CPC Program Library Research Articles

HAWK 2.0: A Monte Carlo program for Higgs production in vector-boson fusion and Higgs strahlung at hadron colliders

The Monte Carlo integrator HAWK provides precision predictions for Higgs production at hadron colliders in vector-boson fusion and Higgs strahlung, i.e. in production processes where the Higgs boson is Attached to WeaK bosons. The fully differential predictions include the full QCD and electroweak next-to-leading-order corrections. Results are computed as integrated cross sections and as binned distributions for important hadron-collider observables. Program summaryProgram title: HAWK, version 2.0Catalogue identifier: AEWT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWT_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.: 132878No. of bytes in distributed program, including test data, etc.: 1400686Distribution format: tar.gzProgramming language: Fortran 77, Fortran 90.Computer: Any computer with a Fortran 90 compiler.Operating system: Linux, Mac OS.RAM: Less than 1 GBClassification: 4.4, 11.1, 11.2.External routines: LHAPDF (https://www.hepforge.org/downloads/lhapdf).Nature of problem:Precision calculation of cross sections and differential distributions for Higgs-boson production in vector-boson fusion and Higgs strahlung at the LHC as described in Refs. [1–3].Solution method:Multi-channel Monte Carlo integration of perturbative matrix elements including higher-order QCD and electroweak corrections which are based on a Feynman-diagrammatic calculation.Restrictions:For vector-boson fusion, only the Higgs-boson decay into a pair of massless singlets is supported. For Higgs strahlung, decay products are not supported, while the Higgs boson can be off shell.Running time:Meaningful results can be obtained within a few hours on a single core. The statistical uncertainty of the results typically improves with the square root of the run time.

HEPMath 1.4: A mathematica package for semi-automatic computations in high energy physics

This article introduces the Mathematica package HEPMath which provides a number of utilities and algorithms for High Energy Physics computations in Mathematica. Its functionality is similar to packages like FormCalc or FeynCalc, but it takes a more complete and extensible approach to implementing common High Energy Physics notations in the Mathematica language, in particular those related to tensors and index contractions. It also provides a more flexible method for the generation of numerical code which is based on new features for C code generation in Mathematica. In particular it can automatically generate Python extension modules which make the compiled functions callable from Python, thus eliminating the need to write any code in a low-level language like C or Fortran. It also contains seamless interfaces to LHAPDF, FeynArts, and LoopTools. Program summaryProgram title: HEPMathCatalogue identifier: AEWU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWU_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.: 27360No. of bytes in distributed program, including test data, etc.: 668749Distribution format: tar.gzProgramming language: Mathematica, C and python.Computer: Workstation.Operating system: Linux.Classification: 11.1, 5, 4.4.External routines: FeynArts (optional), LoopTools (optional), LHAPDF (optional)Nature of problem:Automatisation of (Feynman diagrammatic) computations in High Energy Physics, representation and manipulation of tensors with symbolic indices in the Mathematica language, generation of numerical code and interface to Python.Solution method:A Mathematica package which provides functions to construct and manipulate tensor expressions in Mathematica and interface to other popular tools in High Energy Physics.Unusual features:A code generation method which uses Mathematica’s byte code compiler (Compile) rather than CForm/FortranForm and the automatic generation of Python extension modules.Running time:The examples provided only take a few seconds to run.

Formula omitted]: An open source continuous-time quantum Monte Carlo impurity solver toolkit

Quantum impurity solvers have a broad range of applications in theoretical studies of strongly correlated electron systems. Especially, they play a key role in dynamical mean-field theory calculations of correlated lattice models and realistic materials. Therefore, the development and implementation of efficient quantum impurity solvers is an important task. In this paper, we present an open source interacting quantum impurity solver toolkit (dubbed iQIST). This package contains several highly optimized quantum impurity solvers which are based on the hybridization expansion continuous-time quantum Monte Carlo algorithm, as well as some essential pre- and post-processing tools. We first introduce the basic principle of continuous-time quantum Monte Carlo algorithm and then discuss the implementation details and optimization strategies. The software framework, major features, and installation procedure for iQIST are also explained. Finally, several simple tutorials are presented in order to demonstrate the usage and power of iQIST. Program summaryProgram title:iQISTCatalogue identifier: AEWQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWQ_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.: 226270No. of bytes in distributed program, including test data, etc.: 5263144Distribution format: tar.gzProgramming language: Fortran 2008 and Python.Computer: Desktop PC, laptop, high performance computing cluster.Operating system: Unix, Linux, Mac OS X, Windows.Has the code been vectorized or parallelized?: Yes, it is parallelized by MPI and OpenMPRAM: Depends on the complexity of the problemClassification: 7.3.External routines: BLAS, LAPACK, Latex is required to build the user manual.Nature of problem:Quantum impurity models were originally proposed to describe magnetic impurities in metallic hosts. In these models, the Coulomb interaction acts between electrons occupying the orbitals of the impurity atom. Electrons can hop between the impurity and the host, and in an action formulation, this hopping is described by a time-dependent hybridization function. Nowadays quantum impurity models have a broad range of applications, from the description of heavy fermion systems, and Kondo insulators, to quantum dots in nano-science. They also play an important role as auxiliary problems in dynamical mean-field theory and its diagrammatic extensions [1–3], where an interacting lattice model is mapped onto a quantum impurity model in a self-consistent manner. Thus, the accurate and efficient solution of quantum impurity models becomes an essential task.Solution method:The quantum impurity model can be solved by the numerically exact continuous-time quantum Monte Carlo method, which is the most efficient and powerful impurity solver for finite temperature simulations. In the iQIST software package, we implemented the hybridization expansion version of continuous-time quantum Monte Carlo algorithm. Both the segment representation and general matrix formalism are supported. The key idea of this algorithm is to expand the partition function diagrammatically in powers of the impurity-bath hybridization, and to stochastically sample these diagrams to all relevant orders using the Metropolis Monte Carlo algorithm. For a detailed review of the continuous-time quantum Monte Carlo algorithms, please refer to [4].Running time:Depends on the complexity of the problem. The sample run supplied in the distribution takes about 1.5 minutes.

