A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in Fireball

Fireball is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access Fireball's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation.

Program summary

Program title: FireballUICatalogue identifier: AECF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_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.: 279 784No. of bytes in distributed program, including test data, etc.: 12 836 145Distribution format: tar.gzProgramming language: JavaComputer: PC and workstationOperating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package.RAM: 512 MBWord size: 32 or 64 bitsClassification: 4.14Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations.Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are going to run a simulation on, the user can set up and start the computations of up to hundreds of simulations.Running time: 3 to 5 minutes on a 2 GHz Pentium IV processor.     

S@M, a mathematica implementation of the spinor-helicity formalism

In this paper we present the package S@M (Spinors@Mathematica) which implements the spinor-helicity formalism in Mathematica. The package allows the use of complex-spinor algebra along with the multi-purpose features of Mathematica. The package defines the spinor objects with their basic properties along with functions to manipulate them. It also offers the possibility of evaluating the spinorial objects numerically at every computational step. The package is therefore well suited to be used in the context of on-shell technology, in particular for the evaluation of scattering amplitudes at tree- and loop-level.

Program summary

Program title: S@MCatalogue identifier: AEBF_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBF_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.: 14 404No. of bytes in distributed program, including test data, etc.: 77 536Distribution format: tar.gzProgramming language: MathematicaComputer: All computers running MathematicaOperating system: Any system running MathematicaClassification: 4.4, 5, 11.1Nature of problem: Implementation of the spinor-helicity formalismSolution method: Mathematica implementationRunning time: The notebooks provided with the package take only a few seconds to run.     

TiReX: Replica-exchange molecular dynamics using Tinker

We present a driver program for performing replica-exchange molecular dynamics simulations with the Tinker package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output.

Program summary

Program title: TiReXCatalogue identifier: AEEK_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_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.: 43 385No. of bytes in distributed program, including test data, etc.: 502 262Distribution format: tar.gzProgramming language: Fortran 90/95Computer: Most UNIX machinesOperating system: LinuxHas the code been vectorized or parallelized?: parallelized with MPIClassification: 16.13External routines: TINKER version 4.2 or 5.0, built as a libraryNature of problem: Replica-exchange molecular dynamics.Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals.Running time: The sample run may take up to a few minutes.     

Resolution of singularities for multi-loop integrals

We report on a program for the numerical evaluation of divergent multi-loop integrals. The program is based on iterated sector decomposition. We improve the original algorithm of Binoth and Heinrich such that the program is guaranteed to terminate. The program can be used to compute numerically the Laurent expansion of divergent multi-loop integrals regulated by dimensional regularisation. The symbolic and the numerical steps of the algorithm are combined into one program.

Program summary

Program title: sector_decompositionCatalogue identifier: AEAG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAG_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.: 47 506No. of bytes in distributed program, including test data, etc.: 328 485Distribution format: tar.gzProgramming language: C++Computer: allOperating system: UnixRAM: Depending on the complexity of the problemClassification: 4.4External routines: GiNaC, available from http://www.ginac.de, GNU scientific library, available from http://www.gnu.org/software/gslNature of problem: Computation of divergent multi-loop integrals.Solution method: Sector decomposition.Restrictions: Only limited by the available memory and CPU time.Running time: Depending on the complexity of the problem.     

A completely open source based computing system for computer generation of Fourier holograms

Computer generated holograms are usually generated using commercial software like MATLAB, MATHCAD, Mathematica, etc. This work is an approach in doing the same using freely distributed open source packages and Operating System. A Fourier hologram is generated using this method and tested for simulated and optical reconstruction. The reconstructed images are in good agreement with the objects chosen. The significance of using such a system is also discussed.

Program summary

Program title: FHOLOCatalogue identifier: AEDS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDS_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.: 176 336No. of bytes in distributed program, including test data, etc.: 4 294 872Distribution format: tar.gzProgramming language: C++Computer: any X86 micro computerOperating system: Linux (Debian Etch)RAM: 512 MBClassification: 18Nature of problem: To generate a Fourier Hologram in micro computer only by using open source operating system and packages.Running time: Depends on the matrix size. 10 sec for a matrix of size 256×256.     

Motion4D - A library for lightrays and timelike worldlines in the theory of relativity

The Motion4D-library solves the geodesic equation as well as the parallel- and Fermi-Walker-transport in four-dimensional Lorentzian spacetimes numerically. Initial conditions are given with respect to natural local tetrads which are adapted to the symmetries or the coordinates of the spacetime. Beside some already implemented metrics like the Schwarzschild and Kerr metric, the object oriented structure of the library permits to implement other metrics or integrators in a straight forward manner.

