Computer Physics Communications, Volume 178

Volume 178, Number 1, January 2008

Computational physics

• 
  Shin-ichi Satake, Takafumi Anraku, Hiroyuki Kanamori, Tomoaki Kunugi, Kazuho Sato, Tomoyoshi Ito:
  Study on high speed parallel algorithm using PC grid environment for visualization measurements by Digital Holographic Particle Tracking Velocimetry. 1-7
• 
  Bengt Eliasson:
  A nonuniform nested grid method for simulations of RF induced ionospheric turbulence. 8-14
• 
  Jesús Vigo-Aguiar, J. Martín-Vaquero, Higinio Ramos:
  Exponential fitting BDF-Runge-Kutta algorithms. 15-34
• 
  Angelo A. Schiavi:
  A transmission matrix model for ion beam energy deposition in stack detectors. 35-39
• 
  M. E. Monville, J. D. Lamb, J. C. G. Pereira, J. A. Truter:
  Simulation of laser-induced nanopattern formation. 40-47

Computer programs in physics

• 
  G. E. Ballentine, George F. Bertsch, Naoki Onishi, Kazuhiro Yabana:
  Moment distributions of clusters and molecules in the adiabatic rotor model. 48-51
• 
  Korneel van den Broek:
  Vscape V1.1.0. An interactive tool for metastable vacua. 52-72

Volume 178, Number 2, January 2008

Computational physics

• 
  Ken-ichi Nomura, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta:
  A scalable parallel algorithm for large-scale reactive force-field molecular dynamics simulations. 73-87
• 
  Frederic Wrobel:
  Detailed history of recoiling ions induced by nucleons. 88-104
• 
  Patrick H. Brown, Peter Schuck:
  A new adaptive grid-size algorithm for the simulation of sedimentation velocity profiles in analytical ultracentrifugation. 105-120
• 
  Cheol-O Ahn, Sang Hwan Lee:
  A new treecode for long-range force calculation. 121-127
• 
  Mark J. Rayson, Patrick R. Briddon:
  Rapid iterative method for electronic-structure eigenproblems using localised basis functions. 128-134

Computer programs in physics

• 
  Caroline Collange, Marc Daumas, David Defour:
  Line-by-line spectroscopic simulations on graphics processing units. 135-143
• 
  Oleg Bezshyyko, A. Dolinskii, K. Bezshyyko, Ihor Kadenko, Ruslan Yermolenko, Volker Ziemann:
  PETAG01: A program for the direct simulation of a pellet target. 144-155
• 
  Martin Andersson, Per Jönsson:
  HFSZEEMAN - A program for computing weak and intermediate field fine and hyperfine structure Zeeman splittings from MCDHF wave functions. 156-170

Volume 178, Number 3, February 2008

Computational physics

• 
  Changfeng Xue, Shaozhong Deng:
  New versions of image approximations to the ionic solvent induced reaction field. 171-185
• 
  Pedro R. C. da Silveira, Cesar R. S. da Silva, Renata M. Wentzcovitch:
  Metadata management for distributed first principles calculations in VLab - A collaborative cyberinfrastructure for materials computation. 186-198
• 
  T. E. Simos:
  High-order closed Newton-Cotes trigonometrically-fitted formulae for long-time integration of orbital problems. 199-207
• 
  Francesco Belletti, Maria Cotallo, Andres Cruz Flor, Luis Antonio Fernandez, Antonio Gordillo, Andrea Maiorano, Filippo Mantovani, Enzo Marinari, Victor Martin-Mayor, Antonio Munoz Sudupe, Denis Navarro, Sergio Perez Gaviro, Juan Jesus Ruiz-Lorenzo, Sebastiano Fabio Schifano, Daniele Sciretti, Alfonso Tarancón, Raffaele Tripiccione, Jose Luis Velasco:
  Simulating spin systems on IANUS, an FPGA-based computer. 208-216
• 
  Thomas Hahn:
  A Mathematica interface for FormCalc-generated code. 217-221

Computer programs in physics

• 
  Sergey Belov, L. Dudko, E. Galkin, A. Gusev, W. Pokorski, A. Sherstnev:
  LCG MCDB - a knowledgebase of Monte-Carlo simulated events. 222-229
• 
  Jan-Hendrik Jureit, Christoph A. Stephan:
  Finding the standard model of particle physics a combinatorial problem. 230-247

