the critical point, provided the cluster fugacity is below the value at which the transition becomes discontinuous. Finally, we consider analogous questions for the single-spin Ising heat-bath process.

Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

PubMed Central

Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

2016-01-01

The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

PubMed

Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

2016-08-21

The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

Benchmark Comparison of Dual- and Quad-Core Processor Linux Clusters with Two Global Climate Modeling Workloads

NASA Technical Reports Server (NTRS)

McGalliard, James

2008-01-01

This viewgraph presentation details the science and systems environments that NASA High End computing program serves. Included is a discussion of the workload that is involved in the processing for the Global Climate Modeling. The Goddard Earth Observing System Model, Version 5 (GEOS-5) is a system of models integrated using the Earth System Modeling Framework (ESMF). The GEOS-5 system was used for the Benchmark tests, and the results of the tests are shown and discussed. Tests were also run for the Cubed Sphere system, results for these test are also shown.

Issues in ATM Support of High-Performance, Geographically Distributed Computing

NASA Technical Reports Server (NTRS)

Claus, Russell W.; Dowd, Patrick W.; Srinidhi, Saragur M.; Blade, Eric D.G

1995-01-01

This report experimentally assesses the effect of the underlying network in a cluster-based computing environment. The assessment is quantified by application-level benchmarking, process-level communication, and network file input/output. Two testbeds were considered, one small cluster of Sun workstations and another large cluster composed of 32 high-end IBM RS/6000 platforms. The clusters had Ethernet, fiber distributed data interface (FDDI), Fibre Channel, and asynchronous transfer mode (ATM) network interface cards installed, providing the same processors and operating system for the entire suite of experiments. The primary goal of this report is to assess the suitability of an ATM-based, local-area network to support interprocess communication and remote file input/output systems for distributed computing.

Kohn-Sham Band Structure Benchmark Including Spin-Orbit Coupling for 2D and 3D Solids

NASA Astrophysics Data System (ADS)

Huhn, William; Blum, Volker

2015-03-01

Accurate electronic band structures serve as a primary indicator of the suitability of a material for a given application, e.g., as electronic or catalytic materials. Computed band structures, however, are subject to a host of approximations, some of which are more obvious (e.g., the treatment of the exchange-correlation of self-energy) and others less obvious (e.g., the treatment of core, semicore, or valence electrons, handling of relativistic effects, or the accuracy of the underlying basis set used). We here provide a set of accurate Kohn-Sham band structure benchmarks, using the numeric atom-centered all-electron electronic structure code FHI-aims combined with the ``traditional'' PBE functional and the hybrid HSE functional, to calculate core, valence, and low-lying conduction bands of a set of 2D and 3D materials. Benchmarks are provided with and without effects of spin-orbit coupling, using quasi-degenerate perturbation theory to predict spin-orbit splittings. This work is funded by Fritz-Haber-Institut der Max-Planck-Gesellschaft.

Statistical analysis of activation and reaction energies with quasi-variational coupled-cluster theory

NASA Astrophysics Data System (ADS)

Black, Joshua A.; Knowles, Peter J.

2018-06-01

The performance of quasi-variational coupled-cluster (QV) theory applied to the calculation of activation and reaction energies has been investigated. A statistical analysis of results obtained for six different sets of reactions has been carried out, and the results have been compared to those from standard single-reference methods. In general, the QV methods lead to increased activation energies and larger absolute reaction energies compared to those obtained with traditional coupled-cluster theory.

Coupled-cluster computations of atomic nuclei

NASA Astrophysics Data System (ADS)

Hagen, G.; Papenbrock, T.; Hjorth-Jensen, M.; Dean, D. J.

2014-09-01

In the past decade, coupled-cluster theory has seen a renaissance in nuclear physics, with computations of neutron-rich and medium-mass nuclei. The method is efficient for nuclei with product-state references, and it describes many aspects of weakly bound and unbound nuclei. This report reviews the technical and conceptual developments of this method in nuclear physics, and the results of coupled-cluster calculations for nucleonic matter, and for exotic isotopes of helium, oxygen, calcium, and some of their neighbors.

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

Mobile clusters of single board computers: an option for providing resources to student projects and researchers.

PubMed

Baun, Christian

2016-01-01

Clusters usually consist of servers, workstations or personal computers as nodes. But especially for academic purposes like student projects or scientific projects, the cost for purchase and operation can be a challenge. Single board computers cannot compete with the performance or energy-efficiency of higher-value systems, but they are an option to build inexpensive cluster systems. Because of the compact design and modest energy consumption, it is possible to build clusters of single board computers in a way that they are mobile and can be easily transported by the users. This paper describes the construction of such a cluster, useful applications and the performance of the single nodes. Furthermore, the clusters' performance and energy-efficiency is analyzed by executing the High Performance Linpack benchmark with a different number of nodes and different proportion of the systems total main memory utilized.

Construction and Utilization of a Beowulf Computing Cluster: A User's Perspective

NASA Technical Reports Server (NTRS)

Woods, Judy L.; West, Jeff S.; Sulyma, Peter R.

2000-01-01

Lockheed Martin Space Operations - Stennis Programs (LMSO) at the John C Stennis Space Center (NASA/SSC) has designed and built a Beowulf computer cluster which is owned by NASA/SSC and operated by LMSO. The design and construction of the cluster are detailed in this paper. The cluster is currently used for Computational Fluid Dynamics (CFD) simulations. The CFD codes in use and their applications are discussed. Examples of some of the work are also presented. Performance benchmark studies have been conducted for the CFD codes being run on the cluster. The results of two of the studies are presented and discussed. The cluster is not currently being utilized to its full potential; therefore, plans are underway to add more capabilities. These include the addition of structural, thermal, fluid, and acoustic Finite Element Analysis codes as well as real-time data acquisition and processing during test operations at NASA/SSC. These plans are discussed as well.

Merging symmetry projection methods with coupled cluster theory: Lessons from the Lipkin model Hamiltonian

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

Wahlen-Strothman, J. M.; Henderson, T. H.; Hermes, M. R.

Coupled cluster and symmetry projected Hartree-Fock are two central paradigms in electronic structure theory. However, they are very different. Single reference coupled cluster is highly successful for treating weakly correlated systems, but fails under strong correlation unless one sacrifices good quantum numbers and works with broken-symmetry wave functions, which is unphysical for finite systems. Symmetry projection is effective for the treatment of strong correlation at the mean-field level through multireference non-orthogonal configuration interaction wavefunctions, but unlike coupled cluster, it is neither size extensive nor ideal for treating dynamic correlation. We here examine different scenarios for merging these two dissimilar theories.more » We carry out this exercise over the integrable Lipkin model Hamiltonian, which despite its simplicity, encompasses non-trivial physics for degenerate systems and can be solved via diagonalization for a very large number of particles. We show how symmetry projection and coupled cluster doubles individually fail in different correlation limits, whereas models that merge these two theories are highly successful over the entire phase diagram. Despite the simplicity of the Lipkin Hamiltonian, the lessons learned in this work will be useful for building an ab initio symmetry projected coupled cluster theory that we expect to be accurate in the weakly and strongly correlated limits, as well as the recoupling regime.« less

Combining symmetry collective states with coupled-cluster theory: Lessons from the Agassi model Hamiltonian

NASA Astrophysics Data System (ADS)

Hermes, Matthew R.; Dukelsky, Jorge; Scuseria, Gustavo E.

2017-06-01

The failures of single-reference coupled-cluster theory for strongly correlated many-body systems is flagged at the mean-field level by the spontaneous breaking of one or more physical symmetries of the Hamiltonian. Restoring the symmetry of the mean-field determinant by projection reveals that coupled-cluster theory fails because it factorizes high-order excitation amplitudes incorrectly. However, symmetry-projected mean-field wave functions do not account sufficiently for dynamic (or weak) correlation. Here we pursue a merger of symmetry projection and coupled-cluster theory, following previous work along these lines that utilized the simple Lipkin model system as a test bed [J. Chem. Phys. 146, 054110 (2017), 10.1063/1.4974989]. We generalize the concept of a symmetry-projected mean-field wave function to the concept of a symmetry projected state, in which the factorization of high-order excitation amplitudes in terms of low-order ones is guided by symmetry projection and is not exponential, and combine them with coupled-cluster theory in order to model the ground state of the Agassi Hamiltonian. This model has two separate channels of correlation and two separate physical symmetries which are broken under strong correlation. We show how the combination of symmetry collective states and coupled-cluster theory is effective in obtaining correlation energies and order parameters of the Agassi model throughout its phase diagram.

Experiences Using OpenMP Based on Compiler Directed Software DSM on a PC Cluster

NASA Technical Reports Server (NTRS)

Hess, Matthias; Jost, Gabriele; Mueller, Matthias; Ruehle, Roland; Biegel, Bryan (Technical Monitor)

2002-01-01

In this work we report on our experiences running OpenMP (message passing) programs on a commodity cluster of PCs (personal computers) running a software distributed shared memory (DSM) system. We describe our test environment and report on the performance of a subset of the NAS (NASA Advanced Supercomputing) Parallel Benchmarks that have been automatically parallelized for OpenMP. We compare the performance of the OpenMP implementations with that of their message passing counterparts and discuss performance differences.

Traveling salesman problems with PageRank Distance on complex networks reveal community structure

NASA Astrophysics Data System (ADS)

Jiang, Zhongzhou; Liu, Jing; Wang, Shuai

2016-12-01

In this paper, we propose a new algorithm for community detection problems (CDPs) based on traveling salesman problems (TSPs), labeled as TSP-CDA. Since TSPs need to find a tour with minimum cost, cities close to each other are usually clustered in the tour. This inspired us to model CDPs as TSPs by taking each vertex as a city. Then, in the final tour, the vertices in the same community tend to cluster together, and the community structure can be obtained by cutting the tour into a couple of paths. There are two challenges. The first is to define a suitable distance between each pair of vertices which can reflect the probability that they belong to the same community. The second is to design a suitable strategy to cut the final tour into paths which can form communities. In TSP-CDA, we deal with these two challenges by defining a PageRank Distance and an automatic threshold-based cutting strategy. The PageRank Distance is designed with the intrinsic properties of CDPs in mind, and can be calculated efficiently. In the experiments, benchmark networks with 1000-10,000 nodes and varying structures are used to test the performance of TSP-CDA. A comparison is also made between TSP-CDA and two well-established community detection algorithms. The results show that TSP-CDA can find accurate community structure efficiently and outperforms the two existing algorithms.

An efficient matrix-matrix multiplication based antisymmetric tensor contraction engine for general order coupled cluster.

PubMed

Hanrath, Michael; Engels-Putzka, Anna

2010-08-14

In this paper, we present an efficient implementation of general tensor contractions, which is part of a new coupled-cluster program. The tensor contractions, used to evaluate the residuals in each coupled-cluster iteration are particularly important for the performance of the program. We developed a generic procedure, which carries out contractions of two tensors irrespective of their explicit structure. It can handle coupled-cluster-type expressions of arbitrary excitation level. To make the contraction efficient without loosing flexibility, we use a three-step procedure. First, the data contained in the tensors are rearranged into matrices, then a matrix-matrix multiplication is performed, and finally the result is backtransformed to a tensor. The current implementation is significantly more efficient than previous ones capable of treating arbitrary high excitations.

Classifying Higher Education Institutions in Korea: A Performance-Based Approach

ERIC Educational Resources Information Center

Shin, Jung Cheol

2009-01-01

The purpose of this study was to classify higher education institutions according to institutional performance rather than predetermined benchmarks. Institutional performance was defined as research performance and classified using Hierarchical Cluster Analysis, a statistical method that classifies objects according to specified classification…

High-resolution Self-Organizing Maps for advanced visualization and dimension reduction.

PubMed

Saraswati, Ayu; Nguyen, Van Tuc; Hagenbuchner, Markus; Tsoi, Ah Chung

2018-05-04

Kohonen's Self Organizing feature Map (SOM) provides an effective way to project high dimensional input features onto a low dimensional display space while preserving the topological relationships among the input features. Recent advances in algorithms that take advantages of modern computing hardware introduced the concept of high resolution SOMs (HRSOMs). This paper investigates the capabilities and applicability of the HRSOM as a visualization tool for cluster analysis and its suitabilities to serve as a pre-processor in ensemble learning models. The evaluation is conducted on a number of established benchmarks and real-world learning problems, namely, the policeman benchmark, two web spam detection problems, a network intrusion detection problem, and a malware detection problem. It is found that the visualization resulted from an HRSOM provides new insights concerning these learning problems. It is furthermore shown empirically that broad benefits from the use of HRSOMs in both clustering and classification problems can be expected. Copyright © 2018 Elsevier Ltd. All rights reserved.

Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals?

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

Xu, Xuefei; Zhang, Wenjing; Tang, Mingsheng

2015-05-12

Coupled-cluster (CC) methods have been extensively used as the high-level approach in quantum electronic structure theory to predict various properties of molecules when experimental results are unavailable. It is often assumed that CC methods, if they include at least up to connected-triple-excitation quasiperturbative corrections to a full treatment of single and double excitations (in particular, CCSD(T)), and a very large basis set, are more accurate than Kohn–Sham (KS) density functional theory (DFT). In the present work, we tested and compared the performance of standard CC and KS methods on bond energy calculations of 20 3d transition metal-containing diatomic molecules againstmore » the most reliable experimental data available, as collected in a database called 3dMLBE20. It is found that, although the CCSD(T) and higher levels CC methods have mean unsigned deviations from experiment that are smaller than most exchange-correlation functionals for metal–ligand bond energies of transition metals, the improvement is less than one standard deviation of the mean unsigned deviation. Furthermore, on average, almost half of the 42 exchange-correlation functionals that we tested are closer to experiment than CCSD(T) with the same extended basis set for the same molecule. The results show that, when both relativistic and core–valence correlation effects are considered, even the very high-level (expensive) CC method with single, double, triple, and perturbative quadruple cluster operators, namely, CCSDT(2)Q, averaged over 20 bond energies, gives a mean unsigned deviation (MUD(20) = 4.7 kcal/mol when one correlates only valence, 3p, and 3s electrons of transition metals and only valence electrons of ligands, or 4.6 kcal/mol when one correlates all core electrons except for 1s shells of transition metals, S, and Cl); and that is similar to some good xc functionals (e.g., B97-1 (MUD(20) = 4.5 kcal/mol) and PW6B95 (MUD(20) = 4.9 kcal/mol)) when the same basis set is used. We found that, for both coupled cluster calculations and KS calculations, the T1 diagnostics correlate the errors better than either the M diagnostics or the B1 DFT-based diagnostics. The potential use of practical standard CC methods as a benchmark theory is further confounded by the finding that CC and DFT methods usually have different signs of the error. We conclude that the available experimental data do not provide a justification for using conventional single-reference CC theory calculations to validate or test xc functionals for systems involving 3d transition metals.« less

Basic firefly algorithm for document clustering

NASA Astrophysics Data System (ADS)

Mohammed, Athraa Jasim; Yusof, Yuhanis; Husni, Husniza

2015-12-01

The Document clustering plays significant role in Information Retrieval (IR) where it organizes documents prior to the retrieval process. To date, various clustering algorithms have been proposed and this includes the K-means and Particle Swarm Optimization. Even though these algorithms have been widely applied in many disciplines due to its simplicity, such an approach tends to be trapped in a local minimum during its search for an optimal solution. To address the shortcoming, this paper proposes a Basic Firefly (Basic FA) algorithm to cluster text documents. The algorithm employs the Average Distance to Document Centroid (ADDC) as the objective function of the search. Experiments utilizing the proposed algorithm were conducted on the 20Newsgroups benchmark dataset. Results demonstrate that the Basic FA generates a more robust and compact clusters than the ones produced by K-means and Particle Swarm Optimization (PSO).

Using Hyperfine Electron Paramagnetic Resonance Spectroscopy to Define the Proton-Coupled Electron Transfer Reaction at Fe-S Cluster N2 in Respiratory Complex I.

PubMed

Le Breton, Nolwenn; Wright, John J; Jones, Andrew J Y; Salvadori, Enrico; Bridges, Hannah R; Hirst, Judy; Roessler, Maxie M

2017-11-15

Energy-transducing respiratory complex I (NADH:ubiquinone oxidoreductase) is one of the largest and most complicated enzymes in mammalian cells. Here, we used hyperfine electron paramagnetic resonance (EPR) spectroscopic methods, combined with site-directed mutagenesis, to determine the mechanism of a single proton-coupled electron transfer reaction at one of eight iron-sulfur clusters in complex I, [4Fe-4S] cluster N2. N2 is the terminal cluster of the enzyme's intramolecular electron-transfer chain and the electron donor to ubiquinone. Because of its position and pH-dependent reduction potential, N2 has long been considered a candidate for the elusive "energy-coupling" site in complex I at which energy generated by the redox reaction is used to initiate proton translocation. Here, we used hyperfine sublevel correlation (HYSCORE) spectroscopy, including relaxation-filtered hyperfine and single-matched resonance transfer (SMART) HYSCORE, to detect two weakly coupled exchangeable protons near N2. We assign the larger coupling with A( 1 H) = [-3.0, -3.0, 8.7] MHz to the exchangeable proton of a conserved histidine and conclude that the histidine is hydrogen-bonded to N2, tuning its reduction potential. The histidine protonation state responds to the cluster oxidation state, but the two are not coupled sufficiently strongly to catalyze a stoichiometric and efficient energy transduction reaction. We thus exclude cluster N2, despite its proton-coupled electron transfer chemistry, as the energy-coupling site in complex I. Our work demonstrates the capability of pulse EPR methods for providing detailed information on the properties of individual protons in even the most challenging of energy-converting enzymes.

Cluster-modified function projective synchronisation of complex networks with asymmetric coupling

NASA Astrophysics Data System (ADS)

Wang, Shuguo

2018-02-01

This paper investigates the cluster-modified function projective synchronisation (CMFPS) of a generalised linearly coupled network with asymmetric coupling and nonidentical dynamical nodes. A novel synchronisation scheme is proposed to achieve CMFPS in community networks. We use adaptive control method to derive CMFPS criteria based on Lyapunov stability theory. Each cluster of networks is synchronised with target system by state transformation with scaling function matrix. Numerical simulation results are presented finally to illustrate the effectiveness of this method.

Fan Noise Prediction with Applications to Aircraft System Noise Assessment

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Envia, Edmane; Burley, Casey L.

2009-01-01

This paper describes an assessment of current fan noise prediction tools by comparing measured and predicted sideline acoustic levels from a benchmark fan noise wind tunnel test. Specifically, an empirical method and newly developed coupled computational approach are utilized to predict aft fan noise for a benchmark test configuration. Comparisons with sideline noise measurements are performed to assess the relative merits of the two approaches. The study identifies issues entailed in coupling the source and propagation codes, as well as provides insight into the capabilities of the tools in predicting the fan noise source and subsequent propagation and radiation. In contrast to the empirical method, the new coupled computational approach provides the ability to investigate acoustic near-field effects. The potential benefits/costs of these new methods are also compared with the existing capabilities in a current aircraft noise system prediction tool. The knowledge gained in this work provides a basis for improved fan source specification in overall aircraft system noise studies.

Analysis of 2D Torus and Hub Topologies of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Pedretti, Kevin T.; Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

1997-01-01

A variety of different network technologies and topologies are currently being evaluated as part of the Whitney Project. This paper reports on the implementation and performance of a Fast Ethernet network configured in a 4x4 2D torus topology in a testbed cluster of 'commodity' Pentium Pro PCs. Several benchmarks were used for performance evaluation: an MPI point to point message passing benchmark, an MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2). Our results show that for point to point communication on an unloaded network, the hub and 1 hop routes on the torus have about the same bandwidth and latency. However, the bandwidth decreases and the latency increases on the torus for each additional route hop. Collective communication benchmarks show that the torus provides roughly four times more aggregate bandwidth and eight times faster MPI barrier synchronizations than a hub based network for 16 processor systems. Finally, the SOAPBOX benchmarks, which simulate real-world CFD applications, generally demonstrated substantially better performance on the torus than on the hub. In the few cases the hub was faster, the difference was negligible. In total, our experimental results lead to the conclusion that for Fast Ethernet networks, the torus topology has better performance and scales better than a hub based network.

Relation between financial market structure and the real economy: comparison between clustering methods.

PubMed

Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T

2015-01-01

We quantify the amount of information filtered by different hierarchical clustering methods on correlations between stock returns comparing the clustering structure with the underlying industrial activity classification. We apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree and we compare it with other methods including the Linkage and k-medoids. By taking the industrial sector classification of stocks as a benchmark partition, we evaluate how the different methods retrieve this classification. The results show that the Directed Bubble Hierarchical Tree can outperform other methods, being able to retrieve more information with fewer clusters. Moreover,we show that the economic information is hidden at different levels of the hierarchical structures depending on the clustering method. The dynamical analysis on a rolling window also reveals that the different methods show different degrees of sensitivity to events affecting financial markets, like crises. These results can be of interest for all the applications of clustering methods to portfolio optimization and risk hedging [corrected].

Data-driven cluster reinforcement and visualization in sparsely-matched self-organizing maps.

PubMed

Manukyan, Narine; Eppstein, Margaret J; Rizzo, Donna M

2012-05-01

A self-organizing map (SOM) is a self-organized projection of high-dimensional data onto a typically 2-dimensional (2-D) feature map, wherein vector similarity is implicitly translated into topological closeness in the 2-D projection. However, when there are more neurons than input patterns, it can be challenging to interpret the results, due to diffuse cluster boundaries and limitations of current methods for displaying interneuron distances. In this brief, we introduce a new cluster reinforcement (CR) phase for sparsely-matched SOMs. The CR phase amplifies within-cluster similarity in an unsupervised, data-driven manner. Discontinuities in the resulting map correspond to between-cluster distances and are stored in a boundary (B) matrix. We describe a new hierarchical visualization of cluster boundaries displayed directly on feature maps, which requires no further clustering beyond what was implicitly accomplished during self-organization in SOM training. We use a synthetic benchmark problem and previously published microbial community profile data to demonstrate the benefits of the proposed methods.

Relation between Financial Market Structure and the Real Economy: Comparison between Clustering Methods

PubMed Central

Musmeci, Nicoló; Aste, Tomaso; Di Matteo, T.

2015-01-01

We quantify the amount of information filtered by different hierarchical clustering methods on correlations between stock returns comparing the clustering structure with the underlying industrial activity classification. We apply, for the first time to financial data, a novel hierarchical clustering approach, the Directed Bubble Hierarchical Tree and we compare it with other methods including the Linkage and k-medoids. By taking the industrial sector classification of stocks as a benchmark partition, we evaluate how the different methods retrieve this classification. The results show that the Directed Bubble Hierarchical Tree can outperform other methods, being able to retrieve more information with fewer clusters. Moreover, we show that the economic information is hidden at different levels of the hierarchical structures depending on the clustering method. The dynamical analysis on a rolling window also reveals that the different methods show different degrees of sensitivity to events affecting financial markets, like crises. These results can be of interest for all the applications of clustering methods to portfolio optimization and risk hedging. PMID:25786703

Relativistic coupled-cluster calculations of the 173Yb nuclear quadrupole coupling constant for the YbF molecule

NASA Astrophysics Data System (ADS)

Pašteka, L. F.; Mawhorter, R. J.; Schwerdtfeger, P.

2016-04-01

We report calculations on the q(Yb) electric field gradient (EFG) for the X2Σ+ and A2Π1/2 electronic states of the ytterbium monofluoride (YbF) molecule at the molecular mean-field Dirac-Coulomb-Gaunt as well as scalar-relativistic coupled-cluster levels of theory using large uncontracted basis sets. Vibrational contributions are included in the final results. Our estimated nuclear quadrupole coupling constants of -3386(78) MHz and -2083(153) MHz for the X2Σ+ and A2Π1/2 states of 173YbF are in stark contrast to the only available experimental results (-2050(170) MHz and -1090(160) MHz) respectively, where the only similarity is the difference between the two values. Perturbative triple contributions in the coupled cluster treatment are significant and point towards the necessity to go to higher order in the coupled-cluster treatment in future calculations. We also present density functional calculations which show rather large variations for the Yb EFG with different functionals used; the best result was obtained using the CAM-B3LYP* functional.

Association schemes perspective of microbubble cluster in ultrasonic fields.

PubMed

Behnia, S; Yahyavi, M; Habibpourbisafar, R

2018-06-01

Dynamics of a cluster of chaotic oscillators on a network are studied using coupled maps. By introducing the association schemes, we obtain coupling strength in the adjacency matrices form, which satisfies Markov matrices property. We remark that in general, the stability region of the cluster of oscillators at the synchronization state is characterized by Lyapunov exponent which can be defined based on the N-coupled map. As a detailed physical example, dynamics of microbubble cluster in an ultrasonic field are studied using coupled maps. Microbubble cluster dynamics have an indicative highly active nonlinear phenomenon, were not easy to be explained. In this paper, a cluster of microbubbles with a thin elastic shell based on the modified Keller-Herring equation in an ultrasonic field is demonstrated in the framework of the globally coupled map. On the other hand, a relation between the microbubble elements is replaced by a relation between the vertices. Based on this method, the stability region of microbubbles pulsations at complete synchronization state has been obtained analytically. In this way, distances between microbubbles as coupling strength play the crucial role. In the stability region, we thus observe that the problem of study of dynamics of N-microbubble oscillators reduce to that of a single microbubble. Therefore, the important parameters of the isolated microbubble such as applied pressure, driving frequency and the initial radius have effective behavior on the synchronization state. Copyright © 2018 Elsevier B.V. All rights reserved.

Hierarchical Kohonenen net for anomaly detection in network security.

PubMed

Sarasamma, Suseela T; Zhu, Qiuming A; Huff, Julie

2005-04-01

A novel multilevel hierarchical Kohonen Net (K-Map) for an intrusion detection system is presented. Each level of the hierarchical map is modeled as a simple winner-take-all K-Map. One significant advantage of this multilevel hierarchical K-Map is its computational efficiency. Unlike other statistical anomaly detection methods such as nearest neighbor approach, K-means clustering or probabilistic analysis that employ distance computation in the feature space to identify the outliers, our approach does not involve costly point-to-point computation in organizing the data into clusters. Another advantage is the reduced network size. We use the classification capability of the K-Map on selected dimensions of data set in detecting anomalies. Randomly selected subsets that contain both attacks and normal records from the KDD Cup 1999 benchmark data are used to train the hierarchical net. We use a confidence measure to label the clusters. Then we use the test set from the same KDD Cup 1999 benchmark to test the hierarchical net. We show that a hierarchical K-Map in which each layer operates on a small subset of the feature space is superior to a single-layer K-Map operating on the whole feature space in detecting a variety of attacks in terms of detection rate as well as false positive rate.

Development of New Open-Shell Perturbation and Coupled-Cluster Theories Based on Symmetric Spin Orbitals

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Arnold, James O. (Technical Monitor)

1994-01-01

A new spin orbital basis is employed in the development of efficient open-shell coupled-cluster and perturbation theories that are based on a restricted Hartree-Fock (RHF) reference function. The spin orbital basis differs from the standard one in the spin functions that are associated with the singly occupied spatial orbital. The occupied orbital (in the spin orbital basis) is assigned the delta(+) = 1/square root of 2(alpha+Beta) spin function while the unoccupied orbital is assigned the delta(-) = 1/square root of 2(alpha-Beta) spin function. The doubly occupied and unoccupied orbitals (in the reference function) are assigned the standard alpha and Beta spin functions. The coupled-cluster and perturbation theory wave functions based on this set of "symmetric spin orbitals" exhibit much more symmetry than those based on the standard spin orbital basis. This, together with interacting space arguments, leads to a dramatic reduction in the computational cost for both coupled-cluster and perturbation theory. Additionally, perturbation theory based on "symmetric spin orbitals" obeys Brillouin's theorem provided that spin and spatial excitations are both considered. Other properties of the coupled-cluster and perturbation theory wave functions and models will be discussed.

Near-Edge X-ray Absorption Fine Structure within Multilevel Coupled Cluster Theory.

PubMed

Myhre, Rolf H; Coriani, Sonia; Koch, Henrik

2016-06-14

Core excited states are challenging to calculate, mainly because they are embedded in a manifold of high-energy valence-excited states. However, their locality makes their determination ideal for local correlation methods. In this paper, we demonstrate the performance of multilevel coupled cluster theory in computing core spectra both within the core-valence separated and the asymmetric Lanczos implementations of coupled cluster linear response theory. We also propose a visualization tool to analyze the excitations using the difference between the ground-state and excited-state electron densities.

Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions

PubMed Central

Kluger, Yuval; Basri, Ronen; Chang, Joseph T.; Gerstein, Mark

2003-01-01

Global analyses of RNA expression levels are useful for classifying genes and overall phenotypes. Often these classification problems are linked, and one wants to find “marker genes” that are differentially expressed in particular sets of “conditions.” We have developed a method that simultaneously clusters genes and conditions, finding distinctive “checkerboard” patterns in matrices of gene expression data, if they exist. In a cancer context, these checkerboards correspond to genes that are markedly up- or downregulated in patients with particular types of tumors. Our method, spectral biclustering, is based on the observation that checkerboard structures in matrices of expression data can be found in eigenvectors corresponding to characteristic expression patterns across genes or conditions. In addition, these eigenvectors can be readily identified by commonly used linear algebra approaches, in particular the singular value decomposition (SVD), coupled with closely integrated normalization steps. We present a number of variants of the approach, depending on whether the normalization over genes and conditions is done independently or in a coupled fashion. We then apply spectral biclustering to a selection of publicly available cancer expression data sets, and examine the degree to which the approach is able to identify checkerboard structures. Furthermore, we compare the performance of our biclustering methods against a number of reasonable benchmarks (e.g., direct application of SVD or normalized cuts to raw data). PMID:12671006

Complete characterization of the stability of cluster synchronization in complex dynamical networks.

PubMed

Sorrentino, Francesco; Pecora, Louis M; Hagerstrom, Aaron M; Murphy, Thomas E; Roy, Rajarshi

2016-04-01

Synchronization is an important and prevalent phenomenon in natural and engineered systems. In many dynamical networks, the coupling is balanced or adjusted to admit global synchronization, a condition called Laplacian coupling. Many networks exhibit incomplete synchronization, where two or more clusters of synchronization persist, and computational group theory has recently proved to be valuable in discovering these cluster states based on the topology of the network. In the important case of Laplacian coupling, additional synchronization patterns can exist that would not be predicted from the group theory analysis alone. Understanding how and when clusters form, merge, and persist is essential for understanding collective dynamics, synchronization, and failure mechanisms of complex networks such as electric power grids, distributed control networks, and autonomous swarming vehicles. We describe a method to find and analyze all of the possible cluster synchronization patterns in a Laplacian-coupled network, by applying methods of computational group theory to dynamically equivalent networks. We present a general technique to evaluate the stability of each of the dynamically valid cluster synchronization patterns. Our results are validated in an optoelectronic experiment on a five-node network that confirms the synchronization patterns predicted by the theory.

Spin-orbit splitted excited states using explicitly-correlated equation-of-motion coupled-cluster singles and doubles eigenvectors

NASA Astrophysics Data System (ADS)

Bokhan, Denis; Trubnikov, Dmitrii N.; Perera, Ajith; Bartlett, Rodney J.

2018-04-01

An explicitly-correlated method of calculation of excited states with spin-orbit couplings, has been formulated and implemented. Developed approach utilizes left and right eigenvectors of equation-of-motion coupled-cluster model, which is based on the linearly approximated explicitly correlated coupled-cluster singles and doubles [CCSD(F12)] method. The spin-orbit interactions are introduced by using the spin-orbit mean field (SOMF) approximation of the Breit-Pauli Hamiltonian. Numerical tests for several atoms and molecules show good agreement between explicitly-correlated results and the corresponding values, calculated in complete basis set limit (CBS); the highly-accurate excitation energies can be obtained already at triple- ζ level.

Projected Hartree-Fock theory as a polynomial of particle-hole excitations and its combination with variational coupled cluster theory

NASA Astrophysics Data System (ADS)

Qiu, Yiheng; Henderson, Thomas M.; Scuseria, Gustavo E.

2017-05-01

Projected Hartree-Fock theory provides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems. Coupled cluster theory, in contrast, does the opposite. It therefore seems natural to combine the two so as to describe both strong and weak correlations with high accuracy in a relatively black-box manner. Combining the two approaches, however, is made more difficult by the fact that the two techniques are formulated very differently. In earlier work, we showed how to write spin-projected Hartree-Fock in a coupled-cluster-like language. Here, we fill in the gaps in that earlier work. Further, we combine projected Hartree-Fock and coupled cluster theory in a variational formulation and show how the combination performs for the description of the Hubbard Hamiltonian and for several small molecular systems.

Global cluster synchronization in nonlinearly coupled community networks with heterogeneous coupling delays.

PubMed

Tseng, Jui-Pin

2017-02-01

This investigation establishes the global cluster synchronization of complex networks with a community structure based on an iterative approach. The units comprising the network are described by differential equations, and can be non-autonomous and involve time delays. In addition, units in the different communities can be governed by different equations. The coupling configuration of the network is rather general. The coupling terms can be non-diffusive, nonlinear, asymmetric, and with heterogeneous coupling delays. Based on this approach, both delay-dependent and delay-independent criteria for global cluster synchronization are derived. We implement the present approach for a nonlinearly coupled neural network with heterogeneous coupling delays. Two numerical examples are given to show that neural networks can behave in a variety of new collective ways under the synchronization criteria. These examples also demonstrate that neural networks remain synchronized in spite of coupling delays between neurons across different communities; however, they may lose synchrony if the coupling delays between the neurons within the same community are too large, such that the synchronization criteria are violated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterization of addressability by simultaneous randomized benchmarking.

PubMed

Gambetta, Jay M; Córcoles, A D; Merkel, S T; Johnson, B R; Smolin, John A; Chow, Jerry M; Ryan, Colm A; Rigetti, Chad; Poletto, S; Ohki, Thomas A; Ketchen, Mark B; Steffen, M

2012-12-14

The control and handling of errors arising from cross talk and unwanted interactions in multiqubit systems is an important issue in quantum information processing architectures. We introduce a benchmarking protocol that provides information about the amount of addressability present in the system and implement it on coupled superconducting qubits. The protocol consists of randomized benchmarking experiments run both individually and simultaneously on pairs of qubits. A relevant figure of merit for the addressability is then related to the differences in the measured average gate fidelities in the two experiments. We present results from two similar samples with differing cross talk and unwanted qubit-qubit interactions. The results agree with predictions based on simple models of the classical cross talk and Stark shifts.

Density functional Theory Based Generalized Effective Fragment Potential Method (Postprint)

DTIC Science & Technology

2014-07-01

is acceptable for other applications) leads to induced dipole moments within 10−6 to 10−7 au of the precise values . Thus, the applied field of 10−4...noncovalent interactions. The water-benzene clusters17 and WATER2711 reference values were also ob- tained at the CCSD(T)/CBS level, except for the clusters...with n = 20,42 where MP2/CBS was used. The n-alkane dimers18 benchmark values were CCSD(T)/CBS for ethane to butane and a linear extrapolation method

Network clustering and community detection using modulus of families of loops.

PubMed

Shakeri, Heman; Poggi-Corradini, Pietro; Albin, Nathan; Scoglio, Caterina

2017-01-01

We study the structure of loops in networks using the notion of modulus of loop families. We introduce an alternate measure of network clustering by quantifying the richness of families of (simple) loops. Modulus tries to minimize the expected overlap among loops by spreading the expected link usage optimally. We propose weighting networks using these expected link usages to improve classical community detection algorithms. We show that the proposed method enhances the performance of certain algorithms, such as spectral partitioning and modularity maximization heuristics, on standard benchmarks.

Incremental fuzzy C medoids clustering of time series data using dynamic time warping distance

PubMed Central

Chen, Jingli; Wu, Shuai; Liu, Zhizhong; Chao, Hao

2018-01-01

Clustering time series data is of great significance since it could extract meaningful statistics and other characteristics. Especially in biomedical engineering, outstanding clustering algorithms for time series may help improve the health level of people. Considering data scale and time shifts of time series, in this paper, we introduce two incremental fuzzy clustering algorithms based on a Dynamic Time Warping (DTW) distance. For recruiting Single-Pass and Online patterns, our algorithms could handle large-scale time series data by splitting it into a set of chunks which are processed sequentially. Besides, our algorithms select DTW to measure distance of pair-wise time series and encourage higher clustering accuracy because DTW could determine an optimal match between any two time series by stretching or compressing segments of temporal data. Our new algorithms are compared to some existing prominent incremental fuzzy clustering algorithms on 12 benchmark time series datasets. The experimental results show that the proposed approaches could yield high quality clusters and were better than all the competitors in terms of clustering accuracy. PMID:29795600

Incremental fuzzy C medoids clustering of time series data using dynamic time warping distance.

PubMed

Liu, Yongli; Chen, Jingli; Wu, Shuai; Liu, Zhizhong; Chao, Hao

2018-01-01

Clustering time series data is of great significance since it could extract meaningful statistics and other characteristics. Especially in biomedical engineering, outstanding clustering algorithms for time series may help improve the health level of people. Considering data scale and time shifts of time series, in this paper, we introduce two incremental fuzzy clustering algorithms based on a Dynamic Time Warping (DTW) distance. For recruiting Single-Pass and Online patterns, our algorithms could handle large-scale time series data by splitting it into a set of chunks which are processed sequentially. Besides, our algorithms select DTW to measure distance of pair-wise time series and encourage higher clustering accuracy because DTW could determine an optimal match between any two time series by stretching or compressing segments of temporal data. Our new algorithms are compared to some existing prominent incremental fuzzy clustering algorithms on 12 benchmark time series datasets. The experimental results show that the proposed approaches could yield high quality clusters and were better than all the competitors in terms of clustering accuracy.

