Computer Physics Communications, Volume 183

Volume 183, Number 1, January 2012

Computational physics

• 
  Matthew G. Reuter, Judith C. Hill, Robert J. Harrison:
  Solving PDEs in irregular geometries with multiresolution methods I: Embedded Dirichlet boundary conditions. 1-7
• 
  Nobuya Maeshima, Ken-ichi Hino:
  Parallelization of the R-matrix propagation method for the study of intense-laser-driven semiconductor superlattices. 8-14
• 
  Zhijie Xu, Hai Huang, Xiaoyi Li, Paul Meakin:
  Phase field and level set methods for modeling solute precipitation and/or dissolution. 15-19
• 
  S. Kaprzyk:
  An algebraic formulation of the simplex linear method for multiple integrals over the d-dimensional domain. 20-25
• 
  Filip A. Sala:
  Mobile phone as a platform for numerical simulation. 26-29
• 
  Chuan-Hui Zhang, Qiong Ran, Jiang Shen:
  Structural stability of silicene-like nanotubes. 30-33
• 
  Yoshifumi Nakamura, Ken-Ichi Ishikawa, Yoshinobu Kuramashi, Tetsuya Sakurai, Hiroto Tadano:
  Modified block BiCGSTAB for lattice QCD. 34-37
• 
  Nicolas Bigaouette, Edward Ackad, Lora Ramunno:
  Nonlinear grid mapping applied to an FDTD-based, multi-center 3D Schrödinger equation solver. 38-45
• 
  Jiantong Weng, Tomoyoshi Shimobaba, Minoru Oikawa, Nobuyuki Masuda, Tomoyoshi Ito:
  Fast recurrence relation for computer-generated-hologram. 46-49
• 
  Tao Jiang, Jie Ouyang, Jin-Lian Ren, Bin-Xin Yang, Xiaoyang Xu:
  A mixed corrected symmetric SPH (MC-SSPH) method for computational dynamic problems. 50-62
• 
  Liviu Gr. Ixaru:
  Runge-Kutta method with equation dependent coefficients. 63-69
• 
  Jacob Waltz, T. A. Gianakon:
  A comparison of mix models for the Rayleigh-Taylor instability. 70-79
• 
  Roberto Barrio, Marcos Rodríguez, Fernando Blesa:
  Computer-assisted proof of skeletons of periodic orbits. 80-85
• 
  Zhaoxia Chen, Xiong You, Wei Shi, Zhongli Liu:
  Symmetric and symplectic ERKN methods for oscillatory Hamiltonian systems. 86-98
• 
  Mario S. Reis:
  Models for one-dimensional molecular magnets. 99-105

Computer programs in physics

• 
  Yezhi Lin, Yinping Liu, Zhibin Li:
  Symbolic computation of analytic approximate solutions for nonlinear differential equations with initial conditions. 106-117
• 
  Jaroslaw Adam Miszczak:
  Generating and using truly random quantum states in Mathematica. 118-124
• 
  Valerio Novaresio, María García-Camprubí, Salvador Izquierdo, Pietro Asinari, Norberto Fueyo:
  An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells. 125-146
• 
  Guillem Carles, Carme Ferran, Artur Carnicer, Salvador Bosch:
  Design and implementation of a scene-dependent dynamically selfadaptable wavefront coding imaging system. 147-154
• 
  Beat Röthlisberger, Jörg Lehmann, Daniel Loss:
  libCreme: An optimization library for evaluating convex-roof entanglement measures. 155-165
• 
  Nicolas Schunck, J. Dobaczewski, J. McDonnell, Wojciech Satula, Javid A. Sheikh, Andrzej Staszczak, M. V. Stoitsov, P. Toivanen:
  Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis.: (VII) hfodd (v2.49t): A new version of the program. 166-192
• 
  N. D. Gagunashvili:
  CHICOM: A code of tests for comparing unweighted and weighted histograms and two weighted histograms. 193-196
• 
  Andre E. Botha:
  General R-matrix approach for integrating the multiband k.p equation in layered semiconductor structures. 197-202
• 
  Xevi Biarnés, Fabio Pietrucci, Fabrizio Marinelli, Alessandro Laio:
  METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. 203-211

