Computer Physics Communications, Volume 184

Volume 184, Number 1, January 2013

Computational physics

• 
  Fuyuki Shimojo, Satoshi Ohmura, Weiwei Mou, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta:
  Large nonadiabatic quantum molecular dynamics simulations on parallel computers. 1-8
• 
  Weile Jia, Zongyan Cao, Long Wang, Jiyun Fu, Xuebin Chi, Weiguo Gao, Lin-Wang Wang:
  The analysis of a plane wave pseudopotential density functional theory code on a GPU machine. 9-18
• 
  Katherine Baker, Andrij Baumketner, Yuchun Lin, Shaozhong Deng, Donald Jacobs, Wei Cai:
  ICSM: An order N method for calculating electrostatic interactions added to TINKER. 19-26
• 
  Evangelos Voyiatzis:
  Mechanical properties and elastic constants of atomistic systems through the stress-fluctuation formalism. 27-33
• 
  Tarcísio M. Rocha Filho:
  Solving the Vlasov equation for one-dimensional models with long range interactions on a GPU. 34-39
• 
  Yukihiro Komura, Yutaka Okabe:
  Multi-GPU-based Swendsen-Wang multi-cluster algorithm for the simulation of two-dimensional q-state Potts model. 40-44
• 
  Eliseo García, Lorena Lozano, María Jesús Algar, M. Felipe Cátedra:
  A study of the efficiency of the parallelization of a high frequency electromagnetic approach for the computation of radiation and scattering considering multiple bounces. 45-50
• 
  Changfeng Xue, Shaozhong Deng:
  Coulomb Green's function and image potential near a planar diffuse interface, revisited. 51-59
• 
  Bin Lin:
  Parametric cubic spline method for the solution of the nonlinear Schrödinger equation. 60-65
• 
  T. D. Young, Eloy Romero, José E. Román:
  Parallel finite element density functional computations exploiting grid refinement and subspace recycling. 66-72
• 
  Liang Li, Ting-Zhu Huang, Guang-hui Cheng, Yan-Fei Jing, Zhi-Gang Ren, Hou-Biao Li:
  Solution to 3-D electromagnetic problems discretized by a hybrid FEM/MOM method. 73-78
• 
  Paolo Greppi, Elisabetta Arato:
  Efficient computation paths for the systematic analysis of sensitivities. 79-85
• 
  Dingwen Deng, Chengjian Zhang:
  A family of new fourth-order solvers for a nonlinear damped wave equation. 86-101
• 
  Yutaka Utsuno, Noritaka Shimizu, Takaharu Otsuka, Takashi Abe:
  Efficient computation of Hamiltonian matrix elements between non-orthogonal Slater determinants. 102-108
• 
  Andreas Windisch, Reinhard Alkofer, Gundolf Haase, Manfred Liebmann:
  Examining the analytic structure of Green's functions: Massive parallel complex integration using GPUs. 109-116
• 
  Takumi Doi, Michael G. Endres:
  Unified contraction algorithm for multi-baryon correlators on the lattice. 117-123
• 
  Nuno Cardoso, Paulo J. Silva, Pedro Bicudo, Orlando Oliveira:
  Landau gauge fixing on GPUs. 124-129

Computer programs in physics

• 
  Yezhi Lin, Yinping Liu, Zhibin Li:
  Symbolic computation of analytic approximate solutions for nonlinear fractional differential equations. 130-141
• 
  Gianluca Colò, Ligang Cao, Nguyen Van Giai, Luigi Capelli:
  Self-consistent RPA calculations with Skyrme-type interactions: The skyrme_rpa program. 142-161
• 
  Juan J. Galiana-Merino, Julio L. Rosa-Herranz, Sergio Rosa-Cintas, Juan J. Martinez-Espla:
  SeismicWaveTool: Continuous and discrete wavelet analysis and filtering for multichannel seismic data. 162-171
• 
  I. I. Gontchar, M. V. Chushnyakova:
  A C-code for the double folding interaction potential for reactions involving deformed target nuclei. 172-182
• 
  Alexander P. Bakulev, Vyacheslav L. Khandramai:
  FAPT: A Mathematica package for calculations in QCD Fractional Analytic Perturbation Theory. 183-193
• 
  O. Coufal:
  A method for the accurate and smooth approximation of standard thermodynamic functions. 194-200
• 
  Graham R. Dennis, Joseph J. Hope, Mattias T. Johnsson:
  XMDS2: Fast, scalable simulation of coupled stochastic partial differential equations. 201-208
• 
  Seth Quackenbush, Ryan Gavin, Ye Li, Frank Petriello:
  W physics at the LHC with FEWZ 2.1. 209-214
• 
  Roman A. Sen'kov, Mihai Horoi, Vladimir G. Zelevinsky:
  A high-performance Fortran code to calculate spin- and parity-dependent nuclear level densities. 215-221
• 
  Eric Conte, Benjamin Fuks, Guillaume Serret:
  MadAnalysis 5, a user-friendly framework for collider phenomenology. 222-256

