Computer Physics Communications, Volume 181 (original) (raw)

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Volume 181, Number 1, January 2010

Computational physics

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    Vineet K. Singh, Rajesh Kumar Pandey, Saurabh Singh:
    A stable algorithm for Hankel transforms using hybrid of Block-pulse and Legendre polynomials. 1-10
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    Weiwei Cai, Lin Ma:
    Applications of critical temperature in minimizing functions of continuous variables with simulated annealing algorithm. 11-16
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    Mohankumar Nandagopal, Soubhadra Sen, R. Ramar:
    On the evaluation of correction terms in Gauss-Legendre quadrature. 17-20
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    Marcos Amaku, P. R. Pascholati, V. R. Vanin:
    Decay chain differential equations: Solution through matrix algebra. 21-23
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    Manuel Aldegunde, Natalia Seoane, Antonio J. García-Loureiro, Karol Kalna:
    Reduction of the self-forces in Monte Carlo simulations of semiconductor devices on unstructured meshes. 24-34
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    Mario Zacarés, Miguel Arevalillo-Herráez, S. Abraham:
    A group-theory method to find stationary states in nonlinear discrete symmetry systems. 35-42
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    Mehdi Dehghan, Ameneh Taleei:
    A compact split-step finite difference method for solving the nonlinear Schrödinger equations with constant and variable coefficients. 43-51
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    Liming Zhang, Ali Deng, Minghong Wang, Shaoqing Yang:
    Numerical study of a novel MFIE formulation using monopolar RWG basis functions. 52-60
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    H. Frerichs, D. Reiter, Y. Feng, D. Harting:
    Block-structured grids in Lagrangian 3D edge plasma transport simulations. 61-70
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    Robert C. Tautz:
    A new simulation code for particle diffusion in anisotropic, large-scale and turbulent magnetic fields. 71-77
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    J. Rashidinia, Reza Mohammadi:
    Tension spline approach for the numerical solution of nonlinear Klein-Gordon equation. 78-91
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    Jose L. Movilla, Juan I. Climente, Josep Planelles:
    Dielectric polarization in axially-symmetric nanostructures: A computational approach. 92-98
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    Jae-Suk Yang, Wooseop Kwak:
    Application of Wang-Landau sampling to a protein model using SMMP. 99-104
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    F. Molnár Jr., T. Szakály, Róbert Mészáros, István Lagzi:
    Air pollution modelling using a Graphics Processing Unit with CUDA. 105-112
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    Tetsuya Sakurai, Hiroto Tadano, Yoshinobu Kuramashi:
    Application of block Krylov subspace algorithms to the Wilson-Dirac equation with multiple right-hand sides in lattice QCD. 113-117
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    Anna Manka-Krason, Advera Mwijage, Krzysztof Kulakowski:
    Clustering in random line graphs. 118-121

Computer programs in physics

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    M. ElKacimi, D. Goujdami, H. Przysiezniak, Peter Skands:
    One universal extra dimension in Pythia. 122-127
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    Dajana Conte, Elena Esposito, Beatrice Paternoster, Liviu Gr. Ixaru:
    Some new uses of the etam(Z) functions. 128-137
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    Philip Bechtle, O. Brein, Sven Heinemeyer, Georg Weiglein, K. E. Williams:
    HiggsBounds: Confronting arbitrary Higgs sectors with exclusion bounds from LEP and the Tevatron. 138-167
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    I. I. Gontchar, M. V. Chushnyakova:
    A C-code for the double folding interaction potential of two spherical nuclei. 168-182
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    Michal Januszewski, M. Kostur:
    Accelerating numerical solution of stochastic differential equations with CUDA. 183-188
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    David Eriksson, Johan Rathsman, Oscar Stål:
    2HDMC - two-Higgs-doublet model calculator. 189-205
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    Evgeny Z. Liverts, Nir Barnea:
    The two-electron atomic systems. S-states. 206-212
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    Guy Engelhard, Jonathan L. Feng, Iftah Galon, David Sanford, Felix Yu:
    SPICE: Simulation Package for Including Flavor in Collider Events. 213-226
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    Mattias Blennow, Enrique Fernandez-Martinez:
    Neutrino oscillation parameter sampling with MonteCUBES. 227-231
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    Benjamin C. Allanach, Markus A. Bernhard:
    Including R-parity violation in the numerical computation of the spectrum of the minimal supersymmetric standard model: SOFTSUSY3.0. 232-245

Volume 181, Number 2, February 2010

Computational physics

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    Thomas Unfer, Jean-Pierre Boeuf, François Rogier, Frédéric Thivet:
    Multi-scale gas discharge simulations using asynchronous adaptive mesh refinement. 247-258
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    Andrea Saltelli, Paola Annoni, Ivano Azzini, Francesca Campolongo, Marco Ratto, Stefano Tarantola:
    Variance based sensitivity analysis of model output. Design and estimator for the total sensitivity index. 259-270
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    Liang Li, Ting-Zhu Huang, Yan-Fei Jing, Yong Zhang:
    Application of the incomplete Cholesky factorization preconditioned Krylov subspace method to the vector finite element method for 3-D electromagnetic scattering problems. 271-276
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    Masayuki Toyoda, Taisuke Ozaki:
    Fast spherical Bessel transform via fast Fourier transform and recurrence formula. 277-282
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    Eladio Gutiérrez, Sergio Romero, María A. Trenas, Emilio L. Zapata:
    Quantum computer simulation using the CUDA programming model. 283-300
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    Duo Sun, Rui Jiang, Bing-Hong Wang:
    Timing of traffic lights and phase separation in two-dimensional traffic flow. 301-304
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    A. Andonov, Andrej Arbuzov, D. Bardin, Sergey G. Bondarenko, P. Christova, Lidia Kalinovskaya, V. Kolesnikov, Renat Sadykov:
    Standard SANC modules. 305-312
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    Ji Qiang:
    A high-order fast method for computing convolution integral with smooth kernel. 313-316
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    Cheng-shi Liu:
    Applications of complete discrimination system for polynomial for classifications of traveling wave solutions to nonlinear differential equations. 317-324
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    Hanquan Wang:
    An efficient Chebyshev-Tau spectral method for Ginzburg-Landau-Schrödinger equations. 325-340
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    David W. Holmes, John R. Williams, Peter Tilke:
    An events based algorithm for distributing concurrent tasks on multi-core architectures. 341-354
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    Marco D. Mazzeo, Steven Manos, Peter V. Coveney:
    In situ ray tracing and computational steering for interactive blood flow simulation. 355-370