Volume 183, Number 2, February 2012

Computational physics

• 
  Andrzej Daniluk:
  Visual modeling for scientific software architecture design. A practical approach. 213-230
• 
  Carlos Alberto Jara, Francisco Esquembre, Wolfgang Christian, Francisco A. Candelas Herías, Fernando Torres Medina, Sebastián Dormido:
  A new 3D visualization Java framework based on physics principles. 231-244
• 
  Luciano M. de Andrade Filho, José Manoel de Seixas, Roberto Agostino Vitillo, Brian Thomas Martin:
  Three-dimensional event visualization for the ATLAS calorimeter. 245-250
• 
  K. Roeller, S. Herminghaus, Axel Hager-Fingerle:
  Sinusoidal shaking in event-driven simulations. 251-260
• 
  Yubao Zhen, Chengbiao Chu:
  A deformation-fluctuation hybrid method for fast evaluation of elastic constants with many-body potentials. 261-265
• 
  Sergio Andres Galindo-Torres, D. M. Pedroso, D. J. Williams, Ling Li:
  Breaking processes in three-dimensional bonded granular materials with general shapes. 266-277
• 
  Yong Gan, J. K. Chen:
  A hybrid method for integrated atomistic-continuum simulation of ultrashort-pulsed laser interaction with semiconductors. 278-284
• 
  Farvah Mahmoudi, Sven Heinemeyer, Alexandre Arbey, Aoife Bharucha, Toru Goto, Thomas Hahn, U. Haisch, Sabine Kraml, Margarete Mühlleitner, J. Reuter, Peter Skands, Pietro Slavich:
  Flavour Les Houches Accord: Interfacing flavour related codes. 285-298
• 
  Georg Bergner, Jaïr Wuilloud:
  Acceleration of the Arnoldi method and real eigenvalues of the non-Hermitian Wilson-Dirac operator. 299-304
• 
  Ralf Kleiber, Roman Hatzky:
  A partly matrix-free solver for the gyrokinetic field equation in three-dimensional geometry. 305-308
• 
  Xuesong Li, Lin Ma:
  Minimizing binary functions with simulated annealing algorithm with applications to binary tomography. 309-315
• 
  Mingzhe Liu, Xianguo Tuo, Zhe Li, Jianbo Yang, Yang Gao:
  Asymmetric exclusion process for modeling of information flow. 316-319
• 
  Aleksander A. Stanislavsky, Karina Weron:
  Numerical scheme for calculating of the fractional two-power relaxation laws in time-domain of measurements. 320-323
• 
  Patrick M. C. Rourke, Stephen R. Julian:
  Numerical extraction of de Haas-van Alphen frequencies from calculated band energies. 324-332

Computer programs in physics

• 
  Ben-Hao Sa, Dai-Mei Zhou, Yu-Liang Yan, Xiao-Mei Li, Sheng-Qin Feng, Bao-Guo Dong, Xu Cai:
  PACIAE 2.0: An updated parton and hadron cascade model (program) for the relativistic nuclear collisions. 333-346
• 
  S. Kaprzyk:
  An algebraic formulation and implementation of the tetrahedron linear method for the Brillouin zone integration of spectral functions. 347-362
• 
  Teemu Hynninen, Cristiano L. Dias, A. Mkrtchyan, Vili Heinonen, Mikko Karttunen, Adam S. Foster, Tapio Ala-Nissila:
  A molecular dynamics implementation of the 3D Mercedes-Benz water model. 363-369
• 
  Ulrich Hohenester, Andreas Trügler:
  MNPBEM - A Matlab toolbox for the simulation of plasmonic nanoparticles. 370-381
• 
  Joseph E. Curtis, Sindhu Raghunandan, Hirsh Nanda, Susan Krueger:
  SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints. 382-389
• 
  Dennis M. Elking, Lalith E. Perera, Lee G. Pedersen:
  HPAM: Hirshfeld partitioned atomic multipoles. 390-397
• 
  Matej Batic, Maria Grazia Pia, Sam J. Cipolla:
  ISICSoo: A class for the calculation of ionization cross sections from ECPSSR and PWBA theory. 398-404
• 
  Christian Clason, Gregory von Winckel:
  A general spectral method for the numerical simulation of one-dimensional interacting fermions. 405-417
• 
  N. D. Gagunashvili:
  CHIWEI: A code of goodness of fit tests for weighted and unweighted histograms. 418-421
• 
  Dominik Stöckinger, Philipp Varso:
  FeynArts model file for MSSM transition counterterms from DREG to DRED. 422-430
• 
  Sami Heinäsmäki:
  IONIS: Approximate atomic photoionization intensities. 431-437