Program summary

Program title: Motion4D-libraryCatalogue identifier: AEEX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEX_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.: 150 425No. of bytes in distributed program, including test data, etc.: 5 139 407Distribution format: tar.gzProgramming language: C++Computer: All platforms with a C++ compilerOperating system: Linux, Unix, WindowsRAM: 39 MBytesClassification: 1.5External routines: Gnu Scientific Library (GSL) (http://www.gnu.org/software/gsl/)Nature of problem: Solve geodesic equation, parallel and Fermi-Walker transport in four-dimensional Lorentzian spacetimes.Solution method: Integration of ordinary differential equationsRunning time: The test runs provided with the distribution require only a few seconds to run.     

QCDMAPT: Program package for Analytic approach to QCD

A program package, which facilitates computations in the framework of Analytic approach to QCD, is developed and described in detail. The package includes both the calculated explicit expressions for relevant spectral functions up to the four-loop level and the subroutines for necessary integrals.

Program summary

Program title: QCDMAPTCatalogue identifier: AEGP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGP_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.: 2579No. of bytes in distributed program, including test data, etc.: 180 052Distribution format: tar.gzProgramming language: Maple 9 and higherComputer: Any which supports Maple 9Operating system: Any which supports Maple 9Classification: 11.1, 11.5, 11.6Nature of problem: Subroutines helping computations within Analytic approach to QCD.Solution method: A program package for Maple is provided. It includes both the explicit expressions for relevant spectral functions and the subroutines for basic integrals used in the framework of Analytic approach to QCD.Running time: Template program running time is about a minute (depends on CPU).     

JuNoLo - Jülich nonlocal code for parallel post-processing evaluation of vdW-DF correlation energy

Nowadays the state of the art Density Functional Theory (DFT) codes are based on local (LDA) or semilocal (GGA) energy functionals. Recently the theory of a truly nonlocal energy functional has been developed. It has been used mostly as a post-DFT calculation approach, i.e. by applying the functional to the charge density calculated using any standard DFT code, thus obtaining a new improved value for the total energy of the system. Nonlocal calculation is computationally quite expensive and scales as N² where N is the number of points in which the density is defined, and a massively parallel calculation is welcome for a wider applicability of the new approach. In this article we present a code which accomplishes this goal.

Program summary

Program title: JuNoLoCatalogue identifier: AEFM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFM_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.: 176 980No. of bytes in distributed program, including test data, etc.: 2 126 072Distribution format: tar.gzProgramming language: Fortran 90Computer: any architecture with a Fortran 90 compilerOperating system: Linux, AIXHas the code been vectorised or parallelized?: Yes, from 1 to 65536 processors may be used.RAM: depends strongly on the problem's size.Classification: 7.3External routines:• FFTW (http://www.tw.org/)• MPI (http://www.mcs.anl.gov/research/projects/mpich2/ or http://www.lam-mpi.org/)Nature of problem: Obtaining the value of the nonlocal vdW-DF energy based on the charge density distribution obtained from some Density Functional Theory code.Solution method: Numerical calculation of the double sum is implemented in a parallel F90 code. Calculation of this sum yields the required nonlocal vdW-DF energy.Unusual features: Binds to virtually any DFT program.Additional comments: Excellent parallelization features.Running time: Depends strongly on the size of the problem and the number of CPUs used.     

Algorithmic derivation of Dyson-Schwinger equations

We present an algorithm for the derivation of Dyson-Schwinger equations of general theories that is suitable for an implementation within a symbolic programming language. Moreover, we introduce the Mathematica package DoDSE¹ which provides such an implementation. It derives the Dyson-Schwinger equations graphically once the interactions of the theory are specified. A few examples for the application of both the algorithm and the DoDSE package are provided.

Program summary

Program title: DoDSECatalogue identifier: AECT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECT_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.: 105 874No. of bytes in distributed program, including test data, etc.: 262 446Distribution format: tar.gzProgramming language: Mathematica 6 and higherComputer: all on which Mathematica is availableOperating system: all on which Mathematica is availableClassification: 11.1, 11.4, 11.5, 11.6Nature of problem: Derivation of Dyson-Schwinger equations for a theory with given interactions.Solution method: Implementation of an algorithm for the derivation of Dyson-Schwinger equations.Unusual features: The results can be plotted as Feynman diagrams in Mathematica.Running time: Less than a second to minutes for Dyson-Schwinger equations of higher vertex functions.     

