Computer Physics Communications, Volume 179

Volume 179, Numbers 1-3, July 2008

Special issue based on the Conference on Computational Physics 2007 - CCP 2007

• 
  Michel Mareschal, Paul Geerlings:
  Preface.
• 
  Kurt Binder, Subir K. Das, Jürgen Horbach, Sanjay Puri:
  Simulation of surface-controlled phase separation in slit pores: Diffusive Ginzburg-Landau kinetics versus Molecular Dynamics. 1-7
• 
  D. P. Landau, Fugao Wang, Shan-Ho Tsai:
  Critical endpoint behavior: A Wang-Landau study. 8-12
• 
  Swetlana Jungblut, K. Binder, Tanja Schilling:
  Isotropic-isotropic phase separation in mixtures of rods and spheres: Some aspects of Monte Carlo simulation in the grand canonical ensemble. 13-16
• 
  W. Paul, F. Rampf, T. Strauch, K. Binder:
  Phase transitions in a single polymer chain: A micro-canonical analysis of Wang-Landau simulations. 17-20
• 
  Bernd A. Berg, Wolfhard Janke:
  Multibondic cluster algorithm for finite-size scaling studies of critical phenomena. 21-25

Section 2. Methods in Condensed Matter

• 
  Giovanni Bussi, Michele Parrinello:
  Stochastic thermostats: comparison of local and global schemes. 26-29
• 
  Andreas Tröster:
  Monte Carlo simulation in Fourier space. 30-33
• 
  Titus S. van Erp:
  Efficient path sampling on multiple reaction channels. 34-40
• 
  Harald Oberhofer, Christoph Dellago:
  Optimum bias for fast-switching free energy calculations. 41-45
• 
  J. W. Eastwood:
  The Block-P³M algorithm. 46-50

Section 3. Soft Matter

• 
  Matej Praprotnik, Christoph Junghans, Luigi Delle Site, Kurt Kremer:
  Simulation approaches to soft matter: Generic statistical properties vs. chemical details. 51-60
• 
  David L. Cheung, Lucian Anton, Michael P. Allen, Andrew J. Masters:
  Computer simulation of liquids and liquid crystals. 61-65
• 
  R. Andreea Trasca, Sabine H. L. Klapp:
  Translational order in a nanoconfined dipolar fluid. 66-70
• 
  Christos N. Likos, Bianca M. Mladek, Angel J. Moreno, Dieter Gottwald, Gerhard Kahl:
  Cluster-forming systems of ultrasoft repulsive particles: statics and dynamics. 71-76
• 
  H. H. Wensink, H. Löwen, M. Rex, Christos N. Likos, S. van Teeffelen:
  Long-time self-diffusion for Brownian Gaussian-core particles. 77-81

Section 4. Materials

• 
  Bryan K. Clark, David M. Ceperley:
  Path integral calculations of vacancies in solid Helium. 82-88
• 
  Carlo Pierleoni, Kris T. Delaney, Miguel A. Morales, David M. Ceperley, Markus Holzmann:
  Trial wave functions for high-pressure metallic hydrogen. 89-97
• 
  Keiji Hayashi, Daisuke Tanaka, Tomoki Maruyama, Harumi Araki, Daisuke Matsumura, Misato Kaneko:
  Velocity-dependent threshold behavior of wearless nano-friction as studied in terms of spatial distribution of the local quasi-temperature. 98-101
• 
  Stoyan Pisov, Oksana Melikhova, Marc Hou:
  Mechanical properties of AgCo nanostructured nanowires. 102-106
• 
  Yiming Li, Hui-Wen Cheng:
  Numerical simulation of field emission efficiency of anodic aluminum oxide carbon nanotube field emitter in the triode structure. 107-111

Section 5. Biological Matter

• 
  Cyril Deremble, Richard Lavery, Krystyna Zakrzewska:
  Protein-DNA recognition: Breaking the combinatorial barrier. 112-119
• 
  V. Carnevale, Simone Raugei, Simone Piana, Paolo Carloni:
  On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study. 120-123
• 
  Thomas Wüst, D. P. Landau:
  The HP model of protein folding: A challenging testing ground for Wang-Landau sampling. 124-127
• 
  Rafik Ouared, Bastien Chopard, Bernd Stahl, Daniel A. Rüfenacht, Hasan Yilmaz, Guy Courbebaisse:
  Thrombosis modeling in intracranial aneurysms: a lattice Boltzmann numerical algorithm. 128-131

