FIESTA 2: Parallelizeable multiloop numerical calculations

The program FIESTA has been completely rewritten. Now it can be used not only as a tool to evaluate Feynman integrals numerically, but also to expand Feynman integrals automatically in limits of momenta and masses with the use of sector decompositions and Mellin–Barnes representations. Other important improvements to the code are complete parallelization (even to multiple computers), high-precision arithmetics (allowing to calculate integrals which were undoable before), new integrators, Speer sectors as a strategy, the possibility to evaluate more general parametric integrals.

Program summary

Program title:FIESTA 2Catalogue identifier: AECP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECP_v2_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU GPL version 2No. of lines in distributed program, including test data, etc.: 39 783No. of bytes in distributed program, including test data, etc.: 6 154 515Distribution format: tar.gzProgramming language: Wolfram Mathematica 6.0 (or higher) and CComputer: From a desktop PC to a supercomputerOperating system: Unix, Linux, Windows, Mac OS XHas the code been vectorised or parallelized?: Yes, the code has been parallelized for use on multi-kernel computers as well as clusters via Mathlink over the TCP/IP protocol. The program can work successfully with a single processor, however, it is ready to work in a parallel environment and the use of multi-kernel processor and multi-processor computers significantly speeds up the calculation; on clusters the calculation speed can be improved even further.RAM: Depends on the complexity of the problemClassification: 4.4, 4.12, 5, 6.5Catalogue identifier of previous version: AECP_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 735External routines: QLink [1], Cuba library [2], MPFR [3]Does the new version supersede the previous version?: YesNature of problem: The sector decomposition approach to evaluating Feynman integrals falls apart into the sector decomposition itself, where one has to minimize the number of sectors; the pole resolution and epsilon expansion; and the numerical integration of the resulting expression.Solution method: The sector decomposition is based on a new strategy as well as on classical strategies such as Speer sectors. The sector decomposition, pole resolution and epsilon-expansion are performed in Wolfram Mathematica 6.0 or, preferably, 7.0 (enabling parallelization) [4]. The data is stored on hard disk via a special program, QLink [1]. The expression for integration is passed to the C-part of the code, that parses the string and performs the integration by one of the algorithms in the Cuba library package [2]. This part of the evaluation is perfectly parallelized on multi-kernel computers.Reasons for new version:

• 1. 

  The first version of FIESTA had problems related to numerical instability, so for some classes of integrals it could not produce a result.

• 2. 

  The sector decomposition method can be applied not only for integral calculation.

Summary of revisions:

• 1. 

  New integrator library is used.

• 2. 

  New methods to deal with numerical instability (MPFR library).

• 3. 

  Parallelization in Mathematica.

• 4. 

  Parallelization on multiple computers via TCP-IP.

• 5. 

  New sector decomposition strategy (Speer sectors).

• 6. 

  Possibility of using FIESTA to for integral expansion.

• 7. 

  Possibility of using FIESTA to discover poles in d.

• 8. 

  New negative terms resolution strategies.

Restrictions: The complexity of the problem is mostly restricted by CPU time required to perform the evaluation of the integralRunning time: Depends on the complexity of the problemReferences:

• [1] 

  http://qlink08.sourceforge.net, open source.

• [2] 

  http://www.feynarts.de/cuba/, open source.

• [3] 

  http://www.mpfr.org/, open source.

• [4] 

  http://www.wolfram.com/products/mathematica/index.html.

     

XtalOpt version r7: An open-source evolutionary algorithm for crystal structure prediction

A new version of XtalOpt, a user-friendly GPL-licensed evolutionary algorithm for crystal structure prediction, is available for download from the CPC library or the XtalOpt website, http://xtalopt.openmolecules.net. The new version now supports four external geometry optimization codes (VASP, GULP, PWSCF, and CASTEP), as well as three queuing systems: PBS, SGE, SLURM, and “Local”. The local queuing system allows the geometry optimizations to be performed on the user?s workstation if an external computational cluster is unavailable. Support for the Windows operating system has been added, and a Windows installer is provided. Numerous bugfixes and feature enhancements have been made in the new release as well.

