CPC Program Library Research Articles

3D simulation of the Cluster–Cluster Aggregation model

We write a program to implement the Cluster–Cluster Aggregation (CCA) model with java programming language. By using the simulation program, the fractal aggregation growth process can be displayed dynamically in the form of a three-dimensional (3D) figure. Meanwhile, the related kinetics data of aggregation simulation can be also recorded dynamically. Compared to the traditional programs, the program has better real-time performance and is more helpful to observe the fractal growth process, which contributes to the scientific study in fractal aggregation. Besides, because of adopting java programming language, the program has very good cross-platform performance. Program summaryProgram title: CCACatalogue identifier: AEUK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUK_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 390649No. of bytes in distributed program, including test data, etc.: 83881850Distribution format: tar.gzProgramming language: Java.Computer: Any computer with Windows, java jdk and java3d jdk installed.Operating system: Windows.RAM: Determined by the number of the initial particles in the simulation testClassification: 14, 16.12.Nature of problem:The programs for the CCA model published are very rare, and are mostly in the form of a 2D figure. So, existing computer simulation programs cannot well simulate the fractal aggregation. Compared to the existing programs, our simulation program for the CCA model in the form of a 3D figure can better simulate the process dynamically.Solution method:A program is provided that well simulates CCA model in the form of a 3D figure. The program implementation is based on the java programming language. Especially, we use the java3d technology to display the simulative graphics in form of 3D.Restrictions:In order to show the process of fractal aggregation growth dynamically, this program needs to refresh the graphics of aggregation of colloidal particle frequently. So this program takes up a lot of computer memory. The storage capacity of the computer memory used to run the program will limit the number of single particles which the program can simulate.Unusual features:The program simulates the CCA model in the form of a 3D figure using the java3d technology.Additional comments:!!!!Due to the large file size, CCA is not delivered directly when download or Email is requested. Instead an html file giving details of how the program can be obtained is sent.!!!!Running time:Determined by the size of the problem.

Feynman graph generation and calculations in the Hopf algebra of Feynman graphs

Two programs for the computation of perturbative expansions of quantum field theory amplitudes are provided. feyngen can be used to generate Feynman graphs for Yang–Mills, QED and φk theories. Using dedicated graph theoretic tools feyngen can generate graphs of comparatively high loop orders. feyncop implements the Hopf algebra of those Feynman graphs which incorporates the renormalization procedure necessary to calculate finite results in perturbation theory of the underlying quantum field theory. feyngen is validated by comparison to explicit calculations of zero dimensional quantum field theories and feyncop is validated using a combinatorial identity on the Hopf algebra of graphs. Program summaryProgram title:feyngen, feyncopCatalogue identifier: AEUB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 2657No. of bytes in distributed program, including test data, etc.: 22606Distribution format: tar.gzProgramming language: Python.Computer: PC.Operating system: Unix, GNU/Linux.RAM: 64 m bytesClassification: 4.4.External routines: nauty [1], geng, multig (part of the nauty package)Nature of problem:Performing explicit calculations in quantum field theory Feynman graphs are indispensable. Infinities arising in the perturbative calculations make renormalization necessary. On a combinatorial level renormalization can be encoded using a Hopf algebra [2] whose coproduct incorporates the BPHZ procedure. Upcoming techniques initiated an interest in relatively large loop order Feynman diagrams which are not accessible by traditional tools.Solution method:Both programs use the established nauty package to ensure high performance graph generation at high loop orders. feyngen is capable of generating φk-theory, QED and Yang–Mills Feynman graphs and of filtering these graphs for the properties of connectedness, one-particle-irreducibleness, 2-vertex-connectivity and tadpole-freeness. It can handle graphs with fixed external legs as well as those without fixed external legs.feyncop uses basic graph theoretical algorithms to compute the coproduct of graphs encoding their Hopf algebra structure.Running time:All 130516 1PI, φ4, 8-loop diagrams with four external legs can be generated, together with their symmetry factor, by feyngen within eight hours and all 342430 1PI, QED, vertex residue type, 6-loop diagrams can be generated in three days both on a standard end-user PC. feyncop can calculate the coproduct of all 2346 1PI, φ4, 8-loop diagrams with four external legs within ten minutes.

EHDECAY: An implementation of the Higgs effective Lagrangian into HDECAY

We present eHDECAY, a modified version of the program HDECAY which includes the full list of leading bosonic operators of the Higgs effective Lagrangian with a linear or non-linear realization of the electroweak symmetry and implements two benchmark composite Higgs models. Program summaryProgram title: eHDECAYCatalogue identifier: AEUJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUJ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 71512No. of bytes in distributed program, including test data, etc.: 666827Distribution format: tar.gzProgramming language: Fortran77.Computer: Any with a Fortran77 system.Operating system: Linux, Unix.RAM: 0.5 MBClassification: 11.1.Nature of problem: Numerical calculation of the decay widths and branching ratios of a Higgs-like boson within four different parametrizations: the non-linear Lagrangian, the Strongly-Interacting Light Higgs (SILH) Lagrangian and the MCHM4 and MCHM5 Lagrangians. The Fortran program eHDECAY includes the most important higher-order QCD effects and in case of the SILH and composite Higgs parametrization also the electroweak (EW) higher order corrections. The user furthermore has the possibility to turn off these EW corrections.Solution method: The necessary input values, the choice of the parametrization and the values of the various couplings are set in the input file ehdecay.in. These are read in by the main routine ehdecay.f. The main routine calculates the decay widths and branching ratios through analytical formulae, by using several help routines (dmb.f, elw.f, feynhiggs.f, haber.f, hgaga.f, hgg.f, hsqsq.f, susylha.f). The calculated branching ratios and total width are given out in the files br.eff1 and br.eff2.Restrictions: The EW corrections are included only in the SILH and the composite Higgs parametrization in an approximate way. They are consistently not included in the non-linear case. This would require the explicit calculation of the EW higher order corrections in this framework. The program does not provide any distributions.Running time: Less than one second per point