New version announcement

• 
  Jaroslaw Adam Miszczak:
  Employing online quantum random number generators for generating truly random quantum states in Mathematica. 257-258

Volume 184, Number 2, February 2013

Feature Article

• 
  João Antônio Plascak, P. H. L. Martins:
  Probability distribution function of the order parameter: Mixing fields and universality. 259-269

Computational physics

• 
  Satrajit Adhikari, António J. C. Varandas:
  The coupled 3D wave packet approach for triatomic reactive scattering in hyperspherical coordinates. 270-283
• 
  C. Devi Sudheer, S. Krishnan, Ashok Srinivasan, P. R. C. Kent:
  Dynamic load balancing for petascale quantum Monte Carlo applications: The Alias method. 284-292
• 
  O. Sauter, S. Yu. Medvedev:
  Tokamak coordinate conventions: COCOS. 293-302
• 
  Dongling Wang, Aiguo Xiao, Xueyang Li:
  Parametric symplectic partitioned Runge-Kutta methods with energy-preserving properties for Hamiltonian systems. 303-310
• 
  Jochen Gerhard, Volker Lindenstruth, Marcus Bleicher:
  Relativistic hydrodynamics on graphic cards. 311-319
• 
  Igor V. Sokolov:
  Alternating-order interpolation in a charge-conserving scheme for particle-in-cell simulations. 320-328
• 
  Massimo Bernaschi, Mauro Bisson, Massimiliano Fatica, Simone Melchionna, Sauro Succi:
  Petaflop hydrokinetic simulations of complex flows on massive GPU clusters. 329-341
• 
  Jin-Chun Li, Ping Qian, Zhen-Feng Zhang, Ying Liu, Xiao-Jian Yuan, Jiang Shen, Nan-Xian Chen:
  Theoretical study of structure and lattice vibrations of R₃Co_11-xFe_xB₄ (R=Nd, Gd). 342-347
• 
  Hong Jiang, Ricardo I. Gómez-Abal, Xin-Zheng Li, Christian Meisenbichler, Claudia Ambrosch-Draxl, Matthias Scheffler:
  FHI-gap: A GW code based on the all-electron augmented plane wave method. 348-366
• 
  Jun Liu:
  Least square based method for obtaining one-particle spectral functions from temperature Green functions. 367-373
• 
  Scott Le Grand, Andreas W. Götz, Ross C. Walker:
  SPFP: Speed without compromise - A mixed precision model for GPU accelerated molecular dynamics simulations. 374-380
• 
  Zhi Shang:
  Performance analysis of large scale parallel CFD computing based on Code_Saturne. 381-386
• 
  Yaroslav Pavlyukh, Jamal Berakdar:
  Electron repulsion integrals for self-energy calculations. 387-395

Computer programs in physics

• 
  Sophia Borowka, Jonathon Carter, Gudrun Heinrich:
  Numerical evaluation of multi-loop integrals for arbitrary kinematics with SecDec 2.0. 396-408
• 
  Saulius Mickevicius, Darius Germanas, Ramutis Kazys Kalinauskas:
  Revised calculation of four-particle harmonic-oscillator transformation brackets matrix. 409-413
• 
  Rostislav Chudoba, Václav Sadílek, R. Rypl, Miroslav Vorechovský:
  Using Python for scientific computing: Efficient and flexible evaluation of the statistical characteristics of functions with multivariate random inputs. 414-427
• 
  Victor Zlokazov, Vladimir Utyonkov, Yury Tsyganov:
  VSHEC - A program for the automatic spectrum calibration. 428-431
• 
  Mikhail S. Litsarev:
  The DEPOSIT computer code: Calculations of electron-loss cross-sections for complex ions colliding with neutral atoms. 432-439

New version announcements

• 
  Aleksander Jablonski:
  Improved algorithm for calculating the Chandrasekhar function. 440-442
• 
  Celestino Angeli, Renzo Cimiraglia:
  Automated evaluation of matrix elements between contracted wavefunctions: A Mathematica version of the FRODO program. 443-444