Computer programs in physics

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    Predrag Lazic, Nicolae Atodiresei, Mojtaba Alaei, Vasile Caciuc, Stefan Blügel, Radovan Brako:
    JuNoLo - Jülich nonlocal code for parallel post-processing evaluation of vdW-DF correlation energy. 371-379
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    Matías Tueros, Sergio Sciutto:
    TIERRAS: A package to simulate high energy cosmic ray showers underground, underwater and under-ice. 380-392
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    Stanislaw Jadach, Wieslaw Placzek, Maciej Skrzypek, P. Stoklosa:
    Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations. 393-412
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    Thomas Müller, Frank Grave:
    GeodesicViewer - A tool for exploring geodesics in the theory of relativity. 413-419
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    Darius Germanas, Ramutis Kazys Kalinauskas, Saulius Mickevicius:
    Calculation of four-particle harmonic-oscillator transformation brackets. 420-425
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    Alex Borgoo, O. Scharf, Gediminas Gaigalas, Michel R. Godefroid:
    Multiconfiguration electron density function for the ATSP2K-package. 426-439
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    T. Radtke, Stephan Fritzsche:
    Simulation of n-qubit quantum systems. V. Quantum measurements. 440-453

Volume 181, Number 3, March 2010

Computational physics

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    Xiao-Gang Wang, Tucker Carrington Jr.:
    Parallel methods for high-dimensional quantum dynamics. 455-461
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    Simone Melchionna, Massimo Bernaschi, Sauro Succi, Efthimios Kaxiras, Frank J. Rybicki, Dimitris Mitsouras, Ahmet U. Coskun, Charles L. Feldman:
    Hydrokinetic approach to large-scale cardiovascular blood flow. 462-472
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    Zhen-Ting Huang, Huan-Chun Hsu, Chau-Lyan Chang, Chin-Tien Wu, T. F. Jiang:
    Momentum-time flux conservation method for one-dimensional wave equations. 473-480
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    Sitao Ling, Minghui Wang, Musheng Wei:
    Hermitian tridiagonal solution with the least norm to quaternionic least squares problem. 481-488
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    Leo Brewin:
    A brief introduction to Cadabra: A tool for tensor computations in General Relativity. 489-498
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    Marco Hülsmann, Thorsten Köddermann, Jadran Vrabec, Dirk Reith:
    GROW: A gradient-based optimization workflow for the automated development of molecular models. 499-513
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    P. Kirby:
    Calculation of radial prolate spheroidal wave functions of the second kind. 514-519
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    Tadeusz Wegner, Andrzej Peczak:
    Implementation of a strain energy-based nonlinear finite element in the object-oriented environment. 520-531
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    Matteo Antuono, Andrea Colagrossi, Salvatore Marrone, Diego Molteni:
    Free-surface flows solved by means of SPH schemes with numerical diffusive terms. 532-549
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    Jian-You Guo, Miao Yu, Jing Wang, Bao-Mei Yao, Peng Jiao:
    A relativistic extension of the complex scaling method using oscillator basis functions. 550-556
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    Wei Jiang, Yingzhen Lin:
    Approximate solution of the fractional advection-dispersion equation. 557-561
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    Odysseas T. Kosmas, D. S. Vlachos:
    Phase-fitted discrete Lagrangian integrators. 562-568
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    Marco D. Mazzeo, Matteo Ricci, Claudio Zannoni:
    The Linked Neighbour List (LNL) method for fast off-lattice Monte Carlo simulations of fluids. 569-581
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    Johannes Blümlein, D. J. Broadhurst, J. A. M. Vermaseren:
    The Multiple Zeta Value data mine. 582-625
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    Emmanuel Lorin, André D. Bandrauk:
    Multiresolution scheme for Time-Dependent Schrödinger Equation. 626-638
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    Yonglei Fang, Qinghe Ming, Xinyuan Wu:
    Extended RKN-type methods with minimal dispersion error for perturbed oscillators. 639-650
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    Moritz Riede, Rico Schueppel, Kristian O. Sylvester-Hvid, Martin Kühne, Michael C. Röttger, Klaus Zimmermann, Andreas W. Liehr:
    On the communication of scientific data: The Full-Metadata Format. 651-662
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    Miglena N. Koleva, Lubin G. Vulkov:
    Two-grid quasilinearization approach to ODEs with applications to model problems in physics and mechanics. 663-670
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    Rong Yu, J. Zhu, H. Q. Ye:
    Calculations of single-crystal elastic constants made simple. 671-675

Computer programs in physics

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    Timothy C. Petersen, Simon P. Ringer:
    An electron tomography algorithm for reconstructing 3D morphology using surface tangents of projected scattering interfaces. 676-682
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    Johan Lundberg, Jan Conrad, Wolfgang Rolke, Angel Lopez:
    Limits, discovery and cut optimization for a Poisson process with uncertainty in background and signal efficiency: TRolke 2.0. 683-686
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    Ardavan F. Oskooi, David Roundy, Mihai Ibanescu, Peter Bermel, John D. Joannopoulos, Steven G. Johnson:
    Meep: A flexible free-software package for electromagnetic simulations by the FDTD method. 687-702

New version announcements

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    Thomas Müller, Frank Grave:
    An updated version of the Motion4D-library. 703
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    Jaromir Tosiek:
    The Fedosov *-product in Mathematica. 704
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    Georg M. von Hippel:
    TaylUR 3, a multivariate arbitrary-order automatic differentiation package for Fortran 95. 705-706
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    Andrzej Daniluk:
    Model-Driven Development for scientific computing. Computations of RHEED intensities for a disordered surface. Part I. 707-708
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    Andrzej Daniluk:
    Model-Driven Development for scientific computing. Computations of RHEED intensities for a disordered surface. Part II. 709-710
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    Sean McConnell, Stephan Fritzsche, Andrey Surzhykov:
    DIRAC: A new version of computer algebra tools for studying the properties and behavior of hydrogen-like ions. 711-713

