Computer Physics Communications, Volume 183

Volume 183, Number 1, January 2012

• 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
  
• Y. Nakamura, K.-I. Ishikawa, Y. 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, Xiao-Yang Xu:
  A mixed corrected symmetric SPH (MC-SSPH) method for computational dynamic problems. 50-62
  
• L. Gr. Ixaru:
  Runge-Kutta method with equation dependent coefficients. 63-69
  
• J. 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
  
• M. S. Reis:
  Models for one-dimensional molecular magnets. 99-105
  

• 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, W. Satula, J. 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
  
• A. 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

• 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, 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, A. 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
  
• S. A. Galindo-Torres, D. M. Pedroso, D. J. Williams, L. 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
  
• F. Mahmoudi, Sven Heinemeyer, A. Arbey, A. Bharucha, T. Goto, Thomas Hahn, U. Haisch, S. Kraml, M. Mühlleitner, J. Reuter, P. Skands, P. 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
  
• R. 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
  
• P. M. C. Rourke, S. R. Julian:
  Numerical extraction of de Haas-van Alphen frequencies from calculated band energies. 324-332
  

• 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
  
• T. Hynninen, C. L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A. S. Foster, T. 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
  

• 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

• 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
  
• T. Hahn:
  The high-energy physicistʼs guide to MathLink. 460-469
  
• A. A. 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
  
• C. Espejo, T. Rangel, Yann Pouillon, A. 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
  
• U. D. Jentschura, E. Lötstedt:
  Numerical calculation of Bessel, Hankel and Airy functions. 506-519
  
• A. Gray, I. Bethune, R. Kenway, L. Smith, Martyn F. Guest, Christine A. Kitchen, P. Calleja, A. Korzynski, S. Rankin, Mike Ashworth, A. Porter, Ilian T. Todorov, M. Plummer, E. Jones, L. Steenman-Clark, B. Ralston, C. 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
  

• R. 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
  
• T. C. Petersen, S. 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, M. 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
  
• N. Davidson, G. Nanava, T. Przedzinski, Elzbieta Richter-Was, Z. Was:
  Universal interface of TAUOLA: Technical and physics documentation. 821-843
  

• 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

• 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
  
• C. Bonati, G. Cossu, M. D'Elia, P. 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, C. Kowitz, E. Romero, Jose E. Roman, Frank Jenko:
  Multi-dimensional gyrokinetic parameter studies based on eigenvalue computations. 922-930
  
• V. Ogarko, S. Luding:
  A fast multilevel algorithm for contact detection of arbitrarily polydisperse objects. 931-936
  
• Sergei Kucherenko, Stefano Tarantola, Paola Annoni:
  Estimation of global sensitivity indices for models with dependent variables. 937-946
  
• J. Seebacher, A. Kendl:
  Towards a unified linear kinetic transport model with the trace ion module for EIRENE. 947-959
  
• A. 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
  

• 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
  
• M. Kachelrieß, S. 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
  
• I. V. Grossu, C. Besliu, Al. Jipa, E. Stan, T. Esanu, D. Felea, C. C. Bordeianu:
  Code C# for chaos analysis of relativistic many-body systems with reactions. 1055-1059
  

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

Volume 183, Number 5, May 2012

• Stefano Tarantola, William Becker, Dirk Zeitz:
  A comparison of two sampling methods for global sensitivity analysis. 1061-1072
  
• Omar Awile, Ferit Büyükkeçeci, Sylvain Reboux, Ivo F. Sbalzarini:
  Fast neighbor lists for adaptive-resolution particle simulations. 1073-1081
  
• Yiqiang Xu, Luming Zhang:
  Alternating direction implicit method for solving two-dimensional cubic nonlinear Schrödinger equation. 1082-1093
  
• Takayuki Umeda, Yasuhiro Nariyuki, Daichi Kariya:
  A non-oscillatory and conservative semi-Lagrangian scheme with fourth-degree polynomial interpolation for solving the Vlasov equation. 1094-1100
  
• Omar Ramadan:
  Unified matrix-exponential FDTD formulations for modeling electrically and magnetically dispersive materials. 1101-1106
  