Combinatorial level densities by the real-time method

Levels densities of independent-particle fermionic systems can be calculated easily by using the real-time representation of the evolution operator together with the fast Fourier transform. We describe the method and implement it with a set of Python programs. Examples are provided for the total and partial levels densities of a heavy deformed nucleus (164Dy). The partial level densities that may be calculated are the projected ones on neutron number, proton number, azimuthal angular momentum, and parity. Program summaryProgram title: rt_levels.pyCatalog identifier: AEUI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 6515No. of bytes in distributed program, including test data, etc.: 263821Distribution format: tar.gzProgramming language: Python.Computer: PCs.Operating system: Unix, Apple OSX.RAM: 1 MBClassification: 17.16.External routines: NumpyNature of problem: Compute many-body level densities of finite systems of fermions described by their single-particle spectraSolution method: Fast Fourier transform of the real-time Green’s functionRunning time: A few minutes to one hour

An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale

In this paper we present a massively parallel open source solver for Richards equation, named the RichardsFOAM solver. This solver has been developed in the framework of the open source generalist computational fluid dynamics tool box OpenFOAM® and is capable to deal with large scale problems in both space and time. The source code for RichardsFOAM may be downloaded from the CPC program library website.It exhibits good parallel performances (up to ∼90% parallel efficiency with 1024 processors both in strong and weak scaling), and the conditions required for obtaining such performances are analysed and discussed. These performances enable the mechanistic modelling of water fluxes at the scale of experimental watersheds (up to few square kilometres of surface area), and on time scales of decades to a century. Such a solver can be useful in various applications, such as environmental engineering for long term transport of pollutants in soils, water engineering for assessing the impact of land settlement on water resources, or in the study of weathering processes on the watersheds. Program summaryProgram title: RichardsFOAMCatalogue identifier: AEUF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUF_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 1287No. of bytes in distributed program, including test data, etc.: 9521Distribution format: tar.gzProgramming language: C++.Computer: any x86, tested only on 64-bit machines.Operating system: Generic Linux.Classification: 13.External routines: OpenFOAM® (version 2.0.1 or later)Nature of problem:This software solves the non-linear three-dimensional transient Richards equation, which is a very popular model for water transfer in variably saturated porous media (e.g.: soils). It is designed to take advantage of the massively parallel computing performance of OpenFOAM®. The goal is to be able to model natural hydrosystems on large temporal and spatial scales.Solution method:A mixed implicit (FVM in the object oriented OpenFOAM® framework) and explicit (FVC in the object oriented OpenFOAM® framework) discretization of the equation with a backward time scheme is coupled with a linearization method (Picard algorithm). Due to the linearization loop the final solution of each time step tends towards a fully implicit solution. The implementation has been carried out with a concern for robustness and parallel efficiency.Restrictions:The choice of the maximum and initial time steps must be made carefully in order to avoid stability problems. A careful convergence study of mesh cell size, linear solver precision and linearization method precision must be undertaken for each considered problem, depending on the precision required for the expected results, the spatial and temporal scales at stake, and so on. Finally, the solver in its current version only handles meshes with a constant cell volume (a crash will not necessarily occur with an irregular mesh but some problems may arise with the convergence criterion of the linearization method).Running time:Highly variable, depending on the mesh size and the number and nature of cores involved. The test run provided requires less than 2 s on a 64 bit machine with Intel® CoreTMi7-2760QM CPU @ 2.40 GHz × 8 and 3.8 Gigabytes of RAM.

An accelerated algorithm for full band electron–phonon scattering rate computation