New version program summary

Program title:XtalOptCatalogue identifier: AEGX_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 125 383No. of bytes in distributed program, including test data, etc.: 11 607 415Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: Linux, MS WindowsClassification: 7.7External routines: Qt [2], Open Babel [3], Avogadro [4], and one of: VASP [5], PWSCF [6], GULP [7], CASTEP [8]Catalogue identifier of previous version: AEGX_v1_0Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 372Does the new version supersede the previous version?: YesNature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum of a crystalline structure on its potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available for use and collaboration under the GNU Public License. See the original publication on XtalOpt?s implementation [11] for more information on the method.Reasons for new version: Since XtalOpt?s initial release in June 2010, support for additional optimizers, queuing systems, and an operating system has been added. XtalOpt can now use VASP, GULP, PWSCF, or CASTEP to perform local geometry optimizations. The queue submission code has been rewritten, and now supports running any of the above codes on ssh-accessible computer clusters that use the Portable Batch System (PBS), Sun Grid Engine (SGE), or SLURM queuing systems for managing the optimization jobs. Alternatively, geometry optimizations may be performed on the user?s workstation using the new internal “Local” queuing system if high performance computing resources are unavailable. XtalOpt has been built and tested on the Microsoft Windows operating system (XP or later) in addition to Linux, and a Windows installer is provided. The installer includes a development version of Avogadro that contains expanded crystallography support [12] that is not available in the mainline Avogadro releases. Other notable new developments include:

• • 

  LIBSSH [10] is distributed with the XtalOpt sources and used for communication with the remote clusters, eliminating the previous requirement to set up public-key authentication;

• • 

  Plotting enthalpy (or energy) vs. structure number in the plot tab will trace out the history of the most stable structure as the search progresses A read-only mode has been added to allow inspection of previous searches through the user interface without connecting to a cluster or submitting new jobs;

• • 

  The tutorial [13] has been rewritten to reflect the changes to the interface and the newly supported codes. Expanded sections on optimizations schemes and save/resume have been added;

• • 

  The included version of SPGLIB has been updated. An option has been added to set the Cartesian tolerance of the space group detection. A new option has been added to the Progress table?s right-click menu that copies the selected structure?s POSCAR formatted representation to the clipboard;

• • 

  Numerous other small bugfixes/enhancements.

Summary of revisions: See “Reasons for new version” above.Running time: User dependent. The program runs until stopped by the user.References:

•  [1] 

  http://www.gnu.org/licenses/gpl.html.

•  [2] 

  http://www.trolltech.com/.

•  [3] 

  http://openbabel.org/.

•  [4] 

  http://avogadro.openmolecules.net.

•  [5] 

  http://cms.mpi.univie.ac.at/vasp.

•  [6] 

  http://www.quantum-espresso.org.

•  [7] 

  https://www.ivec.org/gulp.

•  [8] 

  http://www.castep.org.

•  [9] 

  http://spglib.sourceforge.net.

• [10] 

  http://www.libssh.org.

• [11] 

  D. Lonie, E. Zurek, Comp. Phys. Comm. 182 (2011) 372–387, doi:10.1016/j.cpc.2010.07.048.

• [12] 

  http://davidlonie.blogspot.com/2011/03/new-avogadro-crystallography-extension.html.

• [13] 

  http://xtalopt.openmolecules.net/globalsearch/docs/tut-xo.html.

     

XtalOpt: An open-source evolutionary algorithm for crystal structure prediction

The implementation and testing of XtalOpt, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XtalOpt are optimized using a novel benchmarking scheme. XtalOpt is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface.

Program summary

Program title:XtalOptCatalogue identifier: AEGX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GPL v2.1 or later [1]No. of lines in distributed program, including test data, etc.: 36 849No. of bytes in distributed program, including test data, etc.: 1 149 399Distribution format: tar.gzProgramming language: C++Computer: PCs, workstations, or clustersOperating system: LinuxClassification: 7.7External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7].Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics.Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XtalOpt, is freely available to the scientific community for use and collaboration under the GNU Public License.Running time: User dependent. The program runs until stopped by the user.References:

• [1] 

  http://www.gnu.org/licenses/gpl.html.

• [2] 

  http://www.trolltech.com/.

• [3] 

  http://openbabel.org/.

• [4] 

  http://avogadro.openmolecules.net.

• [5] 

  http://cms.mpi.univie.ac.at/vasp.

• [6] 

  http://www.quantum-espresso.org.

• [7] 

  https://www.ivec.org/gulp.

• [8] 

  http://spglib.sourceforge.net.