Volume 178, Number 4, February 2008

Computational physics

• 
  A. I. Mahdy:
  Interactions of two co-propagating laser beams in underdense plasmas using a generalized Peaceman-Rachford ADI form. 249-271
• 
  Byoungseon Jeon, Joel D. Kress, Lee A. Collins, Niels Grønbech-Jensen:
  Parallel TREE code for two-component ultracold plasma analysis. 272-279
• 
  Aiichiro Nakano:
  A space-time-ensemble parallel nudged elastic band algorithm for molecular kinetics simulation. 280-289
• 
  Jin Xu, Peter N. Ostroumov, Jerry Nolen:
  A parallel 3D Poisson solver for space charge simulation in cylindrical coordinates. 290-300

Computer programs in physics

• 
  Ochbadrakh Chuluunbaatar, A. A. Gusev, Vladimir P. Gerdt, V. A. Rostovtsev, Sergey I. Vinitsky, A. G. Abrashkevich, Michail S. Kaschiev, Vladislav V. Serov:
  POTHMF: A program for computing potential curves and matrix elements of the coupled adiabatic radial equations for a hydrogen-like atom in a homogeneous magnetic field. 301-330

Volume 178, Number 5, March 2008

Computational physics

• 
  John Allison, M. Asai, G. Barrand, Mark Dönszelmann, K. Minamimoto, Joseph Perl, S. Tanaka, E. Tcherniaev, J. Tinslay:
  The Geant4 Visualisation System. 331-365
• 
  Radovan Gospavic, Viktor Popov, Goran Todorovic:
  Boundary element - dual reciprocity formulation for bound electron states in semiconductor quantum wires. 366-373
• 
  Sergey Gorbunov, Udo Kebschull, Ivan Kisel, Volker Lindenstruth, Walter F. J. Müller:
  Fast SIMDized Kalman filter based track fit. 374-383
• 
  Jianhui Li, Zhongwu Zhou, Richard J. Sadus:
  Parallel algorithms for molecular dynamics with induction forces. 384-392

Computer programs in physics

• 
  P. Ditz, Alfio Borzì:
  A cascadic monotonic time-discretized algorithm for finite-level quantum control computation. 393-399

Volume 178, Number 6, March 2008

Computational physics

• 
  Lih-Yuan Deng, Rui Guo, Dennis K. J. Lin, Fengshan Bai:
  Improving Random Number Generators in the Monte Carlo simulations via twisting and combining. 401-408
• 
  Liliana Teodorescu, Daniel Sherwood:
  High Energy Physics event selection with Gene Expression Programming. 409-419
• 
  Bayram Deviren, Mustafa Keskin, Osman Canko:
  Dynamic phase transition and multicritical dynamic phase diagrams of the kinetic spin-3/2 Blume-Emery-Griffiths model with repulsive biquadratic coupling under a time-dependent oscillating external field. 420-437
• 
  André Barka, Clément Picard:
  Implementation of spectral basis functions in BEM/FEM/GSM Domain Decomposition Methods devoted to scattering and radiation applications. 438-448
• 
  YiMin Tian, Mengzhao Qin, YongMing Zhang, Tao Ma:
  The multisymplectic numerical method for Gross-Pitaevskii equation. 449-458

Computer programs in physics

• 
  Jan H. Meinke, Sandipan Mohanty, Frank Eisenmenger, Ulrich H. E. Hansmann:
  SMMP v. 3.0 - Simulating proteins and protein interactions in Python and Fortran. 459-470

Volume 178, Number 7, April 2008

Computational physics

• 
  Siham Tabik, Luis F. Romero, Ester M. Garzón, Juan I. Ramos:
  On a model of three-dimensional bursting and its parallel implementation. 471-485
• 
  Yan Feng Li, Kui Fu Chen:
  Eliminating the picket fence effect of the fast Fourier transform. 486-491
• 
  Ruud G. M. van der Sman, S. van der Graaf:
  Emulsion droplet deformation and breakup with Lattice Boltzmann model. 492-504
• 
  Gui-qiong Xu:
  Searching for Painlevé integrable conditions of nonlinear PDEs with constant parameters using symbolic computation. 505-517

