Journal: Computer Physics Communications

Volume 179, Issue 9

617 -- 627Bart van der Holst, Rony Keppens, Zakaria Meliani. A multidimensional grid-adaptive relativistic magnetofluid code
628 -- 633Reza Mazrooei-Sebdani, Mehdi Dehghan. A non-trivial relation between some many-dimensional chaotic discrete dynamical systems and some one-dimensional chaotic discrete dynamical systems
634 -- 641Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Müller-Wittig. Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA
642 -- 646J. Spray, J. Hill, A. Trew. Performance of a Lattice Quantum Chromodynamics kernel on the Cell processor
647 -- 664T. Radtke, S. Fritzsche. Simulation of n-qubit quantum systems. IV. Parametrizations of quantum states, matrices and probability distributions
665 -- 684Alessandro Cafarella, Claudio Corianò, Marco Guzzi. Precision studies of the NNLO DGLAP evolution at the LHC with Candia
685 -- 693Ochbadrakh 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

Volume 179, Issue 8

535 -- 544T. D. Pointon. Second-order, exact charge conservation for electromagnetic particle-in-cell simulation in complex geometry
545 -- 554Mariana Cécere, Luis Lehner, Oscar Reula. Constraint preserving boundary conditions for the Ideal Newtonian MHD equations
555 -- 561Sanjukta Chatterjee, Dhiranjan Roy. A class of new transforms tailored for the hypergeometric series
562 -- 568M. S. Zakynthinaki, J. R. Stirling, A. López Díaz de Durana, C. 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
569 -- 578Marlies 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
579 -- 585G. V. Pereverzev, G. Corrigan. Stable numeric scheme for diffusion equation with a stiff transport
586 -- 590Jose M. Martín-García, David Yllanes, Renato Portugal. The Invar tensor package: Differential invariants of Riemann
597 -- 603Jose M. Martin-Garcia. xPerm: fast index canonicalization for tensor computer algebra
604 -- 606Gary N. Felder. CLUSTEREASY: A program for lattice simulations of scalar fields in an expanding universe on parallel computing clusters
607 -- 613A. Deveikis, A. Juodagalvis. A computer program for two-particle generalized coefficients of fractional parentage
614 -- 615Ioannis G. Tsoulos, Isaac E. Lagaris. MinFinder v2.0: An improved version of MinFinder
616 -- 0Sam 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

Volume 179, Issue 7

449 -- 456Francisco de la Hoz, Fernando Vadillo. An exponential time differencing method for the nonlinear Schrödinger equation
457 -- 465Franz Schreier, Dieter Kohlert. Optimized implementations of rational approximations - a case study on the Voigt and complex error function
466 -- 478Margarit 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
479 -- 485Yongzhi Chen, Yuefan Deng. Task mapping on supercomputers with cellular networks
486 -- 491Jiaqi 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
492 -- 500S. Nath. A Monte Carlo C-code for calculating transmission efficiency of recoil separators and viewing residue trajectories
501 -- 534Daniel Maître, Pierpaolo Mastrolia. S@M, a mathematica implementation of the spinor-helicity formalism

Volume 179, Issue 6

371 -- 379Jalo Liljo, Anupam Karmakar, A. Pukhov, M. Hochbruck. One-dimensional electromagnetic relativistic PIC-hydrodynamic hybrid simulation code H-VLPL (hybrid virtual laser plasma lab)
380 -- 384Marcos Pimenta de Abreu. Diffuse conditions for efficient solution of multislab radiation transport problems
385 -- 390M. Hosseini, A. Tavana, M. Akhavan. MgB::2:: under pressure and plane strain: a DFT study
391 -- 403Yasuhiro Idomura, Masato Ida, Takuma Kano, Nobuyuki Aiba, Shinji Tokuda. Conservative global gyrokinetic toroidal full-f five-dimensional Vlasov simulation
404 -- 408Shin-ichi Satake, Yoshiaki Hiroi, Yuya Suzuki, Nobuyuki Masuda, Tomoyoshi Ito. Special-purpose computer for two-dimensional FFT
409 -- 416Bashir Ahmad, Badra S. Alghamdi. Approximation of solutions of the nonlinear Duffing equation involving both integral and non-integral forcing terms with separated boundary conditions
417 -- 423Lei 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
424 -- 429Vineet K. Singh, Om P. Singh, Rajesh K. Pandey. Numerical evaluation of the Hankel transform by using linear Legendre multi-wavelets
430 -- 437Géza Tóth. QUBIT4MATLAB V3.0: A program package for quantum information science and quantum optics for MATLAB
438 -- 442E. Fredericks, F. M. Mahomed, E. Momoniat, A. Qadir. Constructing a space from the geodesic equations
443 -- 448Bernd A. Berg, Robert C. Harris. From data to probability densities without histograms