Volume 181, Number 4, April 2010

Computational physics

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    B. F. McMillan, S. Jolliet, Alberto Bottino, P. Angelino, Trach-Minh Tran, Laurent Villard:
    Rapid Fourier space solution of linear partial integro-differential equations in toroidal magnetic confinement geometries. 715-719
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    Nobuaki Ohno, Akira Kageyama:
    Region-of-interest visualization by CAVE VR system with automatic control of level-of-detail. 720-725
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    Wei Su, Ping Qian, Ying Liu, Jiang Shen, Nan-Xian Chen:
    First principle calculations of yttrium-doped palladium clusters. 726-731
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    Grégory Geneste:
    Free energies of ferroelectric crystals from a microscopic approach. 732-745
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    Björn Oetzel, Friedhelm Bechstedt, Karsten Hannewald:
    Finite-size modelling of electrodes for quantum transport calculations using k-space ab initio techniques. 746-749
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    Joana G. Freire, Owen J. Brison, Jason Alfredo Carlson Gallas:
    Complete sets of initial vectors for pattern growth with elementary cellular automata. 750-755
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    Mathias Wagner, Andrea Walther, Bernd-Jochen Schaefer:
    On the efficient computation of high-order derivatives for implicitly defined functions. 756-764
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    Oliver Marquardt, Sixten Boeck, Christoph Freysoldt, Tilmann Hickel, Jörg Neugebauer:
    Plane-wave implementation of the real-space k.p formalism and continuum elasticity theory. 765-771
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    Mehdi Dehghan, Arezou Ghesmati:
    Numerical simulation of two-dimensional sine-Gordon solitons via a local weak meshless technique based on the radial point interpolation method (RPIM). 772-786
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    Shaozhong Deng:
    A robust numerical method for self-polarization energy of spherical quantum dots with finite confinement barriers. 787-799
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    Daniel Reith, Peter Virnau:
    Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states. 800-805
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    T. Kunze, Sibylle Gemming, S. Numazawa, Michael Schreiber:
    Low-temperature modeling for degenerate and frustrated Heisenberg systems with anisotropy. 806-812

Computer programs in physics

New version announcements

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    Ioan Valeriu Grossu, D. Felea, Calin Besliu, Alexandru Jipa, Cristian C. Bordeianu, Emil Stan, Tiberiu Esanu:
    A new version of Visual tool for estimating the fractal dimension of images. 831-832
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    David Eriksson, Johan Rathsman, Oscar Stål:
    2HDMC - two-Higgs-doublet model calculator. 833-834
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    M. Bazzotti, G. Carminati, A. Margiotta, Maurizio Spurio:
    An update of the generator of atmospheric muons from parametric formulas (MUPAGE). 835-836

Volume 181, Number 5, May 2010

Computational physics

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    E. T. Meier, V. S. Lukin, Uri Shumlak:
    Spectral element spatial discretization error in solving highly anisotropic heat conduction equation. 837-841
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    N. Mohankumar, A. Natarajan:
    On an interesting variant of the IMT quadrature. 842-847
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    Bongsoo Jang:
    Solving linear and nonlinear initial value problems by the projected differential transform method. 848-854
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    Ivan Duchemin, François Gygi:
    A scalable and accurate algorithm for the computation of Hartree-Fock exchange. 855-860
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    Zhen F. Tian, Peixiang Yu:
    High-order compact ADI (HOC-ADI) method for solving unsteady 2D Schrödinger equation. 861-868
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    Samuel F. Martins, Ricardo A. Fonseca, Luís O. Silva, Wei Lu, Warren B. Mori:
    Numerical simulations of laser wakefield accelerators in optimal Lorentz frames. 869-875
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    Sanjar M. Abrarov, Brendan M. Quine, Rajinder K. Jagpal:
    High-accuracy approximation of the complex probability function by Fourier expansion of exponential multiplier. 876-882
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    Hiroto Tadano, Yoshinobu Kuramashi, Tetsuya Sakurai:
    Application of preconditioned block BiCGGR to the Wilson-Dirac equation with multiple right-hand sides in lattice QCD. 883-886
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    Marco Hülsmann, Jadran Vrabec, Astrid Maaß, Dirk Reith:
    Assessment of numerical optimization algorithms for the development of molecular models. 887-905
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    Jani Sainio:
    CUDAEASY - a GPU accelerated cosmological lattice program. 906-912
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    Monodeep Chakraborty, Jürgen Spitaler, Peter Puschnig, Claudia Ambrosch-Draxl:
    ATAT@WIEN2k: An interface for cluster expansion based on the linearized augmented planewave method. 913-920
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    V. M. Grichine:
    Geant4 hadron elastic diffuse model. 921-927
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    Panagiotis E. Hadjidoukas, C. Bousis, Dimitrios Emfietzoglou:
    Parallelization of a Monte Carlo particle transport simulation code. 928-936
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    Jen-Hao Chen, Jinn-Liang Liu:
    A numerical method for exact diagonalization of semiconductor quantum dot model. 937-946
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    Yongxiang Zhao, Aiguo Xiao:
    Variational iteration method for singular perturbation initial value problems. 947-956
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    Mehrdad Lakestani, Mehdi Dehghan:
    Numerical solution of Riccati equation using the cubic B-spline scaling functions and Chebyshev cardinal functions. 957-966
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    María Eugenia Castro, Alfonso Niño, Camelia Muñoz-Caro:
    A metaheuristic approach to the optimal definition of molecule-fixed axes in rovibrational Hamiltonians. 967-977

Computer programs in physics

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    Weiwei Cai, Laura Kranendonk, Tonghun Lee, Lin Ma:
    Characterization of composite nanoparticles using an improved light scattering program for coated spheres. 978-984

Erratum

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    David Eriksson, Johan Rathsman, Oscar Stål:
    Erratum for "2HDMC - two-Higgs-doublet model calculator" [Comput. Phys. Commun. 181 (2010) 189]. 985