Section 6. Non-equilibrium Systems

• 
  Katrin Rohlf, Simon Fraser, Raymond Kapral:
  Reactive multiparticle collision dynamics. 132-139
• 
  Shyam S. Chikatamarla, Iliya V. Karlin:
  Complete Galilean invariant lattice Boltzmann models. 140-143
• 
  Joaquín Marro:
  A brief comment on the modeling of flow. 144-149
• 
  I. Llopis, Marco Cosentino Lagomarsino, Ignacio Pagonabarraga, C. P. Lowe:
  Cooperativity and hydrodynamic interactions in externally driven semiflexible filaments. 150-154
• 
  D. C. Rapaport:
  Molecular dynamics studies of swimming at the microscopic scale. 155-158
• 
  C. M. Pooley, Julia M. Yeomans:
  Lattice Boltzmann simulation techniques for simulating microscopic swimmers. 159-164

Section 7. Chemistry

• 
  Gregory Van Lier, Christopher P. Ewels, Paul Geerlings:
  Automated determination of chemical functionalisation addition routes based on magnetic susceptibility and nucleus independent chemical shifts. 165-170
• 
  Laurence Leherte, Daniel P. Vercauteren:
  Collective motions in protein structures: Applications of elastic network models built from electron density distributions. 171-180

Section 8. Other fields: Astrophysics, Plasmas and Particle Physics

• 
  Stefan Krieg, Norbert Attig, Thomas Lippert, Nigel Cundy:
  A comparison of methods to calculate the chiral condensate with overlap fermions. 181-183
• 
  Stephan Rosswog, Enrico Ramirez-Ruiz, W. Raphael Hix, M. Dan:
  Simulating black hole white dwarf encounters. 184-189
• 
  Claire Noël, Yves Busegnies, Miltiadis V. Papalexandris, Stephane Goriely:
  Hydrodynamical simulations of detonations in superbursts. 190-193
• 
  F. Subba, Xavier Bonnin, David Coster, R. Zanino:
  2D fluid modeling of the ASDEX upgrade scrape-off layer up to the first wall. 194-198
• 
  Cristian C. Bordeianu, D. Felea, Calin Besliu, Alexandru Jipa, Ioan Valeriu Grossu:
  Chaos analysis of a semi-classical nuclear billiard model. 199-201

Volume 179, Number 4, August 2008

Computational physics

• 
  Minghui Wang, Musheng Wei, Yan Feng:
  An iterative algorithm for least squares problem in quaternionic quantum theory. 203-207
• 
  Shing-Lin Chang, Cheng-Sheng Chien, Zi-Cai Li:
  A finite difference continuation method for computing energy levels of Bose-Einstein condensates. 208-226
• 
  U. Ziegler:
  The NIRVANA code: Parallel computational MHD with adaptive mesh refinement. 227-244
• 
  Klaus Reuter, Frank Jenko, Cary B. Forest, R. Adam Bayliss:
  A parallel implementation of an MHD code for the simulation of mechanically driven, turbulent dynamos in spherical geometry. 245-249
• 
  Weiwei Cai, David J. Ewing, Lin Ma:
  Application of simulated annealing for multispectral tomography. 250-255
• 
  Benjamin C. Allanach, Christopher G. Lester:
  Sampling using a 'bank' of clues. 256-266

Computer programs in physics

• 
  Hridis Kumar Pal, Alok Shukla:
  A Fortran 90 program to solve the Hartree-Fock equations for interacting spin-1/2 fermions confined in harmonic potentials. 267-274
• 
  José Luis Gómez-Muñoz, Julián Bravo-Castillero:
  Calculation of effective conductivity of 2D and 3D composite materials with anisotropic constituents and different inclusion shapes in Mathematica. 275-287