• A. Bierwage, C. Di Troia, Sergio Briguglio, Gregorio Vlad:
  Orbit-based representation of equilibrium distribution functions for low-noise initialization of kinetic simulations of toroidal plasmas. 1107-1123
  

• Tomoyoshi Shimobaba, Jiantong Weng, Takahiro Sakurai, Naohisa Okada, Takashi Nishitsuji, Naoki Takada, Atsushi Shiraki, Nobuyuki Masuda, Tomoyoshi Ito:
  Computational wave optics library for C++: CWO++ library. 1124-1138
  
• Constantinos Voglis, Konstantinos E. Parsopoulos, Dimitris G. Papageorgiou, Isaac E. Lagaris, Michael N. Vrahatis:
  MEMPSODE: A global optimization software based on hybridization of population-based algorithms and local searches. 1139-1154
  

Volume 183, Number 6, June 2012

• Yukihiro Komura, Yutaka Okabe:
  GPU-based Swendsen-Wang multi-cluster algorithm for the simulation of two-dimensional classical spin systems. 1155-1161
  
• Wanjie Xiong, Fan Zhong, Shuangli Fan:
  Positive specific-heat critical exponent of a three-dimensional three-state random-bond Potts model. 1162-1171
  
• Fengshun Lu, Junqiang Song, Fukang Yin, Xiaoqian Zhu:
  Performance evaluation of hybrid programming patterns for large CPU/GPU heterogeneous clusters. 1172-1181
  
• D. Melazzi, D. Curreli, M. Manente, J. Carlsson, D. Pavarin:
  SPIREs: A Finite-Difference Frequency-Domain electromagnetic solver for inhomogeneous magnetized plasma cylinders. 1182-1191
  
• Xingang Ren, Zhixiang Huang, Xianliang Wu, Silong Lu, Hui Wang, Lei Wu, Shen Li:
  High-order unified symplectic FDTD scheme for the metamaterials. 1192-1200
  
• Céline Degrande, Claude Duhr, Benjamin Fuks, David Grellscheid, Olivier Mattelaer, Thomas Reiter:
  UFO - The Universal FeynRules Output. 1201-1214
  
• C. Alexandrou, K. Hadjiyiannakou, G. Koutsou, A. O'Cais, A. Strelchenko:
  Evaluation of fermion loops applied to the calculation of the η mass and the nucleon scalar and electromagnetic form factors. 1215-1224
  
• Kun-Mo Lin, Chieh-Tsan Hung, Feng-Nan Hwang, Matthew R. Smith, Y.-W. Yang, Jong-Shinn Wu:
  Development of a parallel semi-implicit two-dimensional plasma fluid modeling code using finite-volume method. 1225-1236
  
• Janis Timoshenko, Alexei Kuzmin, Juris Purans:
  Reverse Monte Carlo modeling of thermal disorder in crystalline materials from EXAFS spectra. 1237-1245
  
• Michaël Magoga, Fabien Archambault, Jorge I. Cerdá:
  Nt_STM: A step forward in Scanning Tunneling Microscopy (STM) simulations. 1246-1249
  
• Wei Shi, Xinyuan Wu:
  On symplectic and symmetric ARKN methods. 1250-1258
  
• Reza Mokhtari, Majid Mohseni:
  A meshless method for solving mKdV equation. 1259-1268
  

• Jack Deslippe, Georgy Samsonidze, David A. Strubbe, Manish Jain, Marvin L. Cohen, Steven G. Louie:
  BerkeleyGW: A massively parallel computer package for the calculation of the quasiparticle and optical properties of materials and nanostructures. 1269-1289
  
• Markus Q. Huber, Jens Braun:
  Algorithmic derivation of functional renormalization group equations and Dyson-Schwinger equations. 1290-1320
  
• Albert Deuzeman, Siebren Reker, Carsten Urbach:
  Lemon: An MPI parallel I/O library for data encapsulation using LIME. 1321-1335
  
• Simon Catterall, Anosh Joseph:
  An object oriented code for simulating supersymmetric Yang-Mills theories. 1336-1353
  
• Pawel Jakubczyk, Andrzej Wal, D. Jakubczyk, Tadeusz Lulek:
  Computer implementation of the Kerov-Kirillov-Reshetikhin algorithm. 1354-1362
  