Computing scattering rates of electrons and phonons stands at the core of studies of electron transport properties. In the high field regime, the interactions between all electron bands with all phonon bands need to be considered. This full band interaction implies a huge computational burden in calculating scattering rates. In this study, a new accelerated algorithm is presented for this task, which speeds up the computation by two orders of magnitude (100 times) and dramatically simplifies the coding. At the same time, it visually demonstrates the physical process of scattering more clearly. Program summaryProgram title: Scattering_band_by_bandCatalogue identifier: AEUH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 22914No. of bytes in distributed program, including test data, etc.: 5785964Distribution format: tar.gzProgramming language: Matlab.Computer: All.Operating system: All.RAM: Depends on problem, ∼kB to MBClassification: 16.5.Nature of problem:Electron–phonon scattering is a fundamental problem in studying electron transport in condensed matters. There are situations where the scattering rates need to be updated frequently during a simulation, e.g. when hot phonon effects are considered. The speed of scattering calculation is very important in such cases.Solution method:In searching for possible scattering events, we propose here a band-by-band method, instead of the traditional point by point method. The whole calculation is parallelized in this sense and dramatically accelerated. Moreover, we proposed a representation method for all scattering mechanisms, which greatly simplified the coding task. Also, the additional animation part of this program demonstrates many insights into the scattering process.Restrictions:To use the code directly, electron band and phonon band should have the same mesh size. In other words, for each phonon band and electron band, they should have the same number of data points.Additional comments:If high speed is desired, it is best to turn off the animation function.Running time:Running time depends on the problem size. For the example used in this paper, it takes about 144 seconds by 1 CPU on Dell PowerEdge 610 (A dual quad core server with CPU frequency of 3.0 GHz).

An Interactive Data Language software package to calculate ionospheric conductivity by using numerical models

The Inter-university Upper atmosphere Global Observation NETwork (IUGONET) project focuses on handling ground-based observational data of the upper atmosphere. To this end, the project members have been developing a data analysis software package which is based on Interactive Data Language (IDL). Filling the spatial gaps in observational data requires the use of numerical models. In this paper, we discuss an IDL software package for global ionospheric conductivity by integration of 3rd party numerical models. The model can be used to create further derived models. Program summaryProgram title: iug_ionospheric_condCatalogue identifier: AEUG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUG_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 186506No. of bytes in distributed program, including test data, etc.: 16202009Distribution format: tar.gzProgramming language: IDL-7.1.Computer: All Ubuntu based computers. Tested on Virtual Box.Operating system: Ubuntu 12.04 LTS.Classification: 13.External routines: TDAS, UDASNature of problem:To calculate ionospheric conductivity.Solution method:The ionospheric conductivity model was implemented by a mash-up of the three models, a magnetic model, an atmospheric model and an ionospheric model in order to calculate ionospheric conductivity.Running time:The tests provided take only a few seconds to run.

NMSSMCALC: A program package for the calculation of loop-corrected Higgs boson masses and decay widths in the (complex) NMSSM

We present the program package NMSSMCALC for the calculation of the loop-corrected NMSSM Higgs boson masses and decay widths in the CP-conserving and CP-violating NMSSM. The full one-loop corrections to the Higgs boson masses are evaluated in a mixed renormalisation scheme of on-shell and DR¯ conditions. The Higgs decay widths include the dominant higher order QCD corrections, and the decays into bottom quarks, strange quarks and τ leptons are supplemented by higher order SUSY corrections through effective couplings. All relevant off-shell decays into two massive gauge bosons, gauge and Higgs boson and Higgs pair final states as well as into heavy quark pairs are computed. The input and output files feature the SUSY Les Houches Accord so that the program can easily be linked with existing computer tools. Program summaryProgram title: NMSSMCALCCatalogue identifier: AEUE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 53070No. of bytes in distributed program, including test data, etc.: 329132Distribution format: tar.gzProgramming language: Fortran77.Computer: Any with a Fortran77 system.Operating system: Linux, Unix.RAM: 0.5MBClassification: 11.1.Nature of problem:Computation of the NMSSM Higgs mass spectrum including higher order corrections in a mixed renormalisation scheme of on-shell and DRbar conditions, and numerical calculation of the decay widths and branching ratios, both in the CP-conserving and in the CP-violating NMSSM. The decay widths include the dominant higher order QCD corrections and, for the neutral Higgs boson decays into a bottom quark pair, the higher order SUSY–QCD and the approximate SUSY–electroweak (elw) corrections up to one-loop accuracy. The decays into a strange quark pair include the dominant resummed SUSY–QCD corrections and the one into a τ pair the dominant resummed SUSY–elw corrections. Analogously for the charged Higgs boson the higher order SUSY corrections have been implemented for the decays into fermion pairs. In the real NMSSM, the decays into stop and sbottom pairs, respectively, contain the SUSY–QCD corrections. All relevant off-shell decays into massive gauge bosons, into gauge and Higgs bosons, into Higgs pairs and into heavy quark pairs have been taken into account. The input and output files feature the SUSY Les Houches Accord (SLHA).Solution method:The necessary input values are set in the two input files inp.dat (in the SLHA format) and bhdecay.in. The file inp.dat, where the choice between the real and the complex NMSSM can be made, is read in by CalcMasses.F, which calculates the one-loop corrected NMSSM Higgs mass spectrum. CalcMasses.F writes out all necessary parameters, masses and mixing angles in an SLHA format file slha.in, which is read in by bhdecay.f (by bhdecay c.f in the complex case). This Fortran routine then computes the decay widths and branching ratios and writes them out in an SLHA format file slha decay.out. Furthermore it writes out all parameters and mixing angles.Restrictions:At present the NMSSM Higgs spectrum is calculated at one-loop accuracy, the Higgs self-couplings at leading order, and no renormalisation group running of the input parameters is included. However, we are about to implement the two-loop corrections to the NMSSM Higgs boson masses and the Higgs self-couplings. Furthermore, the renormalisation group equations for the input parameters shall be provided in the near future. The program does not provide any distributions.Running time:Less than one second per point