PUQ: A code for non-intrusive uncertainty propagation in computer simulations

We present a software package for the non-intrusive propagation of uncertainties in input parameters through computer simulation codes or mathematical models and associated analysis; we demonstrate its use to drive micromechanical simulations using a phase field approach to dislocation dynamics. The PRISM uncertainty quantification framework (PUQ) offers several methods to sample the distribution of input variables and to obtain surrogate models (or response functions) that relate the uncertain inputs with the quantities of interest (QoIs); the surrogate models are ultimately used to propagate uncertainties. PUQ requires minimal changes in the simulation code, just those required to annotate the QoI(s) for its analysis. Collocation methods include Monte Carlo, Latin Hypercube and Smolyak sparse grids and surrogate models can be obtained in terms of radial basis functions and via generalized polynomial chaos. PUQ uses the method of elementary effects for sensitivity analysis in Smolyak runs. The code is available for download and also available for cloud computing in nanoHUB. PUQ orchestrates runs of the nanoPLASTICITY tool at nanoHUB where users can propagate uncertainties in dislocation dynamics simulations using simply a web browser, without downloading or installing any software. Program summaryProgram title: PUQCatalogue identifier: AEWP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWP_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: MIT licenseNo. of lines in distributed program, including test data, etc.: 45075No. of bytes in distributed program, including test data, etc.: 3318862Distribution format: tar.gzProgramming language: Python, C.Computer: Workstations.Operating system: Linux, Mac OSX.Classification: 4.11, 4.12, 4.13.External routines: SciPy, Matplotlib, h5pyNature of problem: Uncertainty propagation and creation of response surfaces.Solution method: Generalized Polynomial Chaos (gPC) using Smolyak sparse grids.Running time: PUQ performs uncertainty quantification and sensitivity analysis by running a simulation multiple times using different values for input parameters. Its run time will be the product of the run time of the chosen simulation code and the number of runs required to achieve the desired accuracy.

Fortran and C programs for the time-dependent dipolar Gross–Pitaevskii equation in an anisotropic trap

Many of the static and dynamic properties of an atomic Bose–Einstein condensate (BEC) are usually studied by solving the mean-field Gross–Pitaevskii (GP) equation, which is a nonlinear partial differential equation for short-range atomic interaction. More recently, BEC of atoms with long-range dipolar atomic interaction are used in theoretical and experimental studies. For dipolar atomic interaction, the GP equation is a partial integro-differential equation, requiring complex algorithm for its numerical solution. Here we present numerical algorithms for both stationary and non-stationary solutions of the full three-dimensional (3D) GP equation for a dipolar BEC, including the contact interaction. We also consider the simplified one- (1D) and two-dimensional (2D) GP equations satisfied by cigar- and disk-shaped dipolar BECs. We employ the split-step Crank–Nicolson method with real- and imaginary-time propagations, respectively, for the numerical solution of the GP equation for dynamic and static properties of a dipolar BEC. The atoms are considered to be polarized along the z axis and we consider ten different cases, e.g., stationary and non-stationary solutions of the GP equation for a dipolar BEC in 1D (along x and z axes), 2D (in x–y and x–z planes), and 3D, and we provide working codes in Fortran 90/95 and C for these ten cases (twenty programs in all). We present numerical results for energy, chemical potential, root-mean-square sizes and density of the dipolar BECs and, where available, compare them with results of other authors and of variational and Thomas–Fermi approximations. Program summaryProgram title: (i) imag1dZ, (ii) imag1dX, (iii) imag2dXY, (iv) imag2dXZ, (v) imag3d, (vi) real1dZ, (vii) real1dX, (viii) real2dXY, (ix) real2dXZ, (x) real3dCatalogue identifier: AEWL_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWL_v1_0.htmlProgram obtainable from: CPC Program Library, Queens 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.: 111384No. of bytes in distributed program, including test data, etc.: 604013Distribution format: tar.gz

BilKristal 4.0: A tool for crystal parameters extraction and defect quantification

