Computer Physics Communications, Volume 180

Volume 180, Number 1, January 2009

Computational physics

• 
  Hezhu Shao, Zhongcheng Wang:
  Arbitrarily precise numerical solutions of the one-dimensional Schrödinger equation. 1-7
• 
  Benjamin C. Allanach, Csaba Balázs, G. Bélanger, M. Bernhardt, F. Boudjema, D. Choudhury, Klaus Desch, Ulrich Ellwanger, Paolo Gambino, R. Godbole, T. Goto, Jaume Guasch, M. Guchait, Thomas Hahn, Sven Heinemeyer, Cyril Hugonie, T. Hurth, Sabine Kraml, Sven Kreiss, J. Lykken:
  SUSY Les Houches Accord 2. 8-25
• 
  Nigel Cundy, Stefan Krieg, Guido Arnold, Andreas Frommer, Thomas Lippert, Klaus Schilling:
  Numerical methods for the QCD overlap operator IV: Hybrid Monte Carlo. 26-54
• 
  Hong Wei Yang:
  A FDTD analysis on magnetized plasma of Epstein distribution and reflection calculation. 55-60

Computer programs in physics

• 
  Cong-Feng Qiao, Jian Wang, Jian-Xiong Wang, Yangheng Zheng:
  EtabFDC: An eta_b event generator in hadroproduction at LHC. 61-68
• 
  Wojciech Broniowski, Maciej Rybczynski, Piotr Bozek:
  GLISSANDO: GLauber Initial-State Simulation AND mOre... 69-83
• 
  S. Wheaton, J. Cleymans, M. Hauer:
  THERMUS - A thermal model package for ROOT. 84-106
• 
  James Gray, Yang-Hui He, Anton Ilderton, André Lukas:
  STRINGVACUA. A Mathematica package for studying vacuum configurations in string phenomenology. 107-119
• 
  G. P. Salam, Juan Rojo:
  A Higher Order Perturbative Parton Evolution Toolkit (HOPPET). 120-156
• 
  A. Otero-de-la-Roza, M. A. Blanco, Ángel Martín Pendás, Víctor Luaña:
  Critic: a new program for the topological analysis of solid-state electron densities. 157-166

Volume 180, Number 2, February 2009

Computational physics

• 
  Zacharoula Kalogiratou, Th. Monovasilis, Tom E. Simos:
  Computation of the eigenvalues of the Schrödinger equation by exponentially-fitted Runge-Kutta-Nyström methods. 167-176
• 
  J. G. Jiang, Y. N. Huang:
  Simulation of distribution of random walks on a lattice. 177-179
• 
  Nigel Cundy:
  Low-lying Wilson Dirac operator eigenvector mixing in dynamical overlap hybrid Monte Carlo. 180-191
• 
  Guang-hui Cheng, Ting-Zhu Huang, Shu-Qian Shen:
  Block triangular preconditioners for the discretized time-harmonic Maxwell equations in mixed form. 192-196
• 
  Jean-Paul Brichta, Aden N. Seaman, Joseph H. Sanderson:
  Ultrafast imaging of polyatomic molecules with simplex algorithm. 197-200
• 
  Nigel Cundy, Stefan Krieg, Thomas Lippert, Andreas Schäfer:
  Topological tunnelling with dynamical overlap fermions. 201-208
• 
  Yong Duan, P. F. Tang, Ting-Zhu Huang, Sheng-Jian Lai:
  Coupling projection domain decomposition method and Kansa's method in electrostatic problems. 209-214
• 
  Attilio Cucchieri, Axel Maas, Tereza Mendes:
  Linear covariant gauges on the lattice. 215-225
• 
  D. Portes Jr., H. Rodrigues, Basilio Baseia, S. B. Duarte:
  Computational procedure to determine quantum state evolution in Fock space. 226-230
• 
  Byoungseon Jeon, Niels Grønbech-Jensen:
  Efficient parallel algorithm for statistical ion track simulations in crystalline materials. 231-237
• 
  Armen H. Poghosyan, Aram A. Shahinyan:
  A new parameter for validation molecular dynamics simulation (MD) data. 238-240
• 
  Veerle Ledoux, Marnix Van Daele, Guido Vanden Berghe:
  Efficient computation of high index Sturm-Liouville eigenvalues for problems in physics. 241-250
• 
  Panagiotis Vlachos, Ioannis Karafyllidis:
  Simulation of quantum key expansion using quantum cellular automata. 251-255
• 
  Khatuna Kakhiani, Kakha Tsereteli, Paata Tsereteli:
  A program to generate a basis set adaptive radial quadrature grid for density functional theory. 256-268
• 
  A. Nappi:
  A pitfall in the use of extended likelihood for fitting fractions of pure samples in a mixed sample. 269-275