Volume 184, Number 3, March 2013

Computational physics

• 
  Rio Yokota, Lorena A. Barba, Tetsu Narumi, Kenji Yasuoka:
  Petascale turbulence simulation using a highly parallel fast multipole method on GPUs. 445-455
• 
  Simon Portegies Zwart, Stephen L. W. McMillan, Arjen van Elteren, F. Inti Pelupessy, Nathan de Vries:
  Multi-physics simulations using a hierarchical interchangeable software interface. 456-468
• 
  Jorge Francés, Sergio Bleda, Cristian Neipp, Augusto Márquez, Inmaculada Pascual, Augusto Beléndez:
  Performance analysis of the FDTD method applied to holographic volume gratings: Multi-core CPU versus GPU computing. 469-479
• 
  Jing Shen, Wei E. I. Sha, Zhixiang Huang, Mingsheng Chen, Xianliang Wu:
  High-order symplectic FDTD scheme for solving a time-dependent Schrödinger equation. 480-492
• 
  B.-W. Jeng, Y.-S. Wang, C.-S. Chien:
  A two-parameter continuation algorithm for vortex pinning in rotating Bose-Einstein condensates. 493-508
• 
  Nuno Cardoso, Pedro Bicudo:
  Generating pure gauge lattice QCD configurations on GPUs with CUDA. 509-518
• 
  Martin Lüscher, Stefan Schaefer:
  Lattice QCD with open boundary conditions and twisted-mass reweighting. 519-528
• 
  Ali Shokri, Abbas Ali Shokri:
  The new class of implicit L-stable hybrid Obrechkoff method for the numerical solution of first order initial value problems. 529-531
• 
  Florian De Vuyst, Francesco Salvarani:
  GPU-accelerated numerical simulations of the Knudsen gas on time-dependent domains. 532-536
• 
  Marco D. Mazzeo:
  Fast discontinuous Galerkin lattice-Boltzmann simulations on GPUs via maximal kernel fusion. 537-549
• 
  Hossein Ebadi:
  Bound state calculation of two-component Klein-Gordon equation with Damped-Relaxation technique. 550-556
• 
  Baoming Tang, Ehsan Khatami, Marcos Rigol:
  A short introduction to numerical linked-cluster expansions. 557-564
• 
  Zohreh Asgari, S. M. Hosseini:
  Numerical solution of two-dimensional sine-Gordon and MBE models using Fourier spectral and high order explicit time stepping methods. 565-572
• 
  Antonio Brunetti:
  A fast fine-grained genetic algorithm for spectrum fitting: An application to X-ray spectra. 573-578
• 
  Mohankumar Nandagopal, Ajay Rawat:
  Some comments on the evaluation of the Chandrasekhar H function. 579-581
• 
  K. Parand, J. A. Rad:
  Kansa method for the solution of a parabolic equation with an unknown spacewise-dependent coefficient subject to an extra measurement. 582-595
• 
  Hai P. Le, Jean-Luc Cambier, Lord K. Cole:
  GPU-based flow simulation with detailed chemical kinetics. 596-606
• 
  D. W. L. Sprung, M. I. Betti, W. van Dijk:
  Finite Fourier transforms computed by a modified Filon-Euler-Maclaurin method. 607-616
• 
  José M. Domínguez, Alejandro J. C. Crespo, Moncho Gómez-Gesteira:
  Optimization strategies for CPU and GPU implementations of a smoothed particle hydrodynamics method. 617-627
• 
  Edan Lerner, Gustavo Düring, Matthieu Wyart:
  Simulations of driven overdamped frictionless hard spheres. 628-637
• 
  Andreas Galonska, Paul Gibbon, Frederic Imbeaux, Yann Frauel, Bernard Guillerminet, Gabriele Manduchi, Felix Wolf:
  Parallel universal access layer: A scalable I/O library for integrated tokamak modeling. 638-646
• 
  S. J. Ahmed, J. Kivinen, B. Zaporzan, Laura Curiel, Samuel Pichardo, Oleg Rubel:
  BerryPI: A software for studying polarization of crystalline solids with WIEN2k density functional all-electron package. 647-651
• 
  Mohammad Poursina, Kurt S. Anderson:
  Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-and-conquer scheme. 652-660
• 
  Roberto da Silva, Mendeli H. Vainstein, Luís C. Lamb, Sandra D. Prado:
  A simple non-Markovian computational model of the statistics of soccer leagues: Emergence and scaling effects. 661-670
• 
  G. Lanzafame:
  Implicit integrations for SPH in semi-Lagrangian approach: Application to the accretion disc modeling in a microquasar. 671-688
• 
  Chris Johnson, A. D. Kennedy:
  Numerical determination of partial spectrum of Hermitian matrices using a Lánczos method with selective reorthogonalization. 689-697
• 
  L. Basso, Alexander Belyaev, Debtosh Chowdhury, Martin Hirsch, S. Khalil, S. Moretti, B. O'Leary, Werner Porod, Florian Staub:
  Proposal for generalised supersymmetry Les Houches Accord for see-saw models and PDG numbering scheme. 698-719
• 
  Mariano Álvaro, Elena Cebrián, Manuel Carretero, Luis L. Bonilla:
  Numerical methods for kinetic equations in semiconductor superlattices. 720-731
• 
  Antonio Souto-Iglesias, Fabricio Macià, Leo M. González, Jose L. Cercos-Pita:
  On the consistency of MPS. 732-745
• 
  Enrique Comesaña, Manuel Aldegunde, Antonio J. García-Loureiro:
  Simulation of the spin polarization and the charge transport in Zener tunnel junctions based on ferromagnetic GaAs and ZnO. 746-756
• 
  Dieter Bingemann:
  Statistical identification of structural rearrangement events in molecular dynamics trajectories. 757-764
• 
  Hanping Hu, Lingfeng Liu, Nai Da Ding:
  Pseudorandom sequence generator based on the Chen chaotic system. 765-768