• H. P. Nilles, S. Ramos-Sánchez, P. K. S. Vaudrevange, A. Wingerter:
  The orbifolder: A tool to study the low-energy effective theory of heterotic orbifolds. 1363-1380
  
• András Vukics:
  C++QEDv2: The multi-array concept and compile-time algorithms in the definition of composite quantum systems. 1381-1396
  
• A. Deveikis:
  A computer program for two-particle intrinsic coefficients of fractional parentage. 1397-1401
  

Volume 183, Number 7, July 2012

• François Fillion-Gourdeau, Emmanuel Lorin, André D. Bandrauk:
  Numerical solution of the time-dependent Dirac equation in coordinate space without fermion-doubling. 1403-1415
  
• Massimo Bernaschi, Massimiliano Fatica, Giorgio Parisi, L. Parisi:
  Multi-GPU codes for spin systems simulations. 1416-1421
  
• M. Hutchinson, M. Widom:
  VASP on a GPU: Application to exact-exchange calculations of the stability of elemental boron. 1422-1426
  
• Haokai Lu, Peng Li:
  Stochastic projective methods for simulating stiff chemical reacting systems. 1427-1442
  
• Andreas Mayer, Hanna Salopaasi, Katariina Pussi, Renee D. Diehl:
  A novel method for the extraction of intensity-energy spectra from low-energy electron diffraction patterns. 1443-1447
  

• I. Akushevich, O. F. Filoti, A. Ilyichev, N. Shumeiko:
  Monte Carlo generator ELRADGEN 2.0 for simulation of radiative events in elastic ep-scattering of polarized particles. 1448-1467
  
• J. M. Cherfils, G. Pinon, E. Rivoalen:
  JOSEPHINE: A parallel SPH code for free-surface flows. 1468-1480
  
• Birgit Hischenhuber, Florian Frommlet, Wolfgang Schreiner, Bernhard Knapp:
  MH²c: Characterization of major histocompatibility α-helices - an information criterion approach. 1481-1490
  
• Benjamin Lindner, Jeremy C. Smith:
  Sassena - X-ray and neutron scattering calculated from molecular dynamics trajectories using massively parallel computers. 1491-1501
  
• C. Schimeczek, D. Engel, G. Wunner:
  A highly optimized code for calculating atomic data at neutron star magnetic field strengths using a doubly self-consistent Hartree-Fock-Roothaan method. 1502-1510
  
• Luiz C. Mostaço-Guidolin, Rafael B. Frigori, Leonid Ruchko, Ricardo M. O. Galvão:
  SCTE: An open-source Perl framework for testing equipment control and data acquisition. 1511-1518
  
• Feng Feng:
  A recursive method to calculate UV-divergent parts at one-loop level in dimensional regularization. 1519-1524
  
• S. Fritzsche:
  The Ratip program for relativistic calculations of atomic transition, ionization and recombination properties. 1525-1559
  

• Daniel J. Sindhikara:
  Modular reweighting software for statistical mechanical analysis of biased equilibrium data. 1560-1561
  

Volume 183, Number 8, August 2012

• Andrey Asadchev, Mark S. Gordon:
  Mixed-precision evaluation of two-electron integrals by Rys quadrature. 1563-1567
  
• Junqi Yin, D. P. Landau:
  Massively parallel Wang-Landau sampling on multiple GPUs. 1568-1573
  
• Su Do Yi, Beom Jun Kim:
  Force correlations in molecular and stochastic dynamics. 1574-1577
  
• Ezequiel E. Ferrero, Juan Pablo De Francesco, Nicolás Wolovick, Sergio A. Cannas:
  q-state Potts model metastability study using optimized GPU-based Monte Carlo algorithms. 1578-1587
  
• Yan Zhao, Xuesong Li, Lin Ma:
  Multidimensional Monte Carlo model for two-photon laser-induced fluorescence and amplified spontaneous emission. 1588-1595
  
• K. C. Tseng, T. C. Kuo, S. C. Lin, C. C. Su, J. S. Wu:
  Simulations of subsonic vortex-shedding flow past a 2D vertical plate in the near-continuum regime by the parallelized DSMC code. 1596-1608
  
• Liquan Mei, Yaping Chen:
  Numerical solutions of RLW equation using Galerkin method with extrapolation techniques. 1609-1616
  