Development of a two-fluid drag law for clustered particles using direct numerical simulation and validation through experiments

NASA Astrophysics Data System (ADS)

Abbasi Baharanchi, Ahmadreza

This dissertation focused on development and utilization of numerical and experimental approaches to improve the CFD modeling of fluidization flow of cohesive micron size particles. The specific objectives of this research were: (1) Developing a cluster prediction mechanism applicable to Two-Fluid Modeling (TFM) of gas-solid systems (2) Developing more accurate drag models for Two-Fluid Modeling (TFM) of gas-solid fluidization flow with the presence of cohesive interparticle forces (3) using the developed model to explore the improvement of accuracy of TFM in simulation of fluidization flow of cohesive powders (4) Understanding the causes and influential factor which led to improvements and quantification of improvements (5) Gathering data from a fast fluidization flow and use these data for benchmark validations. Simulation results with two developed cluster-aware drag models showed that cluster prediction could effectively influence the results in both the first and second cluster-aware models. It was proven that improvement of accuracy of TFM modeling using three versions of the first hybrid model was significant and the best improvements were obtained by using the smallest values of the switch parameter which led to capturing the smallest chances of cluster prediction. In the case of the second hybrid model, dependence of critical model parameter on only Reynolds number led to the fact that improvement of accuracy was significant only in dense section of the fluidized bed. This finding may suggest that a more sophisticated particle resolved DNS model, which can span wide range of solid volume fraction, can be used in the formulation of the cluster-aware drag model. The results of experiment suing high speed imaging indicated the presence of particle clusters in the fluidization flow of FCC inside the riser of FIU-CFB facility. In addition, pressure data was successfully captured along the fluidization column of the facility and used as benchmark validation data for the second hybrid model developed in the present dissertation. It was shown the second hybrid model could predict the pressure data in the dense section of the fluidization column with better accuracy.

Track structure in radiation biology: theory and applications.

PubMed

Nikjoo, H; Uehara, S; Wilson, W E; Hoshi, M; Goodhead, D T

1998-04-01

A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is deposited by low-energy electrons; the majority of DNA damage lesions are of simple type; the complexity of damage increases with increased LET, while the total yield of strand breaks remains constant; and at high LET values nearly 70% of all double-strand breaks are of complex type.

An overview of the ENEA activities in the field of coupled codes NPP simulation

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

Parisi, C.; Negrenti, E.; Sepielli, M.

2012-07-01

In the framework of the nuclear research activities in the fields of safety, training and education, ENEA (the Italian National Agency for New Technologies, Energy and the Sustainable Development) is in charge of defining and pursuing all the necessary steps for the development of a NPP engineering simulator at the 'Casaccia' Research Center near Rome. A summary of the activities in the field of the nuclear power plants simulation by coupled codes is here presented with the long term strategy for the engineering simulator development. Specifically, results from the participation in international benchmarking activities like the OECD/NEA 'Kalinin-3' benchmark andmore » the 'AER-DYN-002' benchmark, together with simulations of relevant events like the Fukushima accident, are here reported. The ultimate goal of such activities performed using state-of-the-art technology is the re-establishment of top level competencies in the NPP simulation field in order to facilitate the development of Enhanced Engineering Simulators and to upgrade competencies for supporting national energy strategy decisions, the nuclear national safety authority, and the R and D activities on NPP designs. (authors)« less

Symmetries and stability of chimera states in small, globally-coupled networks

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

It has recently been demonstrated that symmetries in a network's topology can help predict the patterns of synchronized clusters that can emerge in a network of coupled oscillators. This and related discoveries have led to increased interest in both network symmetries and cluster synchronization. In parallel with these discoveries, interest in chimera states-dynamical patterns in which a network separates into coherent and incoherent portions-has grown, and chimeras have now been observed in a variety of experimental systems. We present an opto-electronic experiment in which both chimera states and synchronized clusters are observed in a small, globally-coupled network. We show that the symmetries and sub-symmetries of the network permit the formation of the chimera and cluster states. A recently developed group theoretical approach enables us to predict the stability of the observed chimera and cluster states, and highlights the close relationship between chimera and cluster states as belonging to the broader phenomenon of partial synchronization.

A gauge-independent zeroth-order regular approximation to the exact relativistic Hamiltonian—Formulation and applications

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2005-01-01

A simple modification of the zeroth-order regular approximation (ZORA) in relativistic theory is suggested to suppress its erroneous gauge dependence to a high level of approximation. The method, coined gauge-independent ZORA (ZORA-GI), can be easily installed in any existing nonrelativistic quantum chemical package by programming simple one-electron matrix elements for the quasirelativistic Hamiltonian. Results of benchmark calculations obtained with ZORA-GI at the Hartree-Fock (HF) and second-order Møller-Plesset perturbation theory (MP2) level for dihalogens X2 (X=F,Cl,Br,I,At) are in good agreement with the results of four-component relativistic calculations (HF level) and experimental data (MP2 level). ZORA-GI calculations based on MP2 or coupled-cluster theory with single and double perturbations and a perturbative inclusion of triple excitations [CCSD(T)] lead to accurate atomization energies and molecular geometries for the tetroxides of group VIII elements. With ZORA-GI/CCSD(T), an improved estimate for the atomization energy of hassium (Z=108) tetroxide is obtained.

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

Field, Kevin G.; Yang, Ying; Busby, Jeremy T.

Radiation induced segregation (RIS) is a well-studied phenomena which occurs in many structurally relevant nuclear materials including austenitic stainless steels. RIS occurs due to solute atoms preferentially coupling to mobile point defect fluxes that migrate and interact with defect sinks. Here, a 304 stainless steel was neutron irradiated up to 47.1 dpa at 320 °C. Investigations into the RIS response at specific grain boundary types were utilized to determine the sink characteristics of different boundary types as a function of irradiation dose. A rate theory model built on the foundation of the modified inverse Kirkendall (MIK) model is proposed andmore » benchmarked to the experimental results. This model, termed the GiMIK model, includes alterations in the boundary conditions based on grain boundary structure and includes expressions for interstitial binding. This investigation, through experiment and modeling, found specific grain boundary structures exhibit unique defect sink characteristics depending on their local structure. Furthermore, such interactions were found to be consistent across all doses investigated and had larger global implications including precipitation of Ni-Si clusters near different grain boundary types.« less

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

Field, Kevin G.; Yang, Ying; Allen, Todd R.

Radiation induced segregation (RIS) is a well-studied phenomena which occurs in many structurally relevant nuclear materials including austenitic stainless steels. RIS occurs due to solute atoms preferentially coupling to mobile point defect fluxes that migrate and interact with defect sinks. Here, a 304 stainless steel was neutron irradiated up to 47.1 dpa at 320 °C. Investigations into the RIS response at specific grain boundary types were utilized to determine the sink characteristics of different boundary types as a function of irradiation dose. A rate theory model built on the foundation of the modified inverse Kirkendall (MIK) model is proposed andmore » benchmarked to the experimental results. This model, termed the GiMIK model, includes alterations in the boundary conditions based on grain boundary structure and includes expressions for interstitial binding. This investigation, through experiment and modeling, found specific grain boundary structures exhibit unique defect sink characteristics depending on their local structure. Such interactions were found to be consistent across all doses investigated and had larger global implications including precipitation of Ni-Si clusters near different grain boundary types.« less

The Importance of Electron Correlation on Stacking Interaction of Adenine-Thymine Base-Pair Step in B-DNA: A Quantum Monte Carlo Study.

PubMed

Hongo, Kenta; Cuong, Nguyen Thanh; Maezono, Ryo

2013-02-12

We report fixed-node diffusion Monte Carlo (DMC) calculations of stacking interaction energy between two adenine(A)-thymine(T) base pairs in B-DNA (AA:TT), for which reference data are available, obtained from a complete basis set estimate of CCSD(T) (coupled-cluster with singles, doubles, and perturbative triples). We consider four sets of nodal surfaces obtained from self-consistent field calculations and examine how the different nodal surfaces affect the DMC potential energy curves of the AA:TT molecule and the resulting stacking energies. We find that the DMC potential energy curves using the different nodes look similar to each other as a whole. We also benchmark the performance of various quantum chemistry methods, including Hartree-Fock (HF) theory, second-order Møller-Plesset perturbation theory (MP2), and density functional theory (DFT). The DMC and recently developed DFT results of the stacking energy reasonably agree with the reference, while the HF, MP2, and conventional DFT methods give unsatisfactory results.

Toward the Development of a Fundamentally Based Chemical Model for Cyclopentanone: High-Pressure-Limit Rate Constants for H Atom Abstraction and Fuel Radical Decomposition

DOE PAGES

Zhou, Chong-Wen; Simmie, John M.; Pitz, William J.; ...

2016-08-25

Theoretical aspects of the development of a chemical kinetic model for the pyrolysis and combustion of a cyclic ketone, cyclopentanone, are considered. We present calculated thermodynamic and kinetic data for the first time for the principal species including 2- and 3-oxo-cyclopentyl radicals, which are in reasonable agreement with the literature. Furthermore, these radicals can be formed via H atom abstraction reactions by H and Ö atoms and OH, HO 2, and CH 3 radicals, the rate constants of which have been calculated. Abstraction from the β-hydrogen atom is the dominant process when OH is involved, but the reverse holds truemore » for HO 2 radicals. We also determined the subsequent β-scission of the radicals formed, and it is shown that recent tunable VUV photoionization mass spectrometry experiments can be interpreted in this light. The bulk of the calculations used the composite model chemistry G4, which was benchmarked in the simplest case with a coupled cluster treatment, CCSD(T), in the complete basis set limit.« less

Quasi-degenerate perturbation theory using matrix product states

NASA Astrophysics Data System (ADS)

Sharma, Sandeep; Jeanmairet, Guillaume; Alavi, Ali

2016-01-01

In this work, we generalize the recently proposed matrix product state perturbation theory (MPSPT) for calculating energies of excited states using quasi-degenerate (QD) perturbation theory. Our formulation uses the Kirtman-Certain-Hirschfelder canonical Van Vleck perturbation theory, which gives Hermitian effective Hamiltonians at each order, and also allows one to make use of Wigner's 2n + 1 rule. Further, our formulation satisfies Granovsky's requirement of model space invariance which is important for obtaining smooth potential energy curves. Thus, when we use MPSPT with the Dyall Hamiltonian, we obtain a model space invariant version of quasi-degenerate n-electron valence state perturbation theory (NEVPT), a property that the usual formulation of QD-NEVPT2 based on a multipartitioning technique lacked. We use our method on the benchmark problems of bond breaking of LiF which shows ionic to covalent curve crossing and the twist around the double bond of ethylene where significant valence-Rydberg mixing occurs in the excited states. In accordance with our previous work, we find that multi-reference linearized coupled cluster theory is more accurate than other multi-reference theories of similar cost.

Numerically exploring the 1D-2D dimensional crossover on spin dynamics in the doped Hubbard model

DOE PAGES

Kung, Y. F.; Bazin, C.; Wohlfeld, K.; ...

2017-11-02

Using determinant quantum Monte Carlo (DQMC) simulations, we systematically study the doping dependence of the crossover from one to two dimensions and its impact on the magnetic properties of the Hubbard model. A square lattice of chains is used, in which the dimensionality can be tuned by varying the interchain coupling t ⊥. The dynamical spin structure factor and static quantities, such as the static spin susceptibility and nearest-neighbor spin correlation function, are characterized in the one- and two-dimensional limits as a benchmark. When the dimensionality is tuned between these limits, the magnetic properties, while evolving smoothly from one tomore » two dimensions, drastically change regardless of the doping level. This suggests that the spin excitations in the two-dimensional Hubbard model, even in the heavily doped case, cannot be explained using the spinon picture known from one dimension. In conclusion, the DQMC calculations are complemented by cluster perturbation theory studies to form a more complete picture of how the crossover occurs as a function of doping and how doped holes impact magnetic order.« less

Protonation and Proton-Coupled Electron Transfer at S-Ligated [4Fe-4S] Clusters

PubMed Central

Morris, Wesley D.; Darcy, Julia W.; Mayer, James M.

2015-01-01

Biological [Fe-S] clusters are increasingly recognized to undergo proton-coupled electron transfer (PCET), but the site of protonation, mechanism, and role for PCET remains largely unknown. Here we explore this reactivity with synthetic model clusters. Protonation of the arylthiolate-ligated [4Fe-4S] cluster [Fe4S4(SAr)4]2- (1, SAr = S-2,4-6-(iPr)3C6H2) leads to thiol dissociation, reversibly forming [Fe4S4(SAr)3L]1- (2) + ArSH (L = solvent, and/or conjugate base). Solutions of 2 + ArSH react with the nitroxyl radical TEMPO to give [Fe4S4(SAr)4]1- (1ox) and TEMPOH. This reaction involves PCET coupled to thiolate association and may proceed via the unobserved protonated cluster [Fe4S4(SAr)3(HSAr)]1-(1-H). Similar reactions with this and related clusters proceed comparably. An understanding of the PCET thermochemistry of this cluster system has been developed, encompassing three different redox levels and two protonation states. PMID:25965413

Influences of adding negative couplings between cliques of Kuramoto-like oscillators

NASA Astrophysics Data System (ADS)

Yang, Li-xin; Lin, Xiao-lin; Jiang, Jun

2018-06-01

We study the dynamics in a clustered network of coupled oscillators by considering positive and negative coupling schemes. Second order oscillators can be interpreted as a model of consumers and generators working in a power network. Numerical results indicate that coupling strategies play an important role in the synchronizability of the clustered power network. It is found that the synchronizability can be enhanced as the positive intragroup connections increase. Meanwhile, when the intragroup interactions are positive and the probability p that two nodes belonging to different clusters are connected is increased, the synchronization has better performance. Besides, when the intragroup connections are negative, it is observed that the power network has poor synchronizability as the probability p increases. Our simulation results can help us understand the collective behavior of the power network with positive and negative couplings.

[Does implementation of benchmarking in quality circles improve the quality of care of patients with asthma and reduce drug interaction?].

PubMed

Kaufmann-Kolle, Petra; Szecsenyi, Joachim; Broge, Björn; Haefeli, Walter Emil; Schneider, Antonius

2011-01-01

The purpose of this cluster-randomised controlled trial was to evaluate the efficacy of quality circles (QCs) working either with general data-based feedback or with an open benchmark within the field of asthma care and drug-drug interactions. Twelve QCs, involving 96 general practitioners from 85 practices, were randomised. Six QCs worked with traditional anonymous feedback and six with an open benchmark. Two QC meetings supported with feedback reports were held covering the topics "drug-drug interactions" and "asthma"; in both cases discussions were guided by a trained moderator. Outcome measures included health-related quality of life and patient satisfaction with treatment, asthma severity and number of potentially inappropriate drug combinations as well as the general practitioners' satisfaction in relation to the performance of the QC. A significant improvement in the treatment of asthma was observed in both trial arms. However, there was only a slight improvement regarding inappropriate drug combinations. There were no relevant differences between the group with open benchmark (B-QC) and traditional quality circles (T-QC). The physicians' satisfaction with the QC performance was significantly higher in the T-QCs. General practitioners seem to take a critical perspective about open benchmarking in quality circles. Caution should be used when implementing benchmarking in a quality circle as it did not improve healthcare when compared to the traditional procedure with anonymised comparisons. Copyright © 2011. Published by Elsevier GmbH.

X-ray aspects of the DAFT/FADA clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Lima Neto, G. B.; Adami, C.

2012-12-01

We have undertaken the DAFT/FADA survey with the aim of applying constraints on dark energy based on weak lensing tomography as well as obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range [0.4,0.9] for which there are HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. We present preliminary results on the coupled X-ray and dynamical analyses of these clusters.

Efficient electronic structure theory via hierarchical scale-adaptive coupled-cluster formalism: I. Theory and computational complexity analysis

NASA Astrophysics Data System (ADS)

Lyakh, Dmitry I.

2018-03-01

A novel reduced-scaling, general-order coupled-cluster approach is formulated by exploiting hierarchical representations of many-body tensors, combined with the recently suggested formalism of scale-adaptive tensor algebra. Inspired by the hierarchical techniques from the renormalisation group approach, H/H2-matrix algebra and fast multipole method, the computational scaling reduction in our formalism is achieved via coarsening of quantum many-body interactions at larger interaction scales, thus imposing a hierarchical structure on many-body tensors of coupled-cluster theory. In our approach, the interaction scale can be defined on any appropriate Euclidean domain (spatial domain, momentum-space domain, energy domain, etc.). We show that the hierarchically resolved many-body tensors can reduce the storage requirements to O(N), where N is the number of simulated quantum particles. Subsequently, we prove that any connected many-body diagram consisting of a finite number of arbitrary-order tensors, e.g. an arbitrary coupled-cluster diagram, can be evaluated in O(NlogN) floating-point operations. On top of that, we suggest an additional approximation to further reduce the computational complexity of higher order coupled-cluster equations, i.e. equations involving higher than double excitations, which otherwise would introduce a large prefactor into formal O(NlogN) scaling.

Performance of Frozen Density Embedding for Modeling Hole Transfer Reactions.

PubMed

Ramos, Pablo; Papadakis, Markos; Pavanello, Michele

2015-06-18

We have carried out a thorough benchmark of the frozen density-embedding (FDE) method for calculating hole transfer couplings. We have considered 10 exchange-correlation functionals, 3 nonadditive kinetic energy functionals, and 3 basis sets. Overall, we conclude that with a 7% mean relative unsigned error, the PBE and PW91 functionals coupled with the PW91k nonadditive kinetic energy functional and a TZP basis set constitute the most stable and accurate levels of theory for hole transfer coupling calculations. The FDE-ET method is found to be an excellent tool for computing diabatic couplings for hole transfer reactions.

Communication: An improved linear scaling perturbative triples correction for the domain based local pair-natural orbital based singles and doubles coupled cluster method [DLPNO-CCSD(T)].

PubMed

Guo, Yang; Riplinger, Christoph; Becker, Ute; Liakos, Dimitrios G; Minenkov, Yury; Cavallo, Luigi; Neese, Frank

2018-01-07

In this communication, an improved perturbative triples correction (T) algorithm for domain based local pair-natural orbital singles and doubles coupled cluster (DLPNO-CCSD) theory is reported. In our previous implementation, the semi-canonical approximation was used and linear scaling was achieved for both the DLPNO-CCSD and (T) parts of the calculation. In this work, we refer to this previous method as DLPNO-CCSD(T 0 ) to emphasize the semi-canonical approximation. It is well-established that the DLPNO-CCSD method can predict very accurate absolute and relative energies with respect to the parent canonical CCSD method. However, the (T 0 ) approximation may introduce significant errors in absolute energies as the triples correction grows up in magnitude. In the majority of cases, the relative energies from (T 0 ) are as accurate as the canonical (T) results of themselves. Unfortunately, in rare cases and in particular for small gap systems, the (T 0 ) approximation breaks down and relative energies show large deviations from the parent canonical CCSD(T) results. To address this problem, an iterative (T) algorithm based on the previous DLPNO-CCSD(T 0 ) algorithm has been implemented [abbreviated here as DLPNO-CCSD(T)]. Using triples natural orbitals to represent the virtual spaces for triples amplitudes, storage bottlenecks are avoided. Various carefully designed approximations ease the computational burden such that overall, the increase in the DLPNO-(T) calculation time over DLPNO-(T 0 ) only amounts to a factor of about two (depending on the basis set). Benchmark calculations for the GMTKN30 database show that compared to DLPNO-CCSD(T 0 ), the errors in absolute energies are greatly reduced and relative energies are moderately improved. The particularly problematic case of cumulene chains of increasing lengths is also successfully addressed by DLPNO-CCSD(T).

Communication: An improved linear scaling perturbative triples correction for the domain based local pair-natural orbital based singles and doubles coupled cluster method [DLPNO-CCSD(T)

NASA Astrophysics Data System (ADS)

Guo, Yang; Riplinger, Christoph; Becker, Ute; Liakos, Dimitrios G.; Minenkov, Yury; Cavallo, Luigi; Neese, Frank

2018-01-01

In this communication, an improved perturbative triples correction (T) algorithm for domain based local pair-natural orbital singles and doubles coupled cluster (DLPNO-CCSD) theory is reported. In our previous implementation, the semi-canonical approximation was used and linear scaling was achieved for both the DLPNO-CCSD and (T) parts of the calculation. In this work, we refer to this previous method as DLPNO-CCSD(T0) to emphasize the semi-canonical approximation. It is well-established that the DLPNO-CCSD method can predict very accurate absolute and relative energies with respect to the parent canonical CCSD method. However, the (T0) approximation may introduce significant errors in absolute energies as the triples correction grows up in magnitude. In the majority of cases, the relative energies from (T0) are as accurate as the canonical (T) results of themselves. Unfortunately, in rare cases and in particular for small gap systems, the (T0) approximation breaks down and relative energies show large deviations from the parent canonical CCSD(T) results. To address this problem, an iterative (T) algorithm based on the previous DLPNO-CCSD(T0) algorithm has been implemented [abbreviated here as DLPNO-CCSD(T)]. Using triples natural orbitals to represent the virtual spaces for triples amplitudes, storage bottlenecks are avoided. Various carefully designed approximations ease the computational burden such that overall, the increase in the DLPNO-(T) calculation time over DLPNO-(T0) only amounts to a factor of about two (depending on the basis set). Benchmark calculations for the GMTKN30 database show that compared to DLPNO-CCSD(T0), the errors in absolute energies are greatly reduced and relative energies are moderately improved. The particularly problematic case of cumulene chains of increasing lengths is also successfully addressed by DLPNO-CCSD(T).

Improving the accuracy of Møller-Plesset perturbation theory with neural networks

NASA Astrophysics Data System (ADS)

McGibbon, Robert T.; Taube, Andrew G.; Donchev, Alexander G.; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L.; Shaw, David E.

2017-10-01

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol-1 (root-mean-square error 0.09 kcal mol-1), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Improving the accuracy of Møller-Plesset perturbation theory with neural networks.

PubMed

McGibbon, Robert T; Taube, Andrew G; Donchev, Alexander G; Siva, Karthik; Hernández, Felipe; Hargus, Cory; Law, Ka-Hei; Klepeis, John L; Shaw, David E

2017-10-28

Noncovalent interactions are of fundamental importance across the disciplines of chemistry, materials science, and biology. Quantum chemical calculations on noncovalently bound complexes, which allow for the quantification of properties such as binding energies and geometries, play an essential role in advancing our understanding of, and building models for, a vast array of complex processes involving molecular association or self-assembly. Because of its relatively modest computational cost, second-order Møller-Plesset perturbation (MP2) theory is one of the most widely used methods in quantum chemistry for studying noncovalent interactions. MP2 is, however, plagued by serious errors due to its incomplete treatment of electron correlation, especially when modeling van der Waals interactions and π-stacked complexes. Here we present spin-network-scaled MP2 (SNS-MP2), a new semi-empirical MP2-based method for dimer interaction-energy calculations. To correct for errors in MP2, SNS-MP2 uses quantum chemical features of the complex under study in conjunction with a neural network to reweight terms appearing in the total MP2 interaction energy. The method has been trained on a new data set consisting of over 200 000 complete basis set (CBS)-extrapolated coupled-cluster interaction energies, which are considered the gold standard for chemical accuracy. SNS-MP2 predicts gold-standard binding energies of unseen test compounds with a mean absolute error of 0.04 kcal mol -1 (root-mean-square error 0.09 kcal mol -1 ), a 6- to 7-fold improvement over MP2. To the best of our knowledge, its accuracy exceeds that of all extant density functional theory- and wavefunction-based methods of similar computational cost, and is very close to the intrinsic accuracy of our benchmark coupled-cluster methodology itself. Furthermore, SNS-MP2 provides reliable per-conformation confidence intervals on the predicted interaction energies, a feature not available from any alternative method.

Concordance of transcriptional and apical benchmark dose levels for conazole-ind uced liver effects in mice

EPA Science Inventory

The ability to anchor chemical class-based gene expression changes to phenotypic lesions and to describe these changes as a function of dose and time can inform mode of action and improve quantitative risk assessment. Previous research identified a 330-gene cluster commonly resp...

Scalable and cost-effective NGS genotyping in the cloud.

PubMed

Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

2015-10-15

While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

Competencies in Training at the Graduate Student Level: Example of a Pediatric Psychology Seminar Course

PubMed Central

Ievers-Landis, Carolyn E.; Hazen, Rebecca A.; Fehr, Karla K.

2015-01-01

The recently developed competencies in pediatric psychology from the Society of Pediatric Psychology (SPP) Task Force on Competencies and Best Training Practices in Pediatric Psychology provide a benchmark to evaluate training program practices and student progress toward training in level-specific competency goals. Graduate-level training presents a unique challenge for addressing the breadth of competencies required in pediatric psychology while maintaining development of broader clinical psychology training goals. We describe a recurring graduate-level pediatric psychology seminar course that addresses training in a number of the competency cluster areas. The structure of the seminar, examples of classroom topics that correspond with competency cluster areas as well as benchmarks used to evaluate each student’s development in the competency area are provided. Specific challenges in developing and maintaining the seminar in this format are identified, and possible solutions are offered. This training format could serve as a model for established pediatric psychology programs to expand their didactic training goals or for programs without formal pediatric psychology training to address competencies outside of clinical placements. PMID:26900536

A new symmetrical quasi-classical model for electronically non-adiabatic processes: Application to the case of weak non-adiabatic coupling

DOE PAGES

Cotton, Stephen J.; Miller, William H.

2016-10-14

Previous work has shown how a symmetrical quasi-classical (SQC) windowing procedure can be used to quantize the initial and final electronic degrees of freedom in the Meyer-Miller (MM) classical vibronic (i.e, nuclear + electronic) Hamiltonian, and that the approach provides a very good description of electronically non-adiabatic processes within a standard classical molecular dynamics framework for a number of benchmark problems. This study explores application of the SQC/MM approach to the case of very weak non-adiabatic coupling between the electronic states, showing (as anticipated) how the standard SQC/MM approach used to date fails in this limit, and then devises amore » new SQC windowing scheme to deal with it. Finally, application of this new SQC model to a variety of realistic benchmark systems shows that the new model not only treats the weak coupling case extremely well, but it is also seen to describe the “normal” regime (of electronic transition probabilities ≳ 0.1) even more accurately than the previous “standard” model.« less

Relativistic nuclear magnetic resonance J-coupling with ultrasoft pseudopotentials and the zeroth-order regular approximation

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

Green, Timothy F. G., E-mail: tim.green@materials.ox.ac.uk; Yates, Jonathan R., E-mail: jonathan.yates@materials.ox.ac.uk

2014-06-21

We present a method for the first-principles calculation of nuclear magnetic resonance (NMR) J-coupling in extended systems using state-of-the-art ultrasoft pseudopotentials and including scalar-relativistic effects. The use of ultrasoft pseudopotentials is allowed by extending the projector augmented wave (PAW) method of Joyce et al. [J. Chem. Phys. 127, 204107 (2007)]. We benchmark it against existing local-orbital quantum chemical calculations and experiments for small molecules containing light elements, with good agreement. Scalar-relativistic effects are included at the zeroth-order regular approximation level of theory and benchmarked against existing local-orbital quantum chemical calculations and experiments for a number of small molecules containing themore » heavy row six elements W, Pt, Hg, Tl, and Pb, with good agreement. Finally, {sup 1}J(P-Ag) and {sup 2}J(P-Ag-P) couplings are calculated in some larger molecular crystals and compared against solid-state NMR experiments. Some remarks are also made as to improving the numerical stability of dipole perturbations using PAW.« less

A new symmetrical quasi-classical model for electronically non-adiabatic processes: Application to the case of weak non-adiabatic coupling

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

Cotton, Stephen J.; Miller, William H.

Previous work has shown how a symmetrical quasi-classical (SQC) windowing procedure can be used to quantize the initial and final electronic degrees of freedom in the Meyer-Miller (MM) classical vibronic (i.e, nuclear + electronic) Hamiltonian, and that the approach provides a very good description of electronically non-adiabatic processes within a standard classical molecular dynamics framework for a number of benchmark problems. This study explores application of the SQC/MM approach to the case of very weak non-adiabatic coupling between the electronic states, showing (as anticipated) how the standard SQC/MM approach used to date fails in this limit, and then devises amore » new SQC windowing scheme to deal with it. Finally, application of this new SQC model to a variety of realistic benchmark systems shows that the new model not only treats the weak coupling case extremely well, but it is also seen to describe the “normal” regime (of electronic transition probabilities ≳ 0.1) even more accurately than the previous “standard” model.« less

Coupled two-dimensional edge plasma and neutral gas modeling of tokamak scrape-off-layers

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

Maingi, Rajesh

1992-08-01

The objective of this study is to devise a detailed description of the tokamak scrape-off-layer (SOL), which includes the best available models of both the plasma and neutral species and the strong coupling between the two in many SOL regimes. A good estimate of both particle flux and heat flux profiles at the limiter/divertor target plates is desired. Peak heat flux is one of the limiting factors in determining the survival probability of plasma-facing-components at high power levels. Plate particle flux affects the neutral flux to the pump, which determines the particle exhaust rate. A technique which couples a two-dimensionalmore » (2-D) plasma and a 2-D neutral transport code has been developed (coupled code technique), but this procedure requires large amounts of computer time. Relevant physics has been added to an existing two-neutral-species model which takes the SOL plasma/neutral coupling into account in a simple manner (molecular physics model), and this model is compared with the coupled code technique mentioned above. The molecular physics model is benchmarked against experimental data from a divertor tokamak (DIII-D), and a similar model (single-species model) is benchmarked against data from a pump-limiter tokamak (Tore Supra). The models are then used to examine two key issues: free-streaming-limits (ion energy conduction and momentum flux) and the effects of the non-orthogonal geometry of magnetic flux surfaces and target plates on edge plasma parameter profiles.« less

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

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

Zhang, Jianbao; Ma, Zhongjun, E-mail: mzj1234402@163.com; Chen, Guanrong

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding ormore » deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.« less

Robustness of cluster synchronous patterns in small-world networks with inter-cluster co-competition balance

NASA Astrophysics Data System (ADS)

Zhang, Jianbao; Ma, Zhongjun; Chen, Guanrong

2014-06-01

All edges in the classical Watts and Strogatz's small-world network model are unweighted and cooperative (positive). By introducing competitive (negative) inter-cluster edges and assigning edge weights to mimic more realistic networks, this paper develops a modified model which possesses co-competitive weighted couplings and cluster structures while maintaining the common small-world network properties of small average shortest path lengths and large clustering coefficients. Based on theoretical analysis, it is proved that the new model with inter-cluster co-competition balance has an important dynamical property of robust cluster synchronous pattern formation. More precisely, clusters will neither merge nor split regardless of adding or deleting nodes and edges, under the condition of inter-cluster co-competition balance. Numerical simulations demonstrate the robustness of the model against the increase of the coupling strength and several topological variations.

Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators.

PubMed

O'Keeffe, Kevin P; Krapivsky, P L; Strogatz, Steven H

2015-08-07

We consider models of identical pulse-coupled oscillators with global interactions. Previous work showed that under certain conditions such systems always end up in sync, but did not quantify how small clusters of synchronized oscillators progressively coalesce into larger ones. Using tools from the study of aggregation phenomena, we obtain exact results for the time-dependent distribution of cluster sizes as the system evolves from disorder to synchrony.

Configurational coupled cluster approach with applications to magnetic model systems

NASA Astrophysics Data System (ADS)

Wu, Siyuan; Nooijen, Marcel

2018-05-01

A general exponential, coupled cluster like, approach is discussed to extract an effective Hamiltonian in configurational space, as a sum of 1-body, 2-body up to n-body operators. The simplest two-body approach is illustrated by calculations on simple magnetic model systems. A key feature of the approach is that equations up to a certain rank do not depend on higher body cluster operators.

``Dressing'' lines and vertices in calculations of matrix elements with the coupled-cluster method and determination of Cs atomic properties

NASA Astrophysics Data System (ADS)

Derevianko, Andrei; Porsev, Sergey G.

2005-03-01

We consider evaluation of matrix elements with the coupled-cluster method. Such calculations formally involve infinite number of terms and we devise a method of partial summation (dressing) of the resulting series. Our formalism is built upon an expansion of the product C†C of cluster amplitudes C into a sum of n -body insertions. We consider two types of insertions: particle (hole) line insertion and two-particle (two-hole) random-phase-approximation-like insertion. We demonstrate how to “dress” these insertions and formulate iterative equations. We illustrate the dressing equations in the case when the cluster operator is truncated at single and double excitations. Using univalent systems as an example, we upgrade coupled-cluster diagrams for matrix elements with the dressed insertions and highlight a relation to pertinent fourth-order diagrams. We illustrate our formalism with relativistic calculations of the hyperfine constant A(6s) and the 6s1/2-6p1/2 electric-dipole transition amplitude for the Cs atom. Finally, we augment the truncated coupled-cluster calculations with otherwise omitted fourth order diagrams. The resulting analysis for Cs is complete through the fourth order of many-body perturbation theory and reveals an important role of triple and disconnected quadruple excitations.

Zodiacal Exoplanets in Time: Searching for Young Stars in K2

NASA Astrophysics Data System (ADS)

Morris, Nathan Ryan; Mann, Andrew; Rizzuto, Aaron

2018-01-01

Observations of planetary systems around young stars provide insight into the early stages of planetary system formation. Nearby young open clusters such as the Hyades, Pleiades, and Praesepe provide important benchmarks for the properties of stellar systems in general. These clusters are all known to be less than 1 Gyr old, making them ideal targets for a survey of young planetary systems. Few transiting planets have been detected around clusters stars, however, so this alone is too small of a sample. K2, the revived Kepler mission, has provided a vast number of light curves for young stars in clusters and elsewhere in the K2 field. This provides us with the opportunity to extend the sample of young systems to field stars while calibrating with cluster stars. We compute rotational periods from starspot patterns for ~36,000 K2 targets and use gyrochronological relationships derived from cluster stars to determine their ages. From there, we have begun searching for planets around young stars outside the clusters with the ultimate goal of shedding light on how planets and planetary systems evolve in their early, most formative years.

The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison phase results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Rühaak, Wolfram

2016-04-01

Climate change impacts in permafrost regions have received considerable attention recently due to the pronounced warming trends experienced in recent decades and which have been projected into the future. Large portions of these permafrost regions are characterized by surface water bodies (lakes, rivers) that interact with the surrounding permafrost often generating taliks (unfrozen zones) within the permafrost that allow for hydrologic interactions between the surface water bodies and underlying aquifers and thus influence the hydrologic response of a landscape to climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model past and future evolution such units (Kurylyk et al. 2014). However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, which can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. A benchmark exercise was initialized at the end of 2014. Participants convened from USA, Canada, Europe, representing 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones (Kurylyk et al. 2014; Grenier et al. in prep.; Rühaak et al. 2015). They range from simpler, purely thermal 1D cases to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in a cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test case databases at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases TH2 & TH3. Both cases are essentially theoretical but include the full complexity of the coupled non-linear set of equations (heat transfer with conduction, advection, phase change and Darcian flow). The complete set of inter-comparison results shows that the participating codes all produce simulations which are quantitatively similar and correspond to physical intuition. From a quantitative perspective, they agree well over the whole set of performance measures. The differences among the simulation results will be discussed in more depth throughout the test cases especially for the identification of the threshold times for each system as these exhibited the least agreement. However, the results suggest that in spite of the difficulties associated with the resolution of the set of TH equations (coupled and non-linear structure with phase change providing steep slopes), the developed codes provide robust results with a qualitatively reasonable representation of the processes and offer a quantitatively realistic basis. Further perspectives of the exercise will also be presented.

A coupled cluster theory with iterative inclusion of triple excitations and associated equation of motion formulation for excitation energy and ionization potential

NASA Astrophysics Data System (ADS)

Maitra, Rahul; Akinaga, Yoshinobu; Nakajima, Takahito

2017-08-01

A single reference coupled cluster theory that is capable of including the effect of connected triple excitations has been developed and implemented. This is achieved by regrouping the terms appearing in perturbation theory and parametrizing through two different sets of exponential operators: while one of the exponentials, involving general substitution operators, annihilates the ground state but has a non-vanishing effect when it acts on the excited determinant, the other is the regular single and double excitation operator in the sense of conventional coupled cluster theory, which acts on the Hartree-Fock ground state. The two sets of operators are solved as coupled non-linear equations in an iterative manner without significant increase in computational cost than the conventional coupled cluster theory with singles and doubles excitations. A number of physically motivated and computationally advantageous sufficiency conditions are invoked to arrive at the working equations and have been applied to determine the ground state energies of a number of small prototypical systems having weak multi-reference character. With the knowledge of the correlated ground state, we have reconstructed the triple excitation operator and have performed equation of motion with coupled cluster singles, doubles, and triples to obtain the ionization potential and excitation energies of these molecules as well. Our results suggest that this is quite a reasonable scheme to capture the effect of connected triple excitations as long as the ground state remains weakly multi-reference.

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

Burke, Timothy P.; Martz, Roger L.; Kiedrowski, Brian C.

New unstructured mesh capabilities in MCNP6 (developmental version during summer 2012) show potential for conducting multi-physics analyses by coupling MCNP to a finite element solver such as Abaqus/CAE[2]. Before these new capabilities can be utilized, the ability of MCNP to accurately estimate eigenvalues and pin powers using an unstructured mesh must first be verified. Previous work to verify the unstructured mesh capabilities in MCNP was accomplished using the Godiva sphere [1], and this work attempts to build on that. To accomplish this, a criticality benchmark and a fuel assembly benchmark were used for calculations in MCNP using both the Constructivemore » Solid Geometry (CSG) native to MCNP and the unstructured mesh geometry generated using Abaqus/CAE. The Big Ten criticality benchmark [3] was modeled due to its geometry being similar to that of a reactor fuel pin. The C5G7 3-D Mixed Oxide (MOX) Fuel Assembly Benchmark [4] was modeled to test the unstructured mesh capabilities on a reactor-type problem.« less

Manipulating Light with Transition Metal Clusters, Organic Dyes, and Metal Organic Frameworks

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

Ogut, Serdar

The primary goals of our research program is to develop and apply state-of-the-art first-principles methods to predict electronic and optical properties of three systems of significant scientific and technological interest: transition metal clusters, organic dyes, and metal-organic frameworks. These systems offer great opportunities to manipulate light for a wide ranging list of energy-related scientific problems and applications. During this grant period, we focused our investigations on the development, implementation, and benchmarking of many-body Green’s function methods (GW approximation and the Bethe-Salpeter equation) to examine excited-state properties of transition metal/transition-metal-oxide clusters and organic molecules that comprise the building blocks of dyesmore » and metal-organic frameworks.« less

Transition properties from the Hermitian formulation of the coupled cluster polarization propagator

NASA Astrophysics Data System (ADS)

Tucholska, Aleksandra M.; Modrzejewski, Marcin; Moszynski, Robert

2014-09-01

Theory of one-electron transition density matrices has been formulated within the time-independent coupled cluster method for the polarization propagator [R. Moszynski, P. S. Żuchowski, and B. Jeziorski, Coll. Czech. Chem. Commun. 70, 1109 (2005)]. Working expressions have been obtained and implemented with the coupled cluster method limited to single, double, and linear triple excitations (CC3). Selected dipole and quadrupole transition probabilities of the alkali earth atoms, computed with the new transition density matrices are compared to the experimental data. Good agreement between theory and experiment is found. The results obtained with the new approach are of the same quality as the results obtained with the linear response coupled cluster theory. The one-electron density matrices for the ground state in the CC3 approximation have also been implemented. The dipole moments for a few representative diatomic molecules have been computed with several variants of the new approach, and the results are discussed to choose the approximation with the best balance between the accuracy and computational efficiency.