In this paper, we present a revised version of BilKristal 3.0 tool. Raycast screenshot functionality is added to provide improved visual analysis. We added atomic distance analysis functionality to assess crystalline defects. We improved visualization capabilities by adding high level cut function definitions. Discovered bugs are fixed and small performance optimizations are made. New version program summaryProgram title: BilKristal 4.0Catalogue identifier: ADYU_v4_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v4_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.: 370130No. of bytes in distributed program, including test data, etc.: 8350850Distribution format: tar.gzProgramming language: C, C++, Microsoft .NET Framework 2.0 and OpenGL Libraries.Computer: Personal Computers with Windows operating system.Operating system: Windows XP or higher.RAM: 20–60 Megabytes.Classification: 8.External routines: Microsoft .NET Framework 2.0. For the visualization tool, graphics card driver should also support OpenGL.Catalogue identifier of previous version: ADYU_v3_0Journal reference of previous version: Comput. Phys. Comm. 187 (2015) 266Does the new version supersede the previous version?: YesNature of problem: Determining the crystal structure parameters of a material is a very important issue in crystallography. Knowing the crystal structure parameters helps the understanding of the physical behavior of material. For complex structures, particularly for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be very hard.Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identifies the space group from atomic coordinates of crystal structures.Reasons for new version: Additional features, Performance optimizations, Minor bug corrections.Summary of revisions:•Raycast screenshot functionality is added to the visualization tool. A raycasting algorithm similar to the one described in [4, 6] is used. The algorithm is multi-core parallelized as described in [5].•Atomic distance analysis functionality is added. Tool can analyze the crystal structure and give statistical information of atom to atom distances.•In the visualization tool, high level cut function support is added. Users can define cut functions, not just as cut-planes but with more complex functions as well.•Automatic primitive vector and basis vector selection options are added. This way the system selects the simplest primitive and basis vector alternatives and continues without interrupting the user.•In the visualization tool, an unused log file was being created and a redundant configuration file was being used. These issues are corrected.•Dead-codes are removed to improve clarity.Restrictions: Assumptions are explained in [1, 2, 3]. However, none of them can be considered as a restriction to the complexity of the problem.Running time: The tool was able to process input files with more than a million atoms in less than 20 seconds on a PC with an Athlon quad-core CPU at 3.2 GHz using the default parameter values.

Multidimensional integration through Markovian sampling under steered function morphing: A physical guise from statistical mechanics

We present a computational strategy for the evaluation of multidimensional integrals on hyper-rectangles based on Markovian stochastic exploration of the integration domain while the integrand is being morphed by starting from an initial appropriate profile. Thanks to an abstract reformulation of Jarzynski’s equality applied in stochastic thermodynamics to evaluate the free-energy profiles along selected reaction coordinates via non-equilibrium transformations, it is possible to cast the original integral into the exponential average of the distribution of the pseudo-work (that we may term “computational work”) involved in doing the function morphing, which is straightforwardly solved. Several tests illustrate the basic implementation of the idea, and show its performance in terms of computational time, accuracy and precision. The formulation for integrand functions with zeros and possible sign changes is also presented. Program summaryProgram title: JEMDICatalogue identifier: AEWO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWO_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.: 81666No. of bytes in distributed program, including test data, etc.: 1767836Distribution format: tar.gzProgramming language: C++.Computer: PC and Macintosh.Operating system: Unix.RAM: 1 024 000 000 bytesClassification: 4.11, 4.13.External routines: SPRNG included in the distribution file.Nature of problem:Integration of general functions of many variablesSolution method:JEMDI is a library that provides methods for the evaluation of general multidimensional integrals on hyper-rectangles based on Markovian stochastic exploration of the integration domain while the integrand is being morphed by starting from an initial flat profile. Employing a revised abstract reformulation of Jarzynski’s equality, the original integral is cast into the exponential average of the distribution of the pseudo-work involved in doing the morphing of the integrand function.Restrictions:The method is efficiently applicable to the integration of functions of a few hundreds of variables.Running time:Extremely variable, depending on the complexity of the function to integrate and the number of variables. The examples included in the distribution take about 3 min to run.

DMTDHF: A full dimensional time-dependent Hartree–Fock program for diatomic molecules in strong laser fields