Computer programs in physics

• 
  P. J. J. Luukko, Eero Räsänen:
  Imaginary time propagation code for large-scale two-dimensional eigenvalue problems in magnetic fields. 769-776
• 
  Giovanni Luca Masala, Bruno Golosio, Piernicola Oliva:
  An improved Marching Cube algorithm for 3D data segmentation. 777-782
• 
  Ashton S. Reimer, Alexei F. Cheviakov:
  A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet-Neumann boundary conditions. 783-798
• 
  Jacek Kobus:
  A finite difference Hartree-Fock program for atoms and diatomic molecules. 799-811
• 
  Marco Caliari, Stefan Rainer:
  GSGPEs: A MATLAB code for computing the ground state of systems of Gross-Pitaevskii equations. 812-823
• 
  Jan Broeckhove, Kurt Vanmechelen:
  An adaptor for C++ callbacks with C and Fortran libraries. 824-832
• 
  Yury V. Suleimanov, J. W. Allen, W. H. Green:
  RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics. 833-840
• 
  Martin Hoefling, Helmut Grubmüller:
  In silico FRET from simulated dye dynamics. 841-852
• 
  Y. G. Chen, J. B. Wang:
  Qcompiler: Quantum compilation with the CSD method. 853-865
• 
  Richard Marchand, David Purschke, J. Samson:
  LEOrbit: A program to calculate parameters relevant to modeling Low Earth Orbit spacecraft-plasma interaction. 866-872
• 
  David A. Bonhommeau, Marie-Pierre Gaigeot:
  MCMC² : A Monte Carlo code for multiply-charged clusters. 873-884
• 
  Carl McBride, Eva G. Noya, Carlos Vega:
  A computer program to evaluate the NVM propagator for rigid asymmetric tops for use in path integral simulations of rigid bodies. 885-890
• 
  Raoul D. Schram, Gerard T. Barkema, Rob H. Bisseling:
  SAWdoubler: A program for counting self-avoiding walks. 891-898
• 
  Debtosh Chowdhury, Raghuveer Garani, Sudhir K. Vempati:
  SuSeFLAV 1.2: Program for supersymmetric mass spectra with seesaw mechanism and rare lepton flavor violating decays. 899-918
• 
  Borut Paul Kersevan, Elzbieta Richter-Was:
  The Monte Carlo event generator AcerMC versions 2.0 to 3.8 with interfaces to PYTHIA 6.4, HERWIG 6.5 and ARIADNE 4.1. 919-985
• 
  Giuseppe Bevilacqua, Michal Czakon, M. V. Garzelli, Andreas van Hameren, A. Kardos, Costas G. Papadopoulos, R. Pittau, Malgorzata Worek:
  HELAC-NLO. 986-997
• 
  Oliver Brein, Robert V. Harlander, Tom J. E. Zirke:
  vh@nnlo - Higgs Strahlung at hadron colliders. 998-1003
• 
  Andreas Crivellin, Janusz Rosiek, P. H. Chankowski, A. Dedes, S. Jäger, Philip Tanedo:
  SUSY_FLAVOR v2: A computational tool for FCNC and CP-violating processes in the MSSM. 1004-1032
• 
  Lorenzo Botto:
  A geometric multigrid Poisson solver for domains containing solid inclusions. 1033-1044
• 
  G. F. Jefferson, J. Carminati:
  ASP: Automated symbolic computation of approximate symmetries of differential equations. 1045-1063
• 
  B. Azadegan:
  A Mathematica package for calculation of planar channeling radiation spectra of relativistic electrons channeled in a diamond-structure single crystal (quantum approach). 1064-1069