Communication: Finite size correction in periodic coupled cluster theory calculations of solids.

PubMed

Liao, Ke; Grüneis, Andreas

2016-10-14

We present a method to correct for finite size errors in coupled cluster theory calculations of solids. The outlined technique shares similarities with electronic structure factor interpolation methods used in quantum Monte Carlo calculations. However, our approach does not require the calculation of density matrices. Furthermore we show that the proposed finite size corrections achieve chemical accuracy in the convergence of second-order Møller-Plesset perturbation and coupled cluster singles and doubles correlation energies per atom for insulating solids with two atomic unit cells using 2 × 2 × 2 and 3 × 3 × 3 k-point meshes only.

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

A nonperturbative light-front coupled-cluster method

NASA Astrophysics Data System (ADS)

Hiller, J. R.

2012-10-01

The nonperturbative Hamiltonian eigenvalue problem for bound states of a quantum field theory is formulated in terms of Dirac's light-front coordinates and then approximated by the exponential-operator technique of the many-body coupled-cluster method. This approximation eliminates any need for the usual approximation of Fock-space truncation. Instead, the exponentiated operator is truncated, and the terms retained are determined by a set of nonlinear integral equations. These equations are solved simultaneously with an effective eigenvalue problem in the valence sector, where the number of constituents is small. Matrix elements can be calculated, with extensions of techniques from standard coupled-cluster theory, to obtain form factors and other observables.

Coulomb- and Antiferromagnetic-Induced Fission in Doubly Charged Cubelike Fe-S Clusters

NASA Astrophysics Data System (ADS)

Yang, Xin; Wang, Xue-Bin; Niu, Shuqiang; Pickett, Chris J.; Ichiye, Toshiko; Wang, Lai-Sheng

2002-09-01

We report the observation of symmetric fission in doubly charged Fe-S cluster anions, [Fe4S4X4]2- -->2[Fe2S2X2]- (X=Cl,Br), owing to both Coulomb repulsion and antiferromagnetic coupling. Photoelectron spectroscopy shows that both the parent and the fission fragments have similar electronic structures and confirms the inverted energy schemes due to the strong spin polarization of the Fe 3d levels. The current observation provides direct confirmation for the unusual spin couplings in the [Fe4S4X4]2- clusters, which contain two valent-delocalized and ferromagnetically coupled Fe2S2 subunits.

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

NASA Astrophysics Data System (ADS)

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2013-09-01

Building on the framework recently reported for determining general response properties for frozen-density embedding [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)], 10.1063/1.3675845, in this work we report a first implementation of an embedded coupled-cluster in density-functional theory (CC-in-DFT) scheme for electronic excitations, where only the response of the active subsystem is taken into account. The formalism is applied to the calculation of coupled-cluster excitation energies of water and uracil in aqueous solution. We find that the CC-in-DFT results are in good agreement with reference calculations and experimental results. The accuracy of calculations is mainly sensitive to factors influencing the correlation treatment (basis set quality, truncation of the cluster operator) and to the embedding treatment of the ground-state (choice of density functionals). This allows for efficient approximations at the excited state calculation step without compromising the accuracy. This approximate scheme makes it possible to use a first principles approach to investigate environment effects with specific interactions at coupled-cluster level of theory at a cost comparable to that of calculations of the individual subsystems in vacuum.

Scalability and Portability of Two Parallel Implementations of ADI

NASA Technical Reports Server (NTRS)

Phung, Thanh; VanderWijngaart, Rob F.

1994-01-01

Two domain decompositions for the implementation of the NAS Scalar Penta-diagonal Parallel Benchmark on MIMD systems are investigated, namely transposition and multi-partitioning. Hardware platforms considered are the Intel iPSC/860 and Paragon XP/S-15, and clusters of SGI workstations on ethernet, communicating through PVM. It is found that the multi-partitioning strategy offers the kind of coarse granularity that allows scaling up to hundreds of processors on a massively parallel machine. Moreover, efficiency is retained when the code is ported verbatim (save message passing syntax) to a PVM environment on a modest size cluster of workstations.

X-ray and optical substructures of the DAFT/FADA survey clusters

NASA Astrophysics Data System (ADS)

Guennou, L.; Durret, F.; Adami, C.; Lima Neto, G. B.

2013-04-01

We have undertaken the DAFT/FADA survey with the double aim of setting constraints on dark energy based on weak lensing tomography and of obtaining homogeneous and high quality data for a sample of 91 massive clusters in the redshift range 0.4-0.9 for which there were HST archive data. We have analysed the XMM-Newton data available for 42 of these clusters to derive their X-ray temperatures and luminosities and search for substructures. Out of these, a spatial analysis was possible for 30 clusters, but only 23 had deep enough X-ray data for a really robust analysis. This study was coupled with a dynamical analysis for the 26 clusters having at least 30 spectroscopic galaxy redshifts in the cluster range. Altogether, the X-ray sample of 23 clusters and the optical sample of 26 clusters have 14 clusters in common. We present preliminary results on the coupled X-ray and dynamical analyses of these 14 clusters.

The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study.

PubMed

Tabrizi, Shadan Ghassemi; Pelmenschikov, Vladimir; Noodleman, Louis; Kaupp, Martin

2016-01-12

An unprecedented [4Fe-3S] cluster proximal to the regular [NiFe] active site has recently been found to be responsible for the ability of membrane-bound hydrogenases (MBHs) to oxidize dihydrogen in the presence of ambient levels of oxygen. Starting from proximal cluster models of a recent DFT study on the redox-dependent structural transformation of the [4Fe-3S] cluster, (57)Fe Mössbauer parameters (electric field gradients, isomer shifts, and nuclear hyperfine couplings) were calculated using DFT. Our results revise the previously reported correspondence of Mössbauer signals and iron centers in the [4Fe-3S](3+) reduced-state proximal cluster. Similar conflicting assignments are also resolved for the [4Fe-3S](5+) superoxidized state with particular regard to spin-coupling in the broken-symmetry DFT calculations. Calculated (57)Fe hyperfine coupling (HFC) tensors expose discrepancies in the experimental set of HFC tensors and substantiate the need for additional experimental work on the magnetic properties of the MBH proximal cluster in its reduced and superoxidized redox states.

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

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

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance.

PubMed

De Hertogh, Benoît; De Meulder, Bertrand; Berger, Fabrice; Pierre, Michael; Bareke, Eric; Gaigneaux, Anthoula; Depiereux, Eric

2010-01-11

Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods. Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality. Performance analysis refined the results from benchmarks published previously.We show that the Shrinkage t test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized t test and the Window t test performed slightly better. The R scripts used for the analysis are available at http://urbm-cluster.urbm.fundp.ac.be/~bdemeulder/.

Multiscale benchmarking of drug delivery vectors.

PubMed

Summers, Huw D; Ware, Matthew J; Majithia, Ravish; Meissner, Kenith E; Godin, Biana; Rees, Paul

2016-10-01

Cross-system comparisons of drug delivery vectors are essential to ensure optimal design. An in-vitro experimental protocol is presented that separates the role of the delivery vector from that of its cargo in determining the cell response, thus allowing quantitative comparison of different systems. The technique is validated through benchmarking of the dose-response of human fibroblast cells exposed to the cationic molecule, polyethylene imine (PEI); delivered as a free molecule and as a cargo on the surface of CdSe nanoparticles and Silica microparticles. The exposure metrics are converted to a delivered dose with the transport properties of the different scale systems characterized by a delivery time, τ. The benchmarking highlights an agglomeration of the free PEI molecules into micron sized clusters and identifies the metric determining cell death as the total number of PEI molecules presented to cells, determined by the delivery vector dose and the surface density of the cargo. Copyright © 2016 Elsevier Inc. All rights reserved.

RSQRT: AN HEURISTIC FOR ESTIMATING THE NUMBER OF CLUSTERS TO REPORT.

PubMed

Carlis, John; Bruso, Kelsey

2012-03-01

Clustering can be a valuable tool for analyzing large datasets, such as in e-commerce applications. Anyone who clusters must choose how many item clusters, K, to report. Unfortunately, one must guess at K or some related parameter. Elsewhere we introduced a strongly-supported heuristic, RSQRT, which predicts K as a function of the attribute or item count, depending on attribute scales. We conducted a second analysis where we sought confirmation of the heuristic, analyzing data sets from theUCImachine learning benchmark repository. For the 25 studies where sufficient detail was available, we again found strong support. Also, in a side-by-side comparison of 28 studies, RSQRT best-predicted K and the Bayesian information criterion (BIC) predicted K are the same. RSQRT has a lower cost of O(log log n) versus O(n(2)) for BIC, and is more widely applicable. Using RSQRT prospectively could be much better than merely guessing.

RSQRT: AN HEURISTIC FOR ESTIMATING THE NUMBER OF CLUSTERS TO REPORT

PubMed Central

Bruso, Kelsey

2012-01-01

Clustering can be a valuable tool for analyzing large datasets, such as in e-commerce applications. Anyone who clusters must choose how many item clusters, K, to report. Unfortunately, one must guess at K or some related parameter. Elsewhere we introduced a strongly-supported heuristic, RSQRT, which predicts K as a function of the attribute or item count, depending on attribute scales. We conducted a second analysis where we sought confirmation of the heuristic, analyzing data sets from theUCImachine learning benchmark repository. For the 25 studies where sufficient detail was available, we again found strong support. Also, in a side-by-side comparison of 28 studies, RSQRT best-predicted K and the Bayesian information criterion (BIC) predicted K are the same. RSQRT has a lower cost of O(log log n) versus O(n2) for BIC, and is more widely applicable. Using RSQRT prospectively could be much better than merely guessing. PMID:22773923

Performance Comparison of Mainframe, Workstations, Clusters, and Desktop Computers

NASA Technical Reports Server (NTRS)

Farley, Douglas L.

2005-01-01

A performance evaluation of a variety of computers frequently found in a scientific or engineering research environment was conducted using a synthetic and application program benchmarks. From a performance perspective, emerging commodity processors have superior performance relative to legacy mainframe computers. In many cases, the PC clusters exhibited comparable performance with traditional mainframe hardware when 8-12 processors were used. The main advantage of the PC clusters was related to their cost. Regardless of whether the clusters were built from new computers or whether they were created from retired computers their performance to cost ratio was superior to the legacy mainframe computers. Finally, the typical annual maintenance cost of legacy mainframe computers is several times the cost of new equipment such as multiprocessor PC workstations. The savings from eliminating the annual maintenance fee on legacy hardware can result in a yearly increase in total computational capability for an organization.

An international land-biosphere model benchmarking activity for the IPCC Fifth Assessment Report (AR5)

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

Hoffman, Forrest M; Randerson, James T; Thornton, Peter E

2009-12-01

The need to capture important climate feedbacks in general circulation models (GCMs) has resulted in efforts to include atmospheric chemistry and land and ocean biogeochemistry into the next generation of production climate models, called Earth System Models (ESMs). While many terrestrial and ocean carbon models have been coupled to GCMs, recent work has shown that such models can yield a wide range of results (Friedlingstein et al., 2006). This work suggests that a more rigorous set of global offline and partially coupled experiments, along with detailed analyses of processes and comparisons with measurements, are needed. The Carbon-Land Model Intercomparison Projectmore » (C-LAMP) was designed to meet this need by providing a simulation protocol and model performance metrics based upon comparisons against best-available satellite- and ground-based measurements (Hoffman et al., 2007). Recently, a similar effort in Europe, called the International Land Model Benchmark (ILAMB) Project, was begun to assess the performance of European land surface models. These two projects will now serve as prototypes for a proposed international land-biosphere model benchmarking activity for those models participating in the IPCC Fifth Assessment Report (AR5). Initially used for model validation for terrestrial biogeochemistry models in the NCAR Community Land Model (CLM), C-LAMP incorporates a simulation protocol for both offline and partially coupled simulations using a prescribed historical trajectory of atmospheric CO2 concentrations. Models are confronted with data through comparisons against AmeriFlux site measurements, MODIS satellite observations, NOAA Globalview flask records, TRANSCOM inversions, and Free Air CO2 Enrichment (FACE) site measurements. Both sets of experiments have been performed using two different terrestrial biogeochemistry modules coupled to the CLM version 3 in the Community Climate System Model version 3 (CCSM3): the CASA model of Fung, et al., and the carbon-nitrogen (CN) model of Thornton. Comparisons of the CLM3 offline results against observational datasets have been performed and are described in Randerson et al. (2009). CLM version 4 has been evaluated using C-LAMP, showing improvement in many of the metrics. Efforts are now underway to initiate a Nitrogen-Land Model Intercomparison Project (N-LAMP) to better constrain the effects of the nitrogen cycle in biosphere models. Presented will be new results from C-LAMP for CLM4, initial N-LAMP developments, and the proposed land-biosphere model benchmarking activity.« less

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics

NASA Astrophysics Data System (ADS)

Ünal, Aslı; Bozkaya, Uǧur

2018-03-01

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol-1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol-1. Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol-1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Anionic water pentamer and hexamer clusters: An extensive study of structures and energetics.

PubMed

Ünal, Aslı; Bozkaya, Uğur

2018-03-28

An extensive study of structures and energetics for anionic pentamer and hexamer clusters is performed employing high level ab initio quantum chemical methods, such as the density-fitted orbital-optimized linearized coupled-cluster doubles (DF-OLCCD), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods. In this study, sixteen anionic pentamer clusters and eighteen anionic hexamer clusters are reported. Relative, binding, and vertical detachment energies (VDE) are presented at the complete basis set limit (CBS), extrapolating energies of aug4-cc-pVTZ and aug4-cc-pVQZ custom basis sets. The largest VDE values obtained at the CCSD(T)/CBS level are 9.9 and 11.2 kcal mol -1 for pentamers and hexamers, respectively, which are in very good agreement with the experimental values of 9.5 and 11.1 kcal mol -1 . Our binding energy results, at the CCSD(T)/CBS level, indicate strong bindings in anionic clusters due to hydrogen bond interactions. The average binding energy per water molecules is -5.0 and -5.3 kcal mol -1 for pentamers and hexamers, respectively. Furthermore, our results demonstrate that the DF-OLCCD method approaches to the CCSD(T) quality for anionic clusters. The inexpensive analytic gradients of DF-OLCCD compared to CCSD or CCSD(T) make it very attractive for high-accuracy studies.

Experimental observation of chimera and cluster states in a minimal globally coupled network

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

2016-09-01

A "chimera state" is a dynamical pattern that occurs in a network of coupled identical oscillators when the symmetry of the oscillator population is broken into synchronous and asynchronous parts. We report the experimental observation of chimera and cluster states in a network of four globally coupled chaotic opto-electronic oscillators. This is the minimal network that can support chimera states, and our study provides new insight into the fundamental mechanisms underlying their formation. We use a unified approach to determine the stability of all the observed partially synchronous patterns, highlighting the close relationship between chimera and cluster states as belonging to the broader phenomenon of partial synchronization. Our approach is general in terms of network size and connectivity. We also find that chimera states often appear in regions of multistability between global, cluster, and desynchronized states.

RELAP5-3D Results for Phase I (Exercise 2) of the OECD/NEA MHTGR-350 MW Benchmark

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

Gerhard Strydom

2012-06-01

The coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D has recently been initiated at the Idaho National Laboratory (INL) to provide a fully coupled prismatic Very High Temperature Reactor (VHTR) system modeling capability as part of the NGNP methods development program. The PHISICS code consists of three modules: INSTANT (performing 3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and a perturbation/mixer module. As part of the verification and validation activities, steady state results have been obtained for Exercise 2 of Phase I of the newly-defined OECD/NEA MHTGR-350 MW Benchmark. This exercise requiresmore » participants to calculate a steady-state solution for an End of Equilibrium Cycle 350 MW Modular High Temperature Reactor (MHTGR), using the provided geometry, material, and coolant bypass flow description. The paper provides an overview of the MHTGR Benchmark and presents typical steady state results (e.g. solid and gas temperatures, thermal conductivities) for Phase I Exercise 2. Preliminary results are also provided for the early test phase of Exercise 3 using a two-group cross-section library and the Relap5-3D model developed for Exercise 2.« less

RELAP5-3D results for phase I (Exercise 2) of the OECD/NEA MHTGR-350 MW benchmark

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

Strydom, G.; Epiney, A. S.

2012-07-01

The coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D has recently been initiated at the Idaho National Laboratory (INL) to provide a fully coupled prismatic Very High Temperature Reactor (VHTR) system modeling capability as part of the NGNP methods development program. The PHISICS code consists of three modules: INSTANT (performing 3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and a perturbation/mixer module. As part of the verification and validation activities, steady state results have been obtained for Exercise 2 of Phase I of the newly-defined OECD/NEA MHTGR-350 MW Benchmark. This exercise requiresmore » participants to calculate a steady-state solution for an End of Equilibrium Cycle 350 MW Modular High Temperature Reactor (MHTGR), using the provided geometry, material, and coolant bypass flow description. The paper provides an overview of the MHTGR Benchmark and presents typical steady state results (e.g. solid and gas temperatures, thermal conductivities) for Phase I Exercise 2. Preliminary results are also provided for the early test phase of Exercise 3 using a two-group cross-section library and the Relap5-3D model developed for Exercise 2. (authors)« less

Cluster dynamics of pulse coupled oscillators

NASA Astrophysics Data System (ADS)

O'Keeffe, Kevin; Strogatz, Steven; Krapivsky, Paul

2015-03-01

We study the dynamics of networks of pulse coupled oscillators. Much attention has been devoted to the ultimate fate of the system: which conditions lead to a steady state in which all the oscillators are firing synchronously. But little is known about how synchrony builds up from an initially incoherent state. The current work addresses this question. Oscillators start to synchronize by forming clusters of different sizes that fire in unison. First pairs of oscillators, then triplets and so on. These clusters progressively grow by coalescing with others, eventually resulting in the fully synchronized state. We study the mean field model in which the coupling between oscillators is all to all. We use probabilistic arguments to derive a recursive set of evolution equations for these clusters. Using a generating function formalism, we derive simple equations for the moments of these clusters. Our results are in good agreement simulation. We then numerically explore the effects of non-trivial connectivity. Our results have potential application to ultra-low power ``impulse radio'' & sensor networks.

Weak and strong coupling equilibration in nonabelian gauge theories

NASA Astrophysics Data System (ADS)

Keegan, Liam; Kurkela, Aleksi; Romatschke, Paul; van der Schee, Wilke; Zhu, Yan

2016-04-01

We present a direct comparison studying equilibration through kinetic theory at weak coupling and through holography at strong coupling in the same set-up. The set-up starts with a homogeneous thermal state, which then smoothly transitions through an out-of-equilibrium phase to an expanding system undergoing boost-invariant flow. This first apples-to-apples comparison of equilibration provides a benchmark for similar equilibration processes in heavy-ion collisions, where the equilibration mechanism is still under debate. We find that results at weak and strong coupling can be smoothly connected by simple, empirical power-laws for the viscosity, equilibration time and entropy production of the system.

On the accuracy of density functional theory and wave function methods for calculating vertical ionization energies

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

McKechnie, Scott; Booth, George H.; Cohen, Aron J.

The best practice in computational methods for determining vertical ionization energies (VIEs) is assessed, via reference to experimentally determined VIEs that are corroborated by highly accurate coupled-cluster calculations. These reference values are used to benchmark the performance of density-functional theory (DFT) and wave function methods: Hartree-Fock theory (HF), second-order Møller-Plesset perturbation theory (MP2) and Electron Propagator Theory (EPT). The core test set consists of 147 small molecules. An extended set of six larger molecules, from benzene to hexacene, is also considered to investigate the dependence of the results on molecule size. The closest agreement with experiment is found for ionizationmore » energies obtained from total energy diff calculations. In particular, DFT calculations using exchange-correlation functionals with either a large amount of exact exchange or long-range correction perform best. The results from these functionals are also the least sensitive to an increase in molecule size. In general, ionization energies calculated directly from the orbital energies of the neutral species are less accurate and more sensitive to an increase in molecule size. For the single-calculation approach, the EPT calculations are in closest agreement for both sets of molecules. For the orbital energies from DFT functionals, only those with long-range correction give quantitative agreement with dramatic failing for all other functionals considered. The results offer a practical hierarchy of approximations for the calculation of vertical ionization energies. In addition, the experimental and computational reference values can be used as a standardized set of benchmarks, against which other approximate methods can be compared.« less

Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods

NASA Astrophysics Data System (ADS)

Christensen, Anders S.; Kromann, Jimmy C.; Jensen, Jan H.; Cui, Qiang

2017-10-01

To facilitate further development of approximate quantum mechanical methods for condensed phase applications, we present a new benchmark dataset of intermolecular interaction energies in the solution phase for a set of 15 dimers, each containing one charged monomer. The reference interaction energy in solution is computed via a thermodynamic cycle that integrates dimer binding energy in the gas phase at the coupled cluster level and solute-solvent interaction with density functional theory; the estimated uncertainty of such calculated interaction energy is ±1.5 kcal/mol. The dataset is used to benchmark the performance of a set of semi-empirical quantum mechanical (SQM) methods that include DFTB3-D3, DFTB3/CPE-D3, OM2-D3, PM6-D3, PM6-D3H+, and PM7 as well as the HF-3c method. We find that while all tested SQM methods tend to underestimate binding energies in the gas phase with a root-mean-squared error (RMSE) of 2-5 kcal/mol, they overestimate binding energies in the solution phase with an RMSE of 3-4 kcal/mol, with the exception of DFTB3/CPE-D3 and OM2-D3, for which the systematic deviation is less pronounced. In addition, we find that HF-3c systematically overestimates binding energies in both gas and solution phases. As most approximate QM methods are parametrized and evaluated using data measured or calculated in the gas phase, the dataset represents an important first step toward calibrating QM based methods for application in the condensed phase where polarization and exchange repulsion need to be treated in a balanced fashion.

a Protocol for High-Accuracy Theoretical Thermochemistry

NASA Astrophysics Data System (ADS)

Welch, Bradley; Dawes, Richard

2017-06-01

Theoretical studies of spectroscopy and reaction dynamics including the necessary development of potential energy surfaces rely on accurate thermochemical information. The Active Thermochemical Tables (ATcT) approach by Ruscic^{1} incorporates data for a large number of chemical species from a variety of sources (both experimental and theoretical) and derives a self-consistent network capable of making extremely accurate estimates of quantities such as temperature dependent enthalpies of formation. The network provides rigorous uncertainties, and since the values don't rely on a single measurement or calculation, the provenance of each quantity is also obtained. To expand and improve the network it is desirable to have a reliable protocol such as the HEAT approach^{2} for calculating accurate theoretical data. Here we present and benchmark an approach based on explicitly-correlated coupled-cluster theory and vibrational perturbation theory (VPT2). Methyldioxy and Methyl Hydroperoxide are important and well-characterized species in combustion processes and begin the family of (ethyl-, propyl-based, etc) similar compounds (much less is known about the larger members). Accurate anharmonic frequencies are essential to accurately describe even the 0 K enthalpies of formation, but are especially important for finite temperature studies. Here we benchmark the spectroscopic and thermochemical accuracy of the approach, comparing with available data for the smallest systems, and comment on the outlook for larger systems that are less well-known and characterized. ^{1}B. Ruscic, Active Thermochemical Tables (ATcT) values based on ver. 1.118 of the Thermochemical Network (2015); available at ATcT.anl.gov ^{2}A. Tajti, P. G. Szalay, A. G. Császár, M. Kállay, J. Gauss, E. F. Valeev, B. A. Flowers, J. Vázquez, and J. F. Stanton. JCP 121, (2004): 11599.

A suite of benchmark and challenge problems for enhanced geothermal systems

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

White, Mark; Fu, Pengcheng; McClure, Mark

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulation capabilitiesmore » to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: 1) reservoir creation/stimulation, 2) reactive and passive transport, and 3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners. We present the suite of benchmark and challenge problems developed for the GTO-CCS, providing problem descriptions and sample solutions.« less

A scan statistic for binary outcome based on hypergeometric probability model, with an application to detecting spatial clusters of Japanese encephalitis.

PubMed

Zhao, Xing; Zhou, Xiao-Hua; Feng, Zijian; Guo, Pengfei; He, Hongyan; Zhang, Tao; Duan, Lei; Li, Xiaosong

2013-01-01

As a useful tool for geographical cluster detection of events, the spatial scan statistic is widely applied in many fields and plays an increasingly important role. The classic version of the spatial scan statistic for the binary outcome is developed by Kulldorff, based on the Bernoulli or the Poisson probability model. In this paper, we apply the Hypergeometric probability model to construct the likelihood function under the null hypothesis. Compared with existing methods, the likelihood function under the null hypothesis is an alternative and indirect method to identify the potential cluster, and the test statistic is the extreme value of the likelihood function. Similar with Kulldorff's methods, we adopt Monte Carlo test for the test of significance. Both methods are applied for detecting spatial clusters of Japanese encephalitis in Sichuan province, China, in 2009, and the detected clusters are identical. Through a simulation to independent benchmark data, it is indicated that the test statistic based on the Hypergeometric model outweighs Kulldorff's statistics for clusters of high population density or large size; otherwise Kulldorff's statistics are superior.

Communication: Time-dependent optimized coupled-cluster method for multielectron dynamics

NASA Astrophysics Data System (ADS)

Sato, Takeshi; Pathak, Himadri; Orimo, Yuki; Ishikawa, Kenichi L.

2018-02-01

Time-dependent coupled-cluster method with time-varying orbital functions, called time-dependent optimized coupled-cluster (TD-OCC) method, is formulated for multielectron dynamics in an intense laser field. We have successfully derived the equations of motion for CC amplitudes and orthonormal orbital functions based on the real action functional, and implemented the method including double excitations (TD-OCCD) and double and triple excitations (TD-OCCDT) within the optimized active orbitals. The present method is size extensive and gauge invariant, a polynomial cost-scaling alternative to the time-dependent multiconfiguration self-consistent-field method. The first application of the TD-OCC method of intense-laser driven correlated electron dynamics in Ar atom is reported.

Communication: Time-dependent optimized coupled-cluster method for multielectron dynamics.

PubMed

Sato, Takeshi; Pathak, Himadri; Orimo, Yuki; Ishikawa, Kenichi L

2018-02-07

Time-dependent coupled-cluster method with time-varying orbital functions, called time-dependent optimized coupled-cluster (TD-OCC) method, is formulated for multielectron dynamics in an intense laser field. We have successfully derived the equations of motion for CC amplitudes and orthonormal orbital functions based on the real action functional, and implemented the method including double excitations (TD-OCCD) and double and triple excitations (TD-OCCDT) within the optimized active orbitals. The present method is size extensive and gauge invariant, a polynomial cost-scaling alternative to the time-dependent multiconfiguration self-consistent-field method. The first application of the TD-OCC method of intense-laser driven correlated electron dynamics in Ar atom is reported.

A self-consistent density based embedding scheme applied to the adsorption of CO on Pd(111)

NASA Astrophysics Data System (ADS)

Lahav, D.; Klüner, T.

2007-06-01

We derive a variant of a density based embedded cluster approach as an improvement to a recently proposed embedding theory for metallic substrates (Govind et al 1999 J. Chem. Phys. 110 7677; Klüner et al 2001 Phys. Rev. Lett. 86 5954). In this scheme, a local region in space is represented by a small cluster which is treated by accurate quantum chemical methodology. The interaction of the cluster with the infinite solid is taken into account by an effective one-electron embedding operator representing the surrounding region. We propose a self-consistent embedding scheme which resolves intrinsic problems of the former theory, in particular a violation of strict density conservation. The proposed scheme is applied to the well-known benchmark system CO/Pd(111).

Gluon and ghost correlation functions of 2-color QCD at finite density

NASA Astrophysics Data System (ADS)

Hajizadeh, Ouraman; Boz, Tamer; Maas, Axel; Skullerud, Jon-Ivar

2018-03-01

2-color QCD, i. e. QCD with the gauge group SU(2), is the simplest non-Abelian gauge theory without sign problem at finite quark density. Therefore its study on the lattice is a benchmark for other non-perturbative approaches at finite density. To provide such benchmarks we determine the minimal-Landau-gauge 2-point and 3-gluon correlation functions of the gauge sector and the running gauge coupling at finite density. We observe no significant effects, except for some low-momentum screening of the gluons at and above the supposed high-density phase transition.

A stable partitioned FSI algorithm for incompressible flow and deforming beams

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

Li, L., E-mail: lil19@rpi.edu; Henshaw, W.D., E-mail: henshw@rpi.edu; Banks, J.W., E-mail: banksj3@rpi.edu

2016-05-01

An added-mass partitioned (AMP) algorithm is described for solving fluid–structure interaction (FSI) problems coupling incompressible flows with thin elastic structures undergoing finite deformations. The new AMP scheme is fully second-order accurate and stable, without sub-time-step iterations, even for very light structures when added-mass effects are strong. The fluid, governed by the incompressible Navier–Stokes equations, is solved in velocity-pressure form using a fractional-step method; large deformations are treated with a mixed Eulerian-Lagrangian approach on deforming composite grids. The motion of the thin structure is governed by a generalized Euler–Bernoulli beam model, and these equations are solved in a Lagrangian frame usingmore » two approaches, one based on finite differences and the other on finite elements. The key AMP interface condition is a generalized Robin (mixed) condition on the fluid pressure. This condition, which is derived at a continuous level, has no adjustable parameters and is applied at the discrete level to couple the partitioned domain solvers. Special treatment of the AMP condition is required to couple the finite-element beam solver with the finite-difference-based fluid solver, and two coupling approaches are described. A normal-mode stability analysis is performed for a linearized model problem involving a beam separating two fluid domains, and it is shown that the AMP scheme is stable independent of the ratio of the mass of the fluid to that of the structure. A traditional partitioned (TP) scheme using a Dirichlet–Neumann coupling for the same model problem is shown to be unconditionally unstable if the added mass of the fluid is too large. A series of benchmark problems of increasing complexity are considered to illustrate the behavior of the AMP algorithm, and to compare the behavior with that of the TP scheme. The results of all these benchmark problems verify the stability and accuracy of the AMP scheme. Results for one benchmark problem modeling blood flow in a deforming artery are also compared with corresponding results available in the literature.« less

Concordance of transcriptional and apical benchmark dose levels for conazole-induced liver effects in mice.

PubMed

Bhat, Virunya S; Hester, Susan D; Nesnow, Stephen; Eastmond, David A

2013-11-01

The ability to anchor chemical class-based gene expression changes to phenotypic lesions and to describe these changes as a function of dose and time informs mode-of-action determinations and improves quantitative risk assessments. Previous global expression profiling identified a 330-probe cluster differentially expressed and commonly responsive to 3 hepatotumorigenic conazoles (cyproconazole, epoxiconazole, and propiconazole) at 30 days. Extended to 2 more conazoles (triadimefon and myclobutanil), the present assessment encompasses 4 tumorigenic and 1 nontumorigenic conazole. Transcriptional benchmark dose levels (BMDL(T)) were estimated for a subset of the cluster with dose-responsive behavior and a ≥ 5-fold increase or decrease in signal intensity at the highest dose. These genes primarily encompassed CAR/RXR activation, P450 metabolism, liver hypertrophy- glutathione depletion, LPS/IL-1-mediated inhibition of RXR, and NRF2-mediated oxidative stress pathways. Median BMDL(T) estimates from the subset were concordant (within a factor of 2.4) with apical benchmark doses (BMDL(A)) for increased liver weight at 30 days for the 5 conazoles. The 30-day median BMDL(T) estimates were within one-half order of magnitude of the chronic BMDLA for hepatocellular tumors. Potency differences seen in the dose-responsive transcription of certain phase II metabolism, bile acid detoxification, and lipid oxidation genes mirrored each conazole's tumorigenic potency. The 30-day BMDL(T) corresponded to tumorigenic potency on a milligram per kilogram day basis with cyproconazole > epoxiconazole > propiconazole > triadimefon > myclobutanil (nontumorigenic). These results support the utility of measuring short-term gene expression changes to inform quantitative risk assessments from long-term exposures.

Grid Computing Environment using a Beowulf Cluster

NASA Astrophysics Data System (ADS)

Alanis, Fransisco; Mahmood, Akhtar

2003-10-01

Custom-made Beowulf clusters using PCs are currently replacing expensive supercomputers to carry out complex scientific computations. At the University of Texas - Pan American, we built a 8 Gflops Beowulf Cluster for doing HEP research using RedHat Linux 7.3 and the LAM-MPI middleware. We will describe how we built and configured our Cluster, which we have named the Sphinx Beowulf Cluster. We will describe the results of our cluster benchmark studies and the run-time plots of several parallel application codes that were compiled in C on the cluster using the LAM-XMPI graphics user environment. We will demonstrate a "simple" prototype grid environment, where we will submit and run parallel jobs remotely across multiple cluster nodes over the internet from the presentation room at Texas Tech. University. The Sphinx Beowulf Cluster will be used for monte-carlo grid test-bed studies for the LHC-ATLAS high energy physics experiment. Grid is a new IT concept for the next generation of the "Super Internet" for high-performance computing. The Grid will allow scientist worldwide to view and analyze huge amounts of data flowing from the large-scale experiments in High Energy Physics. The Grid is expected to bring together geographically and organizationally dispersed computational resources, such as CPUs, storage systems, communication systems, and data sources.

Coupled multipolar interactions in small-particle metallic clusters.

PubMed

Pustovit, Vitaly N; Sotelo, Juan A; Niklasson, Gunnar A

2002-03-01

We propose a new formalism for computing the optical properties of small clusters of particles. It is a generalization of the coupled dipole-dipole particle-interaction model and allows one in principle to take into account all multipolar interactions in the long-wavelength limit. The method is illustrated by computations of the optical properties of N = 6 particle clusters for different multipolar approximations. We examine the effect of separation between particles and compare the optical spectra with the discrete-dipole approximation and the generalized Mie theory.

Analyzing the errors of DFT approximations for compressed water systems

NASA Astrophysics Data System (ADS)

Alfè, D.; Bartók, A. P.; Csányi, G.; Gillan, M. J.

2014-07-01

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm3 where the experimental pressure is 15 kilobars; second, thermal samples of compressed water clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mEh ≃ 15 meV/monomer for the liquid and the clusters.

Analyzing the errors of DFT approximations for compressed water systems

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

Alfè, D.; London Centre for Nanotechnology, UCL, London WC1H 0AH; Thomas Young Centre, UCL, London WC1H 0AH

We report an extensive study of the errors of density functional theory (DFT) approximations for compressed water systems. The approximations studied are based on the widely used PBE and BLYP exchange-correlation functionals, and we characterize their errors before and after correction for 1- and 2-body errors, the corrections being performed using the methods of Gaussian approximation potentials. The errors of the uncorrected and corrected approximations are investigated for two related types of water system: first, the compressed liquid at temperature 420 K and density 1.245 g/cm{sup 3} where the experimental pressure is 15 kilobars; second, thermal samples of compressed watermore » clusters from the trimer to the 27-mer. For the liquid, we report four first-principles molecular dynamics simulations, two generated with the uncorrected PBE and BLYP approximations and a further two with their 1- and 2-body corrected counterparts. The errors of the simulations are characterized by comparing with experimental data for the pressure, with neutron-diffraction data for the three radial distribution functions, and with quantum Monte Carlo (QMC) benchmarks for the energies of sets of configurations of the liquid in periodic boundary conditions. The DFT errors of the configuration samples of compressed water clusters are computed using QMC benchmarks. We find that the 2-body and beyond-2-body errors in the liquid are closely related to similar errors exhibited by the clusters. For both the liquid and the clusters, beyond-2-body errors of DFT make a substantial contribution to the overall errors, so that correction for 1- and 2-body errors does not suffice to give a satisfactory description. For BLYP, a recent representation of 3-body energies due to Medders, Babin, and Paesani [J. Chem. Theory Comput. 9, 1103 (2013)] gives a reasonably good way of correcting for beyond-2-body errors, after which the remaining errors are typically 0.5 mE{sub h} ≃ 15 meV/monomer for the liquid and the clusters.« less

Novel probabilistic neuroclassifier

NASA Astrophysics Data System (ADS)

Hong, Jiang; Serpen, Gursel

2003-09-01

A novel probabilistic potential function neural network classifier algorithm to deal with classes which are multi-modally distributed and formed from sets of disjoint pattern clusters is proposed in this paper. The proposed classifier has a number of desirable properties which distinguish it from other neural network classifiers. A complete description of the algorithm in terms of its architecture and the pseudocode is presented. Simulation analysis of the newly proposed neuro-classifier algorithm on a set of benchmark problems is presented. Benchmark problems tested include IRIS, Sonar, Vowel Recognition, Two-Spiral, Wisconsin Breast Cancer, Cleveland Heart Disease and Thyroid Gland Disease. Simulation results indicate that the proposed neuro-classifier performs consistently better for a subset of problems for which other neural classifiers perform relatively poorly.

Symmetry, Hopf bifurcation, and the emergence of cluster solutions in time delayed neural networks.