We present the DMTDHF package, which investigates the non-perturbative electronic dynamics of diatomic molecules subjected to strong external laser fields by the fully propagated time-dependent Hartree–Fock theory. The package uses the prolate spheroidal coordinates, together with the finite-element method and discrete-variable representation, while short iterative Lanczos algorithm is employed for the time propagation. This package can be applied to diatomic molecules with many electrons, and is implemented to allow easy extensions for additional capabilities. Program summaryProgram title: DMTDHFCatalogue identifier: AEWN_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWN_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.: 702996No. of bytes in distributed program, including test data, etc.: 7336872Distribution format: tar.gzProgramming language: Fortran 2003.Computer: All computers with a Fortran compiler supporting at least Fortran 2003.Operating system: All operating systems with such a compiler. The makefile depends on a Unix-like system and needs modification under Windows.Has the code been vectorized or parallelized?: The program is able to run both in sequential and parallel mode. For parallel running, the number of processors can be arbitrary.RAM: Several GBs, depends on the size of the molecules and the number of DVR basis functions.Classification: 16.1, 16.2, 16.6.External routines: BLAS, LAPACK, FFTW3, MPINature of problem: The investigation of molecules interacting with intense laser pulses requires non-perturbative theoretical treatment. It has been evidenced that multiorbital and multipole effects come into play for strong-field physics, while the direct numerical integration of TDSE is computationally prohibitive for systems with more than two electrons. TDHF goes beyond the SAE approach and includes the response to the field of all electrons, which is helpful to resolve the multielectron effects from the collective response of electrons.Solution method: The package uses the prolate spheroidal coordinates, together with the finite-elements method and discrete-variable representation, while short iterative Lanczos algorithm is employed for the time propagation.Restrictions: Currently, the spin-restricted form of TDHF is implemented, which can be applied to closed-shell molecules. However, the extension to spin-unrestricted form is straight forward.Unusual features: Due to the prolate spheroidal coordinates, the Coulomb potential is treated accurately. The calculations can converge with only a mild number of basis functions and are highly efficient due to the nature of DVR functions in calculation of the two-electron integrals.Running time: The running time depends on the size of the molecules, the number of basis functions, the duration of laser pulses, and the number of processors used. Depending on these factors, it can vary between a few hours and weeks.

A database of rigorous and high-precision periodic orbits of the Lorenz model

A benchmark database of very high-precision numerical and validated initial conditions of periodic orbits for the Lorenz model is presented. This database is a “computational challenge” and it provides the initial conditions of all periodic orbits of the Lorenz model up to multiplicity 10 and guarantees their existence via computer-assisted proofs methods. The orbits are computed using high-precision arithmetic and mixing several techniques resulting in 1000 digits of precision on the initial conditions of the periodic orbits, and intervals of size 10100 that prove the existence of each orbit. Program summaryProgram title: Lorenz-DatabaseCatalogue identifier: AEWM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWM_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.: 8515No. of bytes in distributed program, including test data, etc.: 6964501Distribution format: tar.gzProgramming language: Data.Computer: Any computer.Operating system: Any.RAM: Database, no requirementsClassification: 4.3, 4.12.Nature of problem: Database of all periodic orbits of the Lorenz model up to multiplicity 10 with 1000 precision digits.Solution method: Advanced search methods for locating unstable periodic orbits combined with the Taylor series method for multiple precision integration of ODEs and interval methods for providing Computer-Assisted proofs of the periodic orbits.Unusual features: The database gives 100 digits rigorously proved using Computer-Assisted techniques and 1000 digits using an optimal adaptive Taylor series method.Running time: Not Applicable.

Plasmonics simulations with the MNPBEM toolbox: Consideration of substrates and layer structures

Within the MNPBEM toolbox, developed for the simulation of plasmonic nanoparticles using a boundary element method approach, we show how to include substrate and layer structure effects. We develop the methodology for solving Maxwell’s equations using scalar and vector potentials within the inhomogeneous dielectric environment of a layer structure. We show that the implementation of our approach allows for fast and efficient simulations of plasmonic nanoparticles situated on top of substrates or embedded in layer structures. The new toolbox provides a number of demo files which can be also used as templates for other simulations. Program summaryProgram title: MNPBEM toolboxCatalogue identifier: AEKJ_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKJ_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.: 56958No. of bytes in distributed program, including test data, etc.: 1258497Distribution format: tar.gzProgramming language: Matlab 8.3.0 (R2014a).Computer: Any which supports Matlab 8.3.0 (R2014a).Operating system: Any which supports Matlab 8.3.0 (R2014a).Has the code been vectorised or parallelized?: YesRAM:≥4 GbyteClassification: 18.Catalogue identifier of previous version: AEKJ_v2_0Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 1177Does the new version supersede the previous version?: YesNature of problem: Simulation of plasmonic nanoparticles placed on substrates or within layer structures.Solution method: Boundary element method using electromagnetic potentialsReasons for new version: Inclusion of substrate and layer structure effectsSummary of revisions:•simulations with layer structures and substrates•simulation control through one options structure•refined boundary element integration•consideration of flat and curved particle boundaries•an improved plot function for particle objects•a new polygon3 class for the extrusion of 2d shapes•a new meshfield class for the computation of electric field mapsRunning time: Depending on surface discretization between seconds and hours.