Volume 179, Number 5, September 2008

Computational physics

• 
  Yosuke Matsumoto, Kanako Seki:
  Implementation of the CIP algorithm to magnetohydrodynamic simulations. 289-296
• 
  N. C. Cassol-Seewald, M. I. M. Copetti, Gastao Krein:
  Numerical approximation of the Ginzburg-Landau equation with memory effects in the dynamics of phase transitions. 297-309
• 
  Kyle Beloy, Andrei Derevianko:
  Application of the dual-kinetic-balance sets in the relativistic many-body problem of atomic structure. 310-319
• 
  Pieter J. in 't Veld, Steven J. Plimpton, Gary S. Grest:
  Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics. 320-329
• 
  Artur Signell, Francisco Ogando, Mats Aspnäs, Jan Westerholm:
  Scalable plasma simulation with ELMFIRE using efficient data structures for process communication. 330-338
• 
  Lixin Zhan:
  A parallel implementation of the Wang-Landau algorithm. 339-344

Computer programs in physics

• 
  Wick Haxton, Cecilia Lunardini:
  SevenOperators, a Mathematica script for harmonic oscillator nuclear matrix elements arising in semileptonic electroweak interactions. 345-358
• 
  Franklin L. Marquezino, Renato Portugal:
  The QWalk simulator of quantum walks. 359-369

Volume 179, Number 6, September 2008

Computational physics

• 
  Jalo Liljo, Anupam Karmakar, Alexander Pukhov, Marlis Hochbruck:
  One-dimensional electromagnetic relativistic PIC-hydrodynamic hybrid simulation code H-VLPL (hybrid virtual laser plasma lab). 371-379
• 
  Marcos Pimenta de Abreu:
  Diffuse conditions for efficient solution of multislab radiation transport problems. 380-384
• 
  M. Hosseini, A. Tavana, M. Akhavan:
  MgB₂ under pressure and plane strain: a DFT study. 385-390
• 
  Yasuhiro Idomura, Masato Ida, Takuma Kano, Nobuyuki Aiba, Shinji Tokuda:
  Conservative global gyrokinetic toroidal full-f five-dimensional Vlasov simulation. 391-403
• 
  Shin-ichi Satake, Yoshiaki Hiroi, Yuya Suzuki, Nobuyuki Masuda, Tomoyoshi Ito:
  Special-purpose computer for two-dimensional FFT. 404-408
• 
  Bashir Ahmad, Badra S. Alghamdi:
  Approximation of solutions of the nonlinear Duffing equation involving both integral and non-integral forcing terms with separated boundary conditions. 409-416
• 
  Lei Liu, Jianguo Du, Jijun Zhao, Hong Liu, Di Wu, Fuliang Zhao:
  Study of high-pressure and high-temperature behaviors and alpha-to-beta phase transition of forsterite by first-principles and quasi-harmonic Debye model. 417-423
• 
  Vineet K. Singh, Om P. Singh, Rajesh K. Pandey:
  Numerical evaluation of the Hankel transform by using linear Legendre multi-wavelets. 424-429

Computer programs in physics

• 
  Géza Tóth:
  QUBIT4MATLAB V3.0: A program package for quantum information science and quantum optics for MATLAB. 430-437
• 
  Ebrahim Fredericks, Fazal Mahmood Mahomed, Ebrahim Momoniat, Asghar Qadir:
  Constructing a space from the geodesic equations. 438-442
• 
  Bernd A. Berg, Robert C. Harris:
  From data to probability densities without histograms. 443-448

Volume 179, Number 7, October 2008

Computational physics

• 
  Francisco de la Hoz, Fernando Vadillo:
  An exponential time differencing method for the nonlinear Schrödinger equation. 449-456
• 
  Franz Schreier, Dieter Kohlert:
  Optimized implementations of rational approximations - a case study on the Voigt and complex error function. 457-465
• 
  Margarit Rizea, Veerle Ledoux, Marnix Van Daele, Guido Vanden Berghe, Nicolae Carjan:
  Finite difference approach for the two-dimensional Schrödinger equation with application to scission-neutron emission. 466-478
• 
  Yongzhi Chen, Yuefan Deng:
  Task mapping on supercomputers with cellular networks. 479-485
• 
  Jiaqi Chen, Zhongcheng Wang, Hezhu Shao, Hailing Hao:
  Highly-accurate ground state energies of the He atom and the He-like ions by Hartree SCF calculation with Obrechkoff method. 486-491

Computer programs in physics

• 
  S. Nath:
  A Monte Carlo C-code for calculating transmission efficiency of recoil separators and viewing residue trajectories. 492-500
• 
  Daniel Maître, Pierpaolo Mastrolia:
  S@M, a mathematica implementation of the spinor-helicity formalism. 501-534