PubMed

Wang, Zhen; Campbell, Sue Ann

2017-11-01

We consider the networks of N identical oscillators with time delayed, global circulant coupling, modeled by a system of delay differential equations with Z N symmetry. We first study the existence of Hopf bifurcations induced by the coupling time delay and then use symmetric Hopf bifurcation theory to determine how these bifurcations lead to different patterns of symmetric cluster oscillations. We apply our results to a case study: a network of FitzHugh-Nagumo neurons with diffusive coupling. For this model, we derive the asymptotic stability, global asymptotic stability, absolute instability, and stability switches of the equilibrium point in the plane of coupling time delay (τ) and excitability parameter (a). We investigate the patterns of cluster oscillations induced by the time delay and determine the direction and stability of the bifurcating periodic orbits by employing the multiple timescales method and normal form theory. We find that in the region where stability switching occurs, the dynamics of the system can be switched from the equilibrium point to any symmetric cluster oscillation, and back to equilibrium point as the time delay is increased.

Chimeras and clusters in networks of hyperbolic chaotic oscillators

NASA Astrophysics Data System (ADS)

Cano, A. V.; Cosenza, M. G.

2017-03-01

We show that chimera states, where differentiated subsets of synchronized and desynchronized dynamical elements coexist, can emerge in networks of hyperbolic chaotic oscillators subject to global interactions. As local dynamics we employ Lozi maps, which possess hyperbolic chaotic attractors. We consider a globally coupled system of these maps and use two statistical quantities to describe its collective behavior: the average fraction of elements belonging to clusters and the average standard deviation of state variables. Chimera states, clusters, complete synchronization, and incoherence are thus characterized on the space of parameters of the system. We find that chimera states are related to the formation of clusters in the system. In addition, we show that chimera states arise for a sufficiently long range of interactions in nonlocally coupled networks of these maps. Our results reveal that, under some circumstances, hyperbolicity does not impede the formation of chimera states in networks of coupled chaotic systems, as it had been previously hypothesized.

Experimental observation of chimera and cluster states in a minimal globally coupled network

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

Hart, Joseph D.; Department of Physics, University of Maryland, College Park, Maryland 20742; Bansal, Kanika

A “chimera state” is a dynamical pattern that occurs in a network of coupled identical oscillators when the symmetry of the oscillator population is broken into synchronous and asynchronous parts. We report the experimental observation of chimera and cluster states in a network of four globally coupled chaotic opto-electronic oscillators. This is the minimal network that can support chimera states, and our study provides new insight into the fundamental mechanisms underlying their formation. We use a unified approach to determine the stability of all the observed partially synchronous patterns, highlighting the close relationship between chimera and cluster states as belongingmore » to the broader phenomenon of partial synchronization. Our approach is general in terms of network size and connectivity. We also find that chimera states often appear in regions of multistability between global, cluster, and desynchronized states.« less

A hybridizable discontinuous Galerkin method for modeling fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-12-01

This work presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid-structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian-Eulerian Navier-Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modeling is coupling together their disparate mathematics on the fluid-solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.

A hybridizable discontinuous Galerkin method for modeling fluid–structure interaction

DOE PAGES

Sheldon, Jason P.; Miller, Scott T.; Pitt, Jonathan S.

2016-08-31

This study presents a novel application of the hybridizable discontinuous Galerkin (HDG) finite element method to the multi-physics simulation of coupled fluid–structure interaction (FSI) problems. Recent applications of the HDG method have primarily been for single-physics problems including both solids and fluids, which are necessary building blocks for FSI modeling. Utilizing these established models, HDG formulations for linear elastostatics, a nonlinear elastodynamic model, and arbitrary Lagrangian–Eulerian Navier–Stokes are derived. The elasticity formulations are written in a Lagrangian reference frame, with the nonlinear formulation restricted to hyperelastic materials. With these individual solid and fluid formulations, the remaining challenge in FSI modelingmore » is coupling together their disparate mathematics on the fluid–solid interface. This coupling is presented, along with the resultant HDG FSI formulation. Verification of the component models, through the method of manufactured solutions, is performed and each model is shown to converge at the expected rate. The individual components, along with the complete FSI model, are then compared to the benchmark problems proposed by Turek and Hron [1]. The solutions from the HDG formulation presented in this work trend towards the benchmark as the spatial polynomial order and the temporal order of integration are increased.« less

Highly anisotropic exchange interactions in a trigonal bipyramidal cyanide-bridged Ni(II)3Os(III)2 cluster.

PubMed

Palii, Andrei V; Reu, Oleg S; Ostrovsky, Sergei M; Klokishner, Sophia I; Tsukerblat, Boris S; Hilfiger, Matthew; Shatruk, Michael; Prosvirin, Andrey; Dunbar, Kim R

2009-06-25

This article is a part of our efforts to control the magnetic anisotropy in cyanide-based exchange-coupled systems with the eventual goal to obtain single-molecule magnets with higher blocking temperatures. We give the theoretical interpretation of the magnetic properties of the new pentanuclear complex {[Ni(II)(tmphen)(2)](3)[Os(III)(CN)(6)](2)} x 6 CH(3)CN (Ni(II)(3)Os(III)(2) cluster). Because the system contains the heavy Os(III) ions, spin-orbit coupling considerably exceeds the contributions from the low-symmetry crystal field and exchange coupling. The magnetic properties of the Ni(II)(3)Os(III)(2) cluster are described in the framework of a highly anisotropic pseudo-spin Hamiltonian that corresponds to the limit of strong spin-orbital coupling and takes into account the complex molecular structure. The model provides a good fit to the experimental data and allows the conclusion that the trigonal axis of the bipyramidal Ni(II)(3)Os(III)(2) cluster is a hard axis of magnetization. This explains the fact that in contrast with the isostructural trigonal bipyramidal Mn(III)(2)Mn(II)(3) cluster, the Ni(II)(3)Os(III)(2) system does not exhibit the single-molecule magnetic behavior.

Localized Ambient Solidity Separation Algorithm Based Computer User Segmentation.

PubMed

Sun, Xiao; Zhang, Tongda; Chai, Yueting; Liu, Yi

2015-01-01

Most of popular clustering methods typically have some strong assumptions of the dataset. For example, the k-means implicitly assumes that all clusters come from spherical Gaussian distributions which have different means but the same covariance. However, when dealing with datasets that have diverse distribution shapes or high dimensionality, these assumptions might not be valid anymore. In order to overcome this weakness, we proposed a new clustering algorithm named localized ambient solidity separation (LASS) algorithm, using a new isolation criterion called centroid distance. Compared with other density based isolation criteria, our proposed centroid distance isolation criterion addresses the problem caused by high dimensionality and varying density. The experiment on a designed two-dimensional benchmark dataset shows that our proposed LASS algorithm not only inherits the advantage of the original dissimilarity increments clustering method to separate naturally isolated clusters but also can identify the clusters which are adjacent, overlapping, and under background noise. Finally, we compared our LASS algorithm with the dissimilarity increments clustering method on a massive computer user dataset with over two million records that contains demographic and behaviors information. The results show that LASS algorithm works extremely well on this computer user dataset and can gain more knowledge from it.

Localized Ambient Solidity Separation Algorithm Based Computer User Segmentation

PubMed Central

Sun, Xiao; Zhang, Tongda; Chai, Yueting; Liu, Yi

2015-01-01

Most of popular clustering methods typically have some strong assumptions of the dataset. For example, the k-means implicitly assumes that all clusters come from spherical Gaussian distributions which have different means but the same covariance. However, when dealing with datasets that have diverse distribution shapes or high dimensionality, these assumptions might not be valid anymore. In order to overcome this weakness, we proposed a new clustering algorithm named localized ambient solidity separation (LASS) algorithm, using a new isolation criterion called centroid distance. Compared with other density based isolation criteria, our proposed centroid distance isolation criterion addresses the problem caused by high dimensionality and varying density. The experiment on a designed two-dimensional benchmark dataset shows that our proposed LASS algorithm not only inherits the advantage of the original dissimilarity increments clustering method to separate naturally isolated clusters but also can identify the clusters which are adjacent, overlapping, and under background noise. Finally, we compared our LASS algorithm with the dissimilarity increments clustering method on a massive computer user dataset with over two million records that contains demographic and behaviors information. The results show that LASS algorithm works extremely well on this computer user dataset and can gain more knowledge from it. PMID:26221133

A clustering algorithm for determining community structure in complex networks

NASA Astrophysics Data System (ADS)

Jin, Hong; Yu, Wei; Li, ShiJun

2018-02-01

Clustering algorithms are attractive for the task of community detection in complex networks. DENCLUE is a representative density based clustering algorithm which has a firm mathematical basis and good clustering properties allowing for arbitrarily shaped clusters in high dimensional datasets. However, this method cannot be directly applied to community discovering due to its inability to deal with network data. Moreover, it requires a careful selection of the density parameter and the noise threshold. To solve these issues, a new community detection method is proposed in this paper. First, we use a spectral analysis technique to map the network data into a low dimensional Euclidean Space which can preserve node structural characteristics. Then, DENCLUE is applied to detect the communities in the network. A mathematical method named Sheather-Jones plug-in is chosen to select the density parameter which can describe the intrinsic clustering structure accurately. Moreover, every node on the network is meaningful so there were no noise nodes as a result the noise threshold can be ignored. We test our algorithm on both benchmark and real-life networks, and the results demonstrate the effectiveness of our algorithm over other popularity density based clustering algorithms adopted to community detection.

Development and Application of a Parallel LCAO Cluster Method

NASA Astrophysics Data System (ADS)

Patton, David C.

1997-08-01

CPU intensive steps in the SCF electronic structure calculations of clusters and molecules with a first-principles LCAO method have been fully parallelized via a message passing paradigm. Identification of the parts of the code that are composed of many independent compute-intensive steps is discussed in detail as they are the most readily parallelized. Most of the parallelization involves spatially decomposing numerical operations on a mesh. One exception is the solution of Poisson's equation which relies on distribution of the charge density and multipole methods. The method we use to parallelize this part of the calculation is quite novel and is covered in detail. We present a general method for dynamically load-balancing a parallel calculation and discuss how we use this method in our code. The results of benchmark calculations of the IR and Raman spectra of PAH molecules such as anthracene (C_14H_10) and tetracene (C_18H_12) are presented. These benchmark calculations were performed on an IBM SP2 and a SUN Ultra HPC server with both MPI and PVM. Scalability and speedup for these calculations is analyzed to determine the efficiency of the code. In addition, performance and usage issues for MPI and PVM are presented.

Verification and benchmark testing of the NUFT computer code

NASA Astrophysics Data System (ADS)

Lee, K. H.; Nitao, J. J.; Kulshrestha, A.

1993-10-01

This interim report presents results of work completed in the ongoing verification and benchmark testing of the NUFT (Nonisothermal Unsaturated-saturated Flow and Transport) computer code. NUFT is a suite of multiphase, multicomponent models for numerical solution of thermal and isothermal flow and transport in porous media, with application to subsurface contaminant transport problems. The code simulates the coupled transport of heat, fluids, and chemical components, including volatile organic compounds. Grid systems may be cartesian or cylindrical, with one-, two-, or fully three-dimensional configurations possible. In this initial phase of testing, the NUFT code was used to solve seven one-dimensional unsaturated flow and heat transfer problems. Three verification and four benchmarking problems were solved. In the verification testing, excellent agreement was observed between NUFT results and the analytical or quasianalytical solutions. In the benchmark testing, results of code intercomparison were very satisfactory. From these testing results, it is concluded that the NUFT code is ready for application to field and laboratory problems similar to those addressed here. Multidimensional problems, including those dealing with chemical transport, will be addressed in a subsequent report.

Benchmarking NNWSI flow and transport codes: COVE 1 results

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

Hayden, N.K.

1985-06-01

The code verification (COVE) activity of the Nevada Nuclear Waste Storage Investigations (NNWSI) Project is the first step in certification of flow and transport codes used for NNWSI performance assessments of a geologic repository for disposing of high-level radioactive wastes. The goals of the COVE activity are (1) to demonstrate and compare the numerical accuracy and sensitivity of certain codes, (2) to identify and resolve problems in running typical NNWSI performance assessment calculations, and (3) to evaluate computer requirements for running the codes. This report describes the work done for COVE 1, the first step in benchmarking some of themore » codes. Isothermal calculations for the COVE 1 benchmarking have been completed using the hydrologic flow codes SAGUARO, TRUST, and GWVIP; the radionuclide transport codes FEMTRAN and TRUMP; and the coupled flow and transport code TRACR3D. This report presents the results of three cases of the benchmarking problem solved for COVE 1, a comparison of the results, questions raised regarding sensitivities to modeling techniques, and conclusions drawn regarding the status and numerical sensitivities of the codes. 30 refs.« less

Magnetic exchange couplings from noncollinear perturbation theory: dinuclear CuII complexes.

PubMed

Phillips, Jordan J; Peralta, Juan E

2014-08-07

To benchmark the performance of a new method based on noncollinear coupled-perturbed density functional theory [J. Chem. Phys. 138, 174115 (2013)], we calculate the magnetic exchange couplings in a series of triply bridged ferromagnetic dinuclear Cu(II) complexes that have been recently synthesized [Phys. Chem. Chem. Phys. 15, 1966 (2013)]. We find that for any basis-set the couplings from our noncollinear coupled-perturbed methodology are practically identical to those of spin-projected energy-differences when a hybrid density functional approximation is employed. This demonstrates that our methodology properly recovers a Heisenberg description for these systems, and is robust in its predictive power of magnetic couplings. Furthermore, this indicates that the failure of density functional theory to capture the subtle variation of the exchange couplings in these complexes is not simply an artifact of broken-symmetry methods, but rather a fundamental weakness of current approximate density functionals for the description of magnetic couplings.

Exchange coupling transformations in Cu (II) heterospin complexes of “breathing crystals” under structural phase transitions

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

Morozov, Vitaly A.; Petrova, Marina V.; Lukzen, Nikita N., E-mail: luk@tomo.nsc.ru

2015-08-15

Family of “breathing crystals” is the polymer-chain complexes of Cu(hfac){sub 2} with nitroxides. The polymer chains consist of one-, two- or three-spin clusters. The “breathing crystals” experience simultaneous magnetic and Jahn-Teller type structural phase transitions with change of total cluster spin and drastic change of bond lengths (ca. 10-12%). For the first time the intra-cluster magnetic couplings in ”breathing crystals” have been calculated both by band structure methods GGA + U and hybrid DFT (B3LYP and PBE0) for the isolated exchange clusters. The temperature dependence of the magnetic coupling constant was calculated for two polymer-chain compounds of the “breathing crystal”more » family - C{sub 21}H{sub 19}CuF{sub 12}N{sub 4}O{sub 6} with the chains containing two-spin clusters and C{sub 22}H{sub 21}CuF{sub 12}N{sub 4}O{sub 6} with the chains of alternating three-spin clusters and one-spin sites. It was found that adding a Hubbard-like parameter not only to the copper 3d electrons but also to the oxygen 2p electrons (GGA + U{sub d} + U{sub p} approach) results in an improved description of exchange coupling in the “breathing crystal” compounds. At the same time treatment of the isolated clusters by a large basis hybrid DFT with high computational cost provides a similar quality fit of the experimental magneto-chemical data as that for the GGA + U{sub d} + U{sub p} band structure calculation scheme. Our calculations also showed that in spite of the abrupt transformation of the magnetic coupling constant under the phase transition, the band gap in the “breathing crystals” remains about the same value with temperature decrease.« less

Ferromagnetic spin coupling in the chromium dimer cation: Measurements by photodissociation spectroscopy combined with coupled-cluster calculations

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

Egashira, Kazuhiro, E-mail: egashira@clusterlab.jp; Yamada, Yurika; Kita, Yukiumi

2015-02-07

The magnetic coupling of the chromium dimer cation, Cr{sub 2}{sup +}, has been an outstanding problem for decades. An optical absorption spectrum of Cr{sub 2}{sup +} has been obtained by photodissociation spectroscopy in the photon-energy range from 2.0 to 5.0 eV. Besides, calculations have been performed by the equation-of-motion coupled-cluster singles and doubles method for vertical excitation of the species. Their coincidence supports our assignment that the ground electronic state exhibits a ferromagnetic spin coupling, which is contrary to those of neutral and negatively charged dimers, Cr{sub 2} and Cr{sub 2}{sup −}, in their lowest spin states.

An energy-based perturbation and a taboo strategy for improving the searching ability of stochastic structural optimization methods

NASA Astrophysics Data System (ADS)

Cheng, Longjiu; Cai, Wensheng; Shao, Xueguang

2005-03-01

An energy-based perturbation and a new idea of taboo strategy are proposed for structural optimization and applied in a benchmark problem, i.e., the optimization of Lennard-Jones (LJ) clusters. It is proved that the energy-based perturbation is much better than the traditional random perturbation both in convergence speed and searching ability when it is combined with a simple greedy method. By tabooing the most wide-spread funnel instead of the visited solutions, the hit rate of other funnels can be significantly improved. Global minima of (LJ) clusters up to 200 atoms are found with high efficiency.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

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

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

Galilean-invariant algorithm coupling immersed moving boundary conditions and Lees-Edwards boundary conditions

NASA Astrophysics Data System (ADS)

Zhou, Guofeng; Wang, Limin; Wang, Xiaowei; Ge, Wei

2011-12-01

Many investigators have coupled the Lees-Edwards boundary conditions (LEBCs) and suspension methods in the framework of the lattice Boltzmann method to study the pure bulk properties of particle-fluid suspensions. However, these suspension methods are all link-based and are more or less exposed to the disadvantages of violating Galilean invariance. In this paper, we have coupled LEBCs with a node-based suspension method, which is demonstrated to be Galilean invariant in benchmark simulations. We use the coupled algorithm to predict the viscosity of a particle-fluid suspension at very low Reynolds number, and the simulation results are in good agreement with the semiempirical Krieger-Dougherty formula.

Weak and strong coupling equilibration in nonabelian gauge theories

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

Keegan, Liam; Kurkela, Aleksi; Romatschke, Paul

2016-04-06

In this study, we present a direct comparison studying equilibration through kinetic theory at weak coupling and through holography at strong coupling in the same set-up. The set-up starts with a homogeneous thermal state, which then smoothly transitions through an out-of-equilibrium phase to an expanding system undergoing boost-invariant flow. This first apples-to-apples comparison of equilibration provides a benchmark for similar equilibration processes in heavy-ion collisions, where the equilibration mechanism is still under debate. We find that results at weak and strong coupling can be smoothly connected by simple, empirical power-laws for the viscosity, equilibration time and entropy production of themore » system.« less

Development and Application of Single-Referenced Perturbation and Coupled-Cluster Theories for Excited Electronic States

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

Recent work on the development of single-reference perturbation theories for the study of excited electronic states will be discussed. The utility of these methods will be demonstrated by comparison to linear-response coupled-cluster excitation energies. Results for some halogen molecules of interest in stratospheric chemistry will be presented.

Multifrequency multi-qubit entanglement based on plasmonic hot spots

PubMed Central

Ren, Jun; Wu, Tong; Zhang, Xiangdong

2015-01-01

The theoretical method to study strong coupling between an ensemble of quantum emitters (QEs) and surface plasmons excited by the nanoparticle cluster has been presented by using a rigorous first-principles electromagnetic Green’s tensor technique. We have demonstrated that multi-qubit entanglements for two-level QEs can be produced at different coupling resonance frequencies, when they locate in the hot spots of the metallic nanoparticle cluster. The duration of quantum beats for such an entanglement can reach two orders longer than that for the entanglement in a photonic cavity. The phenomenon originates from collective coupling resonance excitation of the cluster. At the frequency of single scattering resonance, the entanglement cannot be produced although the single QE spontaneous decay rate is very big. PMID:26350051

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Efficient One-Step Generation of Cluster State with Charge Qubits in Circuit QED

NASA Astrophysics Data System (ADS)

Wang, Yi-Min; Li, Cheng-Zu

2010-01-01

We propose theoretical schemes to generate highly entangled cluster state with superconducting qubits in a circuit QED architecture. Charge qubits are located inside a superconducting transmission line, which serves as a quantum data bus. We show that large clusters state can be efficiently generated in just one step with the long-range Ising-like unitary operators. The quantum operations which are generally realized by two coupling mechanisms: either voltage coupling or current coupling, depend only on global geometric features and are insensitive not only to the thermal state of the transmission line but also to certain random operation errors. Thus high-fidelity one-way quantum computation can be achieved.

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

Assessing the distinguishable cluster approximation based on the triple bond-breaking in the nitrogen molecule

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

Rishi, Varun; Perera, Ajith; Bartlett, Rodney J., E-mail: bartlett@qtp.ufl.edu

2016-03-28

Obtaining the correct potential energy curves for the dissociation of multiple bonds is a challenging problem for ab initio methods which are affected by the choice of a spin-restricted reference function. Coupled cluster (CC) methods such as CCSD (coupled cluster singles and doubles model) and CCSD(T) (CCSD + perturbative triples) correctly predict the geometry and properties at equilibrium but the process of bond dissociation, particularly when more than one bond is simultaneously broken, is much more complicated. New modifications of CC theory suggest that the deleterious role of the reference function can be diminished, provided a particular subset of termsmore » is retained in the CC equations. The Distinguishable Cluster (DC) approach of Kats and Manby [J. Chem. Phys. 139, 021102 (2013)], seemingly overcomes the deficiencies for some bond-dissociation problems and might be of use in quasi-degenerate situations in general. DC along with other approximate coupled cluster methods such as ACCD (approximate coupled cluster doubles), ACP-D45, ACP-D14, 2CC, and pCCSD(α, β) (all defined in text) falls under a category of methods that are basically obtained by the deletion of some quadratic terms in the double excitation amplitude equation for CCD/CCSD (coupled cluster doubles model/coupled cluster singles and doubles model). Here these approximate methods, particularly those based on the DC approach, are studied in detail for the nitrogen molecule bond-breaking. The N{sub 2} problem is further addressed with conventional single reference methods but based on spatial symmetry-broken restricted Hartree–Fock (HF) solutions to assess the use of these references for correlated calculations in the situation where CC methods using fully symmetry adapted SCF solutions fail. The distinguishable cluster method is generalized: 1) to different orbitals for different spins (unrestricted HF based DCD and DCSD), 2) by adding triples correction perturbatively (DCSD(T)) and iteratively (DCSDT-n), and 3) via an excited state approximation through the equation of motion (EOM) approach (EOM-DCD, EOM-DCSD). The EOM-CC method is used to identify lower-energy CC solutions to overcome singularities in the CC potential energy curves. It is also shown that UHF based CC and DC methods behave very similarly in bond-breaking of N{sub 2}, and that using spatially broken but spin preserving SCF references makes the CCSD solutions better than those for DCSD.« less

Coarse-Grained Clustering Dynamics of Heterogeneously Coupled Neurons.

PubMed

Moon, Sung Joon; Cook, Katherine A; Rajendran, Karthikeyan; Kevrekidis, Ioannis G; Cisternas, Jaime; Laing, Carlo R

2015-12-01

The formation of oscillating phase clusters in a network of identical Hodgkin-Huxley neurons is studied, along with their dynamic behavior. The neurons are synaptically coupled in an all-to-all manner, yet the synaptic coupling characteristic time is heterogeneous across the connections. In a network of N neurons where this heterogeneity is characterized by a prescribed random variable, the oscillatory single-cluster state can transition-through [Formula: see text] (possibly perturbed) period-doubling and subsequent bifurcations-to a variety of multiple-cluster states. The clustering dynamic behavior is computationally studied both at the detailed and the coarse-grained levels, and a numerical approach that can enable studying the coarse-grained dynamics in a network of arbitrarily large size is suggested. Among a number of cluster states formed, double clusters, composed of nearly equal sub-network sizes are seen to be stable; interestingly, the heterogeneity parameter in each of the double-cluster components tends to be consistent with the random variable over the entire network: Given a double-cluster state, permuting the dynamical variables of the neurons can lead to a combinatorially large number of different, yet similar "fine" states that appear practically identical at the coarse-grained level. For weak heterogeneity we find that correlations rapidly develop, within each cluster, between the neuron's "identity" (its own value of the heterogeneity parameter) and its dynamical state. For single- and double-cluster states we demonstrate an effective coarse-graining approach that uses the Polynomial Chaos expansion to succinctly describe the dynamics by these quickly established "identity-state" correlations. This coarse-graining approach is utilized, within the equation-free framework, to perform efficient computations of the neuron ensemble dynamics.

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

PubMed

Griss, Johannes; Perez-Riverol, Yasset; The, Matthew; Käll, Lukas; Vizcaíno, Juan Antonio

2018-05-04

In the recent benchmarking article entitled "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra", Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the authors clustered only single MS/MS runs. In one of the reported analyses, three MS/MS runs were processed together, which already led to computational performance issues in many of the tested approaches. This fact highlights the difficulties of using many of the tested algorithms on the nowadays produced average proteomics data sets. Second, the authors only processed identified spectra when merging MS runs. Thereby, all unidentified spectra that are of lower quality were already removed from the data set and could not influence the clustering results. Next, we found that the authors did not analyze the effect of chimeric spectra on the clustering results. In our analysis, we found that 3% of the spectra in the used data sets were chimeric, and this had marked effects on the behavior of the different clustering algorithms tested. Finally, the authors' choice to evaluate the MS-Cluster and spectra-cluster algorithms using a precursor tolerance of 5 Da for high-resolution Orbitrap data only was, in our opinion, not adequate to assess the performance of MS/MS clustering approaches.

Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS-H2

NASA Astrophysics Data System (ADS)

Liu, Jing-Min; Zhai, Yu; Li, Hui

2017-07-01

An effective six-dimensional ab initio potential energy surface (PES) for H2-OCS which explicitly includes the intramolecular stretch normal modes of carbonyl sulfide (OCS) is presented. The electronic structure computations are carried out using the explicitly correlated coupled cluster [CCSD(T)-F12] method with the augmented correlation-consistent aug-cc-pVTZ basis set, and the accuracy is critically tested by performing a series of benchmark calculations. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies to the Morse/long-range potential model. These fits to 13 485 points have a root-mean-square deviation (RMSD) of 0.16 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for five isotopic species of the OCS-hydrogen complexes. The predicted transition frequencies and intensities based on the resulting vibrationally averaged PESs are in good agreement with the available experimental values, whose RMSDs are smaller than 0.004 cm-1 for five different species of OCS-hydrogen complexes. The calculated infrared band origin shifts for all five species of OCS-hydrogen complexes are only 0.03 cm-1 smaller than the corresponding experimental values. These validate the high quality of our PESs which can be used for modeling OCS doped in hydrogen clusters to further study quantum solution and microscopic superfluidity. In addition, the analytic coordinate transformation functions between isotopologues are also derived due to the center of mass shifting of different isotope substitutes.

Verification of ARES transport code system with TAKEDA benchmarks

NASA Astrophysics Data System (ADS)

Zhang, Liang; Zhang, Bin; Zhang, Penghe; Chen, Mengteng; Zhao, Jingchang; Zhang, Shun; Chen, Yixue

2015-10-01

Neutron transport modeling and simulation are central to many areas of nuclear technology, including reactor core analysis, radiation shielding and radiation detection. In this paper the series of TAKEDA benchmarks are modeled to verify the critical calculation capability of ARES, a discrete ordinates neutral particle transport code system. SALOME platform is coupled with ARES to provide geometry modeling and mesh generation function. The Koch-Baker-Alcouffe parallel sweep algorithm is applied to accelerate the traditional transport calculation process. The results show that the eigenvalues calculated by ARES are in excellent agreement with the reference values presented in NEACRP-L-330, with a difference less than 30 pcm except for the first case of model 3. Additionally, ARES provides accurate fluxes distribution compared to reference values, with a deviation less than 2% for region-averaged fluxes in all cases. All of these confirms the feasibility of ARES-SALOME coupling and demonstrate that ARES has a good performance in critical calculation.

Defect sink characteristics of specific grain boundary types in 304 stainless steels under high dose neutron environments

DOE PAGES

Field, Kevin G.; Yang, Ying; Busby, Jeremy T.; ...

2015-03-09

Radiation induced segregation (RIS) is a well-studied phenomena which occurs in many structurally relevant nuclear materials including austenitic stainless steels. RIS occurs due to solute atoms preferentially coupling to mobile point defect fluxes that migrate and interact with defect sinks. Here, a 304 stainless steel was neutron irradiated up to 47.1 dpa at 320 °C. Investigations into the RIS response at specific grain boundary types were utilized to determine the sink characteristics of different boundary types as a function of irradiation dose. A rate theory model built on the foundation of the modified inverse Kirkendall (MIK) model is proposed andmore » benchmarked to the experimental results. This model, termed the GiMIK model, includes alterations in the boundary conditions based on grain boundary structure and includes expressions for interstitial binding. This investigation, through experiment and modeling, found specific grain boundary structures exhibit unique defect sink characteristics depending on their local structure. Furthermore, such interactions were found to be consistent across all doses investigated and had larger global implications including precipitation of Ni-Si clusters near different grain boundary types.« less

Electromagnetic Wave Propagation in Body Area Networks Using the Finite-Difference-Time-Domain Method

PubMed Central

Bringuier, Jonathan N.; Mittra, Raj

2012-01-01

A rigorous full-wave solution, via the Finite-Difference-Time-Domain (FDTD) method, is performed in an attempt to obtain realistic communication channel models for on-body wireless transmission in Body-Area-Networks (BANs), which are local data networks using the human body as a propagation medium. The problem of modeling the coupling between body mounted antennas is often not amenable to attack by hybrid techniques owing to the complex nature of the human body. For instance, the time-domain Green's function approach becomes more involved when the antennas are not conformal. Furthermore, the human body is irregular in shape and has dispersion properties that are unique. One consequence of this is that we must resort to modeling the antenna network mounted on the body in its entirety, and the number of degrees of freedom (DoFs) can be on the order of billions. Even so, this type of problem can still be modeled by employing a parallel version of the FDTD algorithm running on a cluster. Lastly, we note that the results of rigorous simulation of BANs can serve as benchmarks for comparison with the abundance of measurement data. PMID:23012575

Real-case benchmark for flow and tracer transport in the fractured rock

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

Hokr, M.; Shao, H.; Gardner, W. P.

The paper is intended to define a benchmark problem related to groundwater flow and natural tracer transport using observations of discharge and isotopic tracers in fractured, crystalline rock. Three numerical simulators: Flow123d, OpenGeoSys, and PFLOTRAN are compared. The data utilized in the project were collected in a water-supply tunnel in granite of the Jizera Mountains, Bedrichov, Czech Republic. The problem configuration combines subdomains of different dimensions, 3D continuum for hard-rock blocks or matrix and 2D features for fractures or fault zones, together with realistic boundary conditions for tunnel-controlled drainage. Steady-state and transient flow and a pulse injection tracer transport problemmore » are solved. The results confirm mostly consistent behavior of the codes. Both the codes Flow123d and OpenGeoSys with 3D–2D coupling implemented differ by several percent in most cases, which is appropriate to, e.g., effects of discrete unknown placing in the mesh. Some of the PFLOTRAN results differ more, which can be explained by effects of the dispersion tensor evaluation scheme and of the numerical diffusion. Here, the phenomenon can get stronger with fracture/matrix coupling and with parameter magnitude contrasts. Although the study was not aimed on inverse solution, the models were fit to the measured data approximately, demonstrating the intended real-case relevance of the benchmark.« less

Real-case benchmark for flow and tracer transport in the fractured rock

DOE PAGES

Hokr, M.; Shao, H.; Gardner, W. P.; ...

2016-09-19

The paper is intended to define a benchmark problem related to groundwater flow and natural tracer transport using observations of discharge and isotopic tracers in fractured, crystalline rock. Three numerical simulators: Flow123d, OpenGeoSys, and PFLOTRAN are compared. The data utilized in the project were collected in a water-supply tunnel in granite of the Jizera Mountains, Bedrichov, Czech Republic. The problem configuration combines subdomains of different dimensions, 3D continuum for hard-rock blocks or matrix and 2D features for fractures or fault zones, together with realistic boundary conditions for tunnel-controlled drainage. Steady-state and transient flow and a pulse injection tracer transport problemmore » are solved. The results confirm mostly consistent behavior of the codes. Both the codes Flow123d and OpenGeoSys with 3D–2D coupling implemented differ by several percent in most cases, which is appropriate to, e.g., effects of discrete unknown placing in the mesh. Some of the PFLOTRAN results differ more, which can be explained by effects of the dispersion tensor evaluation scheme and of the numerical diffusion. Here, the phenomenon can get stronger with fracture/matrix coupling and with parameter magnitude contrasts. Although the study was not aimed on inverse solution, the models were fit to the measured data approximately, demonstrating the intended real-case relevance of the benchmark.« less

Taxonomy and clustering in collaborative systems: The case of the on-line encyclopedia Wikipedia

NASA Astrophysics Data System (ADS)

Capocci, A.; Rao, F.; Caldarelli, G.

2008-01-01

In this paper we investigate the nature and structure of the relation between imposed classifications and real clustering in a particular case of a scale-free network given by the on-line encyclopedia Wikipedia. We find a statistical similarity in the distributions of community sizes both by using the top-down approach of the categories division present in the archive and in the bottom-up procedure of community detection given by an algorithm based on the spectral properties of the graph. Regardless of the statistically similar behaviour, the two methods provide a rather different division of the articles, thereby signaling that the nature and presence of power laws is a general feature for these systems and cannot be used as a benchmark to evaluate the suitability of a clustering method.

Cluster synchronization in networks of neurons with chemical synapses

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

Juang, Jonq, E-mail: jjuang@math.nctu.edu.tw; Liang, Yu-Hao, E-mail: moonsea.am96g@g2.nctu.edu.tw

2014-03-15

In this work, we study the cluster synchronization of chemically coupled and generally formulated networks which are allowed to be nonidentical. The sufficient condition for the existence of stably synchronous clusters is derived. Specifically, we only need to check the stability of the origins of m decoupled linear systems. Here, m is the number of subpopulations. Examples of nonidentical networks such as Hindmarsh-Rose (HR) neurons with various choices of parameters in different subpopulations, or HR neurons in one subpopulation and FitzHugh-Nagumo neurons in the other subpopulation are provided. Explicit threshold for the coupling strength that guarantees the stably cluster synchronizationmore » can be obtained.« less

Clustering-Based Ensemble Learning for Activity Recognition in Smart Homes

PubMed Central

Jurek, Anna; Nugent, Chris; Bi, Yaxin; Wu, Shengli

2014-01-01

Application of sensor-based technology within activity monitoring systems is becoming a popular technique within the smart environment paradigm. Nevertheless, the use of such an approach generates complex constructs of data, which subsequently requires the use of intricate activity recognition techniques to automatically infer the underlying activity. This paper explores a cluster-based ensemble method as a new solution for the purposes of activity recognition within smart environments. With this approach activities are modelled as collections of clusters built on different subsets of features. A classification process is performed by assigning a new instance to its closest cluster from each collection. Two different sensor data representations have been investigated, namely numeric and binary. Following the evaluation of the proposed methodology it has been demonstrated that the cluster-based ensemble method can be successfully applied as a viable option for activity recognition. Results following exposure to data collected from a range of activities indicated that the ensemble method had the ability to perform with accuracies of 94.2% and 97.5% for numeric and binary data, respectively. These results outperformed a range of single classifiers considered as benchmarks. PMID:25014095

Clustering-based ensemble learning for activity recognition in smart homes.

PubMed

Jurek, Anna; Nugent, Chris; Bi, Yaxin; Wu, Shengli

2014-07-10

Application of sensor-based technology within activity monitoring systems is becoming a popular technique within the smart environment paradigm. Nevertheless, the use of such an approach generates complex constructs of data, which subsequently requires the use of intricate activity recognition techniques to automatically infer the underlying activity. This paper explores a cluster-based ensemble method as a new solution for the purposes of activity recognition within smart environments. With this approach activities are modelled as collections of clusters built on different subsets of features. A classification process is performed by assigning a new instance to its closest cluster from each collection. Two different sensor data representations have been investigated, namely numeric and binary. Following the evaluation of the proposed methodology it has been demonstrated that the cluster-based ensemble method can be successfully applied as a viable option for activity recognition. Results following exposure to data collected from a range of activities indicated that the ensemble method had the ability to perform with accuracies of 94.2% and 97.5% for numeric and binary data, respectively. These results outperformed a range of single classifiers considered as benchmarks.

Generalized Self-Organizing Maps for Automatic Determination of the Number of Clusters and Their Multiprototypes in Cluster Analysis.

PubMed

Gorzalczany, Marian B; Rudzinski, Filip

2017-06-07

This paper presents a generalization of self-organizing maps with 1-D neighborhoods (neuron chains) that can be effectively applied to complex cluster analysis problems. The essence of the generalization consists in introducing mechanisms that allow the neuron chain--during learning--to disconnect into subchains, to reconnect some of the subchains again, and to dynamically regulate the overall number of neurons in the system. These features enable the network--working in a fully unsupervised way (i.e., using unlabeled data without a predefined number of clusters)--to automatically generate collections of multiprototypes that are able to represent a broad range of clusters in data sets. First, the operation of the proposed approach is illustrated on some synthetic data sets. Then, this technique is tested using several real-life, complex, and multidimensional benchmark data sets available from the University of California at Irvine (UCI) Machine Learning repository and the Knowledge Extraction based on Evolutionary Learning data set repository. A sensitivity analysis of our approach to changes in control parameters and a comparative analysis with an alternative approach are also performed.

Aluminum-Mediated Formation of Cyclic Carbonates: Benchmarking Catalytic Performance Metrics.

PubMed

Rintjema, Jeroen; Kleij, Arjan W

2017-03-22

We report a comparative study on the activity of a series of fifteen binary catalysts derived from various reported aluminum-based complexes. A benchmarking of their initial rates in the coupling of various terminal and internal epoxides in the presence of three different nucleophilic additives was carried out, providing for the first time a useful comparison of activity metrics in the area of cyclic organic carbonate formation. These investigations provide a useful framework for how to realistically valorize relative reactivities and which features are important when considering the ideal operational window of each binary catalyst system. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Polynomial Similarity Transformation Theory: A smooth interpolation between coupled cluster doubles and projected BCS applied to the reduced BCS Hamiltonian

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

Degroote, M.; Henderson, T. M.; Zhao, J.