Computer programs in physics

• 
  M. Souaille, H. Loirat, D. Borgis, Marie-Pierre Gaigeot:
  MDVRY: a polarizable classical molecular dynamics package for biomolecules. 276-301
• 
  D. Engel, M. Klews, G. Wunner:
  A fast parallel code for calculating energies and oscillator strengths of many-electron atoms at neutron star magnetic field strengths in adiabatic approximation. 302-311
• 
  J. S. Lee, M. Carena, J. Ellis, A. Pilaftsis, C. E. M. Wagner:
  CPsuperH2.0: An improved computational tool for Higgs phenomenology in the MSSM with explicit CP violation. 312-331
• 
  J. D. Talman:
  NumSBT: A subroutine for calculating spherical Bessel transforms numerically. 332-338

Volume 180, Number 3, March 2009

Computational physics

• 
  V. A. Kudryavtsev:
  Muon simulation codes MUSIC and MUSUN for underground physics. 339-346
• 
  Christoph Friedrich, Arno Schindlmayr, Stefan Blügel:
  Efficient calculation of the Coulomb matrix and its expansion around k=0 within the FLAPW method. 347-359
• 
  Pedro Gonnet, Jens H. Walther, Petros Koumoutsakos:
  theta-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints. 360-364
• 
  Takayuki Umeda, Kentaro Togano, Tatsuki Ogino:
  Two-dimensional full-electromagnetic Vlasov code with conservative scheme and its application to magnetic reconnection. 365-374
• 
  Chia-Chien Huang:
  Semiconductor nanodevice simulation by multidomain spectral method with Chebyshev, prolate spheroidal and Laguerre basis functions. 375-383
• 
  Simone Orlandini, Isabella Baccarelli, Francesco A. Gianturco:
  Variational calculations of structures and energetics in very floppy trimers: A new computational implementation. 384-391
• 
  V. A. Dzuba:
  An universal algorithm of calculating terms of atomic many-body perturbation theory. 392-400

Computer programs in physics

• 
  Alessandro Ballestrero, Aissa Belhouari, Giuseppe Bevilacqua, Vladimir Kashkan, Ezio Maina:
  PHANTOM: A Monte Carlo event generator for six parton final states at high energy colliders. 401-417
• 
  J. Brandon Keith, Jacob R. Fennick, Chad E. Junkermeier, Daniel R. Nelson, James P. Lewis:
  A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in Fireball. 418-426
• 
  Michele Caffo, Henryk Czyz, Michal Gunia, Ettore Remiddi:
  BOKASUN: A fast and precise numerical program to calculate the Master Integrals of the two-loop sunrise diagrams. 427-430
• 
  A. V. Semenov:
  LanHEP - a package for the automatic generation of Feynman rules in field theory. Version 3.0. 431-454
• 
  F. Reinhard, Oliver F. Lange, Jochen S. Hub, Jürgen Haas, Helmut Grubmüller:
  g_permute: Permutation-reduced phase space density compaction. 455-458
• 
  Dimitris Skouteris, Osvaldo Gervasi, Antonio Laganà:
  A program for performing exact quantum dynamics calculations using cylindrical polar coordinates: A nanotube application. 459-465
• 
  Zhe Yuan, Shiwu Gao:
  Linear response approach to collective electronic excitations of solids and surfaces. 466-473

New version announcements

• 
  Bruno Juliá-Díaz, Joseph M. Burdis, Frank Tabakin:
  QDENSITY - A Mathematica quantum computer simulation. 474