Volume 179, Number 8, October 2008

Computational physics

• 
  T. D. Pointon:
  Second-order, exact charge conservation for electromagnetic particle-in-cell simulation in complex geometry. 535-544
• 
  Mariana Cécere, Luis Lehner, Oscar Reula:
  Constraint preserving boundary conditions for the Ideal Newtonian MHD equations. 545-554
• 
  Sanjukta Chatterjee, Dhiranjan Roy:
  A class of new transforms tailored for the hypergeometric series. 555-561
• 
  M. S. Zakynthinaki, James Robert Stirling, A. López Díaz de Durana, Carlos A. Cordente Martínez, M. Sillero Quintana, J. Sampedro Molinuevo:
  Stochastic optimization for the calculation of the optimal critical curve from experimental data in a model of the process of regaining balance after perturbation from quiet stance. 562-568
• 
  Marlies Hankel, Sean C. Smith, Stephen K. Gray, Gabriel G. Balint-Kurti:
  DIFFREALWAVE: A parallel real wavepacket code for the quantum mechanical calculation of reactive state-to-state differential cross sections in atom plus diatom collisions. 569-578
• 
  G. V. Pereverzev, G. Corrigan:
  Stable numeric scheme for diffusion equation with a stiff transport. 579-585

Computer programs in physics

• 
  José M. Martín-García, David Yllanes, Renato Portugal:
  The Invar tensor package: Differential invariants of Riemann. 586-590
• 
  Kálmán Varga:
  Solution of few-body problems with the stochastic variational method II: Two-dimensional systems. 591-596
• 
  José M. Martín-García:
  xPerm: fast index canonicalization for tensor computer algebra. 597-603
• 
  Gary N. Felder:
  CLUSTEREASY: A program for lattice simulations of scalar fields in an expanding universe on parallel computing clusters. 604-606
• 
  Algirdas Deveikis, A. Juodagalvis:
  A computer program for two-particle generalized coefficients of fractional parentage. 607-613

New version announcements

• 
  Ioannis G. Tsoulos, Isaac E. Lagaris:
  MinFinder v2.0: An improved version of MinFinder. 614-615
• 
  Sam J. Cipolla:
  An improved version of ISICS: A program for calculating K-, L- and M-shell cross sections from PWBA and ECPSSR theory using a personal computer. 616

Volume 179, Number 9, November 2008

Computational physics

• 
  Bart van der Holst, Rony Keppens, Zakaria Meliani:
  A multidimensional grid-adaptive relativistic magnetofluid code. 617-627
• 
  Reza Mazrooei-Sebdani, Mehdi Dehghan:
  A non-trivial relation between some many-dimensional chaotic discrete dynamical systems and some one-dimensional chaotic discrete dynamical systems. 628-633
• 
  Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig:
  Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. 634-641
• 
  J. Spray, Jon Hill, Arthur S. Trew:
  Performance of a Lattice Quantum Chromodynamics kernel on the Cell processor. 642-646

Computer programs in physics

• 
  T. Radtke, Stephan Fritzsche:
  Simulation of n-qubit quantum systems. IV. Parametrizations of quantum states, matrices and probability distributions. 647-664
• 
  Alessandro Cafarella, Claudio Corianò, Marco Guzzi:
  Precision studies of the NNLO DGLAP evolution at the LHC with Candia. 665-684
• 
  Ochbadrakh Chuluunbaatar, A. A. Gusev, Sergey I. Vinitsky, A. G. Abrashkevich:
  KANTBP 2.0: New version of a program for computing energy levels, reaction matrix and radial wave functions in the coupled-channel hyperspherical adiabatic approach. 685-693

Volume 179, Number 10, November 2008

Computational physics

• 
  Philippe Boucaud, P. Dimopoulos, Federico Farchioni, Roberto Frezzotti, Vicent Gimenez, Gregorio Herdoiza, Karl Jansen, V. Lubicz, Chris Michael, Gernot Münster, D. Palao, G. C. Rossi, Luigi Scorzato, A. Shindler, Silvano Simula, T. Sudmann, Carsten Urbach, Urs Wenger:
  Dynamical twisted mass fermions with light quarks: simulation and analysis details. 695-715
• 
  Bennett Kalafut, Koen Visscher:
  An objective, model-independent method for detection of non-uniform steps in noisy signals. 716-723
• 
  Jian-Guo Liu, Ye-Zhou Li:
  Auto-Bäcklund transformation and exact solutions of the generalized variable-coefficient Kadomtsev-Petviashvili equation. 724-732