GPELab, a Matlab toolbox to solve Gross–Pitaevskii equations II: Dynamics and stochastic simulations

GPELab is a free Matlab toolbox for modeling and numerically solving large classes of systems of Gross–Pitaevskii equations that arise in the physics of Bose–Einstein condensates. The aim of this second paper, which follows (Antoine and Duboscq, 2014), is to first present the various pseudospectral schemes available in GPELab for computing the deterministic and stochastic nonlinear dynamics of Gross–Pitaevskii equations (Antoine, et al., 2013). Next, the corresponding GPELab functions are explained in detail. Finally, some numerical examples are provided to show how the code works for the complex dynamics of BEC problems. Program summaryProgram title: GPELabCatalogue identifier: AETU_v2_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AETU_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.: 27209No. of bytes in distributed program, including test data, etc.: 283623Distribution format: tar.gzProgramming language: Matlab.Computer: PC, Mac.Operating system: Windows, Mac OS, Linux.Has the code been vectorized or parallelized?: YesRAM: 4000 MegabytesClassification: 2.7, 4.6, 7.7.Catalogue identifier of previous version: AETU_v1_0Journal reference of previous version: Comput. Phys. Comm. 185(2014)2969Does the new version supersede the previous version?: YesNature of problem:Simulation of dynamical solutions for a class of systems (multi-components) of time-dependent Gross–Pitaevskii equations in 1d, 2d and 3d. This program is particularly well designed for the simulation of the dynamics of Bose–Einstein condensates as well as the computation of ground states.Solution method:We use spectral schemes in space and splitting/relaxation scheme in time.Reasons for new version:To include dynamic simulations.Summary of revisions:It is now possible to do dynamical simulations with the code.Running time:From a few seconds for simple problems to a few minutes for more complex situations on a medium computer.

Parallel implementation of inverse adding-doubling and Monte Carlo multi-layered programs for high performance computing systems with shared and distributed memory

Parallel implementation of two numerical tools popular in optical studies of biological materials–Inverse Adding-Doubling (IAD) program and Monte Carlo Multi-Layered (MCML) program–was developed and tested in this study. The implementation was based on Message Passing Interface (MPI) and standard C-language. Parallel versions of IAD and MCML programs were compared to their sequential counterparts in validation and performance tests. Additionally, the portability of the programs was tested using a local high performance computing (HPC) cluster, Penguin-On-Demand HPC cluster, and Amazon EC2 cluster. Parallel IAD was tested with up to 150 parallel cores using 1223 input datasets. It demonstrated linear scalability and the speedup was proportional to the number of parallel cores (up to 150x). Parallel MCML was tested with up to 1001 parallel cores using problem sizes of 104–109 photon packets. It demonstrated classical performance curves featuring communication overhead and performance saturation point. Optimal performance curve was derived for parallel MCML as a function of problem size. Typical speedup achieved for parallel MCML (up to 326x) demonstrated linear increase with problem size. Precision of MCML results was estimated in a series of tests — problem size of 106 photon packets was found optimal for calculations of total optical response and 108 photon packets for spatially-resolved results. The presented parallel versions of MCML and IAD programs are portable on multiple computing platforms. The parallel programs could significantly speed up the simulation for scientists and be utilized to their full potential in computing systems that are readily available without additional costs. Program summaryProgram title: MCMLMPI, IADMPICatalogue identifier: AEWF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWF_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.: 53638No. of bytes in distributed program, including test data, etc.: 731168Distribution format: tar.gzProgramming language: C.Computer: Up to and including HPC/Cloud CPU-based clusters.Operating system: Windows, Linux, Unix, MacOS — requires ANSI C-compatible compiler.Has the code been vectorized or parallelized?: Yes, using MPI directives.RAM: From megabytes to gigabytes (MCMLMPI), kilobytes to megabytes (IADMPI)Classification: 2.2, 2.5, 18.External routines: dcmt-library (MCMLMPI), cweb-package (IADMPI)Nature of problem:Photon transport in multilayered semi-transparent material, estimation of optical properties (IADMPI) and optical response (MCMLMPI) of multilayered material samples.Solution method:Massively-parallel Monte-Carlo method (MCMLMPI), Inverse Adding-Doubling method (IADMPI)Unusual features:Tracking and analysis of photon packets in turbid media (MCMLMPI)Running time:Many small problems can be solved within seconds, large problems might take hours even on HPC clusters (MCMLMPI); hours on single computer and seconds on HPC cluster (IADMPI)

Efficient tool flow for 3D photovoltaic modelling

Performance predictions and optimisation strategies in current nanotechnology-based photovoltaic (PV) require simulation tools that can efficiently and accurately compute optical and electrical performance parameters of intricate 3D geometrical structures. Due to the complexity of each type of simulation it is often the case that a single package excels in either optical or electrical modelling, and the other remains a bottleneck. In this work, an efficient tool flow is described in order to combine the highly effective optical simulator Lumerical with the excellent fabrication and electrical simulation capability of Sentaurus. Interfacing between the two packages is achieved through tool command language and Matlab, offering a fast and accurate electro-optical characteristics of nano-structured PV devices. Program summaryProgram title: Interfacing_Lumerical_SentaurusCatalogue identifier: AEWK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWK_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.: 4525No. of bytes in distributed program, including test data, etc.: 23729Distribution format: tar.gzProgramming language: TCL, Matlab, Lumerical FDTD Solutions Version 8.7.3, TCAD Sentaurus Version j-2014.09.Computer: A multi-core, high ram workstation is recommended for running Lumerical Solutions and TCAD Sentaurus. The scripts provided here were run on a HPZ820 workstation with 2 X Intel Xeon E5-2680 2.70Ghz processors and 128GB DDR3-1600 RAM.Operating system: Linux.Number of processors used: Matlab scripts can be parallel processed. The scripts have been tested on 16 CPUs (32 Threads).RAM: For the TCL files, minimal RAM is needed. For the matlab script, it depends on the structure. The scripts have been tested using an upper limit of 128 GB.Classification: 4, 6, 18.Nature of problem:Create a tool flow that models complex fabrication techniques, as well as accurate and efficient optical and electrical simulations for photovoltaic simulations.Solution method:Code is provided to interface between Lumerical and Sentaurus using TCL and Matlab script.Running time:Depends on structure complexity and number of processors used.