Volume 181, Number 6, June 2010

Computational physics

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    Frederic Imbeaux, J. B. Lister, G. T. A. Huysmans, W. Zwingmann, M. Airaj, L. Appel, V. Basiuk, David Coster, Lars-Goran Eriksson, Bernard Guillerminet, Denis Kalupin, C. Konz, Gabriele Manduchi, M. Ottaviani, G. Pereverzev, Y. Peysson, Olivier Sauter, J. Signoret, Per Strand:
    A generic data structure for integrated modelling of tokamak physics and subsystems. 987-998
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    Hyungson Ki:
    Level set method for two-phase incompressible flows under magnetic fields. 999-1007
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    A. Glazov, N. Raicevic, A. Zhokin:
    Fast simulation of showers in the H1 calorimeter. 1008-1012
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    Jonathan R. Clausen, Daniel A. Reasor Jr., Cyrus K. Aidun:
    Parallel performance of a lattice-Boltzmann/finite element cellular blood flow solver on the IBM Blue Gene/P architecture. 1013-1020
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    Changbum Chun, Rathinasamy Sakthivel:
    Homotopy perturbation technique for solving two-point boundary value problems - comparison with other methods. 1021-1024
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    Matthew R. Smith, Fang-An Kuo, Chih-Wei Hsieh, Jen-Perng Yu, Jong-Shinn Wu, Alex Ferguson:
    Rapid optimization of blast wave mitigation strategies using Quiet Direct Simulation and Genetic Algorithm. 1025-1036
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    Seong-Deog Yang, Hyun Geun Lee, Junseok Kim:
    A phase-field approach for minimizing the area of triply periodic surfaces with volume constraint. 1037-1046
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    Minghui Wang:
    Algorithm Q-LSQR for the least squares problem in quaternionic quantum theory. 1047-1050
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    M. J. Rayson:
    Rapid filtration algorithm to construct a minimal basis on the fly from a primitive Gaussian basis. 1051-1056
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    Constantine Bekas, Alessandro Curioni:
    Very large scale wavefunction orthogonalization in Density Functional Theory electronic structure calculations. 1057-1068
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    S. Satake, Yasuhiro Idomura, Hideo Sugama, Tomohiko Watanabe:
    Benchmark test of drift-kinetic and gyrokinetic codes through neoclassical transport simulations. 1069-1076
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    Florian Staub:
    From superpotential to model files for FeynArts and CalcHep/CompHep. 1077-1086
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  • 
    Aleksey M. Serebrennikov:
    A novel semi-analytic method for the analysis of scattering by dielectric objects immersed in uniform media. 1087-1095
• 
  • 
  • 
  • 
  • 
    K. Parand, Mehdi Dehghan, A. R. Rezaei, S. M. Ghaderi:
    An approximation algorithm for the solution of the nonlinear Lane-Emden type equations arising in astrophysics using Hermite functions collocation method. 1096-1108
• 
  • 
  • 
  • 
  • 
    Shamsul Qamar, Sidrah Mudasser:
    A kinetic flux-vector splitting method for the shallow water magnetohydrodynamics. 1109-1122

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Arturo Rodolfo Samana, F. Krmpotic, C. A. Bertulani:
    QRAP: A numerical code for projected (Q)uasiparticle (RA)ndom (P)hase approximation. 1123-1135
• 
  • 
  • 
  • 
  • 
    B. Gebremariam, T. Duguet, S. K. Bogner:
    Symbolic integration of a product of two spherical Bessel functions with an additional exponential and polynomial factor. 1136-1143
• 
  • 
  • 
  • 
  • 
    Chao-Hsi Chang, Jian-Xiong Wang, Xing-Gang Wu:
    GENXICC2.0: An upgraded version of the generator for hadronic production of double heavy baryons Xicc, Xibc and Xibb. 1144-1149
• 
  • 
  • 
  • 
  • 
    Benzhuo Lu, Xiaolin Cheng, Jingfang Huang, James Andrew McCammon:
    AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems. 1150-1160
• 
  • 
  • 
  • 
  • 
    C. Carasco:
    MCNP Output Data Analysis with ROOT (MODAR). 1161-1166
• 
  • 
  • 
  • 
  • 
    B. Gebremariam, S. K. Bogner, T. Duguet:
    Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at N2LO. 1167-1177

Volume 181, Number 7, July 2010

Computational physics

• 
  • 
  • 
  • 
  • 
    Carlo Manuali, Antonio Laganà, Sergio Rampino:
    GriF: A Grid framework for a Web Service approach to reactive scattering. 1179-1185
• 
  • 
  • 
  • 
  • 
    A. V. Wolkov, N. B. Petrovskaya:
    Higher order discontinuous Galerkin method for acoustic pulse problem. 1186-1194
• 
  • 
  • 
  • 
  • 
    Francisco de la Hoz, Fernando Vadillo:
    An integrating factor for nonlinear Dirac equations. 1195-1203
• 
  • 
  • 
  • 
  • 
    A. D'Angola, Gianni Coppa, Mario Capitelli, Claudine Gorse, Gianpiero Colonna:
    An efficient energy-conserving numerical model for the electron energy distribution function in the presence of electron-electron collisions. 1204-1211
• 
  • 
  • 
  • 
  • 
    Ilya M. Sobol, Sergei S. Kucherenko:
    A new derivative based importance criterion for groups of variables and its link with the global sensitivity indices. 1212-1217
• 
  • 
  • 
  • 
  • 
    F. P. Fernandes, F. W. S. Lima, João Antônio Plascak:
    Blume-Capel model on directed and undirected small-world Voronoi-Delaunay random lattices. 1218-1223
• 
  • 
  • 
  • 
  • 
    Ahmad Golbabai, Seyedeh Mahboubeh Molavi-Arabshahi:
    A numerical method for diffusion-convection equation using high-order difference schemes. 1224-1230
• 
  • 
  • 
  • 
  • 
    Yaming Chen, Huajun Zhu, Songhe Song:
    Multi-symplectic splitting method for the coupled nonlinear Schrödinger equation. 1231-1241
• 
  • 
  • 
  • 
  • 
    Andrei Bourchtein, Ludmila Bourchtein:
    On iterated Crank-Nicolson methods for hyperbolic and parabolic equations. 1242-1250
• 
  • 
  • 
  • 
  • 
    Theodoros Monovasilis, Zacharoula Kalogiratou, Tom E. Simos:
    Symplectic Partitioned Runge-Kutta methods with minimal phase-lag. 1251-1254
• 
  • 
  • 
  • 
  • 
    Mehdi Dehghan, Rezvan Salehi:
    Solution of a nonlinear time-delay model in biology via semi-analytical approaches. 1255-1265
• 
  • 
  • 
  • 
  • 
    Reza Mokhtari, Maryam Mohammadi:
    Numerical solution of GRLW equation using Sinc-collocation method. 1266-1274
• 
  • 
  • 
  • 
  • 
    Omar Ramadan:
    Addendum to: "A FDTD analysis on magnetized plasma of Epstein distribution and reflection calculation" [Computer Physics Communications 180 (1) (2009) 55-60]: A short comment on the equivalence of the shift-operator FDTD method and the bilinear frequency approximation technique for modeling dispersive electromagnetic applications. 1275-1276