Computer programs in physics

• 
  Ning Li, Hua-Xia Zhao, Sang-Hyun Cho, Jung-Gil Choi, Myoung-Hee Kim:
  A fast algorithm for voxel-based deterministic simulation of X-ray imaging. 518-523
• 
  Micael J. T. Oliveira, Fernando Nogueira:
  Generating relativistic pseudo-potentials with explicit incorporation of semi-core states using APE, the Atomic Pseudo-potentials Engine. 524-534
• 
  N. Michel, M. V. Stoitsov:
  Fast computation of the Gauss hypergeometric function with all its parameters complex with application to the Pöschl-Teller-Ginocchio potential wave functions. 535-551

Volume 178, Number 8, April 2008

Computational physics

• 
  Lukas Arnold, Jürgen Dreher, Rainer Grauer:
  A semi-implicit Hall-MHD solver using whistler wave preconditioning. 553-557
• 
  Yousef El-Kurdi, David Fernández, Evgueni Souleimanov, Dennis Giannacopoulos, Warren J. Gross:
  FPGA architecture and implementation of sparse matrix-vector multiplication for the finite element method. 558-570
• 
  T. F. Jiang:
  Calculation of atomic hydrogen and its photoelectron spectra in momentum space. 571-577

Computer programs in physics

• 
  Joris Van Deun, Ronald Cools:
  Integrating products of Bessel functions with an additional exponential or rational factor. 578-590
• 
  Dragoslav Nikezic, K. N. Yu:
  Computer program TRACK_VISION for simulating optical appearance of etched tracks in CR-39 nuclear track detectors. 591-595
• 
  Christian Bogner, Stefan Weinzierl:
  Resolution of singularities for multi-loop integrals. 596-610
• 
  Viktor K. Decyk, Henry J. Gardner:
  Object-oriented design patterns in Fortran 90/95: mazev1, mazev2 and mazev3. 611-620
• 
  Evelio Francisco, Ángel Martín Pendás, M. A. Blanco:
  EDF: Computing electron number probability distribution functions in real space from molecular wave functions. 621-634

Volume 178, Number 9, May 2008

• 
  G. A. Esleta, Christopher P. Monterola:
  Structural reinforcement in a spring-block model of stress-induced fracture propagation. 635-646
• 
  R. De Bartolo, Antonella Greco, Pierluigi Veltri:
  A 3D kinetic-fluid numerical code for stationary equilibrium states in magnetized plasmas. 647-664
• 
  Ivan I. Shevchenko:
  Symbolic computation of the Birkhoff normal form in the problem of stability of the triangular libration points. 665-672
• 
  Bahtiyar A. Mamedov:
  Accurate evaluation of integrals arising from the bulk electron densities in quantum wells of high electron mobility transistors. 673-675

Computer programs in physics

• 
  Sheng-Gui He, Dennis J. Clouthier:
  RT3: A Windows program for the Renner-Teller analysis of 2Pi states of triatomic molecules. 676-684
• 
  Arash A. Mostofi, Jonathan R. Yates, Young-Su Lee, Ivo Souza, David Vanderbilt, Nicola Marzari:
  wannier90: A tool for obtaining maximally-localised Wannier functions. 685-699
• 
  Songxin Liang, David J. Jeffrey:
  Automatic computation of the travelling wave solutions to nonlinear PDEs. 700-712

Volume 178, Number 10, May 2008

• 
  Georg M. von Hippel, Randy Lewis, Robert G. Petry:
  Evolutionary fitting methods for the extraction of mass spectra in lattice field theory. 713-723
• 
  Zak E. Hughes, Lorna M. Stimson, Henk Slim, Juho S. Lintuvuori, Jaroslav M. Ilnytskyi, Mark R. Wilson:
  An investigation of soft-core potentials for the simulation of mesogenic molecules and molecules composed of rigid and flexible segments. 724-731
• 
  Manuel Calvo, J. M. Franco, Juan I. Montijano, Luis Rández:
  Sixth-order symmetric and symplectic exponentially fitted modified Runge-Kutta methods of Gauss type. 732-744