• R.-L. Jiang, C. Fang, P.-F. Chen:
  A new MHD code with adaptive mesh refinement and parallelization for astrophysics. 1617-1633
  
• Adnane Hamiaz, Rudy Klein, Xavier Ferrieres, Olivier Pascal, Jean-Pierre Boeuf, Jean-Rene Poirier:
  Finite Volume Time Domain modelling of microwave breakdown and plasma formation in a metallic aperture. 1634-1640
  
• Andrea Colagrossi, B. Bouscasse, M. Antuono, S. Marrone:
  Particle packing algorithm for SPH schemes. 1641-1653
  
• Hanz Y. Ramírez, Alejandro Santana:
  Two interacting electrons confined in a 3D parabolic cylindrically symmetric potential, in presence of axial magnetic field: A finite element approach. 1654-1657
  
• Xi Chen, Z. J. Ding:
  Solving extra-high-order Rubik's Cube problem by a dynamic simulated annealing. 1658-1663
  
• Nobuko Ohba, Shuji Ogata, Takahisa Kouno, Tomoyuki Tamura, Ryo Kobayashi:
  Linear scaling algorithm of real-space density functional theory of electrons with correlated overlapping domains. 1664-1673
  
• Edoardo Di Napoli, Stefan Blügel, Paolo Bientinesi:
  Correlations in sequences of generalized eigenproblems arising in Density Functional Theory. 1674-1682
  
• Georgios Kalantzis, Dimitrios Emfietzoglou, Panagiotis E. Hadjidoukas:
  A unified spatio-temporal parallelization framework for accelerated Monte Carlo radiobiological modeling of electron tracks and subsequent radiation chemistry. 1683-1695
  
• Asimina Maniopoulou, Erlend R. M. Davidson, Ricardo Grau-Crespo, Aron Walsh, Ian J. Bush, C. Richard A. Catlow, Scott M. Woodley:
  Introducing k-point parallelism into VASP. 1696-1701
  
• B. Pekmen, M. Tezer-Sezgin:
  Differential quadrature solution of nonlinear Klein-Gordon and sine-Gordon equations. 1702-1713
  
• Isaac Gabriel Salib, Shimon Haber:
  Is the cutoff radius in DPD simulations with a fluid of constant density arbitrary? 1714-1718
  
• J. A. Heikkinen, T. Korpilo, S. J. Janhunen, T. P. Kiviniemi, S. Leerink, F. Ogando:
  Interpolation for momentum conservation in 3D toroidal gyrokinetic particle simulation of plasmas. 1719-1727
  
• Pengfei Wei, Zhenzhou Lu, Wenrui Hao, Jun Feng, Bintuan Wang:
  Efficient sampling methods for global reliability sensitivity analysis. 1728-1743
  
• Gary Yuan, François Gygi:
  A distributed approach to verification and validation of electronic structure simulation data using ESTEST. 1744-1748
  
• Gui-Yang Huang, Chong-Yu Wang, Jian-Tao Wang:
  Detailed check of the LDA + U and GGA + U corrected method for defect calculations in wurtzite ZnO. 1749-1752
  
• Elena Eremina, Yuri Eremin, Natalia Grishina, Thomas Wriedt:
  New scheme of the Discrete Sources Method for investigation of a near field enhancement by coupled particles. 1753-1759
  

• J. R. Johansson, P. D. Nation, Franco Nori:
  QuTiP: An open-source Python framework for the dynamics of open quantum systems. 1760-1772
  
• A. Jablonski:
  An effective algorithm for calculating the Chandrasekhar function. 1773-1782
  
• Moti Umansky, Daphne Weihs:
  Novel algorithm and MATLAB-based program for automated power law analysis of single particle, time-dependent mean-square displacement. 1783-1792
  
• Carsten Svaneborg:
  LAMMPS framework for dynamic bonding and an application modeling DNA. 1793-1802
  
• Jingjing Zheng, Steven L. Mielke, Kenneth L. Clarkson, Donald G. Truhlar:
  MSTor: A program for calculating partition functions, free energies, enthalpies, entropies, and heat capacities of complex molecules including torsional anharmonicity. 1803-1812
  