Solving surface structures from normal incidence X-ray standing wave data

A program is provided to determine structural parameters of atoms in or adsorbed on surfaces by refinement of atomistic models towards experimentally determined data generated by the normal incidence X-ray standing wave (NIXSW) technique. The method employs a combination of Differential Evolution Genetic Algorithms and Steepest Descent Line Minimisations to provide a fast, reliable and user friendly tool for experimentalists to interpret complex multidimensional NIXSW data sets.

Program summary

Program title: NIXSW Planewave SolverCatalogue identifier: ADZE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZE_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.: 16 874No. of bytes in distributed program, including test data, etc.: 1 631 874Distribution format: tar.gzProgramming language: Borland C++ Builder 5Computer: Any Windows CompatibleOperating system: Windows 2000 and XPRAM: <10 MBClassification: 7.4Nature of problem: Using NIXSW experimental data to calculate atomic positions of adsorbates.Restrictions: Data from substrates must have cubic, tetragonal or orthorhombic crystal structures i.e. with 90° between conventional cell axes.Running time: Seconds-minutes dependant on the number of plane waves and the number of atomic sites.     

Introducing PROFESS: A new program for orbital-free density functional theory calculations

We present PROFESS (PRinceton Orbital-Free Electronic Structure Software), a new software package that performs orbital-free density functional theory (OF-DFT) calculations. OF-DFT is a first principles quantum mechanics method primarily for condensed matter that can be made to scale linearly with system size. We describe the implementation of energy, force, and stress functionals and the methods used to optimize the electron density under periodic boundary conditions. All electronic energy and potential terms scale linearly while terms involving the ions exhibit quadratic scaling in our code. Despite the latter scaling, the program can treat tens of thousands of atoms with quantum mechanics on a single processor, as we demonstrate here. Limitations of the method are also outlined, the most serious of which is the accuracy of state-of-the-art kinetic energy functionals, which limits the applicability of the method to main group elements at present.

Program summary

Program title: PROFESSCatalogue identifier: AEBN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBN_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.: 35 933No. of bytes in distributed program, including test data, etc.: 329 924Distribution format: tar.gzProgramming language: Fortran 90Computer: Intel with ifort; AMD Opteron with pathf90Operating system: LinuxRAM: Problem dependent, but 2 GB is sufficient for up to 10,000 ionsClassification: 7.3External routines: FFTW (http://www.fftw.org), MINPACK-2Nature of problem: Given a set of coordinates describing the initial ion positions under periodic boundary conditions, recovers the ground state energy, electron density, ion positions, and cell lattice vectors predicted by orbital-free density functional theory. Except for computation of the ion-ion and ion-electron terms, all other terms are effectively linear scaling. Up to ∼10,000 ions may be included in the calculation on just a single processor.Solution method: Computes energies as described in text; minimizes this energy with respect to the electron density, ion positions, and cell lattice vectors.Restrictions: PROFESS cannot use nonlocal (such as ultrasoft) pseudopotentials. Local pseudopotential files for aluminum, magnesium, silver, and silicon are available upon request. Also, due to the current state of the kinetic energy functionals, PROFESS is only reliable for main group metals and some properties of semiconductors.Running time: Problem dependent: the test example provided with the code takes less than a second to run. Timing results for large scale problems are given in the paper.References:[1] Y.A. Wang, N. Govind, E.A. Carter, Phys. Rev. B 58 (1998) 13465;  Y.A. Wang, N. Govind, E.A. Carter, Phys. Rev. B 64 (2001) 129901 (erratum).[2] S.C. Watson, E.A. Carter, Comput. Phys. Comm. 128 (2000) 67.     

Visual tool for estimating the fractal dimension of images

This work presents a new Visual Basic 6.0 application for estimating the fractal dimension of images, based on an optimized version of the box-counting algorithm. Following the attempt to separate the real information from “noise”, we considered also the family of all band-pass filters with the same band-width (specified as parameter). The fractal dimension can be thus represented as a function of the pixel color code. The program was used for the study of paintings cracks, as an additional tool which can help the critic to decide if an artistic work is original or not.

Program summary

Program title: Fractal Analysis v01Catalogue identifier: AEEG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEG_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.: 29 690No. of bytes in distributed program, including test data, etc.: 4 967 319Distribution format: tar.gzProgramming language: MS Visual Basic 6.0Computer: PCOperating system: MS Windows 98 or laterRAM: 30MClassification: 14Nature of problem: Estimating the fractal dimension of images.Solution method: Optimized implementation of the box-counting algorithm. Use of a band-pass filter for separating the real information from “noise”. User friendly graphical interface.Restrictions: Although various file-types can be used, the application was mainly conceived for the 8-bit grayscale, windows bitmap file format.Running time: In a first approximation, the algorithm is linear.     