We present a similarity transformation theory based on a polynomial form of a particle-hole pair excitation operator. In the weakly correlated limit, this polynomial becomes an exponential, leading to coupled cluster doubles. In the opposite strongly correlated limit, the polynomial becomes an extended Bessel expansion and yields the projected BCS wavefunction. In between, we interpolate using a single parameter. The e ective Hamiltonian is non-hermitian and this Polynomial Similarity Transformation Theory follows the philosophy of traditional coupled cluster, left projecting the transformed Hamiltonian onto subspaces of the Hilbert space in which the wave function variance is forced to be zero.more » Similarly, the interpolation parameter is obtained through minimizing the next residual in the projective hierarchy. We rationalize and demonstrate how and why coupled cluster doubles is ill suited to the strongly correlated limit whereas the Bessel expansion remains well behaved. The model provides accurate wave functions with energy errors that in its best variant are smaller than 1% across all interaction stengths. The numerical cost is polynomial in system size and the theory can be straightforwardly applied to any realistic Hamiltonian.« less

Neutron beam characterization measurements at the Manuel Lujan Jr. neutron scattering center

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

Mocko, Michal; Muhrer, Guenter; Daemen, Luke L

We have measured the neutron beam characteristics of neutron moderators at the Manuel Lujan Jr. Neutron Scattering Center at LANSCE. The absolute thermal neutron flux, energy spectra and time emission spectra were measured for the high resolution and high intensity decoupled water, partially coupled liquid hydrogen and partially coupled water moderators. The results of our experimental study will provide an insight into aging of different target-moderator-reflector-shield components as well as new experimental data for benchmarking of neutron transport codes.

Simple mathematical law benchmarks human confrontations.

PubMed

Johnson, Neil F; Medina, Pablo; Zhao, Guannan; Messinger, Daniel S; Horgan, John; Gill, Paul; Bohorquez, Juan Camilo; Mattson, Whitney; Gangi, Devon; Qi, Hong; Manrique, Pedro; Velasquez, Nicolas; Morgenstern, Ana; Restrepo, Elvira; Johnson, Nicholas; Spagat, Michael; Zarama, Roberto

2013-12-10

Many high-profile societal problems involve an individual or group repeatedly attacking another - from child-parent disputes, sexual violence against women, civil unrest, violent conflicts and acts of terror, to current cyber-attacks on national infrastructure and ultrafast cyber-trades attacking stockholders. There is an urgent need to quantify the likely severity and timing of such future acts, shed light on likely perpetrators, and identify intervention strategies. Here we present a combined analysis of multiple datasets across all these domains which account for >100,000 events, and show that a simple mathematical law can benchmark them all. We derive this benchmark and interpret it, using a minimal mechanistic model grounded by state-of-the-art fieldwork. Our findings provide quantitative predictions concerning future attacks; a tool to help detect common perpetrators and abnormal behaviors; insight into the trajectory of a 'lone wolf'; identification of a critical threshold for spreading a message or idea among perpetrators; an intervention strategy to erode the most lethal clusters; and more broadly, a quantitative starting point for cross-disciplinary theorizing about human aggression at the individual and group level, in both real and online worlds.

Simple mathematical law benchmarks human confrontations

NASA Astrophysics Data System (ADS)

Johnson, Neil F.; Medina, Pablo; Zhao, Guannan; Messinger, Daniel S.; Horgan, John; Gill, Paul; Bohorquez, Juan Camilo; Mattson, Whitney; Gangi, Devon; Qi, Hong; Manrique, Pedro; Velasquez, Nicolas; Morgenstern, Ana; Restrepo, Elvira; Johnson, Nicholas; Spagat, Michael; Zarama, Roberto

2013-12-01

Many high-profile societal problems involve an individual or group repeatedly attacking another - from child-parent disputes, sexual violence against women, civil unrest, violent conflicts and acts of terror, to current cyber-attacks on national infrastructure and ultrafast cyber-trades attacking stockholders. There is an urgent need to quantify the likely severity and timing of such future acts, shed light on likely perpetrators, and identify intervention strategies. Here we present a combined analysis of multiple datasets across all these domains which account for >100,000 events, and show that a simple mathematical law can benchmark them all. We derive this benchmark and interpret it, using a minimal mechanistic model grounded by state-of-the-art fieldwork. Our findings provide quantitative predictions concerning future attacks; a tool to help detect common perpetrators and abnormal behaviors; insight into the trajectory of a `lone wolf' identification of a critical threshold for spreading a message or idea among perpetrators; an intervention strategy to erode the most lethal clusters; and more broadly, a quantitative starting point for cross-disciplinary theorizing about human aggression at the individual and group level, in both real and online worlds.

Geographic clusters in underimmunization and vaccine refusal.

PubMed

Lieu, Tracy A; Ray, G Thomas; Klein, Nicola P; Chung, Cindy; Kulldorff, Martin

2015-02-01

Parental refusal and delay of childhood vaccines has increased in recent years and is believed to cluster in some communities. Such clusters could pose public health risks and barriers to achieving immunization quality benchmarks. Our aims were to (1) describe geographic clusters of underimmunization and vaccine refusal, (2) compare clusters of underimmunization with different vaccines, and (3) evaluate whether vaccine refusal clusters may pose barriers to achieving high immunization rates. We analyzed electronic health records among children born between 2000 and 2011 with membership in Kaiser Permanente Northern California. The study population included 154,424 children in 13 counties with continuous membership from birth to 36 months of age. We used spatial scan statistics to identify clusters of underimmunization (having missed 1 or more vaccines by 36 months of age) and vaccine refusal (based on International Classification of Diseases, Ninth Revision, Clinical Modification codes). We identified 5 statistically significant clusters of underimmunization among children who turned 36 months old during 2010-2012. The underimmunization rate within clusters ranged from 18% to 23%, and the rate outside them was 11%. Children in the most statistically significant cluster had 1.58 (P < .001) times the rate of underimmunization as others. Underimmunization with measles, mumps, rubella vaccine and varicella vaccines clustered in similar geographic areas. Vaccine refusal also clustered, with rates of 5.5% to 13.5% within clusters, compared with 2.6% outside them. Underimmunization and vaccine refusal cluster geographically. Spatial scan statistics may be a useful tool to identify locations with challenges to achieving high immunization rates, which deserve focused intervention. Copyright © 2015 by the American Academy of Pediatrics.

Fast graph-based relaxed clustering for large data sets using minimal enclosing ball.

PubMed

Qian, Pengjiang; Chung, Fu-Lai; Wang, Shitong; Deng, Zhaohong

2012-06-01

Although graph-based relaxed clustering (GRC) is one of the spectral clustering algorithms with straightforwardness and self-adaptability, it is sensitive to the parameters of the adopted similarity measure and also has high time complexity O(N(3)) which severely weakens its usefulness for large data sets. In order to overcome these shortcomings, after introducing certain constraints for GRC, an enhanced version of GRC [constrained GRC (CGRC)] is proposed to increase the robustness of GRC to the parameters of the adopted similarity measure, and accordingly, a novel algorithm called fast GRC (FGRC) based on CGRC is developed in this paper by using the core-set-based minimal enclosing ball approximation. A distinctive advantage of FGRC is that its asymptotic time complexity is linear with the data set size N. At the same time, FGRC also inherits the straightforwardness and self-adaptability from GRC, making the proposed FGRC a fast and effective clustering algorithm for large data sets. The advantages of FGRC are validated by various benchmarking and real data sets.

ABCluster: the artificial bee colony algorithm for cluster global optimization.

PubMed

Zhang, Jun; Dolg, Michael

2015-10-07

Global optimization of cluster geometries is of fundamental importance in chemistry and an interesting problem in applied mathematics. In this work, we introduce a relatively new swarm intelligence algorithm, i.e. the artificial bee colony (ABC) algorithm proposed in 2005, to this field. It is inspired by the foraging behavior of a bee colony, and only three parameters are needed to control it. We applied it to several potential functions of quite different nature, i.e., the Coulomb-Born-Mayer, Lennard-Jones, Morse, Z and Gupta potentials. The benchmarks reveal that for long-ranged potentials the ABC algorithm is very efficient in locating the global minimum, while for short-ranged ones it is sometimes trapped into a local minimum funnel on a potential energy surface of large clusters. We have released an efficient, user-friendly, and free program "ABCluster" to realize the ABC algorithm. It is a black-box program for non-experts as well as experts and might become a useful tool for chemists to study clusters.

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

Kim, Junghyun; Gangwon, Jo; Jaehoon, Jung

Applications written solely in OpenCL or CUDA cannot execute on a cluster as a whole. Most previous approaches that extend these programming models to clusters are based on a common idea: designating a centralized host node and coordinating the other nodes with the host for computation. However, the centralized host node is a serious performance bottleneck when the number of nodes is large. In this paper, we propose a scalable and distributed OpenCL framework called SnuCL-D for large-scale clusters. SnuCL-D's remote device virtualization provides an OpenCL application with an illusion that all compute devices in a cluster are confined inmore » a single node. To reduce the amount of control-message and data communication between nodes, SnuCL-D replicates the OpenCL host program execution and data in each node. We also propose a new OpenCL host API function and a queueing optimization technique that significantly reduce the overhead incurred by the previous centralized approaches. To show the effectiveness of SnuCL-D, we evaluate SnuCL-D with a microbenchmark and eleven benchmark applications on a large-scale CPU cluster and a medium-scale GPU cluster.« less

Fast clustering using adaptive density peak detection.

PubMed

Wang, Xiao-Feng; Xu, Yifan

2017-12-01

Common limitations of clustering methods include the slow algorithm convergence, the instability of the pre-specification on a number of intrinsic parameters, and the lack of robustness to outliers. A recent clustering approach proposed a fast search algorithm of cluster centers based on their local densities. However, the selection of the key intrinsic parameters in the algorithm was not systematically investigated. It is relatively difficult to estimate the "optimal" parameters since the original definition of the local density in the algorithm is based on a truncated counting measure. In this paper, we propose a clustering procedure with adaptive density peak detection, where the local density is estimated through the nonparametric multivariate kernel estimation. The model parameter is then able to be calculated from the equations with statistical theoretical justification. We also develop an automatic cluster centroid selection method through maximizing an average silhouette index. The advantage and flexibility of the proposed method are demonstrated through simulation studies and the analysis of a few benchmark gene expression data sets. The method only needs to perform in one single step without any iteration and thus is fast and has a great potential to apply on big data analysis. A user-friendly R package ADPclust is developed for public use.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

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

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

Spatial cluster for clustering the influence factor of birth and death child in Bogor Regency, West Java

NASA Astrophysics Data System (ADS)

Bekti, Rokhana Dwi; Rachmawati, Ro'fah

2014-03-01

The number of birth and death child is the benchmarks to determine and monitor the health and welfare in Indonesia. It can be used to identify groups of people who have a high mortality risk. Identifying group is important to compare the characteristics of human that have high and low risk. These characteristics can be seen from the factors that influenced it. Furthermore, there are factors which influence of birth and death child, such us economic, health facility, education, and others. The influence factors of every individual are different, but there are similarities some individuals which live close together or in the close locations. It means there was spatial effect. To identify group in this research, clustering is done by spatial cluster method, which is view to considering the influence of the location or the relationship between locations. One of spatial cluster method is Spatial 'K'luster Analysis by Tree Edge Removal (SKATER). The research was conducted in Bogor Regency, West Java. The goal was to get a cluster of districts based on the factors that influence birth and death child. SKATER build four number of cluster respectively consists of 26, 7, 2, and 5 districts. SKATER has good performance for clustering which include spatial effect. If it compare by other cluster method, Kmeans has good performance by MANOVA test.

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

Using Grey Wolf Algorithm to Solve the Capacitated Vehicle Routing Problem

NASA Astrophysics Data System (ADS)

Korayem, L.; Khorsid, M.; Kassem, S. S.

2015-05-01

The capacitated vehicle routing problem (CVRP) is a class of the vehicle routing problems (VRPs). In CVRP a set of identical vehicles having fixed capacities are required to fulfill customers' demands for a single commodity. The main objective is to minimize the total cost or distance traveled by the vehicles while satisfying a number of constraints, such as: the capacity constraint of each vehicle, logical flow constraints, etc. One of the methods employed in solving the CVRP is the cluster-first route-second method. It is a technique based on grouping of customers into a number of clusters, where each cluster is served by one vehicle. Once clusters are formed, a route determining the best sequence to visit customers is established within each cluster. The recently bio-inspired grey wolf optimizer (GWO), introduced in 2014, has proven to be efficient in solving unconstrained, as well as, constrained optimization problems. In the current research, our main contributions are: combining GWO with the traditional K-means clustering algorithm to generate the ‘K-GWO’ algorithm, deriving a capacitated version of the K-GWO algorithm by incorporating a capacity constraint into the aforementioned algorithm, and finally, developing 2 new clustering heuristics. The resulting algorithm is used in the clustering phase of the cluster-first route-second method to solve the CVR problem. The algorithm is tested on a number of benchmark problems with encouraging results.

Discontinuities-free complete-active-space state–specific multi–reference coupled cluster theory for describing bond stretching and dissociation

DOE PAGES

Zaporozhets, Irina A.; Ivanov, Vladimir V.; Lyakh, Dmitry I.; ...

2015-07-13

The earlier proposed multi-reference state-specific coupled-cluster theory with the complete active space reference suffered from a problem of energy discontinuities when the formal reference state was changing in the calculation of the potential energy curve (PEC). A simple remedy to the discontinuity problem is found and is presented in this work. It involves using natural complete active space self-consistent field active orbitals in the complete active space coupled-cluster calculations. As a result, the approach gives smooth PECs for different types of dissociation problems, as illustrated in the calculations of the dissociation of the single bond in the hydrogen fluorine moleculemore » and of the symmetric double-bond dissociation in the water molecule.« less

An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs

PubMed Central

2015-01-01

Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the “artificial enrichment” and “analogue bias” of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD. PMID:24749745

An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs.

PubMed

Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon

2014-05-27

Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

Effect of a chameleon scalar field on the cosmic microwave background

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

Davis, Anne-Christine; Schelpe, Camilla A. O.; Shaw, Douglas J.

2009-09-15

We show that a direct coupling between a chameleonlike scalar field and photons can give rise to a modified Sunyaev-Zel'dovich (SZ) effect in the cosmic microwave background (CMB). The coupling induces a mixing between chameleon particles and the CMB photons when they pass through the magnetic field of a galaxy cluster. Both the intensity and the polarization of the radiation are modified. The degree of modification depends strongly on the properties of the galaxy cluster such as magnetic field strength and electron number density. Existing SZ measurements of the Coma cluster enable us to place constraints on the photon-chameleon coupling.more » The constrained conversion probability in the cluster is P{sub Coma}(204 GHz)<6.2x10{sup -5} at 95% confidence, corresponding to an upper bound on the coupling strength of g{sub eff}{sup (cell)}<2.2x10{sup -8} GeV{sup -1} or g{sub eff}{sup (Kolmo)}<(7.2-32.5)x10{sup -10} GeV{sup -1}, depending on the model that is assumed for the cluster magnetic field structure. We predict the radial profile of the chameleonic CMB intensity decrement. We find that the chameleon effect extends farther toward the edges of the cluster than the thermal SZ effect. Thus we might see a discrepancy between the x-ray emission data and the observed SZ intensity decrement. We further predict the expected change to the CMB polarization arising from the existence of a chameleonlike scalar field. These predictions could be verified or constrained by future CMB experiments.« less

Understanding the Irradiation Behavior of Zirconium Carbide

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

Motta, Arthur; Sridharan, Kumar; Morgan, Dane

2013-10-11

Zirconium carbide (ZrC) is being considered for utilization in high-temperature gas-cooled reactor fuels in deep-burn TRISO fuel. Zirconium carbide possesses a cubic B1-type crystal structure with a high melting point, exceptional hardness, and good thermal and electrical conductivities. The use of ZrC as part of the TRISO fuel requires a thorough understanding of its irradiation response. However, the radiation effects on ZrC are still poorly understood. The majority of the existing research is focused on the radiation damage phenomena at higher temperatures (>450{degree}C) where many fundamental aspects of defect production and kinetics cannot be easily distinguished. Little is known aboutmore » basic defect formation, clustering, and evolution of ZrC under irradiation, although some atomistic simulation and phenomenological studies have been performed. Such detailed information is needed to construct a model describing the microstructural evolution in fast-neutron irradiated materials that will be of great technological importance for the development of ZrC-based fuel. The goal of the proposed project is to gain fundamental understanding of the radiation-induced defect formation in zirconium carbide and irradiation response by using a combination of state-of-the-art experimental methods and atomistic modeling. This project will combine (1) in situ ion irradiation at a specialized facility at a national laboratory, (2) controlled temperature proton irradiation on bulk samples, and (3) atomistic modeling to gain a fundamental understanding of defect formation in ZrC. The proposed project will cover the irradiation temperatures from cryogenic temperature to as high as 800{degree}C, and dose ranges from 0.1 to 100 dpa. The examination of this wide range of temperatures and doses allows us to obtain an experimental data set that can be effectively used to exercise and benchmark the computer calculations of defect properties. Combining the examination of radiation-induced microstructures mapped spatially and temporally, microstructural evolution during post-irradiation annealing, and atomistic modeling of defect formation and transport energetics will provide new, critical understanding about property changes in ZrC. The behavior of materials under irradiation is determined by the balance between damage production, defect clustering, and lattice response. In order to predict those effects at high temperatures so targeted testing can be expanded and extrapolated beyond the known database, it is necessary to determine the defect energetics and mobilities as these control damage accumulation and annealing. In particular, low-temperature irradiations are invaluable for determining the regions of defect mobility. Computer simulation techniques are particularly useful for identifying basic defect properties, especially if closely coupled with a well-constructed and complete experimental database. The close coupling of calculation and experiment in this project will provide mutual benchmarking and allow us to glean a deeper understanding of the irradiation response of ZrC, which can then be applied to the prediction of its behavior in reactor conditions.« less

Partial synchronization of relaxation oscillators with repulsive coupling in autocatalytic integrate-and-fire model and electrochemical experiments

NASA Astrophysics Data System (ADS)

Kori, Hiroshi; Kiss, István Z.; Jain, Swati; Hudson, John L.

2018-04-01

Experiments and supporting theoretical analysis are presented to describe the synchronization patterns that can be observed with a population of globally coupled electrochemical oscillators close to a homoclinic, saddle-loop bifurcation, where the coupling is repulsive in the electrode potential. While attractive coupling generates phase clusters and desynchronized states, repulsive coupling results in synchronized oscillations. The experiments are interpreted with a phenomenological model that captures the waveform of the oscillations (exponential increase) followed by a refractory period. The globally coupled autocatalytic integrate-and-fire model predicts the development of partially synchronized states that occur through attracting heteroclinic cycles between out-of-phase two-cluster states. Similar behavior can be expected in many other systems where the oscillations occur close to a saddle-loop bifurcation, e.g., with Morris-Lecar neurons.

A Multifunctional Interface Method for Coupling Finite Element and Finite Difference Methods: Two-Dimensional Scalar-Field Problems

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.

2002-01-01

A multifunctional interface method with capabilities for variable-fidelity modeling and multiple method analysis is presented. The methodology provides an effective capability by which domains with diverse idealizations can be modeled independently to exploit the advantages of one approach over another. The multifunctional method is used to couple independently discretized subdomains, and it is used to couple the finite element and the finite difference methods. The method is based on a weighted residual variational method and is presented for two-dimensional scalar-field problems. A verification test problem and a benchmark application are presented, and the computational implications are discussed.

The charger transfer electronic coupling in diabatic perspective: A multi-state density functional theory study

NASA Astrophysics Data System (ADS)

Guo, Xinwei; Qu, Zexing; Gao, Jiali

2018-01-01

The multi-state density functional theory (MSDFT) provides a convenient way to estimate electronic coupling of charge transfer processes based on a diabatic representation. Its performance has been benchmarked against the HAB11 database with a mean unsigned error (MUE) of 17 meV between MSDFT and ab initio methods. The small difference may be attributed to different representations, diabatic from MSDFT and adiabatic from ab initio calculations. In this discussion, we conclude that MSDFT provides a general and efficient way to estimate the electronic coupling for charge-transfer rate calculations based on the Marcus-Hush model.

Quantum annealing for combinatorial clustering

NASA Astrophysics Data System (ADS)

Kumar, Vaibhaw; Bass, Gideon; Tomlin, Casey; Dulny, Joseph

2018-02-01

Clustering is a powerful machine learning technique that groups "similar" data points based on their characteristics. Many clustering algorithms work by approximating the minimization of an objective function, namely the sum of within-the-cluster distances between points. The straightforward approach involves examining all the possible assignments of points to each of the clusters. This approach guarantees the solution will be a global minimum; however, the number of possible assignments scales quickly with the number of data points and becomes computationally intractable even for very small datasets. In order to circumvent this issue, cost function minima are found using popular local search-based heuristic approaches such as k-means and hierarchical clustering. Due to their greedy nature, such techniques do not guarantee that a global minimum will be found and can lead to sub-optimal clustering assignments. Other classes of global search-based techniques, such as simulated annealing, tabu search, and genetic algorithms, may offer better quality results but can be too time-consuming to implement. In this work, we describe how quantum annealing can be used to carry out clustering. We map the clustering objective to a quadratic binary optimization problem and discuss two clustering algorithms which are then implemented on commercially available quantum annealing hardware, as well as on a purely classical solver "qbsolv." The first algorithm assigns N data points to K clusters, and the second one can be used to perform binary clustering in a hierarchical manner. We present our results in the form of benchmarks against well-known k-means clustering and discuss the advantages and disadvantages of the proposed techniques.

Title: Chimeras in small, globally coupled networks: Experiments and stability analysis

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

Since the initial observation of chimera states, there has been much discussion of the conditions under which these states emerge. The emphasis thus far has mainly been to analyze large networks of coupled oscillators; however, recent studies have begun to focus on the opposite limit: what is the smallest system of coupled oscillators in which chimeras can exist? We experimentally observe chimeras and other partially synchronous patterns in a network of four globally-coupled chaotic opto-electronic oscillators. By examining the equations of motion, we demonstrate that symmetries in the network topology allow a variety of synchronous states to exist, including cluster synchronous states and a chimera state. Using the group theoretical approach recently developed for analyzing cluster synchronization, we show how to derive the variational equations for these synchronous patterns and calculate their linear stability. The stability analysis gives good agreement with our experimental results. Both experiments and simulations suggest that these chimera states often appear in regions of multistability between global, cluster, and desynchronized states.

Isotopic effects in vibrational relaxation dynamics of H on a Si(100) surface

NASA Astrophysics Data System (ADS)

Bouakline, F.; Lorenz, U.; Melani, G.; Paramonov, G. K.; Saalfrank, P.

2017-10-01

In a recent paper [U. Lorenz and P. Saalfrank, Chem. Phys. 482, 69 (2017)], we proposed a robust scheme to set up a system-bath model Hamiltonian, describing the coupling of adsorbate vibrations (system) to surface phonons (bath), from first principles. The method is based on an embedded cluster approach, using orthogonal coordinates for system and bath modes, and an anharmonic phononic expansion of the system-bath interaction up to second order. In this contribution, we use this model Hamiltonian to calculate vibrational relaxation rates of H-Si and D-Si bending modes, coupled to a fully H(D)-covered Si(100)-( 2 × 1 ) surface, at zero temperature. The D-Si bending mode has an anharmonic frequency lying inside the bath frequency spectrum, whereas the H-Si bending mode frequency is outside the bath Debye band. Therefore, in the present calculations, we only take into account one-phonon system-bath couplings for the D-Si system and both one- and two-phonon interaction terms in the case of H-Si. The computation of vibrational lifetimes is performed with two different approaches, namely, Fermi's golden rule, and a generalized Bixon-Jortner model built in a restricted vibrational space of the adsorbate-surface zeroth-order Hamiltonian. For D-Si, the Bixon-Jortner Hamiltonian can be solved by exact diagonalization, serving as a benchmark, whereas for H-Si, an iterative scheme based on the recursive residue generation method is applied, with excellent convergence properties. We found that the lifetimes obtained with perturbation theory, albeit having almost the same order of magnitude—a few hundred fs for D-Si and a couple of ps for H-Si—, are strongly dependent on the discretized numerical representation of the bath spectral density. On the other hand, the Bixon-Jortner model is free of such numerical deficiencies, therefore providing better estimates of vibrational relaxation rates, at a very low computational cost. The results obtained with this model clearly show a net exponential decay of the time-dependent survival probability for the H-Si initial vibrational state, allowing an easy extraction of the bending mode "lifetime." This is in contrast with the D-Si system, whose survival probability exhibits a non-monotonic decay, making it difficult to define such a lifetime. This different behavior of the vibrational decay is rationalized in terms of the power spectrum of the adsorbate-surface system. In the case of D-Si, it consists of several, non-uniformly distributed peaks around the bending mode frequency, whereas the H-Si spectrum exhibits a single Lorentzian lineshape, whose width corresponds to the calculated lifetime. The present work gives some insight into mechanisms of vibration-phonon coupling at surfaces. It also serves as a benchmark for multidimensional system-bath quantum dynamics, for comparison with approximate schemes such as reduced, open-system density matrix theory (where the bath is traced out and a Liouville-von Neumann equation is solved) or approximate wavefunction methods to solve the combined system-bath Schrödinger equation.

PHISICS/RELAP5-3D RESULTS FOR EXERCISES II-1 AND II-2 OF THE OECD/NEA MHTGR-350 BENCHMARK

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

Strydom, Gerhard

2016-03-01

The Idaho National Laboratory (INL) Advanced Reactor Technologies (ART) High-Temperature Gas-Cooled Reactor (HTGR) Methods group currently leads the Modular High-Temperature Gas-Cooled Reactor (MHTGR) 350 benchmark. The benchmark consists of a set of lattice-depletion, steady-state, and transient problems that can be used by HTGR simulation groups to assess the performance of their code suites. The paper summarizes the results obtained for the first two transient exercises defined for Phase II of the benchmark. The Parallel and Highly Innovative Simulation for INL Code System (PHISICS), coupled with the INL system code RELAP5-3D, was used to generate the results for the Depressurized Conductionmore » Cooldown (DCC) (exercise II-1a) and Pressurized Conduction Cooldown (PCC) (exercise II-2) transients. These exercises require the time-dependent simulation of coupled neutronics and thermal-hydraulics phenomena, and utilize the steady-state solution previously obtained for exercise I-3 of Phase I. This paper also includes a comparison of the benchmark results obtained with a traditional system code “ring” model against a more detailed “block” model that include kinetics feedback on an individual block level and thermal feedbacks on a triangular sub-mesh. The higher spatial fidelity that can be obtained by the block model is illustrated with comparisons of the maximum fuel temperatures, especially in the case of natural convection conditions that dominate the DCC and PCC events. Differences up to 125 K (or 10%) were observed between the ring and block model predictions of the DCC transient, mostly due to the block model’s capability of tracking individual block decay powers and more detailed helium flow distributions. In general, the block model only required DCC and PCC calculation times twice as long as the ring models, and it therefore seems that the additional development and calculation time required for the block model could be worth the gain that can be obtained in the spatial resolution« less

Rational synthesis of high nuclearity Mo/Fe/S clusters: the reductive coupling approach in the convenient synthesis of (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et, (n)Pr, (n)Bu] and the new [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl]-1/2(Fe(PEt(3))(2)(MeCN)(4)) and (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) clusters.

PubMed

Han, J; Koutmos, M; Ahmad, S A; Coucouvanis, D

2001-11-05

A general method for the synthesis of high nuclearity Mo/Fe/S clusters is presented and involves the reductive coupling of the (Et(4)N)(2)[(Cl(4)-cat)MoOFeS(2)Cl(2)] (I) and (Et(4)N)(2)[Fe(2)S(2)Cl(4)] (II) clusters. The reaction of I and II with Fe(PR(3))(2)Cl(2) or sodium salts of noncoordinating anions such as NaPF(6) or NaBPh(4) in the presence of PR(3) (R = Et, (n)Pr, or (n)Bu) affords (Cl(4)-cat)(2)Mo(2)Fe(6)S(8)(PR(3))(6) [R = Et (IIIa), (n)Pr (IIIb), (n)Bu (IIIc)], Fe(6)S(6)(PEt(3))(4)Cl(2) (IV) and (PF(6))[Fe(6)S(8)(P(n)Pr(3))(6)] (V) as byproducts. The isolation of (Et(4)N)[Fe(PEt(3))Cl(3)] (VI), NaCl, and SPEt(3) supports a reductive coupling mechanism. Cluster IV and V also have been synthesized by the reductive self-coupling of compound II. The reductive coupling reaction between I and II by PEt(3) and NaPF(6) in a 1:1 ratio produces the (Et(4)N)(2)[(Cl(4)-cat)Mo(L)Fe(3)S(4)Cl(3)] clusters [L = MeCN (VIIa), THF (VIIb)]. The hitherto unknown [(Cl(4)-cat)(2)Mo(2)Fe(2)S(3)O(PEt(3))(3)Cl](+) cluster (VIII) has been isolated as the 2:1 salt of the (Fe(PEt(3))(2)(MeCN)(4))(2+) cation after the reductive self-coupling reaction of I in the presence of Fe(PEt(3))(2)Cl(2). Cluster VIII crystallizes in the monoclinic space group P2(1)/c with a = 11.098(3) A, b = 22.827(6) A, c = 25.855(6) A, beta = 91.680(4) degrees, and Z = 4. The formal oxidation states of metal atoms in VIII have been assigned as Mo(III), Mo(IV), Fe(II), and Fe(III) on the basis of zero-field Mössbauer spectra. The Fe(PEt(3))(2)(MeCN)(4) cation of VIII is also synthesized independently, isolated as the BPh(4)(-) salt (IX), and has been structurally characterized. The reductive coupling of compound I also affords in low yield the new (Cl(4)-cat)(2)Mo(2)Fe(3)S(5)(PEt(3))(5) cluster (X) as a byproduct. Cluster X crystallizes in the monoclinic space group P2(1)/n with a = 14.811(3) A, b = 22.188(4) A, c = 21.864(4) A, beta = 100.124(3) degrees, and Z = 4 and the structure shows very short Mo-Fe, Fe-Fe, Mo-S, Fe-S bonds. The oxidation states of the metal atoms in this neutral cluster (X) have been assigned as Mo(IV)Mo(III)Fe(II)Fe(II)Fe(III) based on zero-field Mössbauer and magnetic measurement. All Fe atoms are high spin and two of the three Fe-Fe distances are found at 2.4683(9) A and 2.4721(9) A.

Reference pricing for drugs: is it compatible with U.S. health care?

PubMed

Kanavos, Panos; Reinhardt, Uwe

2003-01-01

To control spending on prescription drugs, health insurance systems abroad have experimented in recent years with a novel form of patient cost sharing called "reference pricing." Under this approach, the insurer covers only the prices of low-cost, benchmark drugs in therapeutic clusters that are deemed to be close substitutes for one another in treating specific illnesses. Patients who desire a higher-price substitute in a cluster must then pay the full difference between the retail price of that drug and the reference price covered by the insurer. This paper explores the difficult trade-offs that policymakers must make in designing such a system, drawing where relevant from experience abroad.

Probing the Properties of AGN Clustering in the Local Universe with Swift-BAT

NASA Astrophysics Data System (ADS)

Powell, M.; Cappelluti, N.; Urry, M.; Koss, M.; Allevato, V.; Ajello, M.

2017-10-01

I present the benchmark measurement of AGN clustering in the local universe with the all-sky Swift-BAT survey. The hard X-ray selection (14-195 keV) allows for the detection of some of the most obscured AGN, providing the largest, most unbiased sample of local AGN to date. We derive for the first time the halo occupation distribution (HOD) of the sample in various bins of black hole mass, accretion rate, and obscuration. In doing so, we characterize the cosmic environment of growing supermassive black holes with unprecedented precision, and determine which black hole parameters depend on environment. We then compare our results to the current evolutionary models of AGN.

Distance-Based and Low Energy Adaptive Clustering Protocol for Wireless Sensor Networks

PubMed Central

Gani, Abdullah; Anisi, Mohammad Hossein; Ab Hamid, Siti Hafizah; Akhunzada, Adnan; Khan, Muhammad Khurram

2016-01-01

A wireless sensor network (WSN) comprises small sensor nodes with limited energy capabilities. The power constraints of WSNs necessitate efficient energy utilization to extend the overall network lifetime of these networks. We propose a distance-based and low-energy adaptive clustering (DISCPLN) protocol to streamline the green issue of efficient energy utilization in WSNs. We also enhance our proposed protocol into the multi-hop-DISCPLN protocol to increase the lifetime of the network in terms of high throughput with minimum delay time and packet loss. We also propose the mobile-DISCPLN protocol to maintain the stability of the network. The modelling and comparison of these protocols with their corresponding benchmarks exhibit promising results. PMID:27658194

Solution of the sign problem in the Potts model at fixed fermion number

NASA Astrophysics Data System (ADS)

Alexandru, Andrei; Bergner, Georg; Schaich, David; Wenger, Urs

2018-06-01

We consider the heavy-dense limit of QCD at finite fermion density in the canonical formulation and approximate it by a three-state Potts model. In the strong-coupling limit, the model is free of the sign problem. Away from the strong coupling, the sign problem is solved by employing a cluster algorithm which allows to average each cluster over the Z (3 ) sectors. Improved estimators for physical quantities can be constructed by taking into account the triality of the clusters, that is, their transformation properties with respect to Z (3 ) transformations.

Coupled-cluster sum-frequency generation nonlinear susceptibilities of methyl (CH3) and methylene (CH2) groups.

PubMed

Tetsassi Feugmo, Conrard Giresse; Liégeois, Vincent; Champagne, Benoît

2017-11-15

The first vibrational sum frequency generation (SFG) spectra based on molecular properties calculated at the coupled cluster singles and doubles (CCSD) level of approximation have been simulated for interfacial model alkyl chains, providing benchmark data for comparisons with approximate methods, including density functional theory (DFT). The approach proceeds in three steps. In the first two steps, the molecular spectral properties are determined: the vibrational normal modes and frequencies and then the derivatives of the dipole moment and of the polarizability with respect to the normal coordinates. These derivatives are evaluated with a numerical differentiation approach, of which the accuracy was monitored using Romberg's procedure. Then, in the last step, a three-layer model is employed to evaluate the macroscopic second-order nonlinear optical responses and thereby the simulated SFG spectra of the alkyl interface. Results emphasize the following facts: (i) the dipole and polarizability derivatives calculated at the DFT level with the B3LYP exchange-correlation functional can differ, with respect to CCSD, by as much as ±10 to 20% and ±20 to 50% for the CH 3 and CH 2 vibrations, respectively; (ii) these differences are enhanced when considering the SFG intensities as well as their variations as a function of the experimental configuration (ppp versus ssp) and as a function of the tilt and rotation angles, defining the orientation of the alkyl chain at the interface; (iii) these differences originate from both the vibrational normal coordinates and the Cartesian derivatives of the dipole moment and polarizability; (iv) freezing the successive fragments of the alkyl chain strongly modifies the SFG spectrum and enables highlighting the delocalization effects between the terminal CH 3 group and its neighboring CH 2 units; and finally (v) going from the free chain to the free methyl model, and further to C 3v constraints on leads to large variations of two ratios that are frequently used to probe the molecular orientation at the interface, the (r + r)/r + ratio for both antisymmetric and symmetric CH 3 vibrations and the I ppp /I ssp ratio.

Integral Full Core Multi-Physics PWR Benchmark with Measured Data

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

Forget, Benoit; Smith, Kord; Kumar, Shikhar

In recent years, the importance of modeling and simulation has been highlighted extensively in the DOE research portfolio with concrete examples in nuclear engineering with the CASL and NEAMS programs. These research efforts and similar efforts worldwide aim at the development of high-fidelity multi-physics analysis tools for the simulation of current and next-generation nuclear power reactors. Like all analysis tools, verification and validation is essential to guarantee proper functioning of the software and methods employed. The current approach relies mainly on the validation of single physic phenomena (e.g. critical experiment, flow loops, etc.) and there is a lack of relevantmore » multiphysics benchmark measurements that are necessary to validate high-fidelity methods being developed today. This work introduces a new multi-cycle full-core Pressurized Water Reactor (PWR) depletion benchmark based on two operational cycles of a commercial nuclear power plant that provides a detailed description of fuel assemblies, burnable absorbers, in-core fission detectors, core loading and re-loading patterns. This benchmark enables analysts to develop extremely detailed reactor core models that can be used for testing and validation of coupled neutron transport, thermal-hydraulics, and fuel isotopic depletion. The benchmark also provides measured reactor data for Hot Zero Power (HZP) physics tests, boron letdown curves, and three-dimensional in-core flux maps from 58 instrumented assemblies. The benchmark description is now available online and has been used by many groups. However, much work remains to be done on the quantification of uncertainties and modeling sensitivities. This work aims to address these deficiencies and make this benchmark a true non-proprietary international benchmark for the validation of high-fidelity tools. This report details the BEAVRS uncertainty quantification for the first two cycle of operations and serves as the final report of the project.« less

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

Zuniga-Gutierrez, Bernardo, E-mail: bzuniga.51@gmail.com; Camacho-Gonzalez, Monica; Bendana-Castillo, Alfonso

The computation of the spin-rotation tensor within the framework of auxiliary density functional theory (ADFT) in combination with the gauge including atomic orbital (GIAO) scheme, to treat the gauge origin problem, is presented. For the spin-rotation tensor, the calculation of the magnetic shielding tensor represents the most demanding computational task. Employing the ADFT-GIAO methodology, the central processing unit time for the magnetic shielding tensor calculation can be dramatically reduced. In this work, the quality of spin-rotation constants obtained with the ADFT-GIAO methodology is compared with available experimental data as well as with other theoretical results at the Hartree-Fock and coupled-clustermore » level of theory. It is found that the agreement between the ADFT-GIAO results and the experiment is good and very similar to the ones obtained by the coupled-cluster single-doubles-perturbative triples-GIAO methodology. With the improved computational performance achieved, the computation of the spin-rotation tensors of large systems or along Born-Oppenheimer molecular dynamics trajectories becomes feasible in reasonable times. Three models of carbon fullerenes containing hundreds of atoms and thousands of basis functions are used for benchmarking the performance. Furthermore, a theoretical study of temperature effects on the structure and spin-rotation tensor of the H{sup 12}C–{sup 12}CH–DF complex is presented. Here, the temperature dependency of the spin-rotation tensor of the fluorine nucleus can be used to identify experimentally the so far unknown bent isomer of this complex. To the best of our knowledge this is the first time that temperature effects on the spin-rotation tensor are investigated.« less

Entropic multirelaxation-time lattice Boltzmann method for moving and deforming geometries in three dimensions

NASA Astrophysics Data System (ADS)

Dorschner, B.; Chikatamarla, S. S.; Karlin, I. V.