• T. Pálmai:
  Regularization of multi-soliton form factors in sine-Gordon model. 1813-1821
  
• A. Arbey:
  AlterBBN: A program for calculating the BBN abundances of the elements in alternative cosmologies. 1822-1831
  
• M. F. Ciappina, T. Kirchner:
  SymbMat: Symbolic computation of quantum transition matrix elements. 1832-1840
  

• Russell M. Pitzer:
  Atomic self-consistent-field program by the basis set expansion method: Columbus version. 1841-1842
  
• Christian Clason, Gregory von Winckel:
  A general spectral method for the numerical simulation of one-dimensional interacting fermions. 1843-1844
  

Volume 183, Number 9, September 2012

• Barbara Schmidt, Matthias Steinhauser:
  CRunDec: A C++ package for running and decoupling of the strong coupling and quark masses. 1845-1848
  
• Wanxiang Feng, Jun Wen, Jinjian Zhou, Di Xiao, Yugui Yao:
  First-principles calculation of Z₂ topological invariants within the FP-LAPW formalism. 1849-1859
  
• Luigi Brugnano, Felice Iavernaro, Donato Trigiante:
  A two-step, fourth-order method with energy preserving properties. 1860-1868
  
• Elizabeth Williams, James Tickner:
  Efficient Monte Carlo simulation of coincidence effects in radioisotope decays including y-y angular correlations. 1869-1876
  
• Jose Luis Velasco, Andrés Bustos, Francisco Castejón, L. A. Fernandez, Victor Martin-Mayor, Alfonso Tarancón:
  ISDEP: Integrator of stochastic differential equations for plasmas. 1877-1883
  
• Topi Siro, Ari Harju:
  Exact diagonalization of the Hubbard model on graphics processing units. 1884-1889
  
• Saeed Ovaysi, Mohammad Piri:
  Multi-GPU acceleration of direct pore-scale modeling of fluid flow in natural porous media. 1890-1898
  
• Tomasz M. Gwizdalla:
  The hybrid algorithm for the study of geometric configurations of 2D clusters of uniformly charged classical particles. 1899-1903
  
• Alberto Talamo, Zhaopeng Zhong, Yousry Gohar:
  Monte Carlo and deterministic calculation of the Bell and Glasstone spatial correction factor. 1904-1910
  
• Kevin Jorissen, Fernando D. Vila, John J. Rehr:
  A high performance scientific cloud computing environment for materials simulations. 1911-1919
  
• Ydalia Delgado Mercado, Hans Gerd Evertz, Christof Gattringer:
  Worm algorithms for the 3-state Potts model with magnetic field and chemical potential. 1920-1927
  
• André Barka, Nicolas Douchin:
  Asymptotic simplifications for hybrid BEM/GO/PO/PTD techniques based on a Generalized Scattering Matrix approach. 1928-1936
  
• Siham Tabik, Luis F. Romero, Petar Mimica, Oscar G. Plata, Emilio L. Zapata:
  VLBI-resolution radio-map algorithms: Performance analysis of different levels of data-sharing on multi-socket, multi-core architectures. 1937-1946
  
• Enying Li, Hu Wang, Guangyao Li:
  High dimensional model representation (HDMR) coupled intelligent sampling strategy for nonlinear problems. 1947-1955
  
• Haochen Li, Jianqiang Sun:
  A new multi-symplectic scheme for the generalized Kadomtsev-Petviashvili equation. 1956-1965
  
• M. Gherardi, T. Jourdan, S. Le Bourdiec, G. Bencteux:
  Hybrid deterministic/stochastic algorithm for large sets of rate equations. 1966-1973
  
• S. Dalena, P. Chuychai, R. L. Mace, A. Greco, G. Qin, W. H. Matthaeus:
  Streamline generation code for particle dynamics description in numerical models of turbulence. 1974-1985
  
• S. Maeyama, A. Ishizawa, Tomohiko Watanabe, N. Nakajima, S. Tsuji-Iio, H. Tsutsui:
  A hybrid method of semi-Lagrangian and additive semi-implicit Runge-Kutta schemes for gyrokinetic Vlasov simulations. 1986-1992
  
• Waseem Kamleh, Mike Peardon:
  Polynomial filtered HMC-an algorithm for lattice QCD with dynamical quarks. 1993-2000
  