Volume 180, Number 4, April 2009

• 
  João Antônio Plascak, A. T. Bernardes:
  CCP2008 - Modeling a better world.
• 
  Thomas Wüst, D. P. Landau, C. Gervais, Y. Xu:
  Monte Carlo simulations of systems with complex energy landscapes. 475-479
• 
  Mário J. de Oliveira:
  Glassy states in the stochastic Potts model. 480-484
• 
  Shan-Ho Tsai, D. P. Landau:
  Phase diagram of a two-dimensional large-Q Potts model in an external field. 485-487
• 
  Ernesto S. Loscar, Ezequiel V. Albano:
  Hysteretic effects in the first-order irreversible phase transition of the ZGB model. 488-492
• 
  Bertrand Berche, P. Butera, Wolfhard Janke, Lev N. Shchur:
  Universal ratios of critical amplitudes in the Potts model universality class. 493-496
• 
  Marco G. Mazza, Kevin Stokely, Elena G. Strekalova, Harry Eugene Stanley, Giancarlo Franzese:
  Cluster Monte Carlo and numerical mean field analysis for the water liquid-liquid phase transition. 497-502
• 
  L. Nduwayo, R. Lindebaum, Nithaya Chetty:
  Suppressed bond-site percolation. 503-508
• 
  Thomas E. Booth, James E. Gubernatis:
  Sewing algorithm. 509-511
• 
  T. Tallinen, Jan A. Åström, J. Timonen:
  Discrete element simulations of crumpling of thin sheets. 512-516
• 
  Janos M. Kumpula, Jukka-Pekka Onnela, Jari Saramäki, János Kertész, Kimmo Kaski:
  Model of community emergence in weighted social networks. 517-522
• 
  Mary Luz Mouronte, Rosa M. Benito, J. P. Cárdenas, Antonio Santiago, Vicente Feliú Batlle, P. van Wijngaarden, Luis Gregorio Moyano:
  Complexity in Spanish optical fiber and SDH transport networks. 523-526
• 
  Gabriel Baglietto, Ezequiel V. Albano:
  Computer simulations of the collective displacement of self-propelled agents. 527-531
• 
  Enrique Burgos, Horacio Ceva, Laura Hernández, R. P. J. Perazzo:
  Understanding and characterizing nestedness in mutualistic bipartite networks. 532-535
• 
  Tânia Tomé, Áttila Leães Rodrigues, Everaldo Arashiro, Mário J. de Oliveira:
  The stochastic nature of predator-prey cycles. 536-539
• 
  Marcos Rigol, Rajiv R. P. Singh:
  Thermodynamic properties of quantum lattice models from numerical linked cluster expansions. 540-544
• 
  Przemyslaw Klosiewicz, Jan Broeckhove, Wim Vanroose:
  Using pseudo-arclength continuation to trace the resonances of the Schrödinger equation. 545-548
• 
  Myoung Won Cho, Sul-Ah Ahn:
  Efficient and exact computation of Hubbard and t-J models using quantum diagonalization method. 549-554
• 
  Norbert Attig:
  Computational physics with PetaFlops computers. 555-558
• 
  Jamie Shiers:
  Grid today, clouds on the horizon. 559-563
• 
  Gastao Krein, J. M. Machado, A. O. Pereira:
  Dynamics of the deconfinement transition of quarks and gluons in a finite volume. 564-573
• 
  R. L. S. Farias, Rudnei O. Ramos, L. A. da Silva:
  Numerical solutions for non-Markovian stochastic equations of motion. 574-579
• 
  Joan Adler, Polina Pine:
  Visualization techniques for modelling carbon allotropes. 580-582
• 
  A. G. Cunha-Netto, Ronald Dickman, A. A. Caparica:
  Two-dimensional lattice polymers: Adaptive windows simulations. 583-586
• 
  D. T. Seaton, Thomas Wüst, D. P. Landau:
  A Wang-Landau study of the phase transitions in a flexible homopolymer. 587-589
• 
  Cláudio José DaSilva, A. G. Cunha-Netto, Ronald Dickman, A. A. Caparica:
  Constructing ground state configurations of lattice polymers. 590-593
• 
  Aimee Gotway Bailey, C. P. Lowe, A. P. Sutton:
  REVLD: A coarse-grained model for polymers. 594-599
• 
  Marcus Müller, C. Pastorino, J. Servantie:
  Hydrodynamic boundary condition of polymer melts at simple and complex surfaces. 600-604
• 
  Burkhard Dünweg, Ulf D. Schiller, Anthony J. C. Ladd:
  Progress in the understanding of the fluctuating lattice Boltzmann equation. 605-608
• 
  Eric J. R. Parteli, Murilo P. Almeida, Orencio Durán, José S. Andrade Jr., Hans J. Herrmann:
  Sand transport on Mars. 609-611
• 
  Allbens Picardi Faria Atman, P. Claudin, Gaël Combe:
  Departure from elasticity in granular layers: Investigation of a crossover overload force. 612-615
• 
  William F. Oquendo, José D. Muñoz, A. Lizcano:
  Oedometric test, Bauer's law and the micro-macro connection for a dry sand. 616-620
• 
  Reinaldo R. Rosa, Fernando M. Ramos, Cesar A. Caretta, Haroldo F. de Campos Velho:
  Extreme event dynamics in the formation of galaxy-sized dark matter structures. 621-624
• 
  Naoki Yoshida:
  Supercomputer simulations of structure formation in the Universe. 625-627
• 
  Sang Ki Nam, John P. Verboncoeur:
  Global model for high power microwave breakdown at high pressure in air. 628-635
• 
  Seung Min Lee, Yong Jun Hong, Young Sik Seo, Felipe Iza, Gyoo Cheon Kim, Jae Koo Lee:
  Simulations of biomedical atmospheric-pressure discharges. 636-641
• 
  Tiago Kroetz, F. A. Marcus, Marisa Roberto, Iberê L. Caldas, Ricardo L. Viana, E. C. da Silva:
  Transport control in fusion plasmas by changing electric and magnetic field spatial profiles. 642-650
• 
  Min Sup Hur, Jonathan S. Wurtele:
  Two-dimensional simulations of the amplification and focusing of intense laser pulses in the kinetic regime of Raman backward amplification in plasmas. 651-655
• 
  Y. C. Chuang, J. Y. Hsu:
  Particle-in-cell study of microwave confined plasma. 656-658
• 
  J.-Y. Lin, Y.-H. Tang, M.-H. Tsai:
  Electronic structures of the Si(001) thin film under (110)- and (010)-direction uniaxial tensile strains. 659-663
• 
  Fortunato Silva de Menezes, Davi Geiger, Ricardo Martins Abreu e Silva, George Distler, Arefin Hu:
  Forward-backward study of the stereo vision problem. 664-668