PARPLE: Detailed automatized and parallel evaluation of luminescence mappings

Laterally resolved luminescence techniques offer the possibility to examine thin film semiconductors with respect to the inhomogeneities of their opto-electronic, optical and chemical properties. Especially the integrated photoluminescence (PL) yield and splitting of quasi-Fermi levels (QFL) are of interest as well as the derived optical properties like the optical band gap, the Urbach energy and the absorption due to defect states within the band gap. For a large set of individual PL spectra, the integration and determination of the QFL-splitting can be very time-consuming. Especially for films with varying composition, resulting in different band gaps, the fitting parameters can vary from pixel to pixel. With the open source tool PARPLE (PARallel PL Evaluation) the evaluation of recorded maps is automatized regarding the fitting procedure and parallelized using multiple CPU cores for performance improvement. Program summaryProgram title: PARPLECatalogue identifier: AEWJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWJ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: General Public Licence (GPU) v3No. of lines in distributed program, including test data, etc.: 12,173No. of bytes in distributed program, including test data, etc.: 15,156,143Distribution format: tar.gzProgramming language: C.Computer: Any computer running a GCC compiler.Operating system: Linux, Mac OS X, Windows (+Cygwin).RAM: Several ten–several hundred MB depending on number of recorded PL spectra.Classification: 7.4.External routines: GNU Scientific Library, libpng, GNU OpenMPNature of problem:Evaluation of PL spectra and extraction of opto-electronic properties including integrated PL yield, splitting of quasi-Fermi levels and optical band gap. The spectral shift of the PL spectra is covered by use of an adaptive fit procedure.Solution method:Adaptive linear fit of the high energy slope.Restrictions:For a full analysis, the PL spectra must satisfy the requirements of Planck’s generalized law regarding the steady-state condition, the absorption of high-energy photons and that the relaxation time is fast then the recombination time. The experimental setup must be spectrally calibrated.Unusual features:Adaptive linear fit, implemented parallelization.Running time:A few seconds–a few minutes

PyDII: A python framework for computing equilibrium intrinsic point defect concentrations and extrinsic solute site preferences in intermetallic compounds

Point defects play an important role in determining the structural stability and mechanical behavior of intermetallic compounds. To help quantitatively understand the point defect properties in these compounds, we developed PyDII, a Python program that performs thermodynamic calculations of equilibrium intrinsic point defect concentrations and extrinsic solute site preferences in intermetallics. The algorithm implemented in PyDII is built upon a dilute-solution thermodynamic formalism with a set of defect excitation energies calculated from first-principles density-functional theory methods. The analysis module in PyDII enables automated calculations of equilibrium intrinsic antisite and vacancy concentrations as a function of composition and temperature (over ranges where the dilute solution formalism is accurate) and the point defect concentration changes arising from addition of an extrinsic substitutional solute species. To demonstrate the applications of PyDII, we provide examples for intrinsic point defect concentrations in NiAl and Al3 V and site preferences for Ti, Mo and Fe solutes in NiAl. Program summaryProgram title: PyDIICatalogue identifier: AEWI_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWI_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: MIT LicenseNo. of lines in distributed program, including test data, etc.: 6123No. of bytes in distributed program, including test data, etc.: 40988Distribution format: tar.gzProgramming language: Python.Computer: Any computer with a Python interpreter.Operating system: Any which enable Python.RAM: Problem dependentClassification: 7.1.External routines: NumPy [1], Sympy [2], and Pymatgen [3].Nature of problem:Equilibrium intrinsic point defect concentrations and solute site preferences in intermetallic compounds.Solution method:Intrinsic point defect properties and solute site preference as a function of composition and temperature are computed within the grand-canonical, dilute-solution thermodynamic formalism developed by Woodward et al., Phys. Rev. B 63 (2001) 094103.Restrictions:The current version of PyDII supports generating inputs and parsing outputs for density functional calculations implemented in VASP. Defect energetics obtained from other computational methods or software can also be used to compute the defect properties by preparing the input in a format consistent with that of the JSON files provided in the example folder.Additional comments: This article describes version 1.0.0.Running time: Problem dependent

Formula omitted]-diff: An open-source Matlab toolbox for computing multiple scattering problems by disks