• Evandro F. da Silva, Mário J. de Oliveira:
  Two versions of the threshold contact model in two dimensions. 2001-2005
  

• Carroll L. Wainwright:
  CosmoTransitions: Computing cosmological phase transition temperatures and bubble profiles with multiple fields. 2006-2013
  
• Timothy J. McIntyre, Alexis I. Bishop:
  Fringe - A Java-based finite fringe analysis package. 2014-2018
  

• J. Avellar, L. G. S. Duarte, L. A. C. P. da Mota, N. de Melo, J. E. F. Skea:
  The Ndynamics package - Numerical analysis of dynamical systems and the fractal dimension of boundaries. 2019-2020
  
• Dusan Vudragovic, Ivana Vidanovic, Antun Balaz, Paulsamy Muruganandam, Sadhan K. Adhikari:
  C programs for solving the time-dependent Gross-Pitaevskii equation in a fully anisotropic trap. 2021-2025
  

Volume 183, Number 10, October 2012

• Masaharu Matsumoto, Yoshihiro Kajimura, Hideyuki Usui, Ikkoh Funaki, Iku Shinohara:
  Application of a total variation diminishing scheme to electromagnetic hybrid particle-in-cell plasma simulation. 2027-2034
  
• N. Dubray, D. Regnier:
  Numerical search of discontinuities in self-consistent potential energy surfaces. 2035-2041
  
• D. Viganò, J. A. Pons, J. A. Miralles:
  A new code for the Hall-driven magnetic evolution of neutron stars. 2042-2053
  
• Kevin B. Daly, Jay B. Benziger, Pablo G. Debenedetti, Athanassios Z. Panagiotopoulos:
  Massively parallel chemical potential calculation on graphics processing units. 2054-2062
  
• Yanchao Wang, Jian Lv, Li Zhu, Yanming Ma:
  CALYPSO: A method for crystal structure prediction. 2063-2070
  
• Cathal Ó Broin, L. A. A. Nikolopoulos:
  An OpenCL implementation for the solution of the time-dependent Schrödinger equation on GPUs and CPUs. 2071-2080
  
• Bokui Chen, Chuanfei Dong, Yike Liu, Wei Tong, Wenyao Zhang, Jie Liu, Binghong Wang:
  Real-time information feedback based on a sharp decay weighted function. 2081-2088
  
• Alejandro León:
  An efficient model for studying the dynamics of frustrated systems. 2089-2097
  
• Ram K. Pandey, Om P. Singh, Vipul K. Baranwal, Manoj P. Tripathi:
  An analytic solution for the space-time fractional advection-dispersion equation using the optimal homotopy asymptotic method. 2098-2106
  
• Hyun Geun Lee, Junseok Kim:
  An efficient and accurate numerical algorithm for the vector-valued Allen-Cahn equations. 2107-2115
  
• H. Kohno, J. R. Myra, D. A. D'Ippolito:
  A finite element procedure for radio-frequency sheath-plasma interactions in the ion cyclotron range of frequencies. 2116-2127
  
• Alexei Deinega, Sajeev John:
  Finite difference discretization of semiconductor drift-diffusion equations for nanowire solar cells. 2128-2135
  
• Fukuko Yuasa, Elise de Doncker, Nobuyuki Hamaguchi, Tadashi Ishikawa, K. Kato, Yoshimasa Kurihara, Junpei Fujimoto, Yoshimitsu Shimizu:
  Numerical computation of two-loop box diagrams with masses. 2136-2144
  

• Bernd A. Berg, Hao Wu:
  Fortran code for SU(3) lattice gauge theory with and without MPI checkerboard parallelization. 2145-2157
  
• Feng Feng:
  $Apart: A generalized Mathematica Apart function. 2158-2164
  
• Florian Staub, Thorsten Ohl, Werner Porod, Christian Speckner:
  A tool box for implementing supersymmetric models. 2165-2206
  
• Lutz Foucar, Anton Barty, Nicola Coppola, Robert Hartmann, Peter Holl, Uwe Hoppe, Stephan Kassemeyer, Nils Kimmel, Jochen Küpper, Mirko Scholz, Simone Techert, Thomas A. White, Lothar Strüder, Joachim Ullrich:
  CASS - CFEL-ASG software suite. 2207-2213
  