Volume 179, Issue 5

289 -- 296Yosuke Matsumoto, Kanako Seki. Implementation of the CIP algorithm to magnetohydrodynamic simulations
297 -- 309N. C. Cassol-Seewald, M. I. M. Copettiand, G. Krein. Numerical approximation of the Ginzburg-Landau equation with memory effects in the dynamics of phase transitions
320 -- 329Pieter 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
330 -- 338Artur Signell, Francisco Ogando, Mats Aspnäs, Jan Westerholm. Scalable plasma simulation with ELMFIRE using efficient data structures for process communication
339 -- 344Lixin Zhan. A parallel implementation of the Wang-Landau algorithm
345 -- 358Wick Haxton, Cecilia Lunardini. SevenOperators, a Mathematica script for harmonic oscillator nuclear matrix elements arising in semileptonic electroweak interactions
359 -- 369Franklin L. Marquezino, Renato Portugal. The QWalk simulator of quantum walks

Volume 179, Issue 4

203 -- 207Minghui Wang, Musheng Wei, Yan Feng. An iterative algorithm for least squares problem in quaternionic quantum theory
208 -- 226S.-L. Chang, C.-S. Chien, Z.-C. Li. A finite difference continuation method for computing energy levels of Bose-Einstein condensates
227 -- 244U. Ziegler. The NIRVANA code: Parallel computational MHD with adaptive mesh refinement
245 -- 249Klaus 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
250 -- 255Weiwei Cai, David J. Ewing, Lin Ma. Application of simulated annealing for multispectral tomography
256 -- 266Benjamin C. Allanach, Christopher G. Lester. Sampling using a bank of clues
267 -- 274Hridis Kumar Pal, Alok Shukla. A Fortran 90 program to solve the Hartree-Fock equations for interacting spin-1/2 fermions confined in harmonic potentials
275 -- 287José 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

Volume 179, Issue 12

855 -- 864WeiFeng Tao, DongSheng Cai, Xiaoyang Yan, Ken-ichi Nishikawa, Bertrand Lembege. Scalability analysis of parallel Particle-In-Cell codes on computational grids
865 -- 867R. Krivec, V. B. Mandelzweig. Quasilinearization approach to computations with singular potentials
868 -- 880G. M. Petrov, J. Davis. A two-dimensional electromagnetic field algorithm for high-intensity laser-target interactions
888 -- 894M. S. Zakynthinaki, J. R. Stirling. Stochastic optimization for the calculation of the time dependency of the physiological demand during exercise and recovery
895 -- 902Ignace Loris. L1Packv2: A Mathematica package for minimizing an ::::l::::::1::-penalized functional
903 -- 907Alexandre N. Kireev, Olivier J. F. Martin. Real-time Java simulations of multiple interference dielectric filters
908 -- 914A. Deloff. Gauss-Legendre and Chebyshev quadratures for singular integrals
915 -- 923G. Carminati, M. Bazzotti, A. Margiotta, M. Spurio. Atmospheric MUons from PArametric formulas: a fast GEnerator for neutrino telescopes (MUPAGE)
924 -- 930Jaromir Tosiek. The Fedosov *-product in Mathematica
931 -- 935T. Hahn, P. Lang. FeynEdit - a tool for drawing Feynman diagrams