New version announcements

• 
  Paolo Barletta:
  COOL: A code for Dynamic Monte Carlo Simulation of molecular dynamics. 438-439
• 
  Kwang Jin Oh, Ji Hoon Kang, Hun Joo Myung:
  mm_par2.0: An object-oriented molecular dynamics simulation program parallelized using a hierarchical scheme with MPI and OPENMP. 440-441
• 
  Xian-You Wang, Xing-Gang Wu:
  A trick to improve the efficiency of generating unweighted Bc events from BCVEGPY. 442-445
• 
  Min Hyung Cho, Wei Cai:
  Revision of wFMM - A Wideband Fast Multipole Method for the two-dimensional complex Helmholtz equation. 446-447

Volume 183, Number 3, March 2012

Computational physics

• 
  W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington:
  Implementing molecular dynamics on hybrid high performance computers - Particle-particle particle-mesh. 449-459
• 
  Thomas Hahn:
  The high-energy physicistʼs guide to MathLink. 460-469
• 
  Athinoula Kosti, Zacharias A. Anastassi, Tom E. Simos:
  An optimized explicit Runge-Kutta-Nyström method for the numerical solution of orbital and related periodical initial value problems. 470-479
• 
  Camilo Espejo, Tonatiuh Rangel, Yann Pouillon, Aldo H. Romero, Xavier Gonze:
  Wannier functions approach to van der Waals interactions in ABINIT. 480-485
• 
  Manamohan Prusty, Jia Ning Leaw, Shan Shang Chong, Siew Ann Cheong:
  Stochastic boundary conditions for grand-canonical-like molecular dynamics simulations of open systems. 486-496
• 
  Grady Schofield, James R. Chelikowsky, Yousef Saad:
  A spectrum slicing method for the Kohn-Sham problem. 497-505
• 
  Ulrich David Jentschura, Erik Lötstedt:
  Numerical calculation of Bessel, Hankel and Airy functions. 506-519
• 
  Alan Gray, Iain Bethune, Richard D. Kenway, Lorna Smith, Martyn F. Guest, Christine A. Kitchen, Paul Calleja, Aleksander Korzynski, Stuart Rankin, Mike Ashworth, Andrew Porter, Ilian T. Todorov, Martin Plummer, Emma Jones, Lois Steenman-Clark, Ben Ralston, Charles A. Laughton:
  Mapping application performance to HPC architecture. 520-529
• 
  A. Kopp, I. Büsching, R. D. Strauss, M. S. Potgieter:
  A stochastic differential equation code for multidimensional Fokker-Planck type problems. 530-542
• 
  S. Ihnatsenka:
  Computation of electron quantum transport in graphene nanoribbons using GPU. 543-546
• 
  Qiao-Hong Sui, Zhong-Jun Ding, Rui Jiang, Wei Huang, Duo Sun, Bing-Hong Wang:
  Slow-to-start effect in two-dimensional traffic flow. 547-551
• 
  Shu-Sen Xie, Su-Cheol Yi, Tae In Kwon:
  Fourth-order compact difference and alternating direction implicit schemes for telegraph equations. 552-569
• 
  Andrei Bourchtein, Ludmila Bourchtein:
  A semi-implicit time-splitting scheme for a regional nonhydrostatic atmospheric model. 570-587
• 
  Chunye Gong, Jie Liu, Haowei Huang, Zhenghu Gong:
  Particle transport with unstructured grid on GPU. 588-593
• 
  B. Roostaei, Walter C. Ermler:
  Electric dipole transition moments and permanent dipole moments for spin-orbit configuration interaction wave functions. 594-599
• 
  Ram Jiwari, Sapna Pandit, R. C. Mittal:
  Numerical simulation of two-dimensional sine-Gordon solitons by differential quadrature method. 600-616
• 
  Jan L. Cieslinski, Boguslaw Ratkiewicz:
  Discrete gradient algorithms of high order for one-dimensional systems. 617-627
• 
  Lorenzo Pardini, Valerio Bellini, Franca Manghi, Claudia Ambrosch-Draxl:
  First-principles calculation of X-ray dichroic spectra within the full-potential linearized augmented planewave method: An implementation into the Wien2k code. 628-636