• Alfonso García-Parrado Gómez-Lobo, José M. Martín-García:
  Spinors: A Mathematica package for doing spinor calculus in General Relativity. 2214-2225
  
• Gonzalo Alvarez:
  Implementation of the SU(2) Hamiltonian symmetry for the DMRG algorithm. 2226-2232
  
• Victor Liu, Shanhui Fan:
  S⁴ : A free electromagnetic solver for layered periodic structures. 2233-2244
  
• A. Buraczewski, M. Stobinska:
  Numerical model for macroscopic quantum superpositions based on phase-covariant quantum cloning. 2245-2253
  
• Priscila de Aquino, William Link, Fabio Maltoni, Olivier Mattelaer, Tim Stelzer:
  ALOHA: Automatic libraries of helicity amplitudes for Feynman diagram computations. 2254-2263
  
• Piotr Magierski, Gabriel Wlazlowski:
  LINPRO: Linear inverse problem library for data contaminated by statistical noise. 2264-2271
  
• Miguel A. L. Marques, Micael J. T. Oliveira, Tobias Burnus:
  Libxc: A library of exchange and correlation functionals for density functional theory. 2272-2281
  
• Daniel Kuchelmeister, Thomas Müller, Marco Ament, Günter Wunner, Daniel Weiskopf:
  GPU-based four-dimensional general-relativistic ray tracing. 2282-2290
  
• Amna Noreen, Kåre Olaussen:
  High precision series solutions of differential equations: Ordinary and regular singular points of second order ODEs. 2291-2297
  
• Renato M. Fonseca:
  Calculating the renormalisation group equations of a SUSY model with Susyno. 2298-2306
  
• H. Hluchá, H. Eberl, W. Frisch:
  SFOLD - A program package for calculating two-body sfermion decays at full one-loop level in the MSSM. 2307-2312
  

• J. Avellar, L. G. S. Duarte, L. A. C. P. da Mota:
  PSsolver: A Maple implementation to solve first order ordinary differential equations with Liouvillian solutions. 2313-2314
  

Volume 183, Number 11, November 2012

• Tarik Hadzibeganovic, F. Welington S. Lima, Dietrich Stauffer:
  Evolution of tag-mediated altruistic behavior in one-shot encounters on large-scale complex networks. 2315-2321
  
• Mario Arioli, Serge Gratton:
  Linear regression models, least-squares problems, normal equations, and stopping criteria for the conjugate gradient method. 2322-2336
  
• T. V. S. Sekhar, B. Hema Sundar Raju:
  An efficient higher order compact scheme to capture heat transfer solutions in spherical geometry. 2337-2345
  
• P. J. Knight, A. Thyagaraja, T. D. Edwards, J. Hein, M. Romanelli, K. G. McClements:
  CENTORI: A global toroidal electromagnetic two-fluid plasma turbulence code. 2346-2363
  
• Ki-Hwan Kim, Q.-Han Park:
  Overlapping computation and communication of three-dimensional FDTD on a GPU cluster. 2364-2369
  
• Alan R. Levin, Deyin Zhang, Eric Polizzi:
  FEAST fundamental framework for electronic structure calculations: Reformulation and solution of the muffin-tin problem. 2370-2375
  
• Shin-ichi Satake, Hajime Yoshimori, Takayuki Suzuki:
  Optimizations of a GPU accelerated heat conduction equation by a programming of CUDA Fortran from an analysis of a PTX file. 2376-2385
  
• Fernando Casas, Ander Murua, Mladen Nadinic:
  Efficient computation of the Zassenhaus formula. 2386-2391
  
• Venera Khoromskaia, D. Andrae, Boris N. Khoromskij:
  Fast and accurate 3D tensor calculation of the Fock operator in a general basis. 2392-2404
  
• M. Joulaian, A. Pishevar, S. Khajepor, F. Schmid, Y. Afshar:
  A new algorithm for simulating flows of conducting fluids in the presence of electric fields. 2405-2412
  
• Ram Jiwari:
  A Haar wavelet quasilinearization approach for numerical simulation of Burgers' equation. 2413-2423
  