CPMC-Lab: A Matlab package for Constrained Path Monte Carlo calculations

We describe CPMC-Lab, a Matlab program for the constrained-path and phaseless auxiliary-field Monte Carlo methods. These methods have allowed applications ranging from the study of strongly correlated models, such as the Hubbard model, to ab initio calculations in molecules and solids. The present package implements the full ground-state constrained-path Monte Carlo (CPMC) method in Matlab with a graphical interface, using the Hubbard model as an example. The package can perform calculations in finite supercells in any dimensions, under periodic or twist boundary conditions. Importance sampling and all other algorithmic details of a total energy calculation are included and illustrated. This open-source tool allows users to experiment with various model and run parameters and visualize the results. It provides a direct and interactive environment to learn the method and study the code with minimal overhead for setup. Furthermore, the package can be easily generalized for auxiliary-field quantum Monte Carlo (AFQMC) calculations in many other models for correlated electron systems, and can serve as a template for developing a production code for AFQMC total energy calculations in real materials. Several illustrative studies are carried out in one- and two-dimensional lattices on total energy, kinetic energy, potential energy, and charge- and spin-gaps. Program summaryProgram title: CPMC-LabCatalogue identifier: AEUD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUD_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 2850No. of bytes in distributed program, including test data, etc.: 24838Distribution format: tar.gzProgramming language:Matlab.Computer: The non-interactive scripts can be executed on any computer capable of running Matlab with all Matlab versions. The GUI requires Matlab R2010b (version 7.11) and above. Operating system: Windows, Mac OS X, Linux.RAM: Variable.Classification: 7.3.External routines:MatlabNature of problem:Obtaining ground state energy of a repulsive Hubbard model in a supercell in any number of dimensions.Solution method:In the Constrained Path Monte Carlo (CPMC) method, the ground state of a many-fermion system is projected from an initial trial wave function by a branching random walk in an overcomplete basis of Slater determinants. Constraining the determinants according to a trial wave function |ΨT〉 removes the exponential decay of the signal-to-noise ratio characteristic of the sign problem. The method is exact if |ΨT〉 is exact.Unusual features:Direct and interactive environment with a Graphical User Interface for beginners to learn and study the Constrained Path Monte Carlo method with minimal overhead for setup.Running time:The sample provided takes a few seconds to run, the batch sample a few minutes.

EERAD3: Event shapes and jet rates in electron–positron annihilation at order [formula omitted

The program EERAD3 computes the parton-level QCD contributions to event shapes and jet rates in electron–positron annihilation to order αs3. For three-jet production and related observables, this corresponds to next-to-next-to-leading order corrections, and allows for precision QCD studies. We describe the program and its usage in detail. Program summaryProgram title: EERAD3Catalogue identifier: AEUC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 119253No. of bytes in distributed program, including test data, etc.: 1368922Distribution format: tar.gzProgramming language: FORTRAN77 (with some FORTRAN90 features).Computer: All.Operating system: All.Has the code been vectorised or parallelised?: Program code allows the storage and adaptation of Monte Carlo information for producing statistically independent results on many cores. A tool for the combination of these is provided with the code.RAM: 6 MBytesClassification: 11.2, 11.5.Nature of problem:Computation of second-order QCD corrections to event shapes and jet cross sections in electron–positron annihilation.Solution method:Generation of events at parton-level, supplemented by a subtraction method to combine infrared singular contributions among different partonic channels.Running time:The high-precision/high-resolution distributions in [1] required about 700 CPU-days on an Intel Q6800 2.9 GHz. Reasonable precision can be obtained with run times of about 100 hours per coefficient for distributions, or within 5 hours if only single moments are computed.

KANTBP 3.0: New version of a program for computing energy levels, reflection and transmission matrices, and corresponding wave functions in the coupled-channel adiabatic approach

A FORTRAN program for calculating energy values, reflection and transmission matrices, and corresponding wave functions in a coupled-channel approximation of the adiabatic approach is presented. In this approach, a multidimensional Schrodinger equation is reduced to a system of the coupled second-order ordinary differential equations on a finite interval with the homogeneous boundary conditions of the third type at the left- and right-boundary points for continuous spectrum problem. The resulting system of these equations containing the potential matrix elements and first-derivative coupling terms is solved using high-order accuracy approximations of the finite element method. As a test desk, the program is applied to the calculation of the reflection and transmission matrices and corresponding wave functions for the two-dimensional problem with different barrier potentials.