New version announcements

• 
  Xian-You Wang, Xing-Gang Wu:
  GENXICC2.1: An improved version of GENXICC for hadronic production of doubly heavy baryons. 1070-1074
• 
  Alexei Bazavov, Bernd A. Berg:
  Program package for multicanonical simulations of U(1) lattice gauge theory - Second version. 1075-1076

Volume 184, Number 4, April 2013

Computational physics

• 
  T. H. Cho, Wan-Sheng Su, T. C. Leung, Wei Ren, C. T. Chan:
  Electronic and optical properties of bundled single-walled carbon nanotubes investigated by the first-principles method. 1077-1085
• 
  S. A. Galindo-Torres, A. Scheuermann, Ling Li, D. M. Pedroso, D. J. Williams:
  A Lattice Boltzmann model for studying transient effects during imbibition-drainage cycles in unsaturated soils. 1086-1093
• 
  Shamsul Qamar, Sidrah Ahmed:
  The space-time CE/SE method for solving one-dimensional special relativistic magnetohydrodynamics equations. 1094-1105
• 
  Lin Zhang, Jie Ouyang, Xiaohua Zhang:
  The variational multiscale element free Galerkin method for MHD flows at high Hartmann numbers. 1106-1118
• 
  Yaser Afshar, Friederike Schmid, Ahmadreza Pishevar, S. Worley:
  Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics. 1119-1128
• 
  Jonathan D. Halverson, Thomas Brandes, Olaf Lenz, Axel Arnold, Stas Bevc, Vitaliy Starchenko, Kurt Kremer, Torsten Stuehn, Dirk Reith:
  ESPResSo++: A modern multiscale simulation package for soft matter systems. 1129-1149
• 
  Hong Fu, Limin Zheng, Minghui Yang:
  Accelerating modified Shepard interpolated potential energy calculations using graphics processing units. 1150-1154
• 
  Johannes Zierenberg, Martin Marenz, Wolfhard Janke:
  Scaling properties of a parallel implementation of the multicanonical algorithm. 1155-1160
• 
  Yong Zhang, Ting-Zhu Huang, Wei Shao, Sheng-Jian Lai:
  Some new strategies for RCM ordering in solving electromagnetic scattering problems. 1161-1164
• 
  Peter Wittek, Fernando M. Cucchietti:
  A second-order distributed Trotter-Suzuki solver with a hybrid CPU-GPU kernel. 1165-1171
• 
  Andriy O. Lyakhov, Artem R. Oganov, Harold T. Stokes, Qiang Zhu:
  New developments in evolutionary structure prediction algorithm USPEX. 1172-1182
• 
  Markus Hopfer, Reinhard Alkofer, Gundolf Haase:
  Solving the ghost-gluon system of Yang-Mills theory on GPUs. 1183-1190
• 
  Carlos Teijeiro, Godehard Sutmann, Guillermo L. Taboada, Juan Touriño:
  Parallel Brownian dynamics simulations with the message-passing and PGAS programming models. 1191-1202
• 
  Gabor Demeter:
  Solving the Maxwell-Bloch equations for resonant nonlinear optics using GPUs. 1203-1210
• 
  Stéphane Balac, Fabrice Mahé:
  Embedded Runge-Kutta scheme for step-size control in the interaction picture method. 1211-1219

Computer programs in physics

• 
  J. S. Lee, M. Carena, J. Ellis, A. Pilaftsis, C. E. M. Wagner:
  CPsuperH2.3: An updated tool for phenomenology in the MSSM with explicit CP violation. 1220-1233
• 
  J. R. Johansson, Paul D. Nation, Franco Nori:
  QuTiP 2: A Python framework for the dynamics of open quantum systems. 1234-1240
• 
  Shuang Gao, Gregory D. Peterson:
  GASPRNG: GPU accelerated scalable parallel random number generator library. 1241-1249
• 
  Ronald M. Caplan:
  NLSEmagic: Nonlinear Schrödinger equation multi-dimensional Matlab-based GPU-accelerated integrators using compact high-order schemes. 1250-1271
• 
  Kyungwon Chun, Huioon Kim, Hyounggyu Kim, Kil Su Jung, Youngjoo Chung:
  GMES: A Python package for solving Maxwell's equations using the FDTD method. 1272-1279
•