• Tiziano Leidi, Giulio Scocchi, Loris Grossi, Simone Pusterla, Claudio D'Angelo, Jean-Philippe Thiran, Alberto Ortona:
  Computing effective properties of random heterogeneous materials on heterogeneous parallel processors. 2424-2433
  
• Frederick Ira Moxley III, Tim Byrnes, Fumitaka Fujiwara, Weizhong Dai:
  A generalized finite-difference time-domain quantum method for the N-body interacting Hamiltonian. 2434-2440
  

• Markus Q. Huber, Mario Mitter:
  CrasyDSE: A framework for solving Dyson-Schwinger equations. 2441-2457
  
• Werner Porod, Florian Staub:
  SPheno 3.1: extensions including flavour, CP-phases and models beyond the MSSM. 2458-2469
  
• A. A. Azooz, S. H. Al-Nia'emi, M. A. Al-Jubbori:
  A parameterization of nuclear track profiles in CR-39 detector. 2470-2479
  
• Anton Nazarov:
  Affine.m - Mathematica package for computations in representation theory of finite-dimensional and affine Lie algebras. 2480-2493
  

• Ján Busa Jr., Shura Hayryan, Ming-Chya Wu, Ján Busa, Chin-Kun Hu:
  ARVO-CL: The OpenCL version of the ARVO package - An efficient tool for computing the accessible surface area and the excluded volume of proteins via analytical equations. 2494-2497
  

Volume 183, Number 12, December 2012

• Beatrice Paternoster:
  Present state-of-the-art in exponential fitting. A contribution dedicated to Liviu Ixaru on his 70th birthday. 2499-2512
  

• Liang Chen, Cheng Lv, Xunya Jiang:
  A re-formulation of the transfer matrix method for calculating wave-functions in higher dimensional disordered open systems. 2513-2518
  
• Valentin V. Karasiev, Samuel B. Trickey:
  Issues and challenges in orbital-free density functional calculations. 2519-2527
  
• Marcelo Fiori, J. E. Miraglia:
  New approach for approximating the continuum wave function by Gaussian basis set. 2528-2534
  
• Suzanne Varet, Sidonie Lefebvre, Gérard Durand, Antoine Roblin, Serge Cohen:
  Effective discrepancy and numerical experiments. 2535-2541
  
• C. S. Bresolin, A. A. M. Oliveira:
  An algorithm based on collision theory for the lattice Boltzmann simulation of isothermal mass diffusion with chemical reaction. 2542-2549
  
• Kun-Mo Lin, M.-H. Hu, Chieh-Tsan Hung, Jong-Shinn Wu, F.-N. Hwang, Y.-S. Chen, G. Cheng:
  A parallel hybrid numerical algorithm for simulating gas flow and gas discharge of an atmospheric-pressure plasma jet. 2550-2560
  
• Gabriel Voitcu, Marius Echim, Richard Marchand:
  Comparative study of forward and backward test-kinetic simulation approaches. 2561-2569
  
• M. Antuono, Andrea Colagrossi, S. Marrone:
  Numerical diffusive terms in weakly-compressible SPH schemes. 2570-2580
  
• Alejandro Soba, Edgar Alejandro Bea, Guillaume Houzeaux, Hadrien Calmet, José María Cela:
  Real-space density functional theory and time dependent density functional theory using finite/infinite element methods. 2581-2588
  
• E. Hirvijoki, A. Snicker, T. Korpilo, P. Lauber, E. Poli, M. Schneller, T. Kurki-Suonio:
  Alfvén Eigenmodes and Neoclassical tearing modes for orbit-following implementations. 2589-2593
  
• Santos B. Yuste, Joaquín Quintana-Murillo:
  A finite difference method with non-uniform timesteps for fractional diffusion equations. 2594-2600
  
• R. Krivec:
  Numerical regularization of Klauder effect in QLM. 2601-2607
  
• Jean-Luc Fattebert, David F. Richards, James N. Glosli:
  Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions. 2608-2615
  
• Suman Sinha:
  Performance of Wang-Landau algorithm in lattice model of liquid crystals. 2616-2621
  

• Darko Veberic:
  Lambert W function for applications in physics. 2622-2628
  
• T. A. Heltemes, G. A. Moses:
  BADGER v1.0: A Fortran equation of state library. 2629-2646
  

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