     

Continuous-time quantum Monte Carlo impurity solvers

Continuous-time quantum Monte Carlo impurity solvers are algorithms that sample the partition function of an impurity model using diagrammatic Monte Carlo techniques. The present paper describes codes that implement the interaction expansion algorithm originally developed by Rubtsov, Savkin, and Lichtenstein, as well as the hybridization expansion method developed by Werner, Millis, Troyer, et al. These impurity solvers are part of the ALPS-DMFT application package and are accompanied by an implementation of dynamical mean-field self-consistency equations for (single orbital single site) dynamical mean-field problems with arbitrary densities of states.

Program summary

Program title: dmftCatalogue identifier: AEIL_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIL_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: ALPS LIBRARY LICENSE version 1.1No. of lines in distributed program, including test data, etc.: 899 806No. of bytes in distributed program, including test data, etc.: 32 153 916Distribution format: tar.gzProgramming language: C++Operating system: The ALPS libraries have been tested on the following platforms and compilers:

• • 

  Linux with GNU Compiler Collection (g++ version 3.1 and higher), and Intel C++ Compiler (icc version 7.0 and higher)

• • 

  MacOS X with GNU Compiler (g++ Apple-version 3.1, 3.3 and 4.0)

• • 

  IBM AIX with Visual Age C++ (xlC version 6.0) and GNU (g++ version 3.1 and higher) compilers

• • 

  Compaq Tru64 UNIX with Compq C++ Compiler (cxx)

• • 

  SGI IRIX with MIPSpro C++ Compiler (CC)

• • 

  HP-UX with HP C++ Compiler (aCC)

• • 

  Windows with Cygwin or coLinux platforms and GNU Compiler Collection (g++ version 3.1 and higher)

RAM: 10 MB–1 GBClassification: 7.3External routines: ALPS [1], BLAS/LAPACK, HDF5Nature of problem: (See [2].) Quantum impurity models describe an atom or molecule embedded in a host material with which it can exchange electrons. They are basic to nanoscience as representations of quantum dots and molecular conductors and play an increasingly important role in the theory of “correlated electron” materials as auxiliary problems whose solution gives the “dynamical mean field” approximation to the self-energy and local correlation functions.Solution method: Quantum impurity models require a method of solution which provides access to both high and low energy scales and is effective for wide classes of physically realistic models. The continuous-time quantum Monte Carlo algorithms for which we present implementations here meet this challenge. Continuous-time quantum impurity methods are based on partition function expansions of quantum impurity models that are stochastically sampled to all orders using diagrammatic quantum Monte Carlo techniques. For a review of quantum impurity models and their applications and of continuous-time quantum Monte Carlo methods for impurity models we refer the reader to [2].Additional comments: Use of dmft requires citation of this paper. Use of any ALPS program requires citation of the ALPS [1] paper.Running time: 60 s–8 h per iteration.References:

• [1] 

  A. Albuquerque, F. Alet, P. Corboz, et al., J. Magn. Magn. Mater. 310 (2007) 1187.

• [2] 

  http://arxiv.org/abs/1012.4474, Rev. Mod. Phys., in press.

     

Motion4D-library extended

The new version of the Motion4D-library now also includes the integration of a Sachs basis and the Jacobi equation to determine gravitational lensing of pointlike sources for arbitrary spacetimes.