The aim of this paper is to describe a Matlab toolbox, called μ-diff, for modeling and numerically solving two-dimensional complex multiple scattering by a large collection of circular cylinders. The approximation methods in μ-diff are based on the Fourier series expansions of the four basic integral operators arising in scattering theory. Based on these expressions, an efficient spectrally accurate finite-dimensional solution of multiple scattering problems can be simply obtained for complex media even when many scatterers are considered as well as large frequencies. The solution of the global linear system to solve can use either direct solvers or preconditioned iterative Krylov subspace solvers for block Toeplitz matrices. Based on this approach, this paper explains how the code is built and organized. Some complete numerical examples of applications (direct and inverse scattering) are provided to show that μ-diff is a flexible, efficient and robust toolbox for solving some complex multiple scattering problems. Program summaryProgram title:μ-diffCatalogue identifier: AEWH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWH_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.: 13,718No. of bytes in distributed program, including test data, etc.: 1,466,301Distribution format: tar.gzProgramming language: Matlab.Computer: PC, Mac.Operating system: Windows, Mac OS, Linux.Has the code been vectorized or parallelized?: YesRAM: 2000 MegabytesClassification: 4.6, 10, 18.Nature of problem: Modeling and simulation of two-dimensional multiple wave scattering by large clusters of circular cylinders for any frequency. The program is well-designed to manage highly accurate solutions for deterministic or random media, with various boundary conditions and physics properties of the scatterers. Pre- and post-processing facilities are designed specifically for these problems.Solution method: We use spectral Fourier approximation schemes and direct or iterative Krylov subspace methods.Running time: From a few seconds for simple problems to a few minutes for more complex situations on a medium computer.

AQUAgpusph, a new free 3D SPH solver accelerated with OpenCL

In this paper, AQUAgpusph, a new free Smoothed Particle Hydrodynamics (SPH) software accelerated with OpenCL, is described. The main differences and progress with respect to other existing alternatives are considered. These are the use of the Open Computing Language (OpenCL) framework instead of the Compute Unified Device Architecture (CUDA), the implementation of the most popular boundary conditions, the easy customization of the code to different problems, the extensibility with regard to Python scripts, and the runtime output which allows the tracking of simulations in real time, or a higher frequency in saving some results without a significant performance lost. These modifications are shown to improve the solver speed, the results quality, and allow for a wider areas of application. AQUAgpusph has been designed trying to provide researchers and engineers with a valuable tool to test and apply the SPH method. Three practical applications are discussed in detail. The evolution of a dam break is used to quantify and compare the computational performance and modeling accuracy with the most popular SPH Graphics Processing Unit (GPU) accelerated alternatives. The dynamics of a coupled system, a Tuned Liquid Damper (TLD), is discussed in order to show the integration capabilities of the solver with external dynamics. Finally, the sloshing flow inside a nuclear reactor is simulated in order to show the capabilities of the solver to treat 3-D problems with complex geometries and of industrial interest. Program summaryProgram title: AQUAgpusph 1.5Catalogue identifier: AEVG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEVG_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.: 1702666No. of bytes in distributed program, including test data, etc.: 75117178Distribution format: tar.gzProgramming language: C++, OpenCL, Python.Computer: Linux based computers with OpenCL support.Operating system: Linux.Has the code been vectorized or parallelized?: Code is parallelized with OpenCL.Classification: 1.5.Nature of problem: Complex geometry or heavily fragmented free surface fluid dynamics problems where mesh based method cannot be successfully applied.Solution method: SPH is a meshless method where the fluid domain is discretized as a set of fluid particles. The fields in the fluid domain are smoothed using a kernel function, that allows to develop differential operators from the flow field values in scattered sets of particles.Running time: Using an AMD HD-7970 graphic device 2×105 time steps of a 2-D simulation, with 105 particles and 8×102 neighs per particle, is requiring around 9 h of computation. A more detailed performance analysis will be carried out in the practical application section herein.

GPScan.VI: A general-purpose LabVIEW program for scanning imaging or any application requiring synchronous analog voltage generation and data acquisition

A large number of measurement techniques involve the scanning of a probe, while a physical quantity is measured. This is for instance the case for all scanning imaging methods. Data acquisition therefore requires high acquisition rates, together with an accurate synchronization between the probe control and the measurement. The GPScan.VI program is a general purpose LabVIEW program for the control of National Instruments high-speed data acquisition boards, allowing to design scanning imaging systems. Analog output voltages are used to drive a two-dimensional scanning device, while acquisition of analog voltages and TTL pulse counting are run in parallel. Acquisition of megapixel images with pixel dwell times down to the microsecond can be reached with negligible I/O transfer time. The design can be generalized to any situation requiring high speed synchronous generation and acquisition. Program summaryProgram title: GPScan.VICatalogue identifier: AEWG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWG_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.: 1246No. of bytes in distributed program, including test data, etc.: 114456Distribution format: tar.gzProgramming language: LabVIEW (http://www.ni.com/labview/).Computer: Any machine running LabVIEW 2010 or higher.Operating system: Windows XP or higher, OS X.RAM: 5 MbytesClassification: 20.Nature of problem:A large number of measurement techniques involve the scanning of a probe, while a physical quantity is measured. This is, for instance, the case for all scanning imaging methods. Data acquisition therefore requires high acquisition rates, together with an accurate synchronization between the probe control and the measurement.Solution method:The GPScan.VI program allows the setting up of National Instruments multifunction acquisition boards, so that analog output voltage series (used to drive the scanner / probe) are generated, while analog input and counter acquisitions are run synchronously.Restrictions:Requires National Instruments high-speed multifunction boards, such as X Series or S Series, with at least two analog outputs, and a compatible NI-DAQmx driver installed. The program has been tested on X series boards, with LabVIEW 2011, under Windows 7.Running time:Real time data acquisition. Scan rates, up to several millions of samples per second, depend on the specification of the board and may be limited by the response of the physical system used to perform the scanning.