Volume 180, Number 5, May 2009

Computational physics

• 
  Tao Wei, Shengjing Mu, Aiichiro Nakano, Katherine Shing:
  A hybrid multi-loop genetic-algorithm/simplex/spatial-grid method for locating the optimum orientation of an adsorbed protein on a solid surface. 669-674
• 
  Stanislaw Jadach, Wieslaw Placzek, Maciej Skrzypek, P. Stephens, Zbigniew Was:
  Constrained MC for QCD evolution with rapidity ordering and minimum kT. 675-698
• 
  Shyamal Bhar, Soumen Kumar Roy:
  Computer simulation of two continuous spin models using Wang-Landau-Transition-Matrix Monte Carlo algorithm. 699-707
• 
  A. S. V. Ravi Kanth, K. Aruna:
  Differential transform method for solving the linear and nonlinear Klein-Gordon equation. 708-711
• 
  Jacinto Javier Ibáñez, Vicente Hernández, Enrique Arias, Pedro A. Ruiz:
  Solving Initial Value Problems for Ordinary Differential Equations by two approaches: BDF and piecewise-linearized methods. 712-723

Computer programs in physics

• 
  Sridhar Sahu, Alok Shukla:
  Fortran 90 implementation of the Hartree-Fock approach within the CNDO/2 and INDO models. 724-734
• 
  A. V. Smirnov, M. N. Tentyukov:
  Feynman Integral Evaluation by a Sector decomposiTion Approach (FIESTA). 735-746
• 
  G. Bélanger, F. Boudjema, Alexander Pukhov, A. Semenov:
  Dark matter direct detection rate in a generic model with micrOMEGAs_2.2. 747-767
• 
  Juan-Luis Domenech-Garret, Miguel-Angel Sanchis-Lozano:
  QQ-onia package: a numerical solution to the Schrödinger radial equation for heavy quarkonium. 768-778
• 
  I. P. Lokhtin, L. V. Malinina, S. V. Petrushanko, A. M. Snigirev, I. Arsene, Konrad Tywoniuk:
  Heavy ion event generator HYDJET++ (HYDrodynamics plus JETs). 779-799
• 
  A. Otero-de-la-Roza, Víctor Luaña:
  Runwien: a text-based interface for the WIEN package. 800-812