A Breit–Pauli distorted wave implementation for autostructure

We describe the Breit–Pauli distorted wave (BPDW) approach for the electron-impact excitation of atomic ions that we have implemented within the autostructure code.

Program summary

Program title:autostructureCatalogue identifier: AEIV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIV_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.: 130 987No. of bytes in distributed program, including test data, etc.: 1 031 584Distribution format: tar.gzProgramming language: Fortran 77/95Computer: GeneralOperating system: UnixHas the code been vectorized or parallelized?: Yes, a parallel version, with MPI directives, is included in the distribution.RAM: From several kbytes to several GbytesClassification: 2, 2.4Nature of problem: Collision strengths for the electron-impact excitation of atomic ions are calculated using a Breit–Pauli distorted wave approach with the optional inclusion of two-body non-fine-structure and fine-structure interactions.Solution method: General multi-configuration Breit–Pauli atomic structure. A jK-coupling partial wave expansion of the collision problem. Slater state angular algebra. Various model potential non-relativistic or kappa-averaged relativistic radial orbital solutions — the continuum distorted wave orbitals are not required to be orthogonal to the bound.Additional comments: Documentation is provided in the distribution file along with the test-case.Running time: From a few seconds to a few hours.     

LIBERI: Library for numerical evaluation of electron-repulsion integrals

We provide a C library, called LIBERI, for numerical evaluation of four-center electron repulsion integrals, based on successive reduction of integral dimension by using Fourier transforms. LIBERI enables us to compute the integrals for numerically defined basis functions within ¹⁰−5 Hartree accuracy as well as their derivatives with respect to the atomic nuclear positions. Damping of the Coulomb interaction can also be imposed to take account of screening effect.

Program summary

Program title: LIBERICatalogue identifier: AEGG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGG_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.: 44 091No. of bytes in distributed program, including test data, etc.: 1 692 085Distribution format: tar.gzProgramming language: CComputer: allOperating system: any Unix-like systemRAM: 5-10 MbClassification: 7.4External routines: Lapack (http://www.netlib.org/lapack/), Blas (http://www.netlib.org/blas/), FFTW3 (http://www.fftw.org/)Nature of problem: Numerical evaluation of four-center electron-repulsion integrals.Solution method: Four-center electron-repulsion integrals are computed for given basis function set, based on successive reduction of integral dimension using Fourier transform.Running time: 0.5 sec for the demo program supplied with the package.     

PETAG01: A program for the direct simulation of a pellet target

We describe a numerical model of an internal pellet target to study the beam dynamics in storage rings, where the nuclear experiments with such type of target are planned. In this model the Monte Carlo algorithm is applied to evaluate the particle coordinates and momentum deviation depending on time and parameters of the target. One has to mention that due to statistical character of the pellet distribution in the target the analytical techniques are not applicable. This is also true for the particle distribution in the stored beam, which is influenced by various effects (such as a cooling process, intra-beam scattering, betatron oscillation, space charge effect). In this case only the Monte Carlo technique to model energy straggling in combination with the pellet distribution in the target should be considered.

Program summary

Program title: PETAG01Catalogue identifier: ADZV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZV_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.: 1068No. of bytes in distributed program, including test data, etc.: 11 314Distribution format: tar.gzProgramming language: Fortran 77, C/C++Computer: Platform independentOperating system: MS Windows 95/2000/XP, Linux (Unix)RAM: 128 MBClassification: 11.10Nature of problem: Particle beam dynamics with use of the pellet target.Solution method: Monte Carlo with analytical approximation.Running time: dozens of seconds     

PArthENoPE: Public algorithm evaluating the nucleosynthesis of primordial elements

We describe a program for computing the abundances of light elements produced during Big Bang Nucleosynthesis which is publicly available at http://parthenope.na.infn.it/. Starting from nuclear statistical equilibrium conditions the program solves the set of coupled ordinary differential equations, follows the departure from chemical equilibrium of nuclear species, and determines their asymptotic abundances as function of several input cosmological parameters as the baryon density, the number of effective neutrino, the value of cosmological constant and the neutrino chemical potential. The program requires commercial NAG library routines.