Computer programs in physics

• 
  Rafael Ramis, K. Eidmann, J. Meyer-ter-Vehn, S. Hüller:
  MULTI-fs - A computer code for laser-plasma interaction in the femtosecond regime. 637-655
• 
  Aldée Charbonnier, Céline Combet, David Maurin:
  clumpy: A code for γ-ray signals from dark matter structures. 656-668
• 
  I. O. Bespamyatnov, W. L. Rowan, K. T. Liao:
  ALCBEAM - Neutral beam formation and propagation code for beam-based plasma diagnostics. 669-676
• 
  Gundra Kondayya, Alok Shukla:
  A Fortran 90 Hartree-Fock program for one-dimensional periodic π-conjugated systems using Pariser-Parr-Pople model. 677-689
• 
  David C. Lonie, Eva Zurek:
  Identifying duplicate crystal structures: XtalComp, an open-source solution. 690-697
• 
  Timothy C. Petersen, Simon P. Ringer:
  Local electron tomography using angular variations of surface tangents: Stomo version 2. 698-704
• 
  A. Babaev, Yu. L. Pivovarov:
  Resonant coherent excitation of hydrogen-like ions planar channeled in a crystal; Transition into the first excited state. 705-710
• 
  Dean Lambert, Alasdair C. Hamilton, George Constable, Harsh Snehanshu, Sharvil Talati, Johannes Courtial:
  TIM, a ray-tracing program for METATOY research and its dissemination. 711-732
• 
  A. V. Nikitin:
  An efficient code for calculation of the 6C, 9C and 12C symbols for C3v, Td, and Oh point groups. 733-736
• 
  Bruno Juliá-Díaz, Tobias Graß:
  Strongdeco: Expansion of analytical, strongly correlated quantum states into a many-body basis. 737-745
• 
  Mikolaj Chojnacki, Adam Kisiel, Wojciech Florkowski, Wojciech Broniowski:
  THERMINATOR 2: THERMal heavy IoN generATOR 2. 746-773
• 
  Debottam Das, Ulrich Ellwanger, Ana M. Teixeira:
  NMSDECAY: A Fortran code for supersymmetric particle decays in the Next-to-Minimal Supersymmetric Standard Model. 774-779
• 
  Thomas Fischbacher:
  Numerical tools to validate stationary points of SO(8)-gauged N=8D=4 supergravity. 780-784
• 
  Benjamin C. Allanach, C. H. Kom, Marja Hanussek:
  Computation of neutrino masses in R-parity violating supersymmetry: SOFTSUSY3.2. 785-793
• 
  Amparo Gil, Javier Segura, Nico M. Temme:
  An improved algorithm and a Fortran 90 module for computing the conical function f^m_-1/2+iτ(x). 794-799
• 
  Tomasz Dziubak, Jacek Matulewski:
  An object-oriented implementation of a solver of the time-dependent Schrödinger equation using the CUDA technology. 800-812
• 
  Stefan Weinzierl:
  The SISCone jet algorithm optimised for low particle multiplicities. 813-820
• 
  Nadia M. Davidson, G. Nanava, Tomasz Przedzinski, Elzbieta Richter-Was, Zbigniew Was:
  Universal interface of TAUOLA: Technical and physics documentation. 821-843

New version announcements

• 
  Evgeny Z. Liverts, Nir Barnea:
  S-states of helium-like ions. 844-845
• 
  Daniel Maître:
  Extension of HPL to complex arguments. 846