OptQC: An optimized parallel quantum compiler

The software package Qcompiler (Chen and Wang 2013) provides a general quantum compilation framework, which maps any given unitary operation into a quantum circuit consisting of a sequential set of elementary quantum gates. In this paper, we present an extended software OptQC, which finds permutation matrices P and Q for a given unitary matrix U such that the number of gates in the quantum circuit of U=QTPTU′PQ is significantly reduced, where U′ is equivalent to U up to a permutation and the quantum circuit implementation of each matrix component is considered separately. We extend further this software package to make use of high-performance computers with a multiprocessor architecture using MPI. We demonstrate its effectiveness in reducing the total number of quantum gates required for various unitary operators. Program summaryProgram title: OptQCCatalogue identifier: AEUA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEUA_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 178435No. of bytes in distributed program, including test data, etc.: 491574Distribution format: tar.gzProgramming language: Fortran, MPI.Computer: Any computer with Fortran compiler and MPI library.Operating system: Linux.Classification: 4.15.Nature of problem: It aims to minimize the number of quantum gates required to implement a given unitary operation.Solution method: It utilizes a threshold-based acceptance strategy for simulated annealing to select permutation matrices P and Q for a given unitary matrix U such that the number of gates in the quantum circuit of U=QTPTU′PQ is minimized, where U′ is equivalent to U up to a permutation. The decomposition of a unitary operator is performed by recursively applying the cosine–sine decomposition.Running time: Running time increases with the size of the unitary matrix, as well as the prescribed maximum number of iterations for qubit permutation selection and the subsequent simulated annealing algorithm. Running time estimates are provided for each example in Section 4. All simulation results presented in this paper are obtained from running the program on the Fornax supercomputer managed by iVEC@UWA with Intel Xeon X5650 CPUs.

Single particle calculations for a Woods–Saxon potential with triaxial deformations, and large Cartesian oscillator basis (TRIAXIAL 2014, Third version of the code Triaxial)

Theory and FORTRAN program of the first version of this code (TRIAXIAL) have already been described in detail in Computer Physics Comm. 156 (2004) 241–282. A second version of this code (TRIAXIAL 2007) has been given in CPC 176 (2007) 634–635. The present FORTRAN program is the third version (TRIAXIAL 2014) of the same code. Now, It is written in free format. As the former versions, this FORTRAN program solves the same Schrodinger equation of the independent particle model of the atomic nucleus with the same method. However, the present version is much more convenient. In effect, it is characterized by the fact that the eigenvalues and the eigenfunctions can be given by specific subroutines. The latters did not exist in the old versions (2004 and 2007). In addition, it is to be noted that in the previous versions, the eigenfunctions were only given by their coefficients of their expansion onto the harmonic oscillator basis. This method is needed in some cases. But in other cases, it is preferable to treat the eigenfunctions directly in configuration space. For this reason, we have implemented an additional subroutine for this task. Some other practical subroutines have also been implemented. Moreover, eigenvalues and eigenfunctions are recorded onto several files. All these new features of the code and some important aspects of its structure are explained in the document ‘Triaxial2014 use.pdf’. New version program summaryProgram title: Triaxial2014Catalogue identifier: ADSK_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK_v3_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 13672No. of bytes in distributed program, including test data, etc.: 217598Distribution format: tar.gzProgramming language: FORTRAN 77/90 (double precision).Computer: PC. Pentium 4, 2600MHz and beyond.Operating system: WINDOWS XP, WINDOWS 7, LINUX.RAM: 256 Mb (depending on nmax). Swap file: 4Gb (depending on nmax)Classification: 17.7.Does the new version supersede the previous version?: YesCatalogue identifier of previous version: ADSK_v2_0Journal reference of previous version: Comput. Phys. Comm. 176 (2007) 634Nature of problem: The Single particle energies and the single particle wave functions are calculated from one-body Hamiltonian including a central field of Woods–Saxon type, a spin–orbit interaction, and the Coulomb potential for the protons. We consider only ellipsoidal (triaxial) shapes. The deformation of the nuclear shape is fixed by the usual Bohr parameters (β,γ).Solution method: The representative matrix of the Hamiltonian is built by means of the Cartesian basis of the anisotropic harmonic oscillator, and then diagonalized by a set of subroutines of the EISPACK library. Two quadrature methods of Gauss are employed to calculate respectively the integrals of the matrix elements of the Hamiltonian, and the integral defining the Coulomb potential. Two quantum numbers are conserved: the parity and the signature. Due to the Kramers degeneracy, only positive signature is considered. Therefore, calculations are made for positive and negative parity separately (with positive signature only).Reasons for new version: Now, there are several ways to obtain the eigenvalues and the eigenfunctions. The eigenvalues can be obtained from the subroutine ‘eigvals’ or from the array ‘energies’ or also from the formatted files ‘valuu.dat’, ‘eigenvalo.dat’, ‘eigenva.dat’ or better from the unformatted file ‘eigenvaunf.dat’. The eigenfunctions can be obtained straightforwardly in configuration space from the subroutine ‘eigfunc’ or by their components on the oscillator basis from the subroutine ‘compnts’. The latter are also recorded on a formatted file ‘componento.dat’ or on an unformatted file ‘componentounf.dat’.Summary of revisions: This version is characterized by the fact that the eigenvalues and the eigenfunctions can be given by specific subroutines which did not exist in the old versions (2004 and 2007) of the program. Moreover, the eigenvalues and the eigenfunctions can also be deduced directly from files. It is to be noted that this version is now written in free format. All these reasons contribute to make the use of this code easier.Restrictions: There are two restrictions for the code: The number of the major shells of the basis should not exceed Nmax=26 (which is very sufficient in usual cases). For the largest values of Nmax (∼23–26), the diagonalization takes the major part of the running time, but the global run-time remains reasonable.Additional comments: Software used: (1) COMPAC VISUAL FORTRAN (with full optimizations in the settings project options on WINDOWS XP); (2) SILVERFROST PLATO VERSION 4.63 (with debug.net option on WINDOWS 7); (3) APPROXIMATRIX SIMPLY FORTRAN VERSION 2.13 BUILD (on WINDOWS XP and WINDOWS 7).Running time: (With full optimization in the project settings of the Compaq Visual Fortran on Windows XP) With NMAX=23, for the neutrons case, the running time is about 50 s on the intel core i5 processor.