Volume 180, Number 6, June 2009

Computational physics

• 
  Michele Della Morte, Leonardo Giusti:
  Exploiting symmetries for exponential error reduction in path integral Monte Carlo. 813-818
• 
  Michele Della Morte, Leonardo Giusti:
  Symmetries and exponential error reduction in Yang-Mills theories on the lattice. 819-826
• 
  Sumie Yamamoto, Keisuke Fujii, Akiya Miyamoto:
  A handy tool for history keeping of Geant4 tracks - J4HistoryKeeper. 827-834
• 
  L. Welser-Sherrill, J. H. Cooley, D. C. Wilson:
  Interactive tools designed to study mix in inertial confinement fusion implosions. 835-841
• 
  Zhongcheng Wang, Hezhu Shao:
  A new kind of discretization scheme for solving a two-dimensional time-independent Schrödinger equation. 842-849
• 
  C. Timbó, Luiz Antonio Ribeiro da Rosa, Marcello Gonçalves, S. B. Duarte:
  Computational cancer cells identification by fractal dimension analysis. 850-853
• 
  Rong Zeng, Yanzhi Zhang:
  Efficiently computing vortex lattices in rapid rotating Bose-Einstein condensates. 854-860
• 
  Diego Molteni, Andrea Colagrossi:
  A simple procedure to improve the pressure evaluation in hydrodynamic context using the SPH. 861-872
• 
  Mehdi Dehghan, Narges Rastegar:
  On the global behavior of a high-order rational difference equation. 873-878
• 
  Charlotte Froese Fischer, Oleg Zatsarinny:
  A B-spline Galerkin method for the Dirac equation. 879-886
• 
  M. V. Umansky, X. Q. Xu, Ben Dudson, L. L. LoDestro, J. R. Myra:
  Status and verification of edge plasma turbulence code BOUT. 887-903
• 
  Kui Fu Chen, Jing Tao Jiang, Stephen Crowsen:
  Against the long-range spectral leakage of the cosine window family. 904-911
• 
  Adrian Alexandrescu, Alfonso Bueno-Orovio, José R. Salgueiro, Víctor M. Pérez-García:
  Mapped Chebyshev pseudospectral method for the study of multiple scale phenomena. 912-919
• 
  Janis Timoshenko, Alexei Kuzmin:
  Wavelet data analysis of EXAFS spectra. 920-925
• 
  S.-L. Chang, C.-S. Chien:
  Computing multiple peak solutions for Bose-Einstein condensates in optical lattices. 926-947

Computer programs in physics

• 
  Frank Tabakin, Bruno Juliá-Díaz:
  QCMPI: A parallel environment for quantum computing. 948-964
• 
  R. Alkofer, M. Q. Huber, K. Schwenzer:
  Algorithmic derivation of Dyson-Schwinger equations. 965-976
• 
  Rafael Ramis, Jürgen Meyer-ter-Vehn, Julio Ramírez:
  MULTI2D - a computer code for two-dimensional radiation hydrodynamics. 977-994
• 
  Vladimir Horvat:
  ERCS08: A FORTRAN program equipped with a Windows graphics user interface that calculates ECPSSR cross sections for the removal of atomic electrons. 995-1003
• 
  Ling Ti Kong, Guido Bartels, Carlos Campañá, Colin Denniston, Martin H. Müser:
  Implementation of Green's function molecular dynamics: An extension to LAMMPS. 1004-1010

Errata

• 
  Ochbadrakh Chuluunbaatar, A. A. Gusev, Vladimir P. Gerdt, V. A. Rostovtsev, Sergey I. Vinitsky, A. G. Abrashkevich, Michail S. Kaschiev, Vladislav V. Serov:
  Erratum to: Program AEAA_v1_0, "POTHMF: A program for computing potential curves and matrix elements of the coupled adiabatic radial equations for a hydrogen-like atom in a homogeneous magnetic field" [Computer Physics Communications 178 (2008) 301]. 1011
• 
  Ochbadrakh Chuluunbaatar, A. A. Gusev, Sergey I. Vinitsky, A. G. Abrashkevich:
  Erratum to: Program ADZH_v2_0, "KANTBP 2.0: New version of a program for computing energy levels, reaction matrix and radial wave functions in the coupled-channel hyperspherical adiabatic approach" [Computer Physics Communications 179 (2008) 685]. 1012

Volume 180, Number 7, July 2009

Computational physics

• 
  W. Younes:
  Gaussian matrix elements in a cylindrical harmonic oscillator basis. 1013-1040
• 
  Nicholas D. M. Hine, Peter D. Haynes, Arash A. Mostofi, Chris-Kriton Skylaris, Mike C. Payne:
  Linear-scaling density-functional theory with tens of thousands of atoms: Expanding the scope and scale of calculations with ONETEP. 1041-1053
• 
  Jianying Zhang, Guangwu Yan:
  A lattice Boltzmann model for the Korteweg-de Vries equation with two conservation laws. 1054-1062
• 
  Jian Wang:
  Multisymplectic numerical method for the Zakharov system. 1063-1071
• 
  T. E. Simos:
  P-stability, Trigonometric-fitting and the numerical solution of the radial Schrödinger equation. 1072-1085
• 
  Franck Assous, Felix Tsipis:
  Numerical paraxial approximation for highly relativistic beams. 1086-1097
• 
  G. A. Nemnes, Karl-Heinz Hoffmann:
  Spin-box algorithm for low temperature dynamics of short range disordered Ising spin systems. 1098-1103
• 
  Zhen Wang:
  Discrete tanh method for nonlinear difference-differential equations. 1104-1108
• 
  Elisa Stevanato, Roberto Stroili:
  A case study for the handling of data in a skimming control system. 1109-1115
•