2017-06-01

Entropic lattice Boltzmann methods have been developed to alleviate intrinsic stability issues of lattice Boltzmann models for under-resolved simulations. Its reliability in combination with moving objects was established for various laminar benchmark flows in two dimensions in our previous work [B. Dorschner, S. Chikatamarla, F. Bösch, and I. Karlin, J. Comput. Phys. 295, 340 (2015), 10.1016/j.jcp.2015.04.017] as well as for three-dimensional one-way coupled simulations of engine-type geometries in B . Dorschner, F. Bösch, S. Chikatamarla, K. Boulouchos, and I. Karlin [J. Fluid Mech. 801, 623 (2016), 10.1017/jfm.2016.448] for flat moving walls. The present contribution aims to fully exploit the advantages of entropic lattice Boltzmann models in terms of stability and accuracy and extends the methodology to three-dimensional cases, including two-way coupling between fluid and structure and then turbulence and deforming geometries. To cover this wide range of applications, the classical benchmark of a sedimenting sphere is chosen first to validate the general two-way coupling algorithm. Increasing the complexity, we subsequently consider the simulation of a plunging SD7003 airfoil in the transitional regime at a Reynolds number of Re =40 000 and, finally, to access the model's performance for deforming geometries, we conduct a two-way coupled simulation of a self-propelled anguilliform swimmer. These simulations confirm the viability of the new fluid-structure interaction lattice Boltzmann algorithm to simulate flows of engineering relevance.

Application of Hermitian time-dependent coupled-cluster response Ansätze of second order to excitation energies and frequency-dependent dipole polarizabilities

NASA Astrophysics Data System (ADS)

Wälz, Gero; Kats, Daniel; Usvyat, Denis; Korona, Tatiana; Schütz, Martin

2012-11-01

Linear-response methods, based on the time-dependent variational coupled-cluster or the unitary coupled-cluster model, and truncated at the second order according to the Møller-Plesset partitioning, i.e., the TD-VCC[2] and TD-UCC[2] linear-response methods, are presented and compared. For both of these methods a Hermitian eigenvalue problem has to be solved to obtain excitation energies and state eigenvectors. The excitation energies thus are guaranteed always to be real valued, and the eigenvectors are mutually orthogonal, in contrast to response theories based on “traditional” coupled-cluster models. It turned out that the TD-UCC[2] working equations for excitation energies and polarizabilities are equivalent to those of the second-order algebraic diagrammatic construction scheme ADC(2). Numerical tests are carried out by calculating TD-VCC[2] and TD-UCC[2] excitation energies and frequency-dependent dipole polarizabilities for several test systems and by comparing them to the corresponding values obtained from other second- and higher-order methods. It turns out that the TD-VCC[2] polarizabilities in the frequency regions away from the poles are of a similar accuracy as for other second-order methods, as expected from the perturbative analysis of the TD-VCC[2] polarizability expression. On the other hand, the TD-VCC[2] excitation energies are systematically too low relative to other second-order methods (including TD-UCC[2]). On the basis of these results and an analysis presented in this work, we conjecture that the perturbative expansion of the Jacobian converges more slowly for the TD-VCC formalism than for TD-UCC or for response theories based on traditional coupled-cluster models.

Theoretical studies on the coupling interactions in H2SO4···HOO˙···(H2O)n (n = 0-2) clusters: toward understanding the role of water molecules in the uptake of HOO˙ radical by sulfuric acid aerosols.

PubMed

Li, Ping; Ma, Zhiying; Wang, Weihua; Zhai, Yazhou; Sun, Haitao; Bi, Siwei; Bu, Yuxiang

2011-01-21

A detailed knowledge of coupling interactions among sulfuric acid (H(2)SO(4)), the hydroperoxyl radical (HOO˙), and water molecules (H(2)O) is crucial for the better understanding of the uptake of HOO˙ radicals by sulfuric acid aerosols at different atmospheric humidities. In the present study, the equilibrium structures, binding energies, equilibrium distributions, and the nature of the coupling interactions in H(2)SO(4)···HOO˙···(H(2)O)(n) (n = 0-2) clusters have been systematically investigated at the B3LYP/6-311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, natural bond orbital (NBO) method, energy decomposition analyses, and ab initio molecular dynamics. Two binary, five ternary, and twelve tetramer clusters possessing multiple intermolecular H-bonds have been located on their potential energy surfaces. Two different modes for water molecules have been observed to influence the coupling interactions between H(2)SO(4) and HOO˙ through the formations of intermolecular H-bonds with or without breaking the original intermolecular H-bonds in the binary H(2)SO(4)···HOO˙ cluster. It was found that the introduction of one or two water molecules can efficiently enhance the interactions between H(2)SO(4) and HOO˙, implying the positive role of water molecules in the uptake of the HOO˙ radical by sulfuric acid aerosols. Additionally, the coupling interaction modes of the most stable clusters under study have been verified by the ab initio molecular dynamics.

First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

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

Varghese, Jithin J.; Mushrif, Samir H., E-mail: shmushrif@ntu.edu.sg

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barriermore » for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.« less

Cluster assembly in nitrogenase.

PubMed

Sickerman, Nathaniel S; Rettberg, Lee A; Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W

2017-05-09

The versatile enzyme system nitrogenase accomplishes the challenging reduction of N 2 and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe 8 S 7 ]-core P-cluster and a [MoFe 7 S 9 C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N 2 , and both originate from [Fe 4 S 4 ] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe 4 S 4 ] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [Fe 4 S 4 ] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a 'ninth' sulfur atom generates the [Fe 8 S 9 C]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Integrating the Nqueens Algorithm into a Parameterized Benchmark Suite

DTIC Science & Technology

2016-02-01

FOB is a 64-node heterogeneous cluster consisting of 16-IBM dx360M4 nodes, each with one NVIDIA Kepler K20M GPUs and 48-IBM dx360M4 nodes, and each...nodes have 256-GB of memory and an NVIDIA Tesla K40 GPU. More details on Excalibur can be found on the US Army DSRC website.19 Figures 3 and 4 show the

Approximate treatment of semicore states in GW calculations with application to Au clusters.

PubMed

Xian, Jiawei; Baroni, Stefano; Umari, P

2014-03-28

We address the treatment of transition metal atoms in GW electronic-structure calculations within the plane-wave pseudo-potential formalism. The contributions of s and p semi-core electrons to the self-energy, which are essential to grant an acceptable accuracy, are dealt with using a recently proposed scheme whereby the exchange components are treated exactly at the G0W0 level, whereas a suitable approximation to the correlation components is devised. This scheme is benchmarked for small gold nano-clusters, resulting in ionization potentials, electron affinities, and density of states in very good agreement with those obtained from calculations where s and p semicore states are treated as valence orbitals, and allowing us to apply this same scheme to clusters of intermediate size, Au20 and Au32, that would be otherwise very difficult to deal with.

Approximate treatment of semicore states in GW calculations with application to Au clusters

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

Xian, Jiawei; Baroni, Stefano; CNR-IOM Democritos, Theory-Elettra group, Trieste

We address the treatment of transition metal atoms in GW electronic-structure calculations within the plane-wave pseudo-potential formalism. The contributions of s and p semi-core electrons to the self-energy, which are essential to grant an acceptable accuracy, are dealt with using a recently proposed scheme whereby the exchange components are treated exactly at the G{sub 0}W{sub 0} level, whereas a suitable approximation to the correlation components is devised. This scheme is benchmarked for small gold nano-clusters, resulting in ionization potentials, electron affinities, and density of states in very good agreement with those obtained from calculations where s and p semicore statesmore » are treated as valence orbitals, and allowing us to apply this same scheme to clusters of intermediate size, Au{sub 20} and Au{sub 32}, that would be otherwise very difficult to deal with.« less

A high performance scientific cloud computing environment for materials simulations

NASA Astrophysics Data System (ADS)

Jorissen, K.; Vila, F. D.; Rehr, J. J.

2012-09-01

We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials science codes, together with essential interface tools (an SCC toolset) that offers functionality comparable to local compute clusters. In particular, our SCC toolset provides automatic creation of virtual clusters for parallel computing, including tools for execution and monitoring performance, as well as efficient I/O utilities that enable seamless connections to and from the cloud. Our SCC platform is optimized for the Amazon Elastic Compute Cloud (EC2). We present benchmarks for prototypical scientific applications and demonstrate performance comparable to local compute clusters. To facilitate code execution and provide user-friendly access, we have also integrated cloud computing capability in a JAVA-based GUI. Our SCC platform may be an alternative to traditional HPC resources for materials science or quantum chemistry applications.

High-performance scientific computing in the cloud

NASA Astrophysics Data System (ADS)

Jorissen, Kevin; Vila, Fernando; Rehr, John

2011-03-01

Cloud computing has the potential to open up high-performance computational science to a much broader class of researchers, owing to its ability to provide on-demand, virtualized computational resources. However, before such approaches can become commonplace, user-friendly tools must be developed that hide the unfamiliar cloud environment and streamline the management of cloud resources for many scientific applications. We have recently shown that high-performance cloud computing is feasible for parallelized x-ray spectroscopy calculations. We now present benchmark results for a wider selection of scientific applications focusing on electronic structure and spectroscopic simulation software in condensed matter physics. These applications are driven by an improved portable interface that can manage virtual clusters and run various applications in the cloud. We also describe a next generation of cluster tools, aimed at improved performance and a more robust cluster deployment. Supported by NSF grant OCI-1048052.

Multivariate Spatial Condition Mapping Using Subtractive Fuzzy Cluster Means

PubMed Central

Sabit, Hakilo; Al-Anbuky, Adnan

2014-01-01

Wireless sensor networks are usually deployed for monitoring given physical phenomena taking place in a specific space and over a specific duration of time. The spatio-temporal distribution of these phenomena often correlates to certain physical events. To appropriately characterise these events-phenomena relationships over a given space for a given time frame, we require continuous monitoring of the conditions. WSNs are perfectly suited for these tasks, due to their inherent robustness. This paper presents a subtractive fuzzy cluster means algorithm and its application in data stream mining for wireless sensor systems over a cloud-computing-like architecture, which we call sensor cloud data stream mining. Benchmarking on standard mining algorithms, the k-means and the FCM algorithms, we have demonstrated that the subtractive fuzzy cluster means model can perform high quality distributed data stream mining tasks comparable to centralised data stream mining. PMID:25313495

Application of multivariable statistical techniques in plant-wide WWTP control strategies analysis.

PubMed

Flores, X; Comas, J; Roda, I R; Jiménez, L; Gernaey, K V

2007-01-01

The main objective of this paper is to present the application of selected multivariable statistical techniques in plant-wide wastewater treatment plant (WWTP) control strategies analysis. In this study, cluster analysis (CA), principal component analysis/factor analysis (PCA/FA) and discriminant analysis (DA) are applied to the evaluation matrix data set obtained by simulation of several control strategies applied to the plant-wide IWA Benchmark Simulation Model No 2 (BSM2). These techniques allow i) to determine natural groups or clusters of control strategies with a similar behaviour, ii) to find and interpret hidden, complex and casual relation features in the data set and iii) to identify important discriminant variables within the groups found by the cluster analysis. This study illustrates the usefulness of multivariable statistical techniques for both analysis and interpretation of the complex multicriteria data sets and allows an improved use of information for effective evaluation of control strategies.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: Benchmarks approaching the complete basis set limit

NASA Astrophysics Data System (ADS)

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-01

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Møller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

On the accuracy of density-functional theory exchange-correlation functionals for H bonds in small water clusters: benchmarks approaching the complete basis set limit.

PubMed

Santra, Biswajit; Michaelides, Angelos; Scheffler, Matthias

2007-11-14

The ability of several density-functional theory (DFT) exchange-correlation functionals to describe hydrogen bonds in small water clusters (dimer to pentamer) in their global minimum energy structures is evaluated with reference to second order Moller-Plesset perturbation theory (MP2). Errors from basis set incompleteness have been minimized in both the MP2 reference data and the DFT calculations, thus enabling a consistent systematic evaluation of the true performance of the tested functionals. Among all the functionals considered, the hybrid X3LYP and PBE0 functionals offer the best performance and among the nonhybrid generalized gradient approximation functionals, mPWLYP and PBE1W perform best. The popular BLYP and B3LYP functionals consistently underbind and PBE and PW91 display rather variable performance with cluster size.

Interconnect Performance Evaluation of SGI Altix 3700 BX2, Cray X1, Cray Opteron Cluster, and Dell PowerEdge

NASA Technical Reports Server (NTRS)

Fatoohi, Rod; Saini, Subbash; Ciotti, Robert

2006-01-01

We study the performance of inter-process communication on four high-speed multiprocessor systems using a set of communication benchmarks. The goal is to identify certain limiting factors and bottlenecks with the interconnect of these systems as well as to compare these interconnects. We measured network bandwidth using different number of communicating processors and communication patterns, such as point-to-point communication, collective communication, and dense communication patterns. The four platforms are: a 512-processor SGI Altix 3700 BX2 shared-memory machine with 3.2 GB/s links; a 64-processor (single-streaming) Cray XI shared-memory machine with 32 1.6 GB/s links; a 128-processor Cray Opteron cluster using a Myrinet network; and a 1280-node Dell PowerEdge cluster with an InfiniBand network. Our, results show the impact of the network bandwidth and topology on the overall performance of each interconnect.

Intelligent Luminance Control of Lighting Systems Based on Imaging Sensor Feedback

PubMed Central

Liu, Haoting; Zhou, Qianxiang; Yang, Jin; Jiang, Ting; Liu, Zhizhen; Li, Jie

2017-01-01

An imaging sensor-based intelligent Light Emitting Diode (LED) lighting system for desk use is proposed. In contrast to the traditional intelligent lighting system, such as the photosensitive resistance sensor-based or the infrared sensor-based system, the imaging sensor can realize a finer perception of the environmental light; thus it can guide a more precise lighting control. Before this system works, first lots of typical imaging lighting data of the desk application are accumulated. Second, a series of subjective and objective Lighting Effect Evaluation Metrics (LEEMs) are defined and assessed for these datasets above. Then the cluster benchmarks of these objective LEEMs can be obtained. Third, both a single LEEM-based control and a multiple LEEMs-based control are developed to realize a kind of optimal luminance tuning. When this system works, first it captures the lighting image using a wearable camera. Then it computes the objective LEEMs of the captured image and compares them with the cluster benchmarks of the objective LEEMs. Finally, the single LEEM-based or the multiple LEEMs-based control can be implemented to get a kind of optimal lighting effect. Many experiment results have shown the proposed system can tune the LED lamp automatically according to environment luminance changes. PMID:28208781

Intelligent Luminance Control of Lighting Systems Based on Imaging Sensor Feedback.

PubMed

Liu, Haoting; Zhou, Qianxiang; Yang, Jin; Jiang, Ting; Liu, Zhizhen; Li, Jie

2017-02-09

An imaging sensor-based intelligent Light Emitting Diode (LED) lighting system for desk use is proposed. In contrast to the traditional intelligent lighting system, such as the photosensitive resistance sensor-based or the infrared sensor-based system, the imaging sensor can realize a finer perception of the environmental light; thus it can guide a more precise lighting control. Before this system works, first lots of typical imaging lighting data of the desk application are accumulated. Second, a series of subjective and objective Lighting Effect Evaluation Metrics (LEEMs) are defined and assessed for these datasets above. Then the cluster benchmarks of these objective LEEMs can be obtained. Third, both a single LEEM-based control and a multiple LEEMs-based control are developed to realize a kind of optimal luminance tuning. When this system works, first it captures the lighting image using a wearable camera. Then it computes the objective LEEMs of the captured image and compares them with the cluster benchmarks of the objective LEEMs. Finally, the single LEEM-based or the multiple LEEMs-based control can be implemented to get a kind of optimal lighting effect. Many experiment results have shown the proposed system can tune the LED lamp automatically according to environment luminance changes.

Comparison of the PHISICS/RELAP5-3D ring and block model results for phase I of the OECD/NEA MHTGR-350 benchmark

DOE PAGES

Strydom, G.; Epiney, A. S.; Alfonsi, Andrea; ...

2015-12-02

The PHISICS code system has been under development at INL since 2010. It consists of several modules providing improved coupled core simulation capability: INSTANT (3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and modules performing criticality searches, fuel shuffling and generalized perturbation. Coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D was finalized in 2013, and as part of the verification and validation effort the first phase of the OECD/NEA MHTGR-350 Benchmark has now been completed. The theoretical basis and latest development status of the coupled PHISICS/RELAP5-3D tool are described in more detailmore » in a concurrent paper. This paper provides an overview of the OECD/NEA MHTGR-350 Benchmark and presents the results of Exercises 2 and 3 defined for Phase I. Exercise 2 required the modelling of a stand-alone thermal fluids solution at End of Equilibrium Cycle for the Modular High Temperature Reactor (MHTGR). The RELAP5-3D results of four sub-cases are discussed, consisting of various combinations of coolant bypass flows and material thermophysical properties. Exercise 3 required a coupled neutronics and thermal fluids solution, and the PHISICS/RELAP5-3D code suite was used to calculate the results of two sub-cases. The main focus of the paper is a comparison of results obtained with the traditional RELAP5-3D “ring” model approach against a much more detailed model that include kinetics feedback on individual block level and thermal feedbacks on a triangular sub-mesh. The higher fidelity that can be obtained by this “block” model is illustrated with comparison results on the temperature, power density and flux distributions. Furthermore, it is shown that the ring model leads to significantly lower fuel temperatures (up to 10%) when compared with the higher fidelity block model, and that the additional model development and run-time efforts are worth the gains obtained in the improved spatial temperature and flux distributions.« less

Pulse-coupled mixed-mode oscillators: Cluster states and extreme noise sensitivity

NASA Astrophysics Data System (ADS)

Karamchandani, Avinash J.; Graham, James N.; Riecke, Hermann

2018-04-01

Motivated by rhythms in the olfactory system of the brain, we investigate the synchronization of all-to-all pulse-coupled neuronal oscillators exhibiting various types of mixed-mode oscillations (MMOs) composed of sub-threshold oscillations (STOs) and action potentials ("spikes"). We focus particularly on the impact of the delay in the interaction. In the weak-coupling regime, we reduce the system to a Kuramoto-type equation with non-sinusoidal phase coupling and the associated Fokker-Planck equation. Its linear stability analysis identifies the appearance of various cluster states. Their type depends sensitively on the delay and the width of the pulses. Interestingly, long delays do not imply slow population rhythms, and the number of emerging clusters only loosely depends on the number of STOs. Direct simulations of the oscillator equations reveal that for quantitative agreement of the weak-coupling theory the coupling strength and the noise have to be extremely small. Even moderate noise leads to significant skipping of STO cycles, which can enhance the diffusion coefficient in the Fokker-Planck equation by two orders of magnitude. Introducing an effective diffusion coefficient extends the range of agreement significantly. Numerical simulations of the Fokker-Planck equation reveal bistability and solutions with oscillatory order parameters that result from nonlinear mode interactions. These are confirmed in simulations of the full spiking model.

Chimera states in nonlocally coupled phase oscillators with biharmonic interaction

NASA Astrophysics Data System (ADS)

Cheng, Hongyan; Dai, Qionglin; Wu, Nianping; Feng, Yuee; Li, Haihong; Yang, Junzhong

2018-03-01

Chimera states, which consist of coexisting domains of coherent and incoherent parts, have been observed in a variety of systems. Most of previous works on chimera states have taken into account specific form of interaction between oscillators, for example, sinusoidal coupling or diffusive coupling. Here, we investigate chimera dynamics in nonlocally coupled phase oscillators with biharmonic interaction. We find novel chimera states with features such as that oscillators in the same coherent cluster may split into two groups with a phase difference around π/2 and that oscillators in adjacent coherent clusters may have a phase difference close to π/2. The different impacts of the coupling ranges in the first and the second harmonic interactions on chimera dynamics are investigated based on the synchronous dynamics in globally coupled phase oscillators. Our study suggests a new direction in the field of chimera dynamics.

Event-based cluster synchronization of coupled genetic regulatory networks

NASA Astrophysics Data System (ADS)

Yue, Dandan; Guan, Zhi-Hong; Li, Tao; Liao, Rui-Quan; Liu, Feng; Lai, Qiang

2017-09-01

In this paper, the cluster synchronization of coupled genetic regulatory networks with a directed topology is studied by using the event-based strategy and pinning control. An event-triggered condition with a threshold consisting of the neighbors' discrete states at their own event time instants and a state-independent exponential decay function is proposed. The intra-cluster states information and extra-cluster states information are involved in the threshold in different ways. By using the Lyapunov function approach and the theories of matrices and inequalities, we establish the cluster synchronization criterion. It is shown that both the avoidance of continuous transmission of information and the exclusion of the Zeno behavior are ensured under the presented triggering condition. Explicit conditions on the parameters in the threshold are obtained for synchronization. The stability criterion of a single GRN is also given under the reduced triggering condition. Numerical examples are provided to validate the theoretical results.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the 199Hg Atom

NASA Astrophysics Data System (ADS)

Sahoo, B. K.; Das, B. P.

2018-05-01

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P ,T -odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P ,T -odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to 199Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Relativistic Normal Coupled-Cluster Theory for Accurate Determination of Electric Dipole Moments of Atoms: First Application to the ^{199}Hg Atom.

PubMed

Sahoo, B K; Das, B P

2018-05-18

Recent relativistic coupled-cluster (RCC) calculations of electric dipole moments (EDMs) of diamagnetic atoms due to parity and time-reversal violating (P,T-odd) interactions, which are essential ingredients for probing new physics beyond the standard model of particle interactions, differ substantially from the previous theoretical results. It is therefore necessary to perform an independent test of the validity of these results. In view of this, the normal coupled-cluster method has been extended to the relativistic regime [relativistic normal coupled-cluster (RNCC) method] to calculate the EDMs of atoms by simultaneously incorporating the electrostatic and P,T-odd interactions in order to overcome the shortcomings of the ordinary RCC method. This new relativistic method has been applied to ^{199}Hg, which currently has a lower EDM limit than that of any other system. The results of our RNCC and self-consistent RCC calculations of the EDM of this atom are found to be close. The discrepancies between these two results on the one hand and those of previous calculations on the other are elucidated. Furthermore, the electric dipole polarizability of this atom, which has computational similarities with the EDM, is evaluated and it is in very good agreement with its measured value.

Electron and nuclear dynamics of molecular clusters in ultraintense laser fields. IV. Coulomb explosion of molecular heteroclusters

NASA Astrophysics Data System (ADS)

Last, Isidore; Jortner, Joshua

2004-11-01

In this paper we present a theoretical and computational study of the temporal dynamics and energetics of Coulomb explosion of (CD4)n and (CH4)n (n=55-4213) molecular heteroclusters in ultraintense (I=1016-1019W cm-2) laser fields, addressing the manifestation of electron dynamics, together with nuclear energetic and kinematic effects on the heterocluster Coulomb instability. The manifestations of the coupling between electron and nuclear dynamics were explored by molecular dynamics simulations for these heteroclusters coupled to Gaussian laser fields (pulse width τ=25 fs), elucidating outer ionization dynamics, nanoplasma screening effects (being significant for I⩽1017 W cm-2), and the attainment of cluster vertical ionization (CVI) (at I=1017 W cm-2 for cluster radius R0⩽31 Å). Nuclear kinematic effects on heterocluster Coulomb explosion are governed by the kinematic parameter η=qCmA/qAmC for (CA4)n clusters (A=H,D), where qj and mj (j=A,C) are the ionic charges and masses. Nonuniform heterocluster Coulomb explosion (η>1) manifests an overrun effect of the light ions relative to the heavy ions, exhibiting the expansion of two spatially separated subclusters, with the light ions forming the outer subcluster at the outer edge of the spatial distribution. Important features of the energetics of heterocluster Coulomb explosion originate from energetic triggering effects of the driving of the light ions by the heavy ions (C4+ for I=1017-1018W cm-2 and C6+ for I=1019 W cm-2), as well as for kinematic effects. Based on the CVI assumption, scaling laws for the cluster size (radius R0) dependence of the energetics of uniform Coulomb explosion of heteroclusters (η=1) were derived, with the size dependence of the average (Ej,av) and maximal (Ej,M) ion energies being Ej,av=aR02 and Ej,M=(5a/3)R02, as well as for the ion energy distributions P(Ej)∝Ej1/2; Ej⩽Ej,M. These results for uniform Coulomb explosion serve as benchmark reference data for the assessment of the effects of nonuniform explosion, where the CVI scaling law for the energetics still holds, with deviations of the a coefficient, which increase with increasing η. Kinematic effects (for η>1) result in an isotope effect, predicting the enhancement (by 9%-11%) of EH,av for Coulomb explosion of (C4+H4+)η (η=3) relative to ED,av for Coulomb explosion of (C4+D4+)η (η=1.5), with the isotope effect being determined by the ratio of the kinematic parameters for the pair of Coulomb exploding clusters. Kinematic effects for nonuniform explosion also result in a narrow isotope dependent energy distribution (of width ΔE) of the light ions (with ΔE/EH,av≃0.3 and ΔE/ED,av≃0.4), with the distribution peaking at the high energy edge, in marked contrast with the uniform explosion case. Features of laser-heterocluster interactions were inferred from the analyses of the intensity dependent boundary radii (R0)I and the corresponding average D+ ion energies (ED,av)I, which provide a measure for optimization of the cluster size at intensity I for the neutron yield from dd nuclear fusion driven by Coulomb explosion (NFDCE) of these heteroclusters. We infer on the advantage of deuterium containing heteronuclear clusters, e.g., (CD4)n in comparison to homonuclear clusters, e.g., (D2)n/2, for dd NFDCE, where the highly charged heavy ions (e.g., C4+ or C6+) serve as energetic and kinematic triggers driving the D+ ions to a high (10-200 keV) energy domain.

Communication: Relativistic Fock-space coupled cluster study of small building blocks of larger uranium complexes.

PubMed

Tecmer, Paweł; Gomes, André Severo Pereira; Knecht, Stefan; Visscher, Lucas

2014-07-28

We present a study of the electronic structure of the [UO2](+), [UO2](2 +), [UO2](3 +), NUO, [NUO](+), [NUO](2 +), [NUN](-), NUN, and [NUN](+) molecules with the intermediate Hamiltonian Fock-space coupled cluster method. The accuracy of mean-field approaches based on the eXact-2-Component Hamiltonian to incorporate spin-orbit coupling and Gaunt interactions are compared to results obtained with the Dirac-Coulomb Hamiltonian. Furthermore, we assess the reliability of calculations employing approximate density functionals in describing electronic spectra and quantities useful in rationalizing Uranium (VI) species reactivity (hardness, electronegativity, and electrophilicity).

Communication: Relativistic Fock-space coupled cluster study of small building blocks of larger uranium complexes

NASA Astrophysics Data System (ADS)

Tecmer, Paweł; Severo Pereira Gomes, André; Knecht, Stefan; Visscher, Lucas

2014-07-01

We present a study of the electronic structure of the [UO2]+, [UO2]2 +, [UO2]3 +, NUO, [NUO]+, [NUO]2 +, [NUN]-, NUN, and [NUN]+ molecules with the intermediate Hamiltonian Fock-space coupled cluster method. The accuracy of mean-field approaches based on the eXact-2-Component Hamiltonian to incorporate spin-orbit coupling and Gaunt interactions are compared to results obtained with the Dirac-Coulomb Hamiltonian. Furthermore, we assess the reliability of calculations employing approximate density functionals in describing electronic spectra and quantities useful in rationalizing Uranium (VI) species reactivity (hardness, electronegativity, and electrophilicity).

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

PubMed Central

Ding, Jiarui; Shah, Sohrab; Condon, Anne

2016-01-01

Motivation: Many biological data processing problems can be formalized as clustering problems to partition data points into sensible and biologically interpretable groups. Results: This article introduces densityCut, a novel density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K-nearest neighbour graph and then refines the densities via a random walk. A cluster consists of points falling into the basin of attraction of an estimated mode of the underlining density function. A post-processing step merges clusters and generates a hierarchical cluster tree. The number of clusters is selected from the most stable clustering in the hierarchical cluster tree. Experimental results on ten synthetic benchmark datasets and two microarray gene expression datasets demonstrate that densityCut performs better than state-of-the-art algorithms for clustering biological datasets. For applications, we focus on the recent cancer mutation clustering and single cell data analyses, namely to cluster variant allele frequencies of somatic mutations to reveal clonal architectures of individual tumours, to cluster single-cell gene expression data to uncover cell population compositions, and to cluster single-cell mass cytometry data to detect communities of cells of the same functional states or types. densityCut performs better than competing algorithms and is scalable to large datasets. Availability and Implementation: Data and the densityCut R package is available from https://bitbucket.org/jerry00/densitycut_dev. Contact: condon@cs.ubc.ca or sshah@bccrc.ca or jiaruid@cs.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153661

Macroscopic Magnetic Coupling Effect: The Physical Origination of a High-Temperature Superconducting Flux Pump

NASA Astrophysics Data System (ADS)

Wang, Wei; Coombs, Tim

2018-04-01

We have uncovered at the macroscopic scale a magnetic coupling phenomenon in a superconducting YBa2Cu3O7 -δ (YBCO) film, which physically explains the mechanism of the high-temperature superconducting flux pump. The coupling occurs between the applied magnetic poles and clusters of vortices induced in the YBCO film, with each cluster containing millions of vortices. The coupling energy is verified to originate from the inhomogeneous field of the magnetic poles, which reshapes the vortex distribution, aggregates millions of vortices into a single cluster, and accordingly moves with the poles. A contrast study is designed to verify that, to provide the effective coupling energy, the applied wavelength must be short while the field amplitude must be strong, i.e., local-field inhomogeneity is the crucial factor. This finding broadens our understanding of the collective vortex behavior in an applied magnetic field with strong local inhomogeneity. Moreover, this phenomenon largely increases the controlled vortex flow rate by several orders of magnitude compared with existing methods, providing motivation for and physical support to a new branch of wireless superconducting dc power sources, i.e., the high-temperature superconducting flux pump.

A Benchmarking setup for Coupled Earthquake Cycle - Dynamic Rupture - Tsunami Simulations

NASA Astrophysics Data System (ADS)

Behrens, Joern; Bader, Michael; van Dinther, Ylona; Gabriel, Alice-Agnes; Madden, Elizabeth H.; Ulrich, Thomas; Uphoff, Carsten; Vater, Stefan; Wollherr, Stephanie; van Zelst, Iris

2017-04-01

We developed a simulation framework for coupled physics-based earthquake rupture generation with tsunami propagation and inundation on a simplified subduction zone system for the project "Advanced Simulation of Coupled Earthquake and Tsunami Events" (ASCETE, funded by the Volkswagen Foundation). Here, we present a benchmarking setup that can be used for complex rupture models. The workflow begins with a 2D seismo-thermo-mechanical earthquake cycle model representing long term deformation along a planar, shallowly dipping subduction zone interface. Slip instabilities that approximate earthquakes arise spontaneously along the subduction zone interface in this model. The absolute stress field and material properties for a single slip event are used as initial conditions for a dynamic earthquake rupture model.The rupture simulation is performed with SeisSol, which uses an ADER discontinuous Galerkin discretization scheme with an unstructured tetrahedral mesh. The seafloor displacements resulting from this rupture are transferred to the tsunami model with a simple coastal run-up profile. An adaptive mesh discretizing the shallow water equations with a Runge-Kutta discontinuous Galerkin (RKDG) scheme subsequently allows for an accurate and efficient representation of the tsunami evolution and inundation at the coast. This workflow allows for evaluation of how the rupture behavior affects the hydrodynamic wave propagation and coastal inundation. We present coupled results for differing earthquake scenarios. Examples include megathrust only ruptures versus ruptures with splay fault branching off the megathrust near the surface. Coupling to the tsunami simulation component is performed either dynamically (time dependent) or statically, resulting in differing tsunami wave and inundation behavior. The simplified topographical setup allows for systematic parameter studies and reproducible physical studies.

Parameters that affect parallel processing for computational electromagnetic simulation codes on high performance computing clusters

NASA Astrophysics Data System (ADS)

Moon, Hongsik

What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the changing computer hardware platforms in order to provide fast, accurate and efficient solutions to large, complex electromagnetic problems. The research in this dissertation proves that the performance of parallel code is intimately related to the configuration of the computer hardware and can be maximized for different hardware platforms. To benchmark and optimize the performance of parallel CEM software, a variety of large, complex projects are created and executed on a variety of computer platforms. The computer platforms used in this research are detailed in this dissertation. The projects run as benchmarks are also described in detail and results are presented. The parameters that affect parallel CEM software on High Performance Computing Clusters (HPCC) are investigated. This research demonstrates methods to maximize the performance of parallel CEM software code.

Generation of strongly coupled Xe cluster nanoplasmas by low intensive soft x-ray laser irradiation

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

Namba, S.; Hasegawa, N.; Kishimoto, M.

A seeding gas jet including Xe clusters was irradiated with a laser-driven plasma soft x-ray laser pulse ({lambda}=13.9 nm, {approx}7 ps, {<=}5 Multiplication-Sign 10{sup 9} W/cm{sup 2}), where the laser photon energy is high enough to ionize 4d core electrons. In order to clarify how the innershell ionization followed by the Auger electron emission is affected under the intense laser irradiation, the electron energy distribution was measured. Photoelectron spectra showed that the peak position attributed to 4d hole shifted to lower energy and the spectral width was broadened with increasing cluster size. Moreover, the energy distribution exhibited that a stronglymore » coupled cluster nanoplasma with several eV was generated.« less

Stability and Noise-induced Transitions in an Ensemble of Nonlocally Coupled Chaotic Maps

NASA Astrophysics Data System (ADS)

Bukh, Andrei V.; Slepnev, Andrei V.; Anishchenko, Vadim S.; Vadivasova, Tatiana E.

2018-05-01

The influence of noise on chimera states arising in ensembles of nonlocally coupled chaotic maps is studied. There are two types of chimera structures that can be obtained in such ensembles: phase and amplitude chimera states. In this work, a series of numerical experiments is carried out to uncover the impact of noise on both types of chimeras. The noise influence on a chimera state in the regime of periodic dynamics results in the transition to chaotic dynamics. At the same time, the transformation of incoherence clusters of the phase chimera to incoherence clusters of the amplitude chimera occurs. Moreover, it is established that the noise impact may result in the appearance of a cluster with incoherent behavior in the middle of a coherence cluster.

Excitons in Potassium Bromide: A Study using Embedded Time-dependent Density Functional Theory and Equation-of-Motion Coupled Cluster Methods

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

Govind, Niranjan; Sushko, Petr V.; Hess, Wayne P.

2009-03-05

We present a study of the electronic excitations in insulating materials using an embedded- cluster method. The excited states of the embedded cluster are studied systematically using time-dependent density functional theory (TDDFT) and high-level equation-of-motion coupled cluster (EOMCC) methods. In particular, we have used EOMCC models with singles and doubles (EOMCCSD) and two approaches which account for the e®ect of triply excited con¯gurations in non-iterative and iterative fashions. We present calculations of the lowest surface excitations of the well-studied potassium bromide (KBr) system and compare our results with experiment. The bulk-surface exciton shift is also calculated at the TDDFT levelmore » and compared with experiment.« less

Impact of symmetry breaking in networks of globally coupled oscillators

NASA Astrophysics Data System (ADS)

Premalatha, K.; Chandrasekar, V. K.; Senthilvelan, M.; Lakshmanan, M.

2015-05-01

We analyze the consequences of symmetry breaking in the coupling in a network of globally coupled identical Stuart-Landau oscillators. We observe that symmetry breaking leads to increased disorderliness in the dynamical behavior of oscillatory states and consequently results in a rich variety of dynamical states. Depending on the strength of the nonisochronicity parameter, we find various dynamical states such as amplitude chimera, amplitude cluster, frequency chimera, and frequency cluster states. In addition we also find disparate transition routes to recently observed chimera death states in the presence of symmetry breaking even with global coupling. We also analytically verify the chimera death region, which corroborates the numerical results. These results are compared with that of the symmetry-preserving case as well.

Dataset of Fourier transform-infrared coupled with chemometric analysis used to distinguish accessions of Garcinia mangostana L. in Peninsular Malaysia.

PubMed

Samsir, Sri A'jilah; Bunawan, Hamidun; Yen, Choong Chee; Noor, Normah Mohd

2016-09-01

In this dataset, we distinguish 15 accessions of Garcinia mangostana from Peninsular Malaysia using Fourier transform-infrared spectroscopy coupled with chemometric analysis. We found that the position and intensity of characteristic peaks at 3600-3100 cm(-) (1) in IR spectra allowed discrimination of G. mangostana from different locations. Further principal component analysis (PCA) of all the accessions suggests the two main clusters were formed: samples from Johor, Melaka, and Negeri Sembilan (South) were clustered together in one group while samples from Perak, Kedah, Penang, Selangor, Kelantan, and Terengganu (North and East Coast) were in another clustered group.

Modelling charge transfer reactions with the frozen density embedding formalism.

PubMed

Pavanello, Michele; Neugebauer, Johannes

2011-12-21

The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5'-GG-3' and 5'-GT-3'. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.

CCC calculated differential cross sections of electron-H2 scattering

NASA Astrophysics Data System (ADS)

Fursa, Dmitry; Zammit, Mark; Savage, Jeremy; Bray, Igor

2016-09-01

Recently we applied the molecular convergent close-coupling (CCC) method to electron scattering from molecular hydrogen H2. Convergence of the major differential cross sections has been explicitly demonstrated in the fixed-nuclei approximation. A large close-coupling expansion that coupled highly excited states and ionization channels proved to be important to obtain convergent results. Here we present benchmark elastic and electronic excitation differential cross sections for b3Σu+ , a3Σg+ , c3Πu , B1Σu+ , EF1Σg+ , C1Πu , and e3Σu+ states and compare with available experiment and previous calculations. Work supported by Los Alamos National Laboratory and Curtin University.

Communication: Biological applications of coupled-cluster frozen-density embedding

NASA Astrophysics Data System (ADS)

Heuser, Johannes; Höfener, Sebastian

2018-04-01

We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2-in-DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.