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Alexandre Arbey, Farvah Mahmoudi:
    SuperIso Relic: A program for calculating relic density and flavor physics observables in Supersymmetry. 1277-1292
• 
  • 
  • 
  • 
  • 
    C. Studerus:
    Reduze - Feynman integral reduction in C++. 1293-1300
• 
  • 
  • 
  • 
  • 
    T. Reiter:
    Optimising code generation with haggies. 1301-1331

New version announcement

• 
  • 
  • 
  • 
  • 
    Aleksandar I. Ogoyski, Shigeo Kawata, P. H. Popov:
    Code OK3 - An upgraded version of OK2 with beam wobbling function. 1332-1333

Volume 181, Number 8, August 2010

Computational physics

• 
  • 
  • 
  • 
  • 
    Veerle Ledoux, Marnix Van Daele:
    Solving Sturm-Liouville problems by piecewise perturbation methods, revisited. 1335-1345
• 
  • 
  • 
  • 
  • 
    Julián Rincón, Daniel J. García, Karen Hallberg:
    Improved parallelization techniques for the density matrix renormalization group. 1346-1351
• 
  • 
  • 
  • 
  • 
    Toshiaki Kaneko, Takahiro Ueda:
    A geometric method of sector decomposition. 1352-1361
• 
  • 
  • 
  • 
  • 
    Stavros Stavroyiannis, T. E. Simos:
    A nonlinear explicit two-step fourth algebraic order method of order infinity for linear periodic initial value problems. 1362-1368
• 
  • 
  • 
  • 
  • 
    Linghua Kong, Jingjing Zhang, Ying Cao, Yali Duan, Hong Huang:
    Semi-explicit symplectic partitioned Runge-Kutta Fourier pseudo-spectral scheme for Klein-Gordon-Schrödinger equations. 1369-1377
• 
  • 
  • 
  • 
  • 
    Jacques Bloch, Tobias Breu, Andreas Frommer, Simon Heybrock, Katrin Schäfer, Tilo Wettig:
    Short-recurrence Krylov subspace methods for the overlap Dirac operator at nonzero chemical potential. 1378-1387
• 
  • 
  • 
  • 
  • 
    Rafael Bertolini Frigori:
    Universality in short-time critical gluodynamics with heat-bath-inspired algorithms. 1388-1391
• 
  • 
  • 
  • 
  • 
    Mehrdad Lakestani, Mehdi Dehghan:
    Collocation and finite difference-collocation methods for the solution of nonlinear Klein-Gordon equation. 1392-1401
• 
  • 
  • 
  • 
  • 
    Toni Giorgino, Matt J. Harvey, Gianni De Fabritiis:
    Distributed computing as a virtual supercomputer: Tools to run and manage large-scale BOINC simulations. 1402-1409
• 
  • 
  • 
  • 
  • 
    Mehdi Dehghan, Arezou Ghesmati:
    Application of the dual reciprocity boundary integral equation technique to solve the nonlinear Klein-Gordon equation. 1410-1418
• 
  • 
  • 
  • 
  • 
    M. Tentyukov, J. A. M. Vermaseren:
    The multithreaded version of FORM. 1419-1427
• 
  • 
  • 
  • 
  • 
    Moritz J. Pueschel, Tilman Dannert, Frank Jenko:
    On the role of numerical dissipation in gyrokinetic Vlasov simulations of plasma microturbulence. 1428-1437
• 
  • 
  • 
  • 
  • 
    Yago Ascasibar:
    Estimating multidimensional probability fields using the Field Estimator for Arbitrary Spaces (FiEstAS) with applications to astrophysics. 1438-1443
• 
  • 
  • 
  • 
  • 
    S. Bianchi, Roberto Di Leonardo:
    Real-time optical micro-manipulation using optimized holograms generated on the GPU. 1444-1448
• 
  • 
  • 
  • 
  • 
    Christoph Junghans, Simón Poblete:
    A reference implementation of the adaptive resolution scheme in ESPResSo. 1449-1454

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Masayuki Toyoda, Taisuke Ozaki:
    LIBERI: Library for numerical evaluation of electron-repulsion integrals. 1455-1463
• 
  • 
  • 
  • 
  • 
    Ioan Valeriu Grossu, Calin Besliu, Alexandru Jipa, Cristian C. Bordeianu, D. Felea, Emil Stan, Tiberiu Esanu:
    Code C# for chaos analysis of relativistic many-body systems. 1464-1470
• 
  • 
  • 
  • 
  • 
    María Eugenia Castro, Alfonso Niño, Camelia Muñoz-Caro:
    Heuristic computation of the rovibrational G matrix in optimized molecule-fixed axes. Gmat 2.1. 1471-1475

Volume 181, Number 9, September 2010

Feature Article

• 
  • 
  • 
  • 
  • 
    Marat Valiev, Eric J. Bylaska, Niranjan Govind, Karol Kowalski, Tjerk P. Straatsma, Hubertus Johannes Jacobus Van Dam, D. Wang, Jarek Nieplocha, Edoardo Aprà, Theresa L. Windus, Wibe A. de Jong:
    NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations. 1477-1489