A C++11 implementation of arbitrary-rank tensors for high-performance computing

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU. New version program summaryProgram title: cpp-arrayCatalogue identifier: AESA_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESA_v1_1.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU Lesser General Public License, version 3No. of lines in distributed program, including test data, etc.: 12376No. of bytes in distributed program, including test data, etc.: 81669Distribution format: tar.gzProgramming language: C++.Computer: All modern architectures.Operating system: Linux/Unix/Mac OS.RAM: Problem dependentClassification: 5.External routines: GNU CMake build system and BLAS implementation. NVIDIA CUBLAS for GPU computing.Does the new version supersede the previous version?: YesCatalogue identifier of previous version: AESA_v1_0Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 1681Nature of problem:Tensors are a basic building block for any program in scientific computing. Yet, tensors are not a built-in component of the C++ programming language.Solution method:An arbitrary-rank tensor class template is crafted by using the new features introduced by the C++11 set of requirements. In addition, an entire expression template facility is built on top, to provide mathematical straightforward notation without damaging performance.Reasons for new version:The reason for this version is to make the library more portable.Summary of revisions:The first version of the library relied on the presence of a C interface to the BLAS library (CBLAS). This new version gives priority to a Fortran BLAS implementation when a Fortran compiler is provided during the configuration process. Some minor changes have also been made, including an improved Doxygen documentation, fixed installation when using CUDA, and fixed other minor bugs.Running time:Problem dependent. The tests provided take only seconds. The examples take approximately 15 min.

Formula omitted]: A molecular simulation tool for thermodynamic properties, new version release

A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green–Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added. Program summaryProgram title:ms2Catalogue identifier: AEJF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 50375No. of bytes in distributed program, including test data, etc.: 345786Distribution format: tar.gzProgramming language: Fortran90.Computer: The simulation program ms2 is usable on a wide variety of platforms, from single processor machines to modern supercomputers.Operating system: Unix/Linux.Has the code been vectorized or parallelized?: Yes: Message Passing Interface (MPI) protocol and OpenMP Scalability is up to 2000 cores.RAM:ms2 runs on single cores with 512 MB RAM. The memory demand rises with increasing number of cores used per node and increasing number of molecules.Classification: 7.7, 7.9, 12.External routines: Message Passing Interface (MPI)Catalogue identifier of previous version: AEJF_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 2350Does the new version supersede the previous version?: Yes.Nature of problem: Calculation of application oriented thermodynamic properties for fluids consisting of rigid molecules: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal and caloric data as well as transport properties.Solution method: Molecular dynamics, Monte Carlo, various classical ensembles, grand equilibrium method, Green–Kubo formalism, Lustig formalismReasons for new version: The source code was extended to introduce new features.Summary of revisions: The new features of Version 2.0 include: Hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation; Ewald summation for long range interactions; sampling of Massieu potential derivatives; extended Green–Kubo formalism for the sampling of the electric conductivity and the residence time; radial distribution function.Restrictions: None. The system size is user-defined. Typical problems addressed by ms2 can be solved by simulating systems containing typically 1000–4000 molecules.Unusual features: Auxiliary feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories.Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de.Running time: The running time of ms2 depends on the specified problem, the system size and the number of processes used in the simulation. E.g. running four processes on a “Nehalem” processor, simulations calculating vapor–liquid equilibrium data take between two and 12 hours, calculating transport properties between six and 24 hours. Note that the examples given above stand for the total running time as there is no post-processing of any kind involved in property calculations.

HYPERgeometric functions DIfferential REduction (HYPERDIRE): MATHEMATICA based packages for differential reduction of generalized hypergeometric functions: [formula omitted] and [formula omitted] Horn-type hypergeometric functions of three variables

HYPERDIRE is a project devoted to the creation of a set of Mathematica based programs for the differential reduction of hypergeometric functions. The current version includes two parts: the first one, FdFunction, for manipulations with Appell hypergeometric functions FD of r variables; and the second one, FsFunction, for manipulations with Lauricella–Saran hypergeometric functions FS of three variables. Both functions are related with one-loop Feynman diagrams. Program summaryProgram title: HYPERDIRECatalogue identifier: AEPP_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPP_v3_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public LicenseNo. of lines in distributed program, including test data, etc.: 310No. of bytes in distributed program, including test data, etc.: 7666Distribution format: tar.gzProgramming language: MathematicaComputer: All computers running MathematicaOperating system: All operating systems running MathematicaClassification: 4.4.Catalogue identifier of previous version: AEPP_v1_0Journal reference of previous version: Comput. Phys. Comm. 184 (2013) 2332Does the new version supersede the previous version?: No. It is an extension to the previous program, which performs reductions of hypergeometric functions pFp, F1, F2, F3 and F4Nature of problem: Reduction of hypergeometric functions FD and FS to the set of basis functionsSolution method: Differential reductionReasons for new version: New algorithms for the reduction of multivariable Lauricella functions, Horn functions, (hypergeometric functions FD and FS)Summary of revisions: HYPERDIRE is a project devoted to the creation of a set of Mathematica based programs for the differential reduction of hypergeometric functions. The current version includes two parts: the first one, FdFunction, for manipulations with Appell hypergeometric functions FD of r variables; and the second one, FsFunction, for manipulations with Lauricella–Saran hypergeometric functions FS of three variables. Both functions are related with one-loop Feynman diagrams.Running time: Depends on the complexity of problem