Attenuated coupled cluster: a heuristic polynomial similarity transformation incorporating spin symmetry projection into traditional coupled cluster theory

NASA Astrophysics Data System (ADS)

Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

2017-11-01

In electronic structure theory, restricted single-reference coupled cluster (CC) captures weak correlation but fails catastrophically under strong correlation. Spin-projected unrestricted Hartree-Fock (SUHF), on the other hand, misses weak correlation but captures a large portion of strong correlation. The theoretical description of many important processes, e.g. molecular dissociation, requires a method capable of accurately capturing both weak and strong correlation simultaneously, and would likely benefit from a combined CC-SUHF approach. Based on what we have recently learned about SUHF written as particle-hole excitations out of a symmetry-adapted reference determinant, we here propose a heuristic CC doubles model to attenuate the dominant spin collective channel of the quadratic terms in the CC equations. Proof of principle results presented here are encouraging and point to several paths forward for improving the method further.

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

PubMed

Yu, Yang; Li, Chen; Yin, Bing; Li, Jian-Li; Huang, Yuan-He; Wen, Zhen-Yi; Jiang, Zhen-Yi

2013-08-07

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Partially linearized external models to active-space coupled-cluster through connected hextuple excitations.

PubMed

Xu, Enhua; Ten-No, Seiichiro L

2018-06-05

Partially linearized external models to active-space coupled-cluster through hextuple excitations, for example, CC{SDtqph} L , CCSD{tqph} L , and CCSD{tqph} hyb, are implemented and compared with the full active-space CCSDtqph. The computational scaling of CCSDtqph coincides with that for the standard coupled-cluster singles and doubles (CCSD), yet with a much large prefactor. The approximate schemes to linearize the external excitations higher than doubles are significantly cheaper than the full CCSDtqph model. These models are applied to investigate the bond dissociation energies of diatomic molecules (HF, F 2 , CuH, and CuF), and the potential energy surfaces of the bond dissociation processes of HF, CuH, H 2 O, and C 2 H 4 . Among the approximate models, CCSD{tqph} hyb provides very accurate descriptions compared with CCSDtqph for all of the tested systems. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A quantitative study of the clustering of polycyclic aromatic hydrocarbons at high temperatures.

PubMed

Totton, Tim S; Misquitta, Alston J; Kraft, Markus

2012-03-28

The clustering of polycyclic aromatic hydrocarbon (PAH) molecules is investigated in the context of soot particle inception and growth using an isotropic potential developed from the benchmark PAHAP potential. This potential is used to estimate equilibrium constants of dimerisation for five representative PAH molecules based on a statistical mechanics model. Molecular dynamics simulations are also performed to study the clustering of homomolecular systems at a range of temperatures. The results from both sets of calculations demonstrate that at flame temperatures pyrene (C(16)H(10)) dimerisation cannot be a key step in soot particle formation and that much larger molecules (e.g. circumcoronene, C(54)H(18)) are required to form small clusters at flame temperatures. The importance of using accurate descriptions of the intermolecular interactions is demonstrated by comparing results to those calculated with a popular literature potential with an order of magnitude variation in the level of clustering observed. By using an accurate intermolecular potential we are able to show that physical binding of PAH molecules based on van der Waals interactions alone can only be a viable soot inception mechanism if concentrations of large PAH molecules are significantly higher than currently thought.

Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering.

PubMed

Wang, Changqing; Kipping, Judy; Bao, Chenglong; Ji, Hui; Qiu, Anqi

2016-01-01

The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI). For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC). SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organization in children.

Comparative Investigation of Shared Filesystems for the LHCb Online Cluster

NASA Astrophysics Data System (ADS)

Vijay Kartik, S.; Neufeld, Niko

2012-12-01

This paper describes the investigative study undertaken to evaluate shared filesystem performance and suitability in the LHCb Online environment. Particular focus is given to the measurements and field tests designed and performed on an in-house OpenAFS setup; related comparisons with NFSv4 and GPFS (a clustered filesystem from IBM) are presented. The motivation for the investigation and the test setup arises from the need to serve common user-space like home directories, experiment software and control areas, and clustered log areas. Since the operational requirements on such user-space are stringent in terms of read-write operations (in frequency and access speed) and unobtrusive data relocation, test results are presented with emphasis on file-level performance, stability and “high-availability” of the shared filesystems. Use cases specific to the experiment operation in LHCb, including the specific handling of shared filesystems served to a cluster of 1500 diskless nodes, are described. Issues of prematurely expiring authenticated sessions are explicitly addressed, keeping in mind long-running analysis jobs on the Online cluster. In addition, quantitative test results are also presented with alternatives including NFSv4. Comparative measurements of filesystem performance benchmarks are presented, which are seen to be used as reference for decisions on potential migration of the current storage solution deployed in the LHCb online cluster.

Spin-orbit coupling effect on structural and magnetic properties of ConRh13-n (n = 0-13) clusters

NASA Astrophysics Data System (ADS)

Bai, Xi; Lv, Jin; Zhang, Fu-Qiang; Jia, Jian-Feng; Wu, Hai-Shun

2018-04-01

The effect of spin-orbit interaction on the structures and magnetism of ConRh13-n (n = 0-13) clusters have been systematically investigated by using the spin-orbit coupling (SOC) implementation of the density functional theory (DFT). The results calculated without SOC (NSOC) show that Rh13 prefers the double simple-cubic configuration, and icosahedron is the favorable structure for n = 1-9, while n ≥ 10, clusters favor the hexagonal bilayer structure. The inclusion of SOC in calculation does not change the geometries of clusters. Compared with that in NSOC calculation, although the binding energy per atom in clusters with same composition decreases in SOC calculation, the relative stability of clusters with different compositions does not change. An interesting result is that the spin moments of clusters for n = 1-9 are almost constant (21 μB). Spin-orbit interaction recovers orbital moment and its anisotropy by removing crystal-field effect in calculation. The destruction of bonding symmetry and relaxation of bonding account for high anisotropies of orbital moments in Co11Rh2 and CoRh12 clusters. With atomic composition (Co/Rh) around 4/9-5/8 and 9/4, the Co-Rh clusters exhibit high magnetic anisotropy energies.

Inclusion of orbital relaxation and correlation through the unitary group adapted open shell coupled cluster theory using non-relativistic and scalar relativistic Hamiltonians to study the core ionization potential of molecules containing light to medium-heavy elements

NASA Astrophysics Data System (ADS)

Sen, Sangita; Shee, Avijit; Mukherjee, Debashis

2018-02-01

The orbital relaxation attendant on ionization is particularly important for the core electron ionization potential (core IP) of molecules. The Unitary Group Adapted State Universal Coupled Cluster (UGA-SUMRCC) theory, recently formulated and implemented by Sen et al. [J. Chem. Phys. 137, 074104 (2012)], is very effective in capturing orbital relaxation accompanying ionization or excitation of both the core and the valence electrons [S. Sen et al., Mol. Phys. 111, 2625 (2013); A. Shee et al., J. Chem. Theory Comput. 9, 2573 (2013)] while preserving the spin-symmetry of the target states and using the neutral closed-shell spatial orbitals of the ground state. Our Ansatz invokes a normal-ordered exponential representation of spin-free cluster-operators. The orbital relaxation induced by a specific set of cluster operators in our Ansatz is good enough to eliminate the need for different sets of orbitals for the ground and the core-ionized states. We call the single configuration state function (CSF) limit of this theory the Unitary Group Adapted Open-Shell Coupled Cluster (UGA-OSCC) theory. The aim of this paper is to comprehensively explore the efficacy of our Ansatz to describe orbital relaxation, using both theoretical analysis and numerical performance. Whenever warranted, we also make appropriate comparisons with other coupled-cluster theories. A physically motivated truncation of the chains of spin-free T-operators is also made possible by the normal-ordering, and the operational resemblance to single reference coupled-cluster theory allows easy implementation. Our test case is the prediction of the 1s core IP of molecules containing a single light- to medium-heavy nucleus and thus, in addition to demonstrating the orbital relaxation, we have addressed the scalar relativistic effects on the accuracy of the IPs by using a hierarchy of spin-free Hamiltonians in conjunction with our theory. Additionally, the contribution of the spin-free component of the two-electron Gaunt term, not usually taken into consideration, has been estimated at the Self-Consistent Field (ΔSCF) level and is found to become increasingly important and eventually quite prominent for molecules with third period atoms and below. The accuracies of the IPs computed using UGA-OSCC are found to be of the same order as the Coupled Cluster Singles Doubles (ΔCCSD) values while being free from spin contamination. Since the UGA-OSCC uses a common set of orbitals for the ground state and the ion, it obviates the need of two N5 AO to MO transformation in contrast to the ΔCCSD method.

Inclusion of orbital relaxation and correlation through the unitary group adapted open shell coupled cluster theory using non-relativistic and scalar relativistic Hamiltonians to study the core ionization potential of molecules containing light to medium-heavy elements.

PubMed

Sen, Sangita; Shee, Avijit; Mukherjee, Debashis

2018-02-07

The orbital relaxation attendant on ionization is particularly important for the core electron ionization potential (core IP) of molecules. The Unitary Group Adapted State Universal Coupled Cluster (UGA-SUMRCC) theory, recently formulated and implemented by Sen et al. [J. Chem. Phys. 137, 074104 (2012)], is very effective in capturing orbital relaxation accompanying ionization or excitation of both the core and the valence electrons [S. Sen et al., Mol. Phys. 111, 2625 (2013); A. Shee et al., J. Chem. Theory Comput. 9, 2573 (2013)] while preserving the spin-symmetry of the target states and using the neutral closed-shell spatial orbitals of the ground state. Our Ansatz invokes a normal-ordered exponential representation of spin-free cluster-operators. The orbital relaxation induced by a specific set of cluster operators in our Ansatz is good enough to eliminate the need for different sets of orbitals for the ground and the core-ionized states. We call the single configuration state function (CSF) limit of this theory the Unitary Group Adapted Open-Shell Coupled Cluster (UGA-OSCC) theory. The aim of this paper is to comprehensively explore the efficacy of our Ansatz to describe orbital relaxation, using both theoretical analysis and numerical performance. Whenever warranted, we also make appropriate comparisons with other coupled-cluster theories. A physically motivated truncation of the chains of spin-free T-operators is also made possible by the normal-ordering, and the operational resemblance to single reference coupled-cluster theory allows easy implementation. Our test case is the prediction of the 1s core IP of molecules containing a single light- to medium-heavy nucleus and thus, in addition to demonstrating the orbital relaxation, we have addressed the scalar relativistic effects on the accuracy of the IPs by using a hierarchy of spin-free Hamiltonians in conjunction with our theory. Additionally, the contribution of the spin-free component of the two-electron Gaunt term, not usually taken into consideration, has been estimated at the Self-Consistent Field (ΔSCF) level and is found to become increasingly important and eventually quite prominent for molecules with third period atoms and below. The accuracies of the IPs computed using UGA-OSCC are found to be of the same order as the Coupled Cluster Singles Doubles (ΔCCSD) values while being free from spin contamination. Since the UGA-OSCC uses a common set of orbitals for the ground state and the ion, it obviates the need of two N 5 AO to MO transformation in contrast to the ΔCCSD method.

Electric load shape benchmarking for small- and medium-sized commercial buildings

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

Luo, Xuan; Hong, Tianzhen; Chen, Yixing

Small- and medium-sized commercial buildings owners and utility managers often look for opportunities for energy cost savings through energy efficiency and energy waste minimization. However, they currently lack easy access to low-cost tools that help interpret the massive amount of data needed to improve understanding of their energy use behaviors. Benchmarking is one of the techniques used in energy audits to identify which buildings are priorities for an energy analysis. Traditional energy performance indicators, such as the energy use intensity (annual energy per unit of floor area), consider only the total annual energy consumption, lacking consideration of the fluctuation ofmore » energy use behavior over time, which reveals the time of use information and represents distinct energy use behaviors during different time spans. To fill the gap, this study developed a general statistical method using 24-hour electric load shape benchmarking to compare a building or business/tenant space against peers. Specifically, the study developed new forms of benchmarking metrics and data analysis methods to infer the energy performance of a building based on its load shape. We first performed a data experiment with collected smart meter data using over 2,000 small- and medium-sized businesses in California. We then conducted a cluster analysis of the source data, and determined and interpreted the load shape features and parameters with peer group analysis. Finally, we implemented the load shape benchmarking feature in an open-access web-based toolkit (the Commercial Building Energy Saver) to provide straightforward and practical recommendations to users. The analysis techniques were generic and flexible for future datasets of other building types and in other utility territories.« less

Electric load shape benchmarking for small- and medium-sized commercial buildings

DOE PAGES

Luo, Xuan; Hong, Tianzhen; Chen, Yixing; ...

2017-07-28

Small- and medium-sized commercial buildings owners and utility managers often look for opportunities for energy cost savings through energy efficiency and energy waste minimization. However, they currently lack easy access to low-cost tools that help interpret the massive amount of data needed to improve understanding of their energy use behaviors. Benchmarking is one of the techniques used in energy audits to identify which buildings are priorities for an energy analysis. Traditional energy performance indicators, such as the energy use intensity (annual energy per unit of floor area), consider only the total annual energy consumption, lacking consideration of the fluctuation ofmore » energy use behavior over time, which reveals the time of use information and represents distinct energy use behaviors during different time spans. To fill the gap, this study developed a general statistical method using 24-hour electric load shape benchmarking to compare a building or business/tenant space against peers. Specifically, the study developed new forms of benchmarking metrics and data analysis methods to infer the energy performance of a building based on its load shape. We first performed a data experiment with collected smart meter data using over 2,000 small- and medium-sized businesses in California. We then conducted a cluster analysis of the source data, and determined and interpreted the load shape features and parameters with peer group analysis. Finally, we implemented the load shape benchmarking feature in an open-access web-based toolkit (the Commercial Building Energy Saver) to provide straightforward and practical recommendations to users. The analysis techniques were generic and flexible for future datasets of other building types and in other utility territories.« less

Comparison of the PHISICS/RELAP5-3D Ring and Block Model Results for Phase I of the OECD MHTGR-350 Benchmark

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

Gerhard Strydom

2014-04-01

The INL PHISICS code system consists of three modules providing improved core simulation capability: INSTANT (performing 3D nodal transport core calculations), MRTAU (depletion and decay heat generation) and a perturbation/mixer module. Coupling of the PHISICS code suite to the thermal hydraulics system code RELAP5-3D has recently been finalized, and as part of the code verification and validation program the exercises defined for Phase I of the OECD/NEA MHTGR 350 MW Benchmark were completed. This paper provides an overview of the MHTGR Benchmark, and presents selected results of the three steady state exercises 1-3 defined for Phase I. For Exercise 1,more » a stand-alone steady-state neutronics solution for an End of Equilibrium Cycle Modular High Temperature Reactor (MHTGR) was calculated with INSTANT, using the provided geometry, material descriptions, and detailed cross-section libraries. Exercise 2 required the modeling of a stand-alone thermal fluids solution. The RELAP5-3D results of four sub-cases are discussed, consisting of various combinations of coolant bypass flows and material thermophysical properties. Exercise 3 combined the first two exercises in a coupled neutronics and thermal fluids solution, and the coupled code suite PHISICS/RELAP5-3D was used to calculate the results of two sub-cases. The main focus of the paper is a comparison of the traditional RELAP5-3D “ring” model approach vs. a much more detailed model that include kinetics feedback on individual block level and thermal feedbacks on a triangular sub-mesh. The higher fidelity of the block model is illustrated with comparison results on the temperature, power density and flux distributions, and the typical under-predictions produced by the ring model approach are highlighted.« less

Emergent patterns in interacting neuronal sub-populations

NASA Astrophysics Data System (ADS)

Kamal, Neeraj Kumar; Sinha, Sudeshna

2015-05-01

We investigate an ensemble of coupled model neurons, consisting of groups of varying sizes and intrinsic dynamics, ranging from periodic to chaotic, where the inter-group coupling interaction is effectively like a dynamic signal from a different sub-population. We observe that the minority group can significantly influence the majority group. For instance, when a small chaotic group is coupled to a large periodic group, the chaotic group de-synchronizes. However, counter-intuitively, when a small periodic group couples strongly to a large chaotic group, it leads to complete synchronization in the majority chaotic population, which also spikes at the frequency of the small periodic group. It then appears that the small group of periodic neurons can act like a pacemaker for the whole network. Further, we report the existence of varied clustering patterns, ranging from sets of synchronized clusters to anti-phase clusters, governed by the interplay of the relative sizes and dynamics of the sub-populations. So these results have relevance in understanding how a group can influence the synchrony of another group of dynamically different elements, reminiscent of event-related synchronization/de-synchronization in complex networks.

Simple mathematical law benchmarks human confrontations

PubMed Central

Johnson, Neil F.; Medina, Pablo; Zhao, Guannan; Messinger, Daniel S.; Horgan, John; Gill, Paul; Bohorquez, Juan Camilo; Mattson, Whitney; Gangi, Devon; Qi, Hong; Manrique, Pedro; Velasquez, Nicolas; Morgenstern, Ana; Restrepo, Elvira; Johnson, Nicholas; Spagat, Michael; Zarama, Roberto

2013-01-01

Many high-profile societal problems involve an individual or group repeatedly attacking another – from child-parent disputes, sexual violence against women, civil unrest, violent conflicts and acts of terror, to current cyber-attacks on national infrastructure and ultrafast cyber-trades attacking stockholders. There is an urgent need to quantify the likely severity and timing of such future acts, shed light on likely perpetrators, and identify intervention strategies. Here we present a combined analysis of multiple datasets across all these domains which account for >100,000 events, and show that a simple mathematical law can benchmark them all. We derive this benchmark and interpret it, using a minimal mechanistic model grounded by state-of-the-art fieldwork. Our findings provide quantitative predictions concerning future attacks; a tool to help detect common perpetrators and abnormal behaviors; insight into the trajectory of a ‘lone wolf'; identification of a critical threshold for spreading a message or idea among perpetrators; an intervention strategy to erode the most lethal clusters; and more broadly, a quantitative starting point for cross-disciplinary theorizing about human aggression at the individual and group level, in both real and online worlds. PMID:24322528

A Programming Model Performance Study Using the NAS Parallel Benchmarks

DOE PAGES

Shan, Hongzhang; Blagojević, Filip; Min, Seung-Jai; ...

2010-01-01

Harnessing the power of multicore platforms is challenging due to the additional levels of parallelism present. In this paper we use the NAS Parallel Benchmarks to study three programming models, MPI, OpenMP and PGAS to understand their performance and memory usage characteristics on current multicore architectures. To understand these characteristics we use the Integrated Performance Monitoring tool and other ways to measure communication versus computation time, as well as the fraction of the run time spent in OpenMP. The benchmarks are run on two different Cray XT5 systems and an Infiniband cluster. Our results show that in general the threemore » programming models exhibit very similar performance characteristics. In a few cases, OpenMP is significantly faster because it explicitly avoids communication. For these particular cases, we were able to re-write the UPC versions and achieve equal performance to OpenMP. Using OpenMP was also the most advantageous in terms of memory usage. Also we compare performance differences between the two Cray systems, which have quad-core and hex-core processors. We show that at scale the performance is almost always slower on the hex-core system because of increased contention for network resources.« less

Mechanisms contributing to cluster formation in the inferior olivary nucleus in brainstem slices from postnatal mice

PubMed Central

Kølvraa, Mathias; Müller, Felix C; Jahnsen, Henrik; Rekling, Jens C

2014-01-01

Abstract The inferior olivary nucleus (IO) in in vitro slices from postnatal mice (P5.5–P15.5) spontaneously generates clusters of neurons with synchronous calcium transients, and intracellular recordings from IO neurons suggest that electrical coupling between neighbouring IO neurons may serve as a synchronizing mechanism. Here, we studied the cluster-forming mechanism and find that clusters overlap extensively with an overlap distribution that resembles the distribution for a random overlap model. The average somatodendritic field size of single curly IO neurons was ∼6400 μm2, which is slightly smaller than the average IO cluster size. Eighty-seven neurons with overlapping dendrites were estimated to be contained in the principal olive mean cluster size, and about six non-overlapping curly IO neurons could be contained within the largest clusters. Clusters could also be induced by iontophoresis with glutamate. Induced clusters were inhibited by tetrodotoxin, carbenoxelone and 18β-glycyrrhetinic acid, suggesting that sodium action potentials and electrical coupling are involved in glutamate-induced cluster formation, which could also be induced by activation of N-methyl-d-aspartate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors. Spikelets and a small transient depolarizing response were observed during glutamate-induced cluster formation. Calcium transients spread with decreasing velocity during cluster formation, and somatic action potentials and cluster formation are accompanied by large dendritic calcium transients. In conclusion, cluster formation depends on gap junctions, sodium action potentials and spontaneous clusters occur randomly throughout the IO. The relative slow signal spread during cluster formation, combined with a strong dendritic influx of calcium, may signify that active dendritic properties contribute to cluster formation. PMID:24042500

Evaluating the Efficacy of the Cloud for Cluster Computation

NASA Technical Reports Server (NTRS)

Knight, David; Shams, Khawaja; Chang, George; Soderstrom, Tom

2012-01-01

Computing requirements vary by industry, and it follows that NASA and other research organizations have computing demands that fall outside the mainstream. While cloud computing made rapid inroads for tasks such as powering web applications, performance issues on highly distributed tasks hindered early adoption for scientific computation. One venture to address this problem is Nebula, NASA's homegrown cloud project tasked with delivering science-quality cloud computing resources. However, another industry development is Amazon's high-performance computing (HPC) instances on Elastic Cloud Compute (EC2) that promises improved performance for cluster computation. This paper presents results from a series of benchmarks run on Amazon EC2 and discusses the efficacy of current commercial cloud technology for running scientific applications across a cluster. In particular, a 240-core cluster of cloud instances achieved 2 TFLOPS on High-Performance Linpack (HPL) at 70% of theoretical computational performance. The cluster's local network also demonstrated sub-100 ?s inter-process latency with sustained inter-node throughput in excess of 8 Gbps. Beyond HPL, a real-world Hadoop image processing task from NASA's Lunar Mapping and Modeling Project (LMMP) was run on a 29 instance cluster to process lunar and Martian surface images with sizes on the order of tens of gigapixels. These results demonstrate that while not a rival of dedicated supercomputing clusters, commercial cloud technology is now a feasible option for moderately demanding scientific workloads.

Receptive field optimisation and supervision of a fuzzy spiking neural network.

PubMed

Glackin, Cornelius; Maguire, Liam; McDaid, Liam; Sayers, Heather

2011-04-01

This paper presents a supervised training algorithm that implements fuzzy reasoning on a spiking neural network. Neuron selectivity is facilitated using receptive fields that enable individual neurons to be responsive to certain spike train firing rates and behave in a similar manner as fuzzy membership functions. The connectivity of the hidden and output layers in the fuzzy spiking neural network (FSNN) is representative of a fuzzy rule base. Fuzzy C-Means clustering is utilised to produce clusters that represent the antecedent part of the fuzzy rule base that aid classification of the feature data. Suitable cluster widths are determined using two strategies; subjective thresholding and evolutionary thresholding respectively. The former technique typically results in compact solutions in terms of the number of neurons, and is shown to be particularly suited to small data sets. In the latter technique a pool of cluster candidates is generated using Fuzzy C-Means clustering and then a genetic algorithm is employed to select the most suitable clusters and to specify cluster widths. In both scenarios, the network is supervised but learning only occurs locally as in the biological case. The advantages and disadvantages of the network topology for the Fisher Iris and Wisconsin Breast Cancer benchmark classification tasks are demonstrated and directions of current and future work are discussed. Copyright © 2010 Elsevier Ltd. All rights reserved.

The Structure and Stability of Bn(+) Clusters

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The geometries of B+n clusters for n less than 14 have been optimized using density functional theory with the B3LYP functional. The most stable structure for each cluster is planar or quasi-planar. The B3LYP fragmentation energies are calibrated using coupled cluster theory. Overall, our corrected fragmentation energies are in reasonable agreement with experiment. Our results are compared with previous theoretical results.

Multi-task learning with group information for human action recognition

NASA Astrophysics Data System (ADS)

Qian, Li; Wu, Song; Pu, Nan; Xu, Shulin; Xiao, Guoqiang

2018-04-01

Human action recognition is an important and challenging task in computer vision research, due to the variations in human motion performance, interpersonal differences and recording settings. In this paper, we propose a novel multi-task learning framework with group information (MTL-GI) for accurate and efficient human action recognition. Specifically, we firstly obtain group information through calculating the mutual information according to the latent relationship between Gaussian components and action categories, and clustering similar action categories into the same group by affinity propagation clustering. Additionally, in order to explore the relationships of related tasks, we incorporate group information into multi-task learning. Experimental results evaluated on two popular benchmarks (UCF50 and HMDB51 datasets) demonstrate the superiority of our proposed MTL-GI framework.

A new numerical benchmark for variably saturated variable-density flow and transport in porous media

NASA Astrophysics Data System (ADS)

Guevara, Carlos; Graf, Thomas

2016-04-01

In subsurface hydrological systems, spatial and temporal variations in solute concentration and/or temperature may affect fluid density and viscosity. These variations could lead to potentially unstable situations, in which a dense fluid overlies a less dense fluid. These situations could produce instabilities that appear as dense plume fingers migrating downwards counteracted by vertical upwards flow of freshwater (Simmons et al., Transp. Porous Medium, 2002). As a result of unstable variable-density flow, solute transport rates are increased over large distances and times as compared to constant-density flow. The numerical simulation of variable-density flow in saturated and unsaturated media requires corresponding benchmark problems against which a computer model is validated (Diersch and Kolditz, Adv. Water Resour, 2002). Recorded data from a laboratory-scale experiment of variable-density flow and solute transport in saturated and unsaturated porous media (Simmons et al., Transp. Porous Medium, 2002) is used to define a new numerical benchmark. The HydroGeoSphere code (Therrien et al., 2004) coupled with PEST (www.pesthomepage.org) are used to obtain an optimized parameter set capable of adequately representing the data set by Simmons et al., (2002). Fingering in the numerical model is triggered using random hydraulic conductivity fields. Due to the inherent randomness, a large number of simulations were conducted in this study. The optimized benchmark model adequately predicts the plume behavior and the fate of solutes. This benchmark is useful for model verification of variable-density flow problems in saturated and/or unsaturated media.

Comparative study of feature selection with ensemble learning using SOM variants

NASA Astrophysics Data System (ADS)

Filali, Ameni; Jlassi, Chiraz; Arous, Najet

2017-03-01

Ensemble learning has succeeded in the growth of stability and clustering accuracy, but their runtime prohibits them from scaling up to real-world applications. This study deals the problem of selecting a subset of the most pertinent features for every cluster from a dataset. The proposed method is another extension of the Random Forests approach using self-organizing maps (SOM) variants to unlabeled data that estimates the out-of-bag feature importance from a set of partitions. Every partition is created using a various bootstrap sample and a random subset of the features. Then, we show that the process internal estimates are used to measure variable pertinence in Random Forests are also applicable to feature selection in unsupervised learning. This approach aims to the dimensionality reduction, visualization and cluster characterization at the same time. Hence, we provide empirical results on nineteen benchmark data sets indicating that RFS can lead to significant improvement in terms of clustering accuracy, over several state-of-the-art unsupervised methods, with a very limited subset of features. The approach proves promise to treat with very broad domains.

SeMPI: a genome-based secondary metabolite prediction and identification web server.

PubMed

Zierep, Paul F; Padilla, Natàlia; Yonchev, Dimitar G; Telukunta, Kiran K; Klementz, Dennis; Günther, Stefan

2017-07-03

The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceutical-bioinformatics.de/sempi. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Vibrational quenching of excitonic splittings in H-bonded molecular dimers: The electronic Davydov splittings cannot match experiment

NASA Astrophysics Data System (ADS)

Ottiger, Philipp; Leutwyler, Samuel; Köppel, Horst

2012-05-01

The S1/S2 state exciton splittings of symmetric doubly hydrogen-bonded gas-phase dimers provide spectroscopic benchmarks for the excited-state electronic couplings between UV chromophores. These have important implications for electronic energy transfer in multichromophoric systems ranging from photosynthetic light-harvesting antennae to photosynthetic reaction centers, conjugated polymers, molecular crystals, and nucleic acids. We provide laser spectroscopic data on the S1/S2 excitonic splitting Δexp of the doubly H-bonded o-cyanophenol (oCP) dimer and compare to the splittings of the dimers of (2-aminopyridine)2, [(2AP)2], (2-pyridone)2, [(2PY)2], (benzoic acid)2, [(BZA)2], and (benzonitrile)2, [(BN)2]. The experimental S1/S2 excitonic splittings are Δexp = 16.4 cm-1 for (oCP)2, 11.5 cm-1 for (2AP)2, 43.5 cm-1 for (2PY)2, and <1 cm-1 for (BZA)2. In contrast, the vertical S1/S2 energy gaps Δcalc calculated by the approximate second-order coupled cluster (CC2) method for the same dimers are 10-40 times larger than the Δexp values. The qualitative failure of this and other ab initio methods to reproduce the exciton splitting Δexp arises from the Born-Oppenheimer (BO) approximation, which implicitly assumes the strong-coupling case and cannot be employed to evaluate excitonic splittings of systems that are in the weak-coupling limit. Given typical H-bond distances and oscillator strengths, the majority of H-bonded dimers lie in the weak-coupling limit. In this case, the monomer electronic-vibrational coupling upon electronic excitation must be accounted for; the excitonic splittings arise between the vibronic (and not the electronic) transitions. The discrepancy between the BO-based splittings Δcalc and the much smaller experimental Δexp values is resolved by taking into account the quenching of the BO splitting by the intramolecular vibronic coupling in the monomer S1 ← S0 excitation. The vibrational quenching factors Γ for the five dimers (oCP)2, (2AP)2, (2AP)2, (BN)2, and (BZA)2 lie in the range Γ = 0.03-0.2. The quenched excitonic splittings Γ.Δcalc are found to be in very good agreement with the observed splittings Δexp. The vibrational quenching approach predicts reliable Δexp values for the investigated dimers, confirms the importance of vibrational quenching of the electronic Davydov splittings, and provides a sound basis for predicting realistic exciton splittings in multichromophoric systems.

Consensus of satellite cluster flight using an energy-matching optimal control method

NASA Astrophysics Data System (ADS)

Luo, Jianjun; Zhou, Liang; Zhang, Bo

2017-11-01

This paper presents an optimal control method for consensus of satellite cluster flight under a kind of energy matching condition. Firstly, the relation between energy matching and satellite periodically bounded relative motion is analyzed, and the satellite energy matching principle is applied to configure the initial conditions. Then, period-delayed errors are adopted as state variables to establish the period-delayed errors dynamics models of a single satellite and the cluster. Next a novel satellite cluster feedback control protocol with coupling gain is designed, so that the satellite cluster periodically bounded relative motion consensus problem (period-delayed errors state consensus problem) is transformed to the stability of a set of matrices with the same low dimension. Based on the consensus region theory in the research of multi-agent system consensus issues, the coupling gain can be obtained to satisfy the requirement of consensus region and decouple the satellite cluster information topology and the feedback control gain matrix, which can be determined by Linear quadratic regulator (LQR) optimal method. This method can realize the consensus of satellite cluster period-delayed errors, leading to the consistency of semi-major axes (SMA) and the energy-matching of satellite cluster. Then satellites can emerge the global coordinative cluster behavior. Finally the feasibility and effectiveness of the present energy-matching optimal consensus for satellite cluster flight is verified through numerical simulations.

Orbital-ordering-driven multiferroicity and magnetoelectric coupling in GeV₄S₈.

PubMed

Singh, Kiran; Simon, Charles; Cannuccia, Elena; Lepetit, Marie-Bernadette; Corraze, Benoit; Janod, Etienne; Cario, Laurent

2014-09-26

We report here the discovery of multiferroicity and large magnetoelectric coupling in the type I orbital order system GeV₄S₈. Our study demonstrates that this clustered compound displays a para-ferroelectric transition at 32 K. This transition originates from an orbital ordering which reorganizes the charge within the transition metal clusters. Below the antiferromagnetic transition at 17 K, the application of a magnetic field significantly affects the ferroelectric polarization, revealing thus a large magnetoelectric coupling. Our study suggests that the application of a magnetic field induces a metamagnetic transition which significantly affects the ferroelectric polarization thanks to an exchange striction phenomenon.

The multichannel n-propyl + O2 reaction surface: Definitive theory on a model hydrocarbon oxidation mechanism

NASA Astrophysics Data System (ADS)

Bartlett, Marcus A.; Liang, Tao; Pu, Liang; Schaefer, Henry F.; Allen, Wesley D.

2018-03-01

The n-propyl + O2 reaction is an important model of chain branching reactions in larger combustion systems. In this work, focal point analyses (FPAs) extrapolating to the ab initio limit were performed on the n-propyl + O2 system based on explicit quantum chemical computations with electron correlation treatments through coupled cluster single, double, triple, and perturbative quadruple excitations [CCSDT(Q)] and basis sets up to cc-pV5Z. All reaction species and transition states were fully optimized at the rigorous CCSD(T)/cc-pVTZ level of theory, revealing some substantial differences in comparison to the density functional theory geometries existing in the literature. A mixed Hessian methodology was implemented and benchmarked that essentially makes the computations of CCSD(T)/cc-pVTZ vibrational frequencies feasible and thus provides critical improvements to zero-point vibrational energies for the n-propyl + O2 system. Two key stationary points, n-propylperoxy radical (MIN1) and its concerted elimination transition state (TS1), were located 32.7 kcal mol-1 and 2.4 kcal mol-1 below the reactants, respectively. Two competitive β-hydrogen transfer transition states (TS2 and TS2') were found separated by only 0.16 kcal mol-1, a fact unrecognized in the current combustion literature. Incorporating TS2' in master equation (ME) kinetic models might reduce the large discrepancy of 2.5 kcal mol-1 between FPA and ME barrier heights for TS2. TS2 exhibits an anomalously large diagonal Born-Oppenheimer correction (ΔDBOC = 1.71 kcal mol-1), which is indicative of a nearby surface crossing and possible nonadiabatic reaction dynamics. The first systematic conformational search of three hydroperoxypropyl (QOOH) intermediates was completed, uncovering a total of 32 rotamers lying within 1.6 kcal mol-1 of their respective lowest-energy minima. Our definitive energetics for stationary points on the n-propyl + O2 potential energy surface provide key benchmarks for future studies of hydrocarbon oxidation.

Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

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

Burns, Lori A.; Marshall, Michael S.; Sherrill, C. David, E-mail: sherrill@gatech.edu

2014-12-21

A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracymore » and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.« less

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

Wykes, M., E-mail: mikewykes@gmail.com; Parambil, R.; Gierschner, J.

Here, we present a general approach to treating vibronic coupling in molecular crystals based on atomistic simulations of large clusters. Such clusters comprise model aggregates treated at the quantum chemical level embedded within a realistic environment treated at the molecular mechanics level. As we calculate ground and excited state equilibrium geometries and vibrational modes of model aggregates, our approach is able to capture effects arising from coupling to intermolecular degrees of freedom, absent from existing models relying on geometries and normal modes of single molecules. Using the geometries and vibrational modes of clusters, we are able to simulate the fluorescencemore » spectra of aggregates for which the lowest excited state bears negligible oscillator strength (as is the case, e.g., ideal H-aggregates) by including both Franck-Condon (FC) and Herzberg-Teller (HT) vibronic transitions. The latter terms allow the adiabatic excited state of the cluster to couple with vibrations in a perturbative fashion via derivatives of the transition dipole moment along nuclear coordinates. While vibronic coupling simulations employing FC and HT terms are well established for single-molecules, to our knowledge this is the first time they are applied to molecular aggregates. Here, we apply this approach to the simulation of the low-temperature fluorescence spectrum of para-distyrylbenzene single-crystal H-aggregates and draw comparisons with coarse-grained Frenkel-Holstein approaches previously extensively applied to such systems.« less

A quasiparticle-based multi-reference coupled-cluster method.

PubMed

Rolik, Zoltán; Kállay, Mihály

2014-10-07

The purpose of this paper is to introduce a quasiparticle-based multi-reference coupled-cluster (MRCC) approach. The quasiparticles are introduced via a unitary transformation which allows us to represent a complete active space reference function and other elements of an orthonormal multi-reference (MR) basis in a determinant-like form. The quasiparticle creation and annihilation operators satisfy the fermion anti-commutation relations. On the basis of these quasiparticles, a generalization of the normal-ordered operator products for the MR case can be introduced as an alternative to the approach of Mukherjee and Kutzelnigg [Recent Prog. Many-Body Theor. 4, 127 (1995); Mukherjee and Kutzelnigg, J. Chem. Phys. 107, 432 (1997)]. Based on the new normal ordering any quasiparticle-based theory can be formulated using the well-known diagram techniques. Beyond the general quasiparticle framework we also present a possible realization of the unitary transformation. The suggested transformation has an exponential form where the parameters, holding exclusively active indices, are defined in a form similar to the wave operator of the unitary coupled-cluster approach. The definition of our quasiparticle-based MRCC approach strictly follows the form of the single-reference coupled-cluster method and retains several of its beneficial properties. Test results for small systems are presented using a pilot implementation of the new approach and compared to those obtained by other MR methods.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods

NASA Astrophysics Data System (ADS)

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-01

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

Electronic Structure of Ethynyl Substituted Cyclobutadienes

NASA Astrophysics Data System (ADS)

Emmert, Frank Lee Emmert, III; Thompson, Stephanie J.; Slipchenko, Lyudmila V.

2011-06-01

We investigated the effects of ethynyl substitution on the electronic structure of cyclobutadiene. These species are involved in Bergman Cyclization reactionsand are possible intermediates in the formation of fullerenes and graphite sheets. Prediction of the electronic energy of cyclobutadiene is challenging for single-reference ab initio methods such as HF, MP2 or DFT because of Jahn-Teller distortions and the diradical character of the singlet state. We determined the vertical and adiabatic singlet-triplet energy splittings, the natural charges and spin densities in substituted cyclobutadienes, using the equations of motion spin flip coupled cluster with single and double excitations (EOM-SF-CCSD) method that accurately describes diradical states. The adiabatic singlet-triplet gaps decrease upon substituent addition, but the singlet state is always lower in energy. However, we found that the results are affected by spin-contamination of the reference state and deteriorate when an unrestricted HF reference is employed. O. L. Chapman, C. L. McIntosh, J. Pacansky, "Cyclobutadiene" J. Am. Chem. Soc. 1973, 95, (2), 614-617. N. S. Goroff, "Mechanism of Fullerene Formation." Acc. Chem. Res. 1996, 29, (2), 77-83. L.V. Slipchenko and A.I. Krylov, "Singlet-triplet gaps in diradicals by the Spin-Flip approach: A benchmark study", J. Chem. Phys. 2002, 117, 4694-4708.