New version program summary

Program title: Motion4D-libraryCatalogue identifier: AEEX_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEX_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.: 219 441No. of bytes in distributed program, including test data, etc.: 6 968 223Distribution format: tar.gzProgramming language: C++Computer: All platforms with a C++ compilerOperating system: Linux, WindowsRAM: 61 MbytesClassification: 1.5External routines: Gnu Scientic Library (GSL) (http://www.gnu.org/software/gsl/)Catalogue identifier of previous version: AEEX_v2_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 703Does the new version supersede the previous version?: YesNature of problem: Solve geodesic equation, parallel and Fermi-Walker transport in four-dimensional Lorentzian spacetimes. Determine gravitational lensing by integration of Jacobi equation and parallel transport of Sachs basis.Solution method: Integration of ordinary differential equations.Reasons for new version: The main novelty of the current version is the extension to integrate the Jacobi equation and the parallel transport of the Sachs basis along null geodesics. In combination, the change of the cross section of a light bundle and thus the gravitational lensing effect of a spacetime can be determined. Furthermore, we have implemented several new metrics.Summary of revisions: The main novelty of the current version is the integration of the Jacobi equation and the parallel transport of the Sachs basis along null geodesics. The corresponding set of equations read(1)(2)(3) where (1) is the geodesic equation, (2) represents the parallel transport of the two Sachs basis vectors s1,2, and (3) is the Jacobi equation for the two Jacobi fields Y1,2.The initial directions of the Sachs basis vectors are defined perpendicular to the initial direction of the light ray, see also Fig. 1,(4a)(4b)A congruence of null geodesics with central null geodesic γ which starts at the observer O with an infinitesimal circular cross section is defined by the above mentioned two Jacobi fields with initial conditions and . The cross section of this congruence along γ is described by the Jacobian . However, to determine the gravitational lensing of a pointlike source S that is connected to the observer via γ, we need the reverse Jacobian JS→O. Fortunately, the reverse Jacobian is just the negative transpose of the original Jacobian JO→S,(5)J:=JS→O=−T(JO→S). The Jacobian J transforms the circular shape of the congruence into an ellipse whose shape parameters (M_±: major/minor axis, ψ: angle of major axis, ε: ellipticity) read(6a)(6b)ψ=arctan2(J₂₁cosζ₊+J₂₂sinζ₊,J₁₁cosζ₊+J₁₂sinζ₊),(6c) with(7) and the parameters α=J₁₁J₁₂+J₂₁J₂₂, . The magnification factor is given by(8) These shape parameters can be easily visualized in the new version of the GeodesicViewer, see Ref. [1]. A detailed discussion of gravitational lensing can be found, for example, in Schneider et al. [2].In the following, a list of newly implemented metrics is given:

• • 

  BertottiKasner: see Rindler [3].

• • 

  BesselGravWaveCart: gravitational Bessel wave from Kramer [4].

• • 

  DeSitterUniv, DeSitterUnivConf: de Sitter universe in Cartesian and conformal coordinates.

• • 

  Ernst: Black hole in a magnetic universe by Ernst [5].

• • 

  ExtremeReissnerNordstromDihole: see Chandrasekhar [6].

• • 

  HalilsoyWave: see Ref. [7].

• • 

  JaNeWi: Janis–Newman–Winicour metric, see Ref. [8].

• • 

  MinkowskiConformal: Minkowski metric in conformally rescaled coordinates.

• • 

  PTD_AI, PTD_AII, PTD_AIII, PTD_BI, PTD_BII, PTD_BIII, PTD_C Petrov-Type D – Levi-Civita spacetimes, see Ref. [7].

• • 

  PainleveGullstrand: Schwarzschild metric in Painlevé–Gullstrand coordinates, see Ref. [9].

• • 

  PlaneGravWave: Plane gravitational wave, see Ref. [10].

• • 

  SchwarzschildIsotropic: Schwarzschild metric in isotropic coordinates, see Ref. [11].

• • 

  SchwarzschildTortoise: Schwarzschild metric in tortoise coordinates, see Ref. [11].

• • 

  Sultana-Dyer: A black hole in the Einstein–de Sitter universe by Sultana and Dyer [12].

• • 

  TaubNUT: see Ref. [13].

The Christoffel symbols and the natural local tetrads of these new metrics are given in the Catalogue of Spacetimes, Ref. [14].To study the behavior of geodesics, it is often useful to determine an effective potential like in classical mechanics. For several metrics, we followed the Euler–Lagrangian approach as described by Rindler [10] and implemented an effective potential for a specific situation. As an example, consider the Lagrangian for timelike geodesics in the ?=π/2 hypersurface in the Schwarzschild spacetime with α=1−2m/r. The Euler–Lagrangian equations lead to the energy balance equation with the effective potential V(r)=(r−2m)(r²+h²)/r³ and the constants of motion and . The constants of motion for a timelike geodesic that starts at (r=10m,φ=0) with initial direction ξ=π/4 with respect to the black hole direction and with initial velocity β=0.7 read k≈1.252 and h≈6.931. Then, from the energy balance equation we immediately obtain the radius of closest approach rmin≈5.927.Beside a standard Runge–Kutta fourth-order integrator and the integrators of the Gnu Scientific Library (GSL), we also implemented a standard Bulirsch–Stoer integrator.Running time: The test runs provided with the distribution require only a few seconds to run.References:

• [1] 

  T. Müller, New version announcement to the GeodesicViewer, http://cpc.cs.qub.ac.uk/summaries/AEFP_v2_0.html.

• [2] 

  P. Schneider, J. Ehlers, E. E. Falco, Gravitational Lenses, Springer, 1992.

• [3] 

  W. Rindler, Phys. Lett. A 245 (1998) 363.

• [4] 

  D. Kramer, Ann. Phys. 9 (2000) 331.

• [5] 

  F.J. Ernst, J. Math. Phys. 17 (1976) 54.