A [formula omitted] dimensional viscous hydrodynamic code for relativistic heavy ion collisions

We describe the details of 3+1 dimensional relativistic hydrodynamic code for the simulations of quark–gluon/hadron matter expansion in ultra-relativistic heavy ion collisions. The code solves the equations of relativistic viscous hydrodynamics in the Israel–Stewart framework. With the help of ideal–viscous splitting, we keep the ability to solve the equations of ideal hydrodynamics in the limit of zero viscosities using a Godunov-type algorithm. Milne coordinates are used to treat the predominant expansion in longitudinal (beam) direction effectively. The results are successfully tested against known analytical relativistic inviscid and viscous solutions, as well as against existing 2+1D relativistic viscous code. Program summaryProgram title: vHLLECatalogue identifier: AETZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETZ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 13825No. of bytes in distributed program, including test data, etc.: 92750Distribution format: tar.gzProgramming language: C++.Computer: any with a C++ compiler and the CERN ROOT libraries.Operating system: tested on GNU/Linux Ubuntu 12.04 x64 (gcc 4.6.3), GNU/Linux Ubuntu 13.10 (gcc 4.8.2), Red Hat Linux 6 (gcc 4.4.7).RAM: scales with the number of cells in hydrodynamic grid; 1900 Mbytes for 3D 160×160×100 grid.Classification: 1.5, 4.3, 12.External routines: CERN ROOT (http://root.cern.ch), Gnuplot (http://www.gnuplot.info/) for plotting the results.Nature of problem:relativistic hydrodynamical description of the 3-dimensional quark–gluon/hadron matter expansion in ultra-relativistic heavy ion collisions.Solution method:finite volume Godunov-type method.Running time:scales with the number of hydrodynamic cells; typical running times on Intel(R) Core(TM) i7-3770 CPU @ 3.40 GHz, single thread mode, 160×160×100 grid and p=ε/3 EoS (setup discussed in Sec. 4.4):7.6 sec/timestep for ideal hydro evolution;15.7 sec/timestep for viscous hydro evolution;37 sec/timestep for tabulated EoS and ideal hydro evolution.

PyFR: An open source framework for solving advection–diffusion type problems on streaming architectures using the flux reconstruction approach

High-order numerical methods for unstructured grids combine the superior accuracy of high-order spectral or finite difference methods with the geometric flexibility of low-order finite volume or finite element schemes. The Flux Reconstruction (FR) approach unifies various high-order schemes for unstructured grids within a single framework. Additionally, the FR approach exhibits a significant degree of element locality, and is thus able to run efficiently on modern streaming architectures, such as Graphical Processing Units (GPUs). The aforementioned properties of FR mean it offers a promising route to performing affordable, and hence industrially relevant, scale-resolving simulations of hitherto intractable unsteady flows within the vicinity of real-world engineering geometries. In this paper we present PyFR, an open-source Python based framework for solving advection–diffusion type problems on streaming architectures using the FR approach. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language based on the Mako templating engine. The current release of PyFR is able to solve the compressible Euler and Navier–Stokes equations on grids of quadrilateral and triangular elements in two dimensions, and hexahedral elements in three dimensions, targeting clusters of CPUs, and NVIDIA GPUs. Results are presented for various benchmark flow problems, single-node performance is discussed, and scalability of the code is demonstrated on up to 104 NVIDIA M2090 GPUs. The software is freely available under a 3-Clause New Style BSD license (see www.pyfr.org). Program summaryProgram title: PyFR v0.1.0Catalogue identifier: AETY_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETY_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: New style BSD licenseNo. of lines in distributed program, including test data, etc.: 12733No. of bytes in distributed program, including test data, etc.: 214183Distribution format: tar.gzProgramming language: Python, CUDA and C.Computer: Variable, up to and including GPU clusters.Operating system: Recent version of Linux/UNIX.RAM: Variable, from hundreds of megabytes to gigabytes.Classification: 6.5, 12.External routines: Python 2.7, numpy, PyCUDA, mpi4py, SymPy, MakoNature of problem:Compressible Euler and Navier–Stokes equations of fluid dynamics; potential for any advection–diffusion type problem.Solution method:High-order flux reconstruction approach suitable for curved, mixed, unstructured grids.Unusual features:Code makes extensive use of symbolic manipulation and runtime code generation through a domain specific language.Running time:Many small problems can be solved on a recent workstation in minutes to hours.