Computational physics

• 
  • 
  • 
  • 
  • 
    Mitsuru Honda:
    Simulation technique of free-boundary equilibrium evolution in plasma ramp-up phase. 1490-1500
• 
  • 
  • 
  • 
  • 
    C. A. Duarte:
    Convergence and instability of iterative procedures on the one-dimensional Schrödinger-Poisson problem. 1501-1509
• 
  • 
  • 
  • 
  • 
    Ian Mondragon-Shem, Boris A. Rodríguez, Francisco E. López:
    Efficient calculation of Coulomb matrix elements for bilayers of confined charge carriers with arbitrary spatial separation. 1510-1516
• 
  • 
  • 
  • 
  • 
    Michael A. Clark, Ronald Babich, Kipton Barros, Richard C. Brower, Claudio Rebbi:
    Solving lattice QCD systems of equations using mixed precision solvers on GPUs. 1517-1528
• 
  • 
  • 
  • 
  • 
    Feng-Nan Hwang, Shang-Rong Cai, Yun-Long Shao, Jong-Shinn Wu:
    Parallel Newton-Krylov-Schwarz algorithms for the three-dimensional Poisson-Boltzmann equation in numerical simulation of colloidal particle interactions. 1529-1537
• 
  • 
  • 
  • 
  • 
    Yonglei Fang, Qinghong Li, Xinyuan Wu:
    Extended RKN methods with FSAL property for oscillatory systems. 1538-1548
• 
  • 
  • 
  • 
  • 
    Benjamin Block, Peter Virnau, Tobias Preis:
    Multi-GPU accelerated multi-spin Monte Carlo simulations of the 2D Ising model. 1549-1556
• 
  • 
  • 
  • 
  • 
    Robert Hammerling, Othmar Koch, Christa Simon, Ewa Weinmüller:
    Numerical solution of singular ODE eigenvalue problems in electronic structure computations. 1557-1561
• 
  • 
  • 
  • 
  • 
    Ruud G. M. van der Sman:
    MRT Lattice Boltzmann schemes for confined suspension flows. 1562-1569
• 
  • 
  • 
  • 
  • 
    Gunnar S. Bali, Sara Collins, Andreas Schäfer:
    Effective noise reduction techniques for disconnected loops in Lattice QCD. 1570-1583
• 
  • 
  • 
  • 
  • 
    G. M. Doctors, Marco D. Mazzeo, Peter V. Coveney:
    A computationally efficient method for simulating fluid flow in elastic pipes in three dimensions. 1584-1592
• 
  • 
  • 
  • 
  • 
    Stefan Ask, I. V. Akin, L. Benucci, A. De Roeck, Martin Goebel, Johannes Haller:
    Real emission and virtual exchange of gravitons and unparticles in Pythia8. 1593-1604
• 
  • 
  • 
  • 
  • 
    Gaurav Khanna, Justin McKennon:
    Numerical modeling of gravitational wave sources accelerated by OpenCL. 1605-1611
• 
  • 
  • 
  • 
  • 
    Thomas Binoth, Fawzi Boudjema, Günther Dissertori, A. Lazopoulos, Ansgar Denner, Stefan Dittmaier, Rikkert Frederix, Nicolas Greiner, S. Höche, W. Giele, Peter Skands, J. Winter, T. Gleisberg, J. Archibald, Gudrun Heinrich, Frank Krauss, D. Maître, M. Huber, J. Huston, Nikolas Kauer, Fabio Maltoni, Carlo Oleari, Giampiero Passarino, R. Pittau, Stefano Pozzorini, T. Reiter, Steffen Schumann, Giulia Zanderighi:
    A proposal for a standard interface between Monte Carlo tools and one-loop programs. 1612-1622
• 
  • 
  • 
  • 
  • 
    Andriy O. Lyakhov, Artem R. Oganov, Mario Valle:
    How to predict very large and complex crystal structures. 1623-1632

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Bernie D. Shizgal, Raouf Dridi:
    Maple code for the calculation of the matrix elements of the Boltzmann collision operators for mixtures. 1633-1640
• 
  • 
  • 
  • 
  • 
    B. Gillis Carlsson, Jacek Dobaczewski, Jussi Toivanen, Petr Veselý:
    Solution of self-consistent equations for the N3LO nuclear energy density functional in spherical symmetry. The program hosphe (v1.02). 1641-1657

Erratum

• 
  • 
  • 
  • 
  • 
    Xinyuan Wu:
    Erratum to "Extended RKN-type methods for numerical integration of perturbed oscillators" [Computer Physics Communications 180 (2009) 1777-1794]. 1658
• 
  • 
  • 
  • 
  • 
    Subir Nath:
    Erratum to "TERS v2.0: An improved version of TERS" [Comput. Phys. Commun. 180 (2009) 2392]. 1659

Volume 181, Number 10, October 2010

Computational physics

• 
  • 
  • 
  • 
  • 
    Joshua A. Breslau, Guo-Yong Fu:
    Implementation of an implicit shear Alfvén operator in the M3D code. 1661-1670
• 
  • 
  • 
  • 
  • 
    Pablo M. Dupuy, Hallvard F. Svendsen, Luciano E. Patruno, Hugo A. Jakobsen:
    Finite-difference stable stencils based on least-square quadric fitting. 1671-1681
• 
  • 
  • 
  • 
  • 
    Wanqing Li, Tang Ying, Jian Wan, Dong-Jin Yu:
    Comparison research on the neighbor list algorithms: Verlet table and linked-cell. 1682-1686
• 
  • 
  • 
  • 
  • 
    Larry A. Viehland, Yongbin Chang:
    Transport cross sections for collisions between particles. 1687-1696
• 
  • 
  • 
  • 
  • 
    Jie Cheng, Yanqing Hu, Zengru Di, Ying Fan:
    Local adaptive mechanism and hierarchic social entropy in opinion formation on complex networks. 1697-1701
• 
  • 
  • 
  • 
  • 
    Malgorzata J. Krawczyk:
    Application of the differential equations method for identifying communities in sparse networks. 1702-1706
• 
  • 
  • 
  • 
  • 
    Richard G. Edgar, Michael A. Clark, Kevin Dale, Daniel A. Mitchell, Stephen M. Ord, Randall B. Wayth, Hanspeter Pfister, Lincoln J. Greenhill:
    Enabling a high throughput real time data pipeline for a large radio telescope array with GPUs. 1707-1714
• 
  • 
  • 
  • 
  • 
    Jakub T. Moscicki, Maciej Wos, Massimo Lamanna, Philippe de Forcrand, Owe Philipsen:
    Lattice QCD thermodynamics on the Grid. 1715-1726
• 
  • 
  • 
  • 
  • 
    Cheng-Sheng Chien, Shing-Lin Chang, Biao Wu:
    Two-stage continuation algorithms for Bloch waves of Bose-Einstein condensates in optical lattices. 1727-1737
• 
  • 
  • 
  • 
  • 
    Liviu Gr. Ixaru:
    New numerical method for the eigenvalue problem of the 2D Schrödinger equation. 1738-1742
• 
  • 
  • 
  • 
  • 
    Alexei V. Snytnikov, Vitalii A. Vshivkov, W. J. Goedheer:
    Adaptive mass alteration to model ion-ion recombination in a Particle-in-Cell simulation of silane radio-frequency discharges. 1743-1749
• 
  • 
  • 
  • 
  • 
    Michael Watson, Ken-ichi Nishikawa:
    A method for incorporating the Kerr-Schild metric in electromagnetic particle-in-cell code. 1750-1757