Computer programs in physics

• 
  Markus Kuhn, Hans Walliser:
  Program for calculating SU(4) Clebsch-Gordan coefficients. 733-740
• 
  Jordi Mayneris, Miguel González, Stephen K. Gray:
  Real wavepacket code for ABC+D->AB+CD reactive scattering. 741-747
• 
  Damien Caliste, Yann Pouillon, Matthieu J. Verstraete, V. Olevano, Xavier Gonze:
  Sharing electronic structure and crystallographic data with ETSF_IO. 748-758
• 
  Giuseppe Degrassi, Paolo Gambino, P. Slavich:
  SusyBSG: a Fortran code for BR[B->X_sgamma] in the MSSM with Minimal Flavor Violation. 759-771

Volume 179, Number 11, December 2008

Computational physics

• 
  N. Mohankumar, Scott M. Auerbach:
  Some comments on the use of higher-order formula for numerical derivatives in scientific computing. 773-776
• 
  Michael L. Parks, Richard B. Lehoucq, Steven J. Plimpton, Stewart A. Silling:
  Implementing peridynamics within a molecular dynamics code. 777-783
• 
  Fabien Tran, Jan Kunes, Pavel Novák, Peter Blaha, Laurence D. Marks, Karlheinz Schwarz:
  Force calculation for orbital-dependent potentials with FP-(L)APW + lo basis sets. 784-790
• 
  Shaozhong Deng:
  On the immersed interface method for solving time-domain Maxwell's equations in materials with curved dielectric interfaces. 791-800
• 
  Yonglei Fang, Yongzhong Song, Xinyuan Wu:
  Trigonometrically fitted explicit Numerov-type method for periodic IVPs with two frequencies. 801-811
• 
  Vineet K. Singh, Om P. Singh, Rajesh K. Pandey:
  Efficient algorithms to compute Hankel transforms using wavelets. 812-818
• 
  N. Mohankumar:
  Comments on the accurate evaluation of integrals arising from the bulk electron densities in quantum wells. 819-820

Computer programs in physics

• 
  David López-Durán, Enrico Bodo, Franco A. Gianturco:
  ASPIN: An all spin scattering code for atom-molecule rovibrationally inelastic cross sections. 821-838
• 
  Gregory S. Ho, Vincent L. Lignères, Emily A. Carter:
  Introducing PROFESS: A new program for orbital-free density functional theory calculations. 839-854

Volume 179, Number 12, December 2008

Computational physics

• 
  WeiFeng Tao, DongSheng Cai, Xiaoyang Yan, Ken-ichi Nishikawa, Bertrand Lembege:
  Scalability analysis of parallel Particle-In-Cell codes on computational grids. 855-864
• 
  Rajmund Krivec, V. B. Mandelzweig:
  Quasilinearization approach to computations with singular potentials. 865-867
• 
  G. M. Petrov, J. Davis:
  A two-dimensional electromagnetic field algorithm for high-intensity laser-target interactions. 868-880
• 
  Yago Ascasibar:
  FiEstAS sampling - a Monte Carlo algorithm for multidimensional numerical integration. 881-887
• 
  M. S. Zakynthinaki, James Robert Stirling:
  Stochastic optimization for the calculation of the time dependency of the physiological demand during exercise and recovery. 888-894

Computer programs in physics

• 
  Ignace Loris:
  L1Packv2: A Mathematica package for minimizing an l₁-penalized functional. 895-902
• 
  Alexandre N. Kireev, Olivier J. F. Martin:
  Real-time Java simulations of multiple interference dielectric filters. 903-907
• 
  A. Deloff:
  Gauss-Legendre and Chebyshev quadratures for singular integrals. 908-914
• 
  G. Carminati, M. Bazzotti, A. Margiotta, Maurizio Spurio:
  Atmospheric MUons from PArametric formulas: a fast GEnerator for neutrino telescopes (MUPAGE). 915-923
• 
  Jaromir Tosiek:
  The Fedosov *-product in Mathematica. 924-930
• 
  Thomas Hahn, Philipp Lang:
  FeynEdit - a tool for drawing Feynman diagrams. 931-935