SLIMP: Strong laser interaction model package for atoms and molecules

We present the SLIMP package, which provides an efficient way for the calculation of strong-field ionization rate and high-order harmonic spectra based on the single active electron approximation. The initial states are taken as single-particle orbitals directly from output files of the general purpose quantum chemistry programs GAMESS, Firefly and Gaussian. For ionization, the molecular Ammosov–Delone–Krainov theory, and both the length gauge and velocity gauge Keldysh–Faisal–Reiss theories are implemented, while the Lewenstein model is used for harmonic spectra. Furthermore, it is also efficient for the evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment and calculation of orbital integrations. This package can be applied to quite large basis sets and complex molecules with many atoms, and is implemented to allow easy extensions for additional capabilities. Program summaryProgram title: SLIMPCatalogue identifier: AEWE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEWE_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.: 90277No. of bytes in distributed program, including test data, etc.: 927942Distribution format: tar.gzProgramming language: Fortran 90.Computer: All computers with a Fortran compiler supporting at least Fortran 90.Operating system: All operating systems with such a compiler. The makefile depends on a Unix-like system and needs modification under Windows.RAM: Memory requirement depends on the size of the molecules and the number of basis functions. For instance, about 2.8MB RAM is required for N2 molecules with the acc-pvqz basis set (210 basis functions). However, the SF6 molecules require 22MB RAM with the same basis set (739 basis functions).Classification: 16.1, 16.10, 2.7.Nature of problem: In modeling of atoms and molecules subjected to intense laser pulses, there is a general need for the calculation of theoretical models. However, the application of these models requires the effective evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment or calculation of orbital integrations. This package provides an efficient way for these calculations directly from the output files of the widely used GAMESS, Firefly and Gaussian programs.Solution method: The molecular orbital is constructed from a linear combination of atomic orbitals, which is further expanded with Cartesian gaussian type orbitals (GTO). The orbital momentum wavefunction and dipole moment can be constructed with the Fourier transformed GTOs. Orbital integrations rely on the elementary integrations of GTOs. These results are used directly as input in the subsequent models calculations.Restrictions: Current implementation supports the S, P L, D, F and G types, of GTOs. Here L indicates the diffuse basis. However, the extension to higher order basis is straight-forward. This package supports the versions of GAMESS (US, 2013), Firefly (8.1), and Gaussian (both 09 and 03). For older versions, mild modifications on the reading formats may be necessary in the modules.Running time: The running time depends on the size of the molecules, the number of basis functions, and most importantly, on the problem to which this package has been employed. Typically for a single-processor PC-type computer it can vary between a few seconds and days.

Phonon Transport Simulator (PhonTS)

Thermal conductivity prediction remains an important subject in many scientific and engineering areas. Only recently has such prediction become possible on the basis of the first principles calculations, thus ensuring high quality results. Implementation of the methodology, however, is technically challenging and requires a lengthy development process. We thus introduce the Phonon Transport Simulator (PhonTS), a Fortran90, fully parallel code to perform such calculations. PhonTS possesses a large array of options and returns the thermal conductivity tensor together with related quantities, such as spectral thermal conductivity, phonon lifetimes, mean free paths and Grüneisen parameters. First principles calculations are implemented via convenient interfaces to widely-used third-party codes, while many classical potentials are included in PhonTS itself. The code is carefully validated against data published in the literature from various thermal conductivity computational techniques and against experimental data. Program summaryProgram title: PhonTSCatalogue identifier: AEVO_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEVO_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.: 7060788No. of bytes in distributed program, including test data, etc.: 58119383Distribution format: tar.gzProgramming language: Fortran90.Computer: Linux cluster.Operating system: Linux.Has the code been vectorised or parallelized?: Yes, via the MPI-librariesRAM: 200 MBClassification: 7.8, 7.9.External routines: LAPACK, MPI-librariesNature of problem: Computes thermal conductivity in crystal solids from the level of the interatomic interactions.Solution method: Iterative or variational solution of the Boltzmann Transport Equation for phonons, by treating anharmonicity as a perturbation to the harmonic problem.Additional comments: Due to the large file size, PhonTS 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: Problem dependent. For solid argon (4 atoms in the conventional cell, k-space mesh of 9×9×9, classical potential, fully convergent results) simulations take ∼104 seconds on a single processor.