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Sergey Belov, Lev Dudko, D. Kekelidze, A. Sherstnev:
    HepML, an XML-based format for describing simulated data in high energy physics. 1758-1768
• 
  • 
  • 
  • 
  • 
    A. V. Nesterenko, C. Simolo:
    QCDMAPT: Program package for Analytic approach to QCD. 1769-1775
• 
  • 
  • 
  • 
  • 
    Pietro Asinari:
    Nonlinear Boltzmann equation for the homogeneous isotropic case: Minimal deterministic Matlab program. 1776-1788
• 
  • 
  • 
  • 
  • 
    Wafaa M. Fawzy:
    A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a 3Sigma state and a closed-shell molecule. 1789-1801
• 
  • 
  • 
  • 
  • 
    Kouhei Hasegawa, Sven-Olaf Moch, Peter Uwer:
    AutoDipole - Automated generation of dipole subtraction terms -. 1802-1817

New version announcements

• 
  • 
  • 
  • 
  • 
    Stamatis Stamatiadis, Stavros C. Farantos:
    auto_deriv: Tool for automatic differentiation of a Fortran code. 1818-1819

Volume 181, Number 11, November 2010

Computational physics

• 
  • 
  • 
  • 
  • 
    James Tickner:
    Monte Carlo simulation of X-ray and gamma-ray photon transport on a graphics-processing unit. 1821-1832
• 
  • 
  • 
  • 
  • 
    Higinio Ramos, Cesáreo Lorenzo:
    Review of explicit Falkner methods and its modifications for solving special second-order I.V.P.s. 1833-1841
• 
  • 
  • 
  • 
  • 
    Jorge Eduardo Macías-Díaz:
    On the simulation of the energy transmission in the forbidden band-gap of a spatially discrete double sine-Gordon system. 1842-1849
• 
  • 
  • 
  • 
  • 
    Xiaofan Li, Tong Zhu, Meigen Zhang, Guihua Long:
    Seismic scalar wave equation with variable coefficients modeling by a new convolutional differentiator. 1850-1858
• 
  • 
  • 
  • 
  • 
    N. Mohankumar, Tucker Carrington Jr.:
    A new approach for determining the time step when propagating with the Lanczos algorithm. 1859-1861
• 
  • 
  • 
  • 
  • 
    Marc Torrent, N. A. W. Holzwarth, François Jollet, David Harris, Nicholas Lepley, Xiao Xu:
    Electronic structure packages: Two implementations of the projector augmented wave (PAW) formalism. 1862-1867
• 
  • 
  • 
  • 
  • 
    Reza Jalilian:
    Non-polynomial spline method for solving Bratu's problem. 1868-1872
• 
  • 
  • 
  • 
  • 
    Xinyuan Wu, Xiong You, Wei Shi, Bin Wang:
    ERKN integrators for systems of oscillatory second-order differential equations. 1873-1887
• 
  • 
  • 
  • 
  • 
    Jan Kunes, Ryotaro Arita, Philipp Wissgott, Alessandro Toschi, Hiroaki Ikeda, Karsten Held:
    Wien2wannier: From linearized augmented plane waves to maximally localized Wannier functions. 1888-1895

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    Gary A. Huber, James Andrew McCammon:
    Browndye: A software package for Brownian dynamics. 1896-1905
• 
  • 
  • 
  • 
  • 
    Ajay Rawat, Mohankumar Nandagopal:
    Milne, a routine for the numerical solution of Milne's problem. 1906-1910
• 
  • 
  • 
  • 
  • 
    Natan Osterman:
    TweezPal - Optical tweezers analysis and calibration software. 1911-1916
• 
  • 
  • 
  • 
  • 
    Douglas M. Gingrich:
    Monte Carlo event generator for black hole production and decay in proton-proton collisions - QBH version 1.02. 1917-1924

New version announcements

• 
  • 
  • 
  • 
  • 
    Jean Luc Lamotte, Jean Marie Chesneaux, Fabienne Jézéquel:
    CADNA_C: A version of CADNA for use with C or C++ programs. 1925-1926
• 
  • 
  • 
  • 
  • 
    Fabienne Jézéquel, Jean Marie Chesneaux, Jean Luc Lamotte:
    A new version of the CADNA library for estimating round-off error propagation in Fortran programs. 1927-1928