Computer programs in physics

• 
  Farvah Mahmoudi:
  SuperIso: A program for calculating the isospin asymmetry of B -> K^*gamma in the MSSM. 745-754
• 
  Tobias Huber, Daniel Maître:
  HypExp 2, Expanding hypergeometric functions about half-integer parameters. 755-776
• 
  George Opletal, Timothy C. Petersen, Brendan O'Malley, I. K. Snook, D. G. McCulloch, Irene Yarovsky:
  HRMC: Hybrid Reverse Monte Carlo method with silicon and carbon potentials. 777-787
• 
  Cristian C. Bordeianu, Calin Besliu, Alexandru Jipa, D. Felea, Ioan Valeriu Grossu:
  Scilab software package for the study of dynamical systems. 788-793

Erratum

• 
  P.-Y. Chen, Y.-L. Shao, K.-W. Cheng, K.-H. Hsu, Jong-Shinn Wu, J.-P. Yu:
  Erratum to "Three-dimensional simulation studies on electrostatic predictions for carbon nanotube field effect transistors" [Computer Physics Communications 177 (2007) 683-688]. 794

Volume 178, Number 11, June 2008

• 
  Tongsong Jiang, Li Chen:
  An algebraic method for Schrödinger equations in quaternionic quantum mechanics. 795-799
• 
  Luis F. Romero, Siham Tabik, Jesús M. Vías, Emilio L. Zapata:
  Fast clear-sky solar irradiation computation for very large digital elevation models. 800-808
• 
  Gianpiero Colonna, Annarita Laricchiuta:
  General numerical algorithm for classical collision integral calculation. 809-816
• 
  Tirath Ramdas, Gregory K. Egan, David Abramson, Kim K. Baldridge:
  On ERI sorting for SIMD execution of large-scale Hartree-Fock SCF. 817-834

Computer programs in physics

• 
  S. Janecek, E. Krotscheck:
  A fast and simple program for solving local Schrödinger equations in two and three dimensions. 835-842
• 
  Ioannis G. Tsoulos, Isaac E. Lagaris:
  GenMin: An enhanced genetic algorithm for global optimization. 843-851
• 
  Torbjörn Sjöstrand, Stephen Mrenna, Peter Skands:
  A brief introduction to PYTHIA 8.1. 852-867
• 
  Guido R. Mocken, Christoph H. Keitel:
  FFT-split-operator code for solving the Dirac equation in 2+1 dimensions. 868-882

Erratum

• 
  Daniela Tordella, Michele Iovieno, Silvano Massaglia:
  Erratum to: Small scale localization in turbulent flows. A priori tests applied to a possible Large Eddy Simulation of compressible turbulent flows [Computer Physics Communications 176 (2007) 539-549]. 883-884

Volume 178, Number 12, June 2008

• 
  Bülent Karasözen, Andrew D. Nemtsev, V. G. Tsybulin:
  Staggered grids discretization in three-dimensional Darcy convection. 885-893
• 
  Marco D. Mazzeo, Peter V. Coveney:
  HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries. 894-914
• 
  Keizo Fujimoto, Richard D. Sydora:
  Electromagnetic particle-in-cell simulations on magnetic reconnection with adaptive mesh refinement. 915-923
• 
  Kui Fu Chen, Yan Feng Li:
  Combining the Hanning windowed interpolated FFT in both directions. 924-928

Computer programs in physics

• 
  Gary N. Felder, Igor Tkachev:
  LATTICEEASY: A program for lattice simulations of scalar fields in an expanding universe. 929-932
• 
  Fabienne Jézéquel, Jean Marie Chesneaux:
  CADNA: a library for estimating round-off error propagation. 933-955
• 
  Ofelia Pisanti, A. Cirillo, Salvatore Esposito, F. Iocco, Giuseppe Mangano, Gennaro Miele, Pasquale Dario Serpico:
  PArthENoPE: Public algorithm evaluating the nucleosynthesis of primordial elements. 956-971

Erratum

• 
  Kurt Siegfried Kölbig, B. Schorr:
  Erratum to: "A program package for the Landau distribution" [Computer Physics Communications 31 (1984) 97-111]. 972