Program summary

Program title: PArthENoPECatalogue identifier: AEAV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAV_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.: 10 033No. of bytes in distributed program, including test data, etc.: 46 002Distribution format: tar.gzProgramming language: Fortran 77Computer: PC-compatible running Fortran on Unix, MS Windows or LinuxOperating system: Windows 2000, Windows XP, LinuxClassification: 1.2, 1.9, 17.8External routines: NAG LibrariesNature of problem: Computation of yields of light elements synthesized in the primordial universe.Solution method: BDF method for the integration of the ODEs, implemented in a NAG routine.Running time: 90 sec with default parameters on a Dual Xeon Processor 2.4 GHz with 2 GB RAM.     

FracMAP: A user-interactive package for performing simulation and orientation-specific morphology analysis of fractal-like solid nano-agglomerates

Computer simulation techniques have found extensive use in establishing empirical relationships between three-dimensional (3d) and two-dimensional (2d) projected properties of particles produced by the process of growth through the agglomeration of smaller particles (monomers). In this paper, we describe a package, FracMAP, that has been written to simulate 3d quasi-fractal agglomerates and create their 2d pixelated projection images by restricting them to stable orientations as commonly encountered for quasi-fractal agglomerates collected on filter media for electron microscopy. Resulting 2d images are analyzed for their projected morphological properties.

Program summary

Program title: FracMAPCatalogue identifier: AEDD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDD_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.: 4722No. of bytes in distributed program, including test data, etc.: 27 229Distribution format: tar.gzProgramming language: C++Computer: PCOperating system: Windows, LinuxRAM: 2.0 MegabytesClassification: 7.7Nature of problem: Solving for a suitable fractal agglomerate construction under constraints of typical morphological parameters.Solution method: Monte Carlo approximation.Restrictions: Problem complexity is not representative of run-time, since Monte Carlo iterations are of a constant complexity.Additional comments: The distribution file contains two versions of the FracMAP code, one for Windows and one for Linux.Running time: 1 hour for a fractal agglomerate of size 25 on a single processor.     

Plato: A localised orbital based density functional theory code

The Plato package allows both orthogonal and non-orthogonal tight-binding as well as density functional theory (DFT) calculations to be performed within a single framework. The package also provides extensive tools for analysing the results of simulations as well as a number of tools for creating input files. The code is based upon the ideas first discussed in Sankey and Niklewski (1989) [1] with extensions to allow high-quality DFT calculations to be performed. DFT calculations can utilise either the local density approximation or the generalised gradient approximation. Basis sets from minimal basis through to ones containing multiple radial functions per angular momenta and polarisation functions can be used. Illustrations of how the package has been employed are given along with instructions for its utilisation.

Program summary

Program title: PlatoCatalogue identifier: AEFC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_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.: 219 974No. of bytes in distributed program, including test data, etc.: 1 821 493Distribution format: tar.gzProgramming language: C/MPI and PERLComputer: Apple Macintosh, PC, Unix machinesOperating system: Unix, Linux and Mac OS XHas the code been vectorised or parallelised?: Yes, up to 256 processors testedRAM: Up to 2 Gbytes per processorClassification: 7.3External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTWNature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces.Solution method: Localised orbital based density functional theory.Restrictions: Tight-binding and density functional theory only, no exact exchange.Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater–Koster tables for accuracy.Running time: Test cases will run in a few minutes, large calculations may run for several days.     

Milne, a routine for the numerical solution of Milne's problem

The routine Milne provides accurate numerical values for the classical Milne's problem of neutron transport for the planar one speed and isotropic scattering case. The solution is based on the Case eigen-function formalism. The relevant X functions are evaluated accurately by the Double Exponential quadrature. The calculated quantities are the extrapolation distance and the scalar and the angular fluxes. Also, the H function needed in astrophysical calculations is evaluated as a byproduct.

Program summary

Program title: MilneCatalogue identifier: AEGS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGS_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.: 701No. of bytes in distributed program, including test data, etc.: 6845Distribution format: tar.gzProgramming language: Fortran 77Computer: PC under Linux or WindowsOperating system: Ubuntu 8.04 (Kernel version 2.6.24-16-generic), Windows-XPClassification: 4.11, 21.1, 21.2Nature of problem: The X functions are integral expressions. The convergence of these regular and Cauchy Principal Value integrals are impaired by the singularities of the integrand in the complex plane. The DE quadrature scheme tackles these singularities in a robust manner compared to the standard Gauss quadrature.Running time: The test included in the distribution takes a few seconds to run.