Computer Physics Communications, Volume 178

Volume 178, Number 1, January 2008

• 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
  
• B. Eliasson:
  A nonuniform nested grid method for simulations of RF induced ionospheric turbulence. 8-14
  
• Jesús Vigo-Aguiar, J. Martín-Vaquero, H. Ramos:
  Exponential fitting BDF-Runge-Kutta algorithms. 15-34
  
• 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
  

• G. E. Ballentine, G. F. Bertsch, N. Onishi, K. 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

• 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
  
• F. 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
  

• Sylvain Collange, Marc Daumas, David Defour:
  Line-by-line spectroscopic simulations on graphics processing units. 135-143
  
• O. Bezshyyko, A. Dolinskii, K. Bezshyyko, I. Kadenko, R. Yermolenko, V. 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

• 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 Tarancon, Raffaele Tripiccione, Jose Luis Velasco:
  Simulating spin systems on IANUS, an FPGA-based computer. 208-216
  
• T. Hahn:
  A Mathematica interface for FormCalc-generated code. 217-221
  

• S. 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

• 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
  

• Ochbadrakh Chuluunbaatar, A. A. Gusev, Vladimir P. Gerdt, V. A. Rostovtsev, Sergey I. Vinitsky, A. G. Abrashkevich, Michail S. Kaschiev, V. 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

• J. Allison, M. Asai, G. Barrand, Mark Dönszelmann, K. Minamimoto, J. 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
  
• S. Gorbunov, Udo Kebschull, I. Kisel, Volker Lindenstruth, W. 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
  

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

Volume 178, Number 6, March 2008

• 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
  

• 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

• Siham Tabik, Luis F. Romero, Ester M. Garzón, J. 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
  
• R. 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
  

• 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

• 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
  

• Joris Van Deun, Ronald Cools:
  Integrating products of Bessel functions with an additional exponential or rational factor. 578-590
  
• D. 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
  
• E. Francisco, A. 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, C. Monterola:
  Structural reinforcement in a spring-block model of stress-induced fracture propagation. 635-646
  
• R. De Bartolo, A. Greco, P. Veltri:
  A 3D kinetic-fluid numerical code for stationary equilibrium states in magnetized plasmas. 647-664
  
• I. I. Shevchenko:
  Symbolic computation of the Birkhoff normal form in the problem of stability of the triangular libration points. 665-672
  
• B. A. Mamedov:
  Accurate evaluation of integrals arising from the bulk electron densities in quantum wells of high electron mobility transistors. 673-675
  

• 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
  
• M. Calvo, J. M. Franco, J. I. Montijano, L. Rández:
  Sixth-order symmetric and symplectic exponentially fitted modified Runge-Kutta methods of Gauss type. 732-744
  

• F. 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
  
• G. Opletal, T. C. Petersen, B. O'Malley, I. K. Snook, D. G. McCulloch, I. Yarovsky:
  HRMC: Hybrid Reverse Monte Carlo method with silicon and carbon potentials. 777-787
  
• C. C. Bordeianu, C. Besliu, Al. Jipa, D. Felea, I. V. Grossu:
  Scilab software package for the study of dynamical systems. 788-793
  

• P.-Y. Chen, Y.-L. Shao, K.-W. Cheng, K.-H. Hsu, J.-S. 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 Baldridge:
  On ERI sorting for SIMD execution of large-scale Hartree-Fock SCF. 817-834
  

• 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
  

• 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
  
• M. D. Mazzeo, P. 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
  

• 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
  
• O. Pisanti, A. Cirillo, S. Esposito, F. Iocco, Giuseppe Mangano, Gennaro Miele, P. D. Serpico:
  PArthENoPE: Public algorithm evaluating the nucleosynthesis of primordial elements. 956-971
  

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