Volume 183, Number 4, April 2012

Computational physics

• 
  Juraci P. Reis, Artur F. Menezes, Edmilson M. Souza, Alessandro Facure, Jose A. C. C. Medeiros, Ademir X. Silva:
  Dose optimization in ¹²⁵I permanent prostate seed implants using the Monte Carlo method. 847-852
• 
  Claudio Bonati, Guido Cossu, Massimo D'Elia, Pietro Incardona:
  QCD simulations with staggered fermions on GPUs. 853-863
• 
  Francisco de la Hoz, Fernando Vadillo:
  Numerical simulation of the N-dimensional sine-Gordon equation via operational matrices. 864-879
• 
  Mathias Winkel, Robert Speck, Helge Hübner, Lukas Arnold, Rolf Krause, Paul Gibbon:
  A massively parallel, multi-disciplinary Barnes-Hut tree code for extreme-scale N-body simulations. 880-889
• 
  Nathan Schmid, Clara D. Christ, Markus Christen, Andreas P. Eichenberger, Wilfred F. van Gunsteren:
  Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. 890-903
• 
  Cristóbal Bertoglio, Boris N. Khoromskij:
  Low-rank quadrature-based tensor approximation of the Galerkin projected Newton/Yukawa kernels. 904-912
• 
  Feng-Gong Lang, Xiao-Ping Xu:
  Quintic B-spline collocation method for second order mixed boundary value problem. 913-921
• 
  F. Merz, Christoph Kowitz, Eloy Romero, José E. Román, Frank Jenko:
  Multi-dimensional gyrokinetic parameter studies based on eigenvalue computations. 922-930
• 
  Vitaliy Ogarko, Stefan Luding:
  A fast multilevel algorithm for contact detection of arbitrarily polydisperse objects. 931-936
• 
  Sergei S. Kucherenko, Stefano Tarantola, Paola Annoni:
  Estimation of global sensitivity indices for models with dependent variables. 937-946
• 
  J. Seebacher, Alexander Kendl:
  Towards a unified linear kinetic transport model with the trace ion module for EIRENE. 947-959
• 
  Andy Buckley, A. Shilton, M. J. White:
  Fast supersymmetry phenomenology at the Large Hadron Collider using machine learning techniques. 960-970
• 
  M. Fitzgerald, J. Khachan:
  A 2-D PIC/MC/Vlasov method for electrostatic fusion discharges. 971-979
• 
  Eiji Tsuchida, Yoong-Kee Choe:
  Iterative diagonalization of symmetric matrices in mixed precision and its application to electronic structure calculations. 980-985
• 
  Christian Ringl, Herbert M. Urbassek:
  A LAMMPS implementation of granular mechanics: Inclusion of adhesive and microscopic friction forces. 986-992
• 
  C. A. Duarte:
  Compact expressions for the magnetoresistance and the electron/hole density of states under the application of magnetic fields. 993-997
• 
  Yueh-Cheng Kuo, Shih-Feng Shieh, Weichung Wang:
  Rotational quotient procedure: A tracking control continuation method for PDEs on radially symmetric domains. 998-1001

Computer programs in physics

• 
  M. Hirai, S. Kumano:
  Numerical solution of Q² evolution equations for fragmentation functions. 1002-1013
• 
  Shigeru Odaka, Yoshimasa Kurihara:
  GR@PPA 2.8: Initial-state jet matching for weak-boson production processes at hadron collisions. 1014-1028
• 
  R. J. Casperson:
  IBAR: Interacting boson model calculations for large system sizes. 1029-1035
• 
  Michael Kachelrieß, Sergei Stanislavovich Ostapchenko, R. Tomàs:
  ELMAG: A Monte Carlo simulation of electromagnetic cascades on the extragalactic background light and in magnetic fields. 1036-1043
• 
  K. T. Vu, G. F. Jefferson, J. Carminati:
  Finding higher symmetries of differential equations using the MAPLE package DESOLVII. 1044-1054
• 
  Ioan Valeriu Grossu, Calin Besliu, Alexandru Jipa, Emil Stan, Tiberiu Esanu, D. Felea, Cristian C. Bordeianu:
  Code C# for chaos analysis of relativistic many-body systems with reactions. 1055-1059

New version announcement

• 
  Tobias Huber, Daniel Maître:
  HypExp 2, expanding hypergeometric functions about half-integer parameters. 1060

Volume 183, Number 5, May 2012

Computational physics

• 
  Stefano Tarantola, William Becker, Dirk Zeitz:
  A comparison of two sampling methods for global sensitivity analysis. 1061-1072
•