Volume 179, Issue 11

773 -- 776N. Mohankumar, Scott M. Auerbach. Some comments on the use of higher-order formula for numerical derivatives in scientific computing
777 -- 783Michael L. Parks, Richard B. Lehoucq, Steven J. Plimpton, Stewart A. Silling. Implementing peridynamics within a molecular dynamics code
784 -- 790Fabien 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
791 -- 800Shaozhong Deng. On the immersed interface method for solving time-domain Maxwell s equations in materials with curved dielectric interfaces
801 -- 811Yonglei Fang, Yongzhong Song, Xinyuan Wu. Trigonometrically fitted explicit Numerov-type method for periodic IVPs with two frequencies
812 -- 818Vineet K. Singh, Om P. Singh, Rajesh K. Pandey. Efficient algorithms to compute Hankel transforms using wavelets
819 -- 820N. Mohankumar. Comments on the accurate evaluation of integrals arising from the bulk electron densities in quantum wells
821 -- 838David López-Durán, Enrico Bodo, Franco A. Gianturco. ASPIN: An all spin scattering code for atom-molecule rovibrationally inelastic cross sections
839 -- 854Gregory S. Ho, Vincent L. Lignères, Emily A. Carter. Introducing PROFESS: A new program for orbital-free density functional theory calculations

Volume 179, Issue 10

695 -- 715Philippe Boucaud, P. Dimopoulos, Federico Farchioni, R. Frezzotti, Vicent Gimenez, G. Herdoiza, K. Jansen, V. Lubicz, C. Michael, G. Münster, D. Palao, G. C. Rossi, L. Scorzato, A. Shindler, S. Simula, T. Sudmann, C. Urbach, U. Wenger. Dynamical twisted mass fermions with light quarks: simulation and analysis details
716 -- 723Bennett Kalafut, Koen Visscher. An objective, model-independent method for detection of non-uniform steps in noisy signals
724 -- 732Jian-Guo Liu, Ye-Zhou Li. Auto-Bäcklund transformation and exact solutions of the generalized variable-coefficient Kadomtsev-Petviashvili equation
733 -- 740Markus Kuhn, Hans Walliser. Program for calculating SU(4) Clebsch-Gordan coefficients
741 -- 747Jordi Mayneris, Miguel González, Stephen K. Gray. Real wavepacket code for ABC+D->AB+CD reactive scattering
748 -- 758D. Caliste, Y. Pouillon, M. J. Verstraete, V. Olevano, X. Gonze. Sharing electronic structure and crystallographic data with ETSF_IO
759 -- 771G. Degrassi, P. Gambino, P. Slavich. SusyBSG: a Fortran code for BR[B->X::s::gamma] in the MSSM with Minimal Flavor Violation