A New Integrated Threshold Selection Methodology for Spatial Forecast Verification of Extreme Events

NASA Astrophysics Data System (ADS)

Kholodovsky, V.

2017-12-01

Extreme weather and climate events such as heavy precipitation, heat waves and strong winds can cause extensive damage to the society in terms of human lives and financial losses. As climate changes, it is important to understand how extreme weather events may change as a result. Climate and statistical models are often independently used to model those phenomena. To better assess performance of the climate models, a variety of spatial forecast verification methods have been developed. However, spatial verification metrics that are widely used in comparing mean states, in most cases, do not have an adequate theoretical justification to benchmark extreme weather events. We proposed a new integrated threshold selection methodology for spatial forecast verification of extreme events that couples existing pattern recognition indices with high threshold choices. This integrated approach has three main steps: 1) dimension reduction; 2) geometric domain mapping; and 3) thresholds clustering. We apply this approach to an observed precipitation dataset over CONUS. The results are evaluated by displaying threshold distribution seasonally, monthly and annually. The method offers user the flexibility of selecting a high threshold that is linked to desired geometrical properties. The proposed high threshold methodology could either complement existing spatial verification methods, where threshold selection is arbitrary, or be directly applicable in extreme value theory.

Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods.

PubMed

Ben Amor, Nadia; Hoyau, Sophie; Maynau, Daniel; Brenner, Valérie

2018-05-14

A benchmark set of relevant geometries of a model protein, the N-acetylphenylalanylamide, is presented to assess the validity of the approximate second-order coupled cluster (CC2) method in studying low-lying excited states of such bio-relevant systems. The studies comprise investigations of basis-set dependence as well as comparison with two multireference methods, the multistate complete active space 2nd order perturbation theory (MS-CASPT2) and the multireference difference dedicated configuration interaction (DDCI) methods. First of all, the applicability and the accuracy of the quasi-linear multireference difference dedicated configuration interaction method have been demonstrated on bio-relevant systems by comparison with the results obtained by the standard MS-CASPT2. Second, both the nature and excitation energy of the first low-lying excited state obtained at the CC2 level are very close to the Davidson corrected CAS+DDCI ones, the mean absolute deviation on the excitation energy being equal to 0.1 eV with a maximum of less than 0.2 eV. Finally, for the following low-lying excited states, if the nature is always well reproduced at the CC2 level, the differences on excitation energies become more important and can depend on the geometry.

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

Hill, J. Grant, E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu; Peterson, Kirk A., E-mail: grant.hill@sheffield.ac.uk, E-mail: kipeters@wsu.edu

New correlation consistent basis sets, cc-pVnZ-PP-F12 (n = D, T, Q), for all the post-d main group elements Ga–Rn have been optimized for use in explicitly correlated F12 calculations. The new sets, which include not only orbital basis sets but also the matching auxiliary sets required for density fitting both conventional and F12 integrals, are designed for correlation of valence sp, as well as the outer-core d electrons. The basis sets are constructed for use with the previously published small-core relativistic pseudopotentials of the Stuttgart-Cologne variety. Benchmark explicitly correlated coupled-cluster singles and doubles with perturbative triples [CCSD(T)-F12b] calculations of themore » spectroscopic properties of numerous diatomic molecules involving 4p, 5p, and 6p elements have been carried out and compared to the analogous conventional CCSD(T) results. In general the F12 results obtained with a n-zeta F12 basis set were comparable to conventional aug-cc-pVxZ-PP or aug-cc-pwCVxZ-PP basis set calculations obtained with x = n + 1 or even x = n + 2. The new sets used in CCSD(T)-F12b calculations are particularly efficient at accurately recovering the large correlation effects of the outer-core d electrons.« less

Driven similarity renormalization group: Third-order multireference perturbation theory.

PubMed

Li, Chenyang; Evangelista, Francesco A

2017-03-28

A third-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT3) approach is presented. The DSRG-MRPT3 method has several appealing features: (a) it is intruder free, (b) it is size consistent, (c) it leads to a non-iterative algorithm with O(N 6 ) scaling, and (d) it includes reference relaxation effects. The DSRG-MRPT3 scheme is benchmarked on the potential energy curves of F 2 , H 2 O 2 , C 2 H 6 , and N 2 along the F-F, O-O, C-C, and N-N bond dissociation coordinates, respectively. The nonparallelism errors of DSRG-MRPT3 are consistent with those of complete active space third-order perturbation theory and multireference configuration interaction with singles and doubles and show significant improvements over those obtained from DSRG second-order multireference perturbation theory. Our efficient implementation of the DSRG-MRPT3 based on factorized electron repulsion integrals enables studies of medium-sized open-shell organic compounds. This point is demonstrated with computations of the singlet-triplet splitting (Δ ST =E T -E S ) of 9,10-anthracyne. At the DSRG-MRPT3 level of theory, our best estimate of the adiabatic Δ ST is 3.9 kcal mol -1 , a value that is within 0.1 kcal mol -1 from multireference coupled cluster results.

Auxiliary basis sets for density-fitting second-order Møller-Plesset perturbation theory: weighted core-valence correlation consistent basis sets for the 4d elements Y-Pd.

PubMed

Hill, J Grant

2013-09-30

Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit. Copyright © 2013 Wiley Periodicals, Inc.

Energy saving in WWTP: Daily benchmarking under uncertainty and data availability limitations.

PubMed

Torregrossa, D; Schutz, G; Cornelissen, A; Hernández-Sancho, F; Hansen, J

2016-07-01

Efficient management of Waste Water Treatment Plants (WWTPs) can produce significant environmental and economic benefits. Energy benchmarking can be used to compare WWTPs, identify targets and use these to improve their performance. Different authors have performed benchmark analysis on monthly or yearly basis but their approaches suffer from a time lag between an event, its detection, interpretation and potential actions. The availability of on-line measurement data on many WWTPs should theoretically enable the decrease of the management response time by daily benchmarking. Unfortunately this approach is often impossible because of limited data availability. This paper proposes a methodology to perform a daily benchmark analysis under database limitations. The methodology has been applied to the Energy Online System (EOS) developed in the framework of the project "INNERS" (INNovative Energy Recovery Strategies in the urban water cycle). EOS calculates a set of Key Performance Indicators (KPIs) for the evaluation of energy and process performances. In EOS, the energy KPIs take in consideration the pollutant load in order to enable the comparison between different plants. For example, EOS does not analyse the energy consumption but the energy consumption on pollutant load. This approach enables the comparison of performances for plants with different loads or for a single plant under different load conditions. The energy consumption is measured by on-line sensors, while the pollutant load is measured in the laboratory approximately every 14 days. Consequently, the unavailability of the water quality parameters is the limiting factor in calculating energy KPIs. In this paper, in order to overcome this limitation, the authors have developed a methodology to estimate the required parameters and manage the uncertainty in the estimation. By coupling the parameter estimation with an interval based benchmark approach, the authors propose an effective, fast and reproducible way to manage infrequent inlet measurements. Its use enables benchmarking on a daily basis and prepares the ground for further investigation. Copyright © 2016 Elsevier Inc. All rights reserved.

Benchmarking Gas Path Diagnostic Methods: A Public Approach

NASA Technical Reports Server (NTRS)

Simon, Donald L.; Bird, Jeff; Davison, Craig; Volponi, Al; Iverson, R. Eugene

2008-01-01

Recent technology reviews have identified the need for objective assessments of engine health management (EHM) technology. The need is two-fold: technology developers require relevant data and problems to design and validate new algorithms and techniques while engine system integrators and operators need practical tools to direct development and then evaluate the effectiveness of proposed solutions. This paper presents a publicly available gas path diagnostic benchmark problem that has been developed by the Propulsion and Power Systems Panel of The Technical Cooperation Program (TTCP) to help address these needs. The problem is coded in MATLAB (The MathWorks, Inc.) and coupled with a non-linear turbofan engine simulation to produce "snap-shot" measurements, with relevant noise levels, as if collected from a fleet of engines over their lifetime of use. Each engine within the fleet will experience unique operating and deterioration profiles, and may encounter randomly occurring relevant gas path faults including sensor, actuator and component faults. The challenge to the EHM community is to develop gas path diagnostic algorithms to reliably perform fault detection and isolation. An example solution to the benchmark problem is provided along with associated evaluation metrics. A plan is presented to disseminate this benchmark problem to the engine health management technical community and invite technology solutions.

Electrostatic effects on clustering and ion dynamics in ionomer melts

NASA Astrophysics Data System (ADS)

Ma, Boran; Nguyen, Trung; Pryamitsyn, Victor; Olvera de La Cruz, Monica

An understanding of the relationships between ionomer chain morphology, dynamics and counter-ion mobility is a key factor in the design of ion conducting membranes for battery applications. In this study, we investigate the influence of electrostatic coupling between randomly charged copolymers (ionomers) and counter ions on the structural and dynamic features of a model system of ionomer melts. Using coarse-grained molecular dynamics (CGMD) simulations, we found that variations in electrostatic coupling strength (Γ) remarkably affect the formation of ion-counter ion clusters, ion mobility, and polymer dynamics for a range of charged monomer fractions. Specifically, an increase in Γ leads to larger ionic cluster sizes and reduced polymer and ion mobility. Analysis of the distribution of the radius of gyration of the clusters further reveals that the fractal dimension of the ion clusters is nearly independent from Γ for all the cases studied. Finally, at sufficiently high values of Γ, we observed arrested heterogeneous ions mobility, which is correlated with an increase in ion cluster size. These findings provide insight into the role of electrostatics in governing the nanostructures formed by ionomers.

Heterogeneous delays making parents synchronized: A coupled maps on Cayley tree model

NASA Astrophysics Data System (ADS)

Singh, Aradhana; Jalan, Sarika

2014-06-01

We study the phase synchronized clusters in the diffusively coupled maps on the Cayley tree networks for heterogeneous delay values. Cayley tree networks comprise of two parts: the inner nodes and the boundary nodes. We find that heterogeneous delays lead to various cluster states, such as; (a) cluster state consisting of inner nodes and boundary nodes, and (b) cluster state consisting of only boundary nodes. The former state may comprise of nodes from all the generations forming self-organized cluster or nodes from few generations yielding driven clusters depending upon on the parity of heterogeneous delay values. Furthermore, heterogeneity in delays leads to the lag synchronization between the siblings lying on the boundary by destroying the exact synchronization among them. The time lag being equal to the difference in the delay values. The Lyapunov function analysis sheds light on the destruction of the exact synchrony among the last generation nodes. To the end we discuss the relevance of our results with respect to their applications in the family business as well as in understanding the occurrence of genetic diseases.

A comparison of the coupled cluster and internally contracted averaged coupled-pair functional levels of theory for the calculation of the MCH2(+) binding energies for M = Sc to Cu

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry; Scuseria, Gustavo E.

1992-01-01

The correlation contribution to the M-C binding energy for the MCH2(+) systems can exceed 100 kcal/mol. At the self-consistent field (SCF) level, these systems can be more than 50 kcal/mol above the fragment energies. In spite of the poor zeroth-order reference, the coupled cluster single and double excitation method with a perturbational estimate of triple excitations, CCSD(T), method is shown to provide an accurate description of these systems. The maximum difference between the CCSD(T) and internally contracted averaged coupled-pair functional binding energies is 1.5 kcal/mol for CrCH2(+), with the remaining systems agreeing to within 1.0 kcal/mol.

Pattern formation for NO+N H3 on Pt(100): Two-dimensional numerical results

NASA Astrophysics Data System (ADS)

Uecker, Hannes

2005-01-01

The Lombardo-Fink-Imbihl model of the NO+NH3 reaction on a Pt(100) surface consists of seven coupled ordinary differential equations (ODE) and shows stable relaxation oscillations with sharp transitions in the relevant temperature range. Here we study numerically the effect of coupling of these oscillators by surface diffusion in two dimensions. We find different types of patterns, in particular phase clusters and standing waves. In models of related surface reactions such clustered solutions are known to exist only under a global coupling through the gas phase. This global coupling is replaced here by relatively fast diffusion of two variables which are kinetically slaved in the ODE. We also compare our simulations with experimental results and discuss some shortcomings of the model.

Gap-junction coupling and ATP-sensitive potassium channels in human β -cell clusters: Effects on emergent dynamics

NASA Astrophysics Data System (ADS)

Loppini, A.; Pedersen, M. G.; Braun, M.; Filippi, S.

2017-09-01

The importance of gap-junction coupling between β cells in pancreatic islets is well established in mouse. Such ultrastructural connections synchronize cellular activity, confine biological heterogeneity, and enhance insulin pulsatility. Dysfunction of coupling has been associated with diabetes and altered β -cell function. However, the role of gap junctions between human β cells is still largely unexplored. By using patch-clamp recordings of β cells from human donors, we previously estimated electrical properties of these channels by mathematical modeling of pairs of human β cells. In this work we revise our estimate by modeling triplet configurations and larger heterogeneous clusters. We find that a coupling conductance in the range 0.005 -0.020 nS/pF can reproduce experiments in almost all the simulated arrangements. We finally explore the consequence of gap-junction coupling of this magnitude between β cells with mutant variants of the ATP-sensitive potassium channels involved in some metabolic disorders and diabetic conditions, translating studies performed on rodents to the human case. Our results are finally discussed from the perspective of therapeutic strategies. In summary, modeling of more realistic clusters with more than two β cells slightly lowers our previous estimate of gap-junction conductance and gives rise to patterns that more closely resemble experimental traces.

PID controller tuning using metaheuristic optimization algorithms for benchmark problems

NASA Astrophysics Data System (ADS)

Gholap, Vishal; Naik Dessai, Chaitali; Bagyaveereswaran, V.

2017-11-01

This paper contributes to find the optimal PID controller parameters using particle swarm optimization (PSO), Genetic Algorithm (GA) and Simulated Annealing (SA) algorithm. The algorithms were developed through simulation of chemical process and electrical system and the PID controller is tuned. Here, two different fitness functions such as Integral Time Absolute Error and Time domain Specifications were chosen and applied on PSO, GA and SA while tuning the controller. The proposed Algorithms are implemented on two benchmark problems of coupled tank system and DC motor. Finally, comparative study has been done with different algorithms based on best cost, number of iterations and different objective functions. The closed loop process response for each set of tuned parameters is plotted for each system with each fitness function.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Translating an AI application from Lisp to Ada: A case study

NASA Technical Reports Server (NTRS)

Davis, Gloria J.

1991-01-01

A set of benchmarks was developed to test the performance of a newly designed computer executing both Lisp and Ada. Among these was AutoClassII -- a large Artificial Intelligence (AI) application written in Common Lisp. The extraction of a representative subset of this complex application was aided by a Lisp Code Analyzer (LCA). The LCA enabled rapid analysis of the code, putting it in a concise and functionally readable form. An equivalent benchmark was created in Ada through manual translation of the Lisp version. A comparison of the execution results of both programs across a variety of compiler-machine combinations indicate that line-by-line translation coupled with analysis of the initial code can produce relatively efficient and reusable target code.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Gatemon Benchmarking and Two-Qubit Operation

NASA Astrophysics Data System (ADS)

Casparis, Lucas; Larsen, Thorvald; Olsen, Michael; Petersson, Karl; Kuemmeth, Ferdinand; Krogstrup, Peter; Nygard, Jesper; Marcus, Charles

Recent experiments have demonstrated superconducting transmon qubits with semiconductor nanowire Josephson junctions. These hybrid gatemon qubits utilize field effect tunability singular to semiconductors to allow complete qubit control using gate voltages, potentially a technological advantage over conventional flux-controlled transmons. Here, we present experiments with a two-qubit gatemon circuit. We characterize qubit coherence and stability and use randomized benchmarking to demonstrate single-qubit gate errors of ~0.5 % for all gates, including voltage-controlled Z rotations. We show coherent capacitive coupling between two gatemons and coherent SWAP operations. Finally, we perform a two-qubit controlled-phase gate with an estimated fidelity of ~91 %, demonstrating the potential of gatemon qubits for building scalable quantum processors. We acknowledge financial support from Microsoft Project Q and the Danish National Research Foundation.

Analysis of Fiber Clustering in Composite Materials Using High-Fidelity Multiscale Micromechanics

NASA Technical Reports Server (NTRS)

Bednarcyk, Brett A.; Aboudi, Jacob; Arnold, Steven M.

2015-01-01

A new multiscale micromechanical approach is developed for the prediction of the behavior of fiber reinforced composites in presence of fiber clustering. The developed method is based on a coupled two-scale implementation of the High-Fidelity Generalized Method of Cells theory, wherein both the local and global scales are represented using this micromechanical method. Concentration tensors and effective constitutive equations are established on both scales and linked to establish the required coupling, thus providing the local fields throughout the composite as well as the global properties and effective nonlinear response. Two nondimensional parameters, in conjunction with actual composite micrographs, are used to characterize the clustering of fibers in the composite. Based on the predicted local fields, initial yield and damage envelopes are generated for various clustering parameters for a polymer matrix composite with both carbon and glass fibers. Nonlinear epoxy matrix behavior is also considered, with results in the form of effective nonlinear response curves, with varying fiber clustering and for two sets of nonlinear matrix parameters.

Development of a Typology of Dual-Earner Couples Caring for Children and Aging Parents

ERIC Educational Resources Information Center

Cullen, Jennifer C.; Hammer, Leslie B.; Neal, Margaret B.; Sinclair, Robert R.

2009-01-01

Using a national sample of 267 couples, the authors identify distinct profiles of dual-earner couples in the sandwiched generation (i.e., those caring for children and aging parents) using cluster analysis and then assess the relationship between these profiles and work-family conflict. The profiles are defined by characteristics of couples' child…

The [(AI 2O 3) 2] - Anion Cluster: Electron Localization-Delocalization Isomerism

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

Sierka, Marek; Dobler, Jens; Sauer, Joachim

2009-10-05

Three-dimensional bulk alumina and its two-dimensional thin films show great structural diversity, posing considerable challenges to their experimental structural characterization and computational modeling. Recently, structural diversity has also been demonstrated for zerodimensional gas phase aluminum oxide clusters. Mass-selected clusters not only make systematic studies of the structural and electronic properties as a function of size possible, but lately have also emerged as powerful molecular models of complex surfaces and solid catalysts. In particular, the [(Al 2O 3) 3-5] + clusters were the first example of polynuclear maingroup metal oxide cluster that are able to thermally activate CH 4. Over themore » past decades gas phase aluminum oxide clusters have been extensively studied both experimentally and computationally, but definitive structural assignments were made for only a handful of them: the planar [Al 3O 3] - and [Al 5O 4] - cluster anions, and the [(Al 2O 3) 1-4(AlO)] + cluster cations. For stoichiometric clusters only the atomic structures of [(Al 2O 3) 4] +/0 have been nambiguously resolved. Here we report on the structures of the [(Al 2O 3) 2] -/0 clusters combining photoelectron spectroscopy (PES) and quantum chemical calculations employing a genetic algorithm as a global optimization technique. The [(Al 2O 3) 2] - cluster anion show energetically close lying but structurally distinct cage and sheet-like isomers which differ by delocalization/localization of the extra electron. The experimental results are crucial for benchmarking the different computational methods applied with respect to a proper description of electron localization and the relative energies for the isomers which will be of considerable value for future computational studies of aluminum oxide and related systems.« less

Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).

PubMed

Batiste, Laurent; Unzue, Andrea; Dolbois, Aymeric; Hassler, Fabrice; Wang, Xuan; Deerain, Nicholas; Zhu, Jian; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo

2018-02-28

Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.

Observation time scale, free-energy landscapes, and molecular symmetry

PubMed Central

Wales, David J.; Salamon, Peter

2014-01-01

When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely atomic clusters and alanine dipeptide, highlighting the connections to broken ergodicity, local equilibrium, and “feasible” symmetry operations of the molecular Hamiltonian. PMID:24374625

Root-cause analysis of the better performance of the coarse-mesh finite-difference method for CANDU-type reactors

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

Shen, W.

2012-07-01

Recent assessment results indicate that the coarse-mesh finite-difference method (FDM) gives consistently smaller percent differences in channel powers than the fine-mesh FDM when compared to the reference MCNP solution for CANDU-type reactors. However, there is an impression that the fine-mesh FDM should always give more accurate results than the coarse-mesh FDM in theory. To answer the question if the better performance of the coarse-mesh FDM for CANDU-type reactors was just a coincidence (cancellation of errors) or caused by the use of heavy water or the use of lattice-homogenized cross sections for the cluster fuel geometry in the diffusion calculation, threemore » benchmark problems were set up with three different fuel lattices: CANDU, HWR and PWR. These benchmark problems were then used to analyze the root cause of the better performance of the coarse-mesh FDM for CANDU-type reactors. The analyses confirm that the better performance of the coarse-mesh FDM for CANDU-type reactors is mainly caused by the use of lattice-homogenized cross sections for the sub-meshes of the cluster fuel geometry in the diffusion calculation. Based on the analyses, it is recommended to use 2 x 2 coarse-mesh FDM to analyze CANDU-type reactors when lattice-homogenized cross sections are used in the core analysis. (authors)« less

Recovery of evolution of Grad-Shafranov equilibria from single-spacecraft data: Benchmarking and application to a flux transfer event

NASA Astrophysics Data System (ADS)

Sonnerup, B. U.; Hasegawa, H.; Nakamura, T.

2010-12-01

Even after the advent of multi-spacecraft missions such as Cluster and THEMIS, it has been difficult to distinguish between time evolution of, and spatial variation within, a space plasma structure on the basis of in situ measurements. We present a method for analyzing time evolution of two-dimensional (2D) and magnetohydrostatic, namely Grad-Shafranov equilibria, using data recorded by an observing probe as it traverses a quasi-static, 2D magnetic-field/plasma structure. The method recovers spatial initial values used in the classical Grad-Shafranov (GS) reconstruction [Sonnerup et al., JGR, 2006] for an interval before and after the time of actual measurements, by advancing them backward and forward in time based on a set of equation for an incompressible plasma; the consequence is generation of multiple GS maps or a movie of the 2D field structure. The method is successfully benchmarked by use of a 2D magnetohydrodynamic simulation of time-dependent magnetic reconnection, and then is applied to a magnetic flux transfer event (FTE) seen by Cluster at the dayside high-latitude magnetopause, which has been analyzed with the GS method [Hasegawa et al., Ann. Geophys., 2006]. The application shows that the field lines constituting the FTE flux rope were contracting toward its center as a result of modest convective flow in the region around the core of the flux rope.

Running Neuroimaging Applications on Amazon Web Services: How, When, and at What Cost?

PubMed

Madhyastha, Tara M; Koh, Natalie; Day, Trevor K M; Hernández-Fernández, Moises; Kelley, Austin; Peterson, Daniel J; Rajan, Sabreena; Woelfer, Karl A; Wolf, Jonathan; Grabowski, Thomas J

2017-01-01

The contribution of this paper is to identify and describe current best practices for using Amazon Web Services (AWS) to execute neuroimaging workflows "in the cloud." Neuroimaging offers a vast set of techniques by which to interrogate the structure and function of the living brain. However, many of the scientists for whom neuroimaging is an extremely important tool have limited training in parallel computation. At the same time, the field is experiencing a surge in computational demands, driven by a combination of data-sharing efforts, improvements in scanner technology that allow acquisition of images with higher image resolution, and by the desire to use statistical techniques that stress processing requirements. Most neuroimaging workflows can be executed as independent parallel jobs and are therefore excellent candidates for running on AWS, but the overhead of learning to do so and determining whether it is worth the cost can be prohibitive. In this paper we describe how to identify neuroimaging workloads that are appropriate for running on AWS, how to benchmark execution time, and how to estimate cost of running on AWS. By benchmarking common neuroimaging applications, we show that cloud computing can be a viable alternative to on-premises hardware. We present guidelines that neuroimaging labs can use to provide a cluster-on-demand type of service that should be familiar to users, and scripts to estimate cost and create such a cluster.

Clustering by soft-constraint affinity propagation: applications to gene-expression data.

PubMed

Leone, Michele; Sumedha; Weigt, Martin

2007-10-15

Similarity-measure-based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck (2007a). In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, e.g. in analyzing gene expression data. This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new a priori free parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.

Hydrodynamical simulations of coupled and uncoupled quintessence models - II. Galaxy clusters

NASA Astrophysics Data System (ADS)

Carlesi, Edoardo; Knebe, Alexander; Lewis, Geraint F.; Yepes, Gustavo

2014-04-01

We study the z = 0 properties of clusters (and large groups) of galaxies within the context of interacting and non-interacting quintessence cosmological models, using a series of adiabatic SPH simulations. Initially, we examine the average properties of groups and clusters, quantifying their differences in ΛCold Dark Matter (ΛCDM), uncoupled Dark Energy (uDE) and coupled Dark Energy (cDE) cosmologies. In particular, we focus upon radial profiles of the gas density, temperature and pressure, and we also investigate how the standard hydrodynamic equilibrium hypothesis holds in quintessence cosmologies. While we are able to confirm previous results about the distribution of baryons, we also find that the main discrepancy (with differences up to 20 per cent) can be seen in cluster pressure profiles. We then switch attention to individual structures, mapping each halo in quintessence cosmology to its ΛCDM counterpart. We are able to identify a series of small correlations between the coupling in the dark sector and halo spin, triaxiality and virialization ratio. When looking at spin and virialization of dark matter haloes, we find a weak (5 per cent) but systematic deviation in fifth force scenarios from ΛCDM.

Solar Wind/Magnetosphere/Ionosphere Coupling and the Temporal and Spatial Evolution of Boundary Layers using Cluster, Polar and other ISTP Satellites

NASA Technical Reports Server (NTRS)

Maynard, Nelson C.

2004-01-01

Our analysis concerns macro and meso-scale aspects of coupling between the IMF and the magnetosphere-ionosphere system, as opposed to the microphysics of determining how electron gyrotropy is broken and merging actually occurs. We correlate observed behaviors at Cluster and at Polar with temporal variations in other regions, such as in the ionosphere as measured by SuperDARN. Addressing problems with simultaneous observations from diverse locations properly constrains our interpretations.

Modelling charge transfer reactions with the frozen density embedding formalism

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

Pavanello, Michele; Neugebauer, Johannes

2011-12-21

The frozen density embedding (FDE) subsystem formulation of density-functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two {pi}-stacked nucleobase dimers of B-DNA: 5{sup '}-GG-3{sup '} and 5{sup '}-GT-3{sup '}. The calculations rely on two assumptions: the two-state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionalsmore » are used the electronic couplings are grossly overestimated.« less

Performance Measurement, Visualization and Modeling of Parallel and Distributed Programs

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Sarukkai, Sekhar R.; Mehra, Pankaj; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

This paper presents a methodology for debugging the performance of message-passing programs on both tightly coupled and loosely coupled distributed-memory machines. The AIMS (Automated Instrumentation and Monitoring System) toolkit, a suite of software tools for measurement and analysis of performance, is introduced and its application illustrated using several benchmark programs drawn from the field of computational fluid dynamics. AIMS includes (i) Xinstrument, a powerful source-code instrumentor, which supports both Fortran77 and C as well as a number of different message-passing libraries including Intel's NX Thinking Machines' CMMD, and PVM; (ii) Monitor, a library of timestamping and trace -collection routines that run on supercomputers (such as Intel's iPSC/860, Delta, and Paragon and Thinking Machines' CM5) as well as on networks of workstations (including Convex Cluster and SparcStations connected by a LAN); (iii) Visualization Kernel, a trace-animation facility that supports source-code clickback, simultaneous visualization of computation and communication patterns, as well as analysis of data movements; (iv) Statistics Kernel, an advanced profiling facility, that associates a variety of performance data with various syntactic components of a parallel program; (v) Index Kernel, a diagnostic tool that helps pinpoint performance bottlenecks through the use of abstract indices; (vi) Modeling Kernel, a facility for automated modeling of message-passing programs that supports both simulation -based and analytical approaches to performance prediction and scalability analysis; (vii) Intrusion Compensator, a utility for recovering true performance from observed performance by removing the overheads of monitoring and their effects on the communication pattern of the program; and (viii) Compatibility Tools, that convert AIMS-generated traces into formats used by other performance-visualization tools, such as ParaGraph, Pablo, and certain AVS/Explorer modules.

TRUST. I. A 3D externally illuminated slab benchmark for dust radiative transfer

NASA Astrophysics Data System (ADS)

Gordon, K. D.; Baes, M.; Bianchi, S.; Camps, P.; Juvela, M.; Kuiper, R.; Lunttila, T.; Misselt, K. A.; Natale, G.; Robitaille, T.; Steinacker, J.

2017-07-01

Context. The radiative transport of photons through arbitrary three-dimensional (3D) structures of dust is a challenging problem due to the anisotropic scattering of dust grains and strong coupling between different spatial regions. The radiative transfer problem in 3D is solved using Monte Carlo or Ray Tracing techniques as no full analytic solution exists for the true 3D structures. Aims: We provide the first 3D dust radiative transfer benchmark composed of a slab of dust with uniform density externally illuminated by a star. This simple 3D benchmark is explicitly formulated to provide tests of the different components of the radiative transfer problem including dust absorption, scattering, and emission. Methods: The details of the external star, the slab itself, and the dust properties are provided. This benchmark includes models with a range of dust optical depths fully probing cases that are optically thin at all wavelengths to optically thick at most wavelengths. The dust properties adopted are characteristic of the diffuse Milky Way interstellar medium. This benchmark includes solutions for the full dust emission including single photon (stochastic) heating as well as two simplifying approximations: One where all grains are considered in equilibrium with the radiation field and one where the emission is from a single effective grain with size-distribution-averaged properties. A total of six Monte Carlo codes and one Ray Tracing code provide solutions to this benchmark. Results: The solution to this benchmark is given as global spectral energy distributions (SEDs) and images at select diagnostic wavelengths from the ultraviolet through the infrared. Comparison of the results revealed that the global SEDs are consistent on average to a few percent for all but the scattered stellar flux at very high optical depths. The image results are consistent within 10%, again except for the stellar scattered flux at very high optical depths. The lack of agreement between different codes of the scattered flux at high optical depths is quantified for the first time. Convergence tests using one of the Monte Carlo codes illustrate the sensitivity of the solutions to various model parameters. Conclusions: We provide the first 3D dust radiative transfer benchmark and validate the accuracy of this benchmark through comparisons between multiple independent codes and detailed convergence tests.

Optical potential from first principles

DOE PAGES

Rotureau, J.; Danielewicz, P.; Hagen, G.; ...

2017-02-15

Here, we develop a method to construct a microscopic optical potential from chiral interactions for nucleon-nucleus scattering. The optical potential is constructed by combining the Green’s function approach with the coupled-cluster method. To deal with the poles of the Green’s function along the real energy axis we employ a Berggren basis in the complex energy plane combined with the Lanczos method. Using this approach, we perform a proof-of-principle calculation of the optical potential for the elastic neutron scattering on 16O. For the computation of the ground-state of 16O, we use the coupled-cluster method in the singles-and-doubles approximation, while for themore » A ±1 nuclei we use particle-attached/removed equation-of-motion method truncated at two-particle-one-hole and one-particle-two-hole excitations, respectively. We verify the convergence of the optical potential and scattering phase shifts with respect to the model-space size and the number of discretized complex continuum states. We also investigate the absorptive component of the optical potential (which reflects the opening of inelastic channels) by computing its imaginary volume integral and find an almost negligible absorptive component at low-energies. To shed light on this result, we computed excited states of 16O using equation-of-motion coupled-cluster method with singles-and- doubles excitations and we found no low-lying excited states below 10 MeV. Furthermore, most excited states have a dominant two-particle-two-hole component, making higher-order particle-hole excitations necessary to achieve a precise description of these core-excited states. We conclude that the reduced absorption at low-energies can be attributed to the lack of correlations coming from the low-order cluster truncation in the employed coupled-cluster method.« less

A four-component Fock-space coupled cluster investigation of the HM(CO)5, (M = Mn, Re) photoelectron spectra

NASA Astrophysics Data System (ADS)

Nikoobakht, Behnam; Siebert, Max; Pernpointner, Markus

2015-11-01

In this work, we readdress the photoelectron spectra of the HM(CO)5, (M=Mn, Re) carbonyl complexes by applying four-component Fock-space coupled cluster (FSCC) methods for their calculation in order to extend earlier studies based on less demanding approaches. The final-state characterisation was based on group theoretical considerations of the contributing orbitals and allowed for an unambiguous assignment. Energy level diagrams show the effect of spin-orbit (SO) coupling starting from scalar relativistic results and for the heavy representative HRe(CO)5 nonadditivity effects of SO and electron correlation can be observed requiring a consistent treatment of both contributions.

Four-Nozzle Benchmark Wind Tunnel Model USA Code Solutions for Simulation of Multiple Rocket Base Flow Recirculation at 145,000 Feet Altitude

NASA Technical Reports Server (NTRS)

Dougherty, N. S.; Johnson, S. L.

1993-01-01

Multiple rocket exhaust plume interactions at high altitudes can produce base flow recirculation with attendant alteration of the base pressure coefficient and increased base heating. A search for a good wind tunnel benchmark problem to check grid clustering technique and turbulence modeling turned up the experiment done at AEDC in 1961 by Goethert and Matz on a 4.25-in. diameter domed missile base model with four rocket nozzles. This wind tunnel model with varied external bleed air flow for the base flow wake produced measured p/p(sub ref) at the center of the base as high as 3.3 due to plume flow recirculation back onto the base. At that time in 1961, relatively inexpensive experimentation with air at gamma = 1.4 and nozzle A(sub e)/A of 10.6 and theta(sub n) = 7.55 deg with P(sub c) = 155 psia simulated a LO2/LH2 rocket exhaust plume with gamma = 1.20, A(sub e)/A of 78 and P(sub c) about 1,000 psia. An array of base pressure taps on the aft dome gave a clear measurement of the plume recirculation effects at p(infinity) = 4.76 psfa corresponding to 145,000 ft altitude. Our CFD computations of the flow field with direct comparison of computed-versus-measured base pressure distribution (across the dome) provide detailed information on velocities and particle traces as well eddy viscosity in the base and nozzle region. The solution was obtained using a six-zone mesh with 284,000 grid points for one quadrant taking advantage of symmetry. Results are compared using a zero-equation algebraic and a one-equation pointwise R(sub t) turbulence model (work in progress). Good agreement with the experimental pressure data was obtained with both; and this benchmark showed the importance of: (1) proper grid clustering and (2) proper choice of turbulence modeling for rocket plume problems/recirculation at high altitude.

Robust and Efficient Biomolecular Clustering of Tumor Based on ${p}$ -Norm Singular Value Decomposition.

PubMed

Kong, Xiang-Zhen; Liu, Jin-Xing; Zheng, Chun-Hou; Hou, Mi-Xiao; Wang, Juan

2017-07-01

High dimensionality has become a typical feature of biomolecular data. In this paper, a novel dimension reduction method named p-norm singular value decomposition (PSVD) is proposed to seek the low-rank approximation matrix to the biomolecular data. To enhance the robustness to outliers, the Lp-norm is taken as the error function and the Schatten p-norm is used as the regularization function in the optimization model. To evaluate the performance of PSVD, the Kmeans clustering method is then employed for tumor clustering based on the low-rank approximation matrix. Extensive experiments are carried out on five gene expression data sets including two benchmark data sets and three higher dimensional data sets from the cancer genome atlas. The experimental results demonstrate that the PSVD-based method outperforms many existing methods. Especially, it is experimentally proved that the proposed method is more efficient for processing higher dimensional data with good robustness, stability, and superior time performance.

Adding-point strategy for reduced-order hypersonic aerothermodynamics modeling based on fuzzy clustering

NASA Astrophysics Data System (ADS)

Chen, Xin; Liu, Li; Zhou, Sida; Yue, Zhenjiang

2016-09-01

Reduced order models(ROMs) based on the snapshots on the CFD high-fidelity simulations have been paid great attention recently due to their capability of capturing the features of the complex geometries and flow configurations. To improve the efficiency and precision of the ROMs, it is indispensable to add extra sampling points to the initial snapshots, since the number of sampling points to achieve an adequately accurate ROM is generally unknown in prior, but a large number of initial sampling points reduces the parsimony of the ROMs. A fuzzy-clustering-based adding-point strategy is proposed and the fuzzy clustering acts an indicator of the region in which the precision of ROMs is relatively low. The proposed method is applied to construct the ROMs for the benchmark mathematical examples and a numerical example of hypersonic aerothermodynamics prediction for a typical control surface. The proposed method can achieve a 34.5% improvement on the efficiency than the estimated mean squared error prediction algorithm and shows same-level prediction accuracy.

II Zw 40 - 30 Doradus on Steroids

NASA Astrophysics Data System (ADS)

Leitherer, Claus; Lee, Janice C.; Levesque, Emily M.

2017-11-01

We obtained HST COS G140L spectra of the enigmatic nearby blue compact dwarf galaxy II Zw 40. The galaxy hosts a nuclear super star cluster embedded in a radio-bright nebula, similar to those observed in the related blue compact dwarfs NGC 5253 and Henize 2-10. The ultraviolet spectrum of II Zw 40 is exceptional in terms of the strength of He II 1640, O III] 1666 and C III] 1909. We determined reddening, age, and the cluster mass from the ultraviolet data. The super nebula and the ionizing cluster exceed the ionizing luminosity and stellar mass of the local benchmark 30 Doradus by an order of magnitude. Comparison with stellar evolution models accounting for rotation reveals serious short-comings: these models do not account for the presence of Wolf-Rayet-like stars at young ages observed in II Zw 40. Photoionization modeling is used to probe the origin of the nebular lines and determine gas phase abundances. C/O is solar, in agreement with the result of the stellar-wind modeling.