Volume 181, Number 12, December 2010

Computational physics

• 
  • 
  • 
  • 
  • 
    Enrique Ramos, José E. Román, Salvador Cardona-Serra, Juan M. Clemente-Juan:
    Parallel implementation of the MAGPACK package for the analysis of high-nuclearity spin clusters. 1929-1940
• 
  • 
  • 
  • 
  • 
    R. Pittau:
    Testing and improving the numerical accuracy of the NLO predictions. 1941-1946
• 
  • 
  • 
  • 
  • 
    Akbar Mohebbi, Mehdi Dehghan:
    High-order scheme for determination of a control parameter in an inverse problem from the over-specified data. 1947-1954
• 
  • 
  • 
  • 
  • 
    Xinyuan Wu, Bin Wang:
    Multidimensional adapted Runge-Kutta-Nyström methods for oscillatory systems. 1955-1962
• 
  • 
  • 
  • 
  • 
    Jorge Francés, Cristian Neipp, Manuel Pérez-Molina, Augusto Beléndez:
    Rigorous interference and diffraction analysis of diffractive optic elements using the finite-difference time-domain method. 1963-1973
• 
  • 
  • 
  • 
  • 
    Weiwei Cai, Lin Ma:
    Comparison of approaches based on optimization and algebraic iteration for binary tomography. 1974-1981
• 
  • 
  • 
  • 
  • 
    M. Carrettoni, O. Cremonesi:
    Generation of noise time series with arbitrary power spectrum. 1982-1985
• 
  • 
  • 
  • 
  • 
    Nobuyuki Masuda, Takashige Sugie, Tomoyoshi Ito, Shinjiro Tanaka, Yu Hamada, Shin-ichi Satake, Tomoaki Kunugi, Kazuho Sato:
    Special purpose computer system with highly parallel pipelines for flow visualization using holography technology. 1986-1989
• 
  • 
  • 
  • 
  • 
    Ali Shokri, Mehdi Dehghan:
    A Not-a-Knot meshless method using radial basis functions and predictor-corrector scheme to the numerical solution of improved Boussinesq equation. 1990-2000
• 
  • 
  • 
  • 
  • 
    J. Ambia-Garrido, Arnold Vainrub, B. Montgomery Pettitt:
    A model for structure and thermodynamics of ssDNA and dsDNA near a surface: A coarse grained approach. 2001-2007
• 
  • 
  • 
  • 
  • 
    Emily M. Ryan, Alexandre M. Tartakovsky, Cristina H. Amon:
    A novel method for modeling Neumann and Robin boundary conditions in smoothed particle hydrodynamics. 2008-2023
• 
  • 
  • 
  • 
  • 
    Ji Qiang, Xiaoye Sherry Li:
    Particle-field decomposition and domain decomposition in parallel particle-in-cell beam dynamics simulation. 2024-2034
• 
  • 
  • 
  • 
  • 
    Magdalena Mierzwiczak, Jan Adam Kolodziej:
    Application of the method of fundamental solutions and radial basis functions for inverse transient heat source problem. 2035-2043
• 
  • 
  • 
  • 
  • 
    Manuel Calvo, J. M. Franco, Juan I. Montijano, Luis Rández:
    Symmetric and symplectic exponentially fitted Runge-Kutta methods of high order. 2044-2056
• 
  • 
  • 
  • 
  • 
    Tian Qiu, Tarik Hadzibeganovic, Guang Chen, Li-Xin Zhong, Xiao-Run Wu:
    Cooperation in the snowdrift game on directed small-world networks under self-questioning and noisy conditions. 2057-2062
• 
  • 
  • 
  • 
  • 
    Spencer E. Olson, Andrew J. Christlieb, Fredrik K. Fatemi:
    PID feedback for load-balanced parallel gridless DSMC. 2063-2071
• 
  • 
  • 
  • 
  • 
    Edoardo Patelli, Helmut J. Pradlwarter, Gerhart I. Schuëller:
    Global sensitivity of structural variability by random sampling. 2072-2081

Computer programs in physics

• 
  • 
  • 
  • 
  • 
    William J. Menz, Matthew J. Penna, Mark J. Biggs:
    TNAMD: Implementation of TIGER2 in NAMD. 2082-2085
• 
  • 
  • 
  • 
  • 
    Min Hyung Cho, Wei Cai:
    A Wideband Fast Multipole Method for the two-dimensional complex Helmholtz equation. 2086-2090
• 
  • 
  • 
  • 
  • 
    Barry I. Schneider, Javier Segura, Amparo Gil, Xiaoxu Guan, Klaus Bartschat:
    A new Fortran 90 program to compute regular and irregular associated Legendre functions. 2091-2097
• 
  • 
  • 
  • 
  • 
    Liang-You Peng, Qihuang Gong:
    An accurate Fortran code for computing hydrogenic continuum wave functions at a wide range of parameters. 2098-2101
• 
  • 
  • 
  • 
  • 
    Arnaud Marmier, Zoe A. D. Lethbridge, Richard I. Walton, Christopher W. Smith, Stephen C. Parker, Kenneth E. Evans:
    ElAM: A computer program for the analysis and representation of anisotropic elastic properties. 2102-2115
• 
  • 
  • 
  • 
  • 
    Ján Busa, Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Ming-Chya Wu:
    CAVE: A package for detection and quantitative analysis of internal cavities in a system of overlapping balls: Application to proteins. 2116-2125
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    Sergio M. Davis, Claudia Loyola, Felipe González, Joaquín Peralta:
    Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code. 2126-2139
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    Jesse Noffsinger, Feliciano Giustino, Brad D. Malone, Cheol-Hwan Park, Steven G. Louie, Marvin L. Cohen:
    EPW: A program for calculating the electron-phonon coupling using maximally localized Wannier functions. 2140-2148
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    Martin Kröger, Markus Hütter:
    Automated symbolic calculations in nonequilibrium thermodynamics. 2149-2157
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    Gregory von Winckel, Alfio Borzì:
    QUCON: A fast Krylov-Newton code for dipole quantum control problems. 2158-2163
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    Scott Rostrup, Hans De Sterck:
    Parallel hyperbolic PDE simulation on clusters: Cell versus GPU. 2164-2179
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    Janusz Rosiek, P. H. Chankowski, Athanasios Dedes, Sebastian Jäger, Philip Tanedo:
    SUSY_FLAVOR: A computational tool for FCNC and CP-violating processes in the MSSM. 2180-2205

New version announcements

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    Bo Zhang, Jingfang Huang, Nikos Pitsianis, Xiaobai Sun:
    Revision of FMM-Yukawa: An adaptive fast multipole method for screened Coulomb interactions. 2206-2207
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    Linda Hung, Chen Huang, Ilgyou Shin, Gregory S. Ho, Vincent L. Lignères, Emily A. Carter:
    Introducing PROFESS 2.0: A parallelized, fully linear scaling program for orbital-free density functional theory calculations. 2208-2209
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    C. Carasco:
    MCNP output data analysis with ROOT (MODAR). 2210-2211
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    Peter Koval, J. D. Talman:
    Update of spherical Bessel transform: FFTW and OpenMP. 2212-2213