Computer Physics Communications
Published on behalf of Elsevier
ISSN: 00104655
Datasets associated with articles published in Computer Physics Communications

Multiple elastic scattering of electrons in condensed matter
Since the 1940s, much attention has been devoted to the problem of accurate theoretical description of electron transport in condensed matter. The needed information for describing different aspects of the electron transport is the angular distribution of This… 
OpenMP, OpenMP/MPI, and CUDA/MPI C programs for solving the timedependent dipolar GrossPitaevskii equation
We present new versions of the previously published C and CUDA programs for solving the dipolar Gross–Pitaevskii equation in one, two, and three spatial dimensions, which calculate stationary and nonstationary solutions by propagation in imaginary or real are… 
Hybrid OpenMP/MPI programs for solving the timedependent GrossPitaevskii equation in a fully anisotropic trap
We present hybrid OpenMP/MPI (Open MultiProcessing/Message Passing Interface) parallelized versions of earlier published C programs (D. Vudragovi\'{c} et al. (2012) [1]) for calculating both stationary and nonstationary solutions of the timedependent (GP)… 
OpenMP GNU and Intel Fortran programs for solving the timedependent GrossPitaevskii equation
We present Open MultiProcessing (OpenMP) version of Fortran 90 programs for solving the Gross–Pitaevskii (GP) equation for a Bose–Einstein condensate in one, two, and three spatial dimensions, optimized for use with GNU and Intel compilers. We use the for and… 
Geant4DNA simulations using complex DNA geometries generated by the DnaFabric tool
Several DNA representations are used to study radioinduced complex DNA damages depending on the approach and the required level of granularity. Among all approaches, the mechanistic one requires the most resolved DNA models that can go down to atomistic DNA a… 
QDENSITY/QCWAVE: A Mathematica quantum computer simulation update
The Mathematica quantum computer simulation packages QDENSITY and QCWAVE are updated for Mathematica 910.3. An overview is given of the new QDensity, QCWave, BTSystem and Circuits packages, which includes: (1) improved treatment of tensor products of states… 
CUDA programs for solving the timedependent dipolar GrossPitaevskii equation in an anisotropic trap
In this paper we present new versions of previously published numerical programs for solving the dipolar Gross–Pitaevskii (GP) equation including the contact interaction in two and three spatial dimensions in imaginary and in real time, yielding both and New a… 
TIMEDELn: A programme for the detection and parametrization of overlapping resonances using the timedelay method
TIMEDELn implements the timedelay method of determining resonance parameters from the characteristic Lorentzian form displayed by the largest eigenvalues of the timedelay matrix. TIMEDELn constructs the timedelay matrix from input Kmatrices and analyses be… 
TRIQS/DFTTools: A TRIQS application for ab initio calculations of correlated materials
We present the TRIQS/DFTTools package, an application based on the TRIQS library that connects this toolbox to realistic materials calculations based on density functional theory (DFT). In particular, TRIQS/DFTTools together with TRIQS allows an efficient of a… 
MEAMfit: A referencefree modified embedded atom method (RFMEAM) energy and forcefitting code
MEAMfit v1.02. Changes: various bug fixes; speed of singleshot energy and force calculations (not optimization) increased by x10; elements up to Cn (Z=112) now correctly read from vasprun.xml files; EAM fits now produce Camelion output files; changed max of… 
METHES: A Monte Carlo collision code for the simulation of electron transport in low temperature plasmas
We present a freely available MATLAB code for the simulation of electron transport in arbitrary gas mixtures in the presence of uniform electric fields. For steadystate electron transport, the program provides the transport coefficients, reaction rates and is… 
HOSocean: Opensource solver for nonlinear waves in open ocean based on HighOrder Spectral method
HOSocean is an efficient HighOrder Spectral code developed to solve the deterministic propagation of nonlinear wavefields in open ocean. HOSocean is released as opensource, developed and distributed under the terms of GNU General Public License (GPLv3). a… 
LennardJones type pairpotential method for coarsegrained lipid bilayer membrane simulations in LAMMPS
Lipid bilayer membranes have been extensively studied by coarsegrained molecular dynamics simulations. Numerical efficiencies have been reported in the cases of aggressive coarsegraining, where several lipids are coarsegrained into a particle of size 4∼6 nm… 
Amp: A modular approach to machine learning in atomistic simulations
Electronic structure calculations, such as those employing Kohn–Sham density functional theory or ab initio wavefunction theories, have allowed for atomisticlevel understandings of a wide variety of phenomena and properties of matter at small scales. However,… 
RHEED intensities from twodimensional heteroepitaxial nanoscale systems of GaN on an Si surface
This paper presents a computer program, which facilitates the calculation of changes the intensity of RHEED oscillations from the heteroepitaxial structures of (0001)GaN films nucleated on a Si surface. The calculations are based on the use of a dynamical and… 
MAGE (Mfile/Mif Automatic GEnerator): A graphical interface tool for automatic generation of Object Oriented Micromagnetic Framework configuration files and Matlab scripts for results analysis
We present a tool for fullyautomated generation of both simulations configuration files (Mif) and Matlab scripts for automated data analysis, dedicated for Object Oriented Micromagnetic Framework (OOMMF). We introduce extended graphical user interface (GUI)… 
pyIAST: Ideal Adsorbed Solution Theory (IAST) Python Package
Ideal adsorbed solution theory (IAST) is a widelyused thermodynamic framework to readily predict mixedgas adsorption isotherms from a set of purecomponent adsorption isotherms. We present an opensource, userfriendly Python package, pyIAST, to perform IAST… 
Efficient computation of Laguerre polynomials
An efficient algorithm and a Fortran 90 module (LaguerrePol) for computing Laguerre polynomials L_n^(α)(z) are presented. The standard threeterm recurrence relation satisfied by the polynomials and different types of asymptotic expansions valid for n large α… 
BASDet: Bayesian Approach(es) for Structure Determination from Single Molecule Xray Diffraction Images
Xray free electron lasers (XFEL) are expected to enable molecular structure determination in single molecule diffraction experiments. In this paper, we describe an implementation of two orthogonal Bayesian approaches, previously introduced in Walczak and of a… 
SOSpin, a C++ library for Yukawa decomposition in SO(2N) models
We present in this paper the SOSpin library, which calculates an analytic decomposition of the Yukawa interactions invariant under any SO(2N) group in terms of an SU(N) basis. We make use of the oscillator expansion formalism, where the SO(2N) spinor are in of…