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins

SLDMOL is a program for modeling the 1-D scattering length density (SLD) profile of proteins at the lipid membrane–solution interface or adsorbed to other surfaces. The program reads experimental SLD data from neutron or X-ray reflectivity measurements and compares the results to a trajectory of protein structures, finding the conformation and orientation that best fits the experimental data. SLDMOL is a freely distributed open source program written in python that can be run independently using command lines or a GUI. SLDMOL has also been integrated into the larger SASSIE package extending molecular modeling capabilities. Sample environment conditions can be replicated including H2O/D2O solvent contrasts, specific amino acid deuteration and complex molecular assemblies. Ensembles of protein conformations can be generated independently (e.g. molecular dynamics simulations) or with SASSIE. For each individual structure a best-fit SLD profile is outputted along with a goodness of fit parameter, protein depth penetration and surface coverage. In addition to individual comparisons SLD profiles can be calculated over ensemble averages of protein structures. As a result, SLDMOL provides a detailed molecular interpretation of reflectivity data or conversely can be used to predict experimental outcomes for different protein conformation and specific deuteration schemes prior to measurements. Program summaryProgram title: SLDMOLCatalogue identifier: AETX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License, version 3No. of lines in distributed program, including test data, etc.: 3302107No. of bytes in distributed program, including test data, etc.: 125715760Distribution format: tar.gzProgramming language: Python.Computer: PC/Mac.Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.7–10.9).RAM: 1 GBClassification: 3.External routines: Python 2.6.5, numpy 1.4.0, scipy 0.8.0, Tcl 8.5, Tk 8.5, Mac installation requires Xcode 3 development tools.Subprograms used:CatIdTitleReferenceAEKL_v1_0SASSIECPC 183(2012)382Nature of problem:Reflectivity is a powerful technique to study the conformation of biological molecules at surface and interfaces. Open source software that facilitates computational modeling and interpretation of experimental results in terms of detailed molecular structure is currently lacking.Solution method:SLDMOL takes one or an ensemble of atomistic configurations of proteins and compares them to 1-D scattering length density (SLD) profiles determined from reflectivity experiments. Protein structures can be generated independently (e.g. molecular dynamics simulations) or through the SASSIE software package. SLDMOL performs an optimization to determine which structure best fits the SLD profile. Structures can also be averaged either directly or through a Monte-Carlo weighting algorithm. Finally SLDMOL allows the modeling of reflectivity experiments through the in silico selective deuteration of amino acids and the calculation of SLD profiles in a number of different aqueous solvent contrasts.Additional comments:!!!!Due to the large file size, SLDMOL is not delivered directly when download or Email is requested. Instead an html file giving details of how the program can be obtained is sent.!!!!Running time:Varies depending on application. Typically 10 min to 24 h depending on the number of structures to be evaluated.

RHEED intensities from two-dimensional heteroepitaxial nanoscale systems

A practical computing algorithm has been developed for calculating the reflection high-energy electron diffraction (RHEED) from the molecular beam epitaxy growing surface. The calculations are based on the use of the dynamical diffraction theory in which the electrons are taken to be diffracted by a potential, which is periodic in the dimension perpendicular to the surface. The computer program presented in this paper enables calculations for three basic types of diffuse potential for crystalline heteroepitaxial structures, including the possible existence of various diffuse scattering models through the layer parallel to the surface. Program SummaryProgram title: RHEED_DIFFCatalogue identifier: AETW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETW_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 68483No. of bytes in distributed program, including test data, etc.: 480831Distribution format: tar.gzProgramming language: C++.Computer: Intel i7-based PC.Operating system: Windows, Linux.RAM: The presented algorithm belongs to the linear memory class of the computational complexity O(n).Word size: 64 bitsClassification: 4.6, 6.2, 7.2.Nature of problem:RHEED rocking curves (the specular beam intensities versus the glancing angle) recorded from heteroepitaxial layers are used for the non-destructive evaluation of epilayer thickness and composition with a high degree of accuracy. Rocking curves from such heterostructures are often very complex because the thickness fringes from every layer beat together. Simulations based on the dynamical diffraction theory are generally used to interpret the rocking curves of such structures from which very small changes in thickness and composition can be obtained. Rocking curves are also used to determine the level of strain and its relaxation mechanism in a lattice-mismatched system.Solution method:RHEED intensities are calculated within the framework of the general matrix formulation described in Ref. [1] under the one-beam condition [2,3]. The dynamical diffraction calculations presented in this paper utilize the systematic reflection case in RHEED, in which the atomic potential in the planes parallel to the surface are projected onto the surface normal, so that the results are insensitive to the atomic arrangement in the layers parallel to the surface. In this paper, an approach in which oscillating changes in the intensity appear as a combined effect of changes in the refraction conditions and changes in diffuse scattering for different models of the scattering potential is implemented.Running time:Numerically, the problem of calculating the changes in RHEED oscillation intensity from growing layers is an NP problem. The time computational complexity of the presented algorithm depends on the number of layers for both the substrate and the growing layers included in the calculations. The time-computational complexity of the presented solution is O(n2), where n is the total number of layers used in the calculations.