Volume 179, Issue 1-3

0 -- 0Michel Mareschal, Paul Geerlings. Preface
1 -- 7Kurt Binder, Subir K. Das, Jürgen Horbach, Sanjay Puri. Simulation of surface-controlled phase separation in slit pores: Diffusive Ginzburg-Landau kinetics versus Molecular Dynamics
8 -- 12D. P. Landau, Fugao Wang, Shan-Ho Tsai. Critical endpoint behavior: A Wang-Landau study
13 -- 16S. Jungblut, K. Binder, T. Schilling. Isotropic-isotropic phase separation in mixtures of rods and spheres: Some aspects of Monte Carlo simulation in the grand canonical ensemble
17 -- 20W. Paul, F. Rampf, T. Strauch, K. Binder. Phase transitions in a single polymer chain: A micro-canonical analysis of Wang-Landau simulations
21 -- 25Bernd A. Berg, Wolfhard Janke. Multibondic cluster algorithm for finite-size scaling studies of critical phenomena
26 -- 29Giovanni Bussi, Michele Parrinello. Stochastic thermostats: comparison of local and global schemes
34 -- 40Titus S. van Erp. Efficient path sampling on multiple reaction channels
41 -- 45Harald Oberhofer, Christoph Dellago. Optimum bias for fast-switching free energy calculations
46 -- 50J. W. Eastwood. The Block-P:::3:::M algorithm
51 -- 60Matej Praprotnik, Christoph Junghans, Luigi Delle Site, Kurt Kremer. Simulation approaches to soft matter: Generic statistical properties vs. chemical details
61 -- 65David L. Cheung, Lucian Anton, Michael P. Allen, Andrew J. Masters. Computer simulation of liquids and liquid crystals
66 -- 70R. Andreea Trasca, Sabine H. L. Klapp. Translational order in a nanoconfined dipolar fluid
71 -- 76Christos N. Likos, Bianca M. Mladek, Angel J. Moreno, Dieter Gottwald, Gerhard Kahl. Cluster-forming systems of ultrasoft repulsive particles: statics and dynamics
77 -- 81H. H. Wensink, H. Löwen, M. Rex, C. N. Likos, S. van Teeffelen. Long-time self-diffusion for Brownian Gaussian-core particles
82 -- 88Bryan K. Clark, David M. Ceperley. Path integral calculations of vacancies in solid Helium
89 -- 97Carlo Pierleoni, Kris T. Delaney, Miguel A. Morales, David M. Ceperley, Markus Holzmann. Trial wave functions for high-pressure metallic hydrogen
98 -- 101Keiji 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
102 -- 106Stoyan Pisov, Oksana Melikhova, Marc Hou. Mechanical properties of AgCo nanostructured nanowires
107 -- 111Yiming Li, Hui-Wen Cheng. Numerical simulation of field emission efficiency of anodic aluminum oxide carbon nanotube field emitter in the triode structure
112 -- 119Cyril Deremble, Richard Lavery, Krystyna Zakrzewska. Protein-DNA recognition: Breaking the combinatorial barrier
120 -- 123V. Carnevale, S. Raugei, S. Piana, P. Carloni. On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study
124 -- 127T. Wüst, D. P. Landau. The HP model of protein folding: A challenging testing ground for Wang-Landau sampling
128 -- 131Rafik Ouared, Bastien Chopard, Bernd Stahl, Daniel A. Rüfenacht, H. Yilmaz, Guy Courbebaisse. Thrombosis modeling in intracranial aneurysms: a lattice Boltzmann numerical algorithm
132 -- 139Katrin Rohlf, Simon Fraser, Raymond Kapral. Reactive multiparticle collision dynamics
140 -- 143Shyam S. Chikatamarla, I. V. Karlin. Complete Galilean invariant lattice Boltzmann models
144 -- 149J. Marro. A brief comment on the modeling of flow
150 -- 154I. Llopis, M. Cosentino Lagomarsino, I. Pagonabarraga, C. P. Lowe. Cooperativity and hydrodynamic interactions in externally driven semiflexible filaments
155 -- 158D. C. Rapaport. Molecular dynamics studies of swimming at the microscopic scale
159 -- 164C. M. Pooley, Julia M. Yeomans. Lattice Boltzmann simulation techniques for simulating microscopic swimmers
165 -- 170G. Van Lier, C. P. Ewels, Paul Geerlings. Automated determination of chemical functionalisation addition routes based on magnetic susceptibility and nucleus independent chemical shifts
171 -- 180Laurence Leherte, Daniel P. Vercauteren. Collective motions in protein structures: Applications of elastic network models built from electron density distributions
181 -- 183Stefan Krieg, Norbert Attig, Thomas Lippert, Nigel Cundy. A comparison of methods to calculate the chiral condensate with overlap fermions
184 -- 189Stephan Rosswog, Enrico Ramirez-Ruiz, W. Raphael Hix, M. Dan. Simulating black hole white dwarf encounters
190 -- 193Claire Noël, Yves Busegnies, Miltiadis V. Papalexandris, Stephane Goriely. Hydrodynamical simulations of detonations in superbursts
194 -- 198F. Subba, Xavier Bonnin, David Coster, R. Zanino. 2D fluid modeling of the ASDEX upgrade scrape-off layer up to the first wall
199 -- 201C. C. Bordeianu, D. Felea, C. Besliu, Al. Jipa, I. V. Grossu. Chaos analysis of a semi-classical nuclear billiard model