• [6] 

  S. Chandrasekhar, Proc. R. Soc. Lond. A 421 (1989) 227.

• [7] 

  H. Stephani, D. Kramer, M. MacCallum, C. Hoenselaers, E. Herlt, Exact Solutions of the Einstein Field Equations, Cambridge University Press, 2009.

• [8] 

  A.I. Janis, E.T. Newman, J. Winicour, Phys. Rev. Lett. 20 (1968) 878.

• [9] 

  K. Martel, E. Poisson, Am. J. Phys. 69 (2001) 476.

• [10] 

  W. Rindler, Relativity – Special, General, and Cosmology, Oxford University Press, Oxford, 2007.

• [11] 

  C.W. Misner, K.S. Thorne, J.A. Wheeler, Gravitation, W.H. Freeman, 1973.

• [12] 

  J. Sultana, C.C. Dyer, Gen. Relativ. Gravit. 37 (2005) 1349.

• [13] 

  D. Bini, C. Cherubini, Robert T. Jantzen, Class. Quantum Grav. 19 (2002) 5481.

• [14] 

  T. Muller, F. Grave, arXiv:0904.4184 [gr-qc].

     

ROOT — A C++ framework for petabyte data storage, statistical analysis and visualization

A new stable version (“production version”) v5.28.00 of ROOT [1] has been published [2]. It features several major improvements in many areas, most noteworthy data storage performance as well as statistics and graphics features. Some of these improvements have already been predicted in the original publication Antcheva et al. (2009) [3]. This version will be maintained for at least 6 months; new minor revisions (“patch releases”) will be published [4] to solve problems reported with this version.

New version program summary

Program title: ROOTCatalogue identifier: AEFA_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFA_v2_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU Lesser Public License v.2.1No. of lines in distributed program, including test data, etc.: 2 934 693No. of bytes in distributed program, including test data, etc.: 1009Distribution format: tar.gzProgramming language: C++Computer: Intel i386, Intel x86-64, Motorola PPC, Sun Sparc, HP PA-RISCOperating system: GNU/Linux, Windows XP/Vista/7, Mac OS X, FreeBSD, OpenBSD, Solaris, HP-UX, AIXHas the code been vectorized or parallelized?: YesRAM: > 55 MbytesClassification: 4, 9, 11.9, 14Catalogue identifier of previous version: AEFA_v1_0Journal reference of previous version: Comput. Phys. Commun. 180 (2009) 2499Does the new version supersede the previous version?: YesNature of problem: Storage, analysis and visualization of scientific dataSolution method: Object store, wide range of analysis algorithms and visualization methodsReasons for new version: Added features and corrections of deficienciesSummary of revisions: The release notes at http://root.cern.ch/root/v528/Version528.news.html give a module-oriented overview of the changes in v5.28.00. Highlights include

• • 

  File format Reading of TTrees has been improved dramatically with respect to CPU time (30%) and notably with respect to disk space.

• • 

  Histograms A new TEfficiency class has been provided to handle the calculation of efficiencies and their uncertainties, TH2Poly for polygon-shaped bins (e.g. maps), TKDE for kernel density estimation, and TSVDUnfold for singular value decomposition.

• • 

  Graphics Kerning is now supported in TLatex, PostScript and PDF; a table of contents can be added to PDF files. A new font provides italic symbols. A TPad containing GL can be stored in a binary (i.e. non-vector) image file; add support for full-scene anti-aliasing. Usability enhancements to EVE.

• • 

  Math New interfaces for generating random number according to a given distribution, goodness of fit tests of unbinned data, binning multidimensional data, and several advanced statistical functions were added.

• • 

  RooFit Introduction of HistFactory; major additions to RooStats.

• • 

  TMVA Updated to version 4.1.0, adding e.g. the support for simultaneous classification of multiple output classes for several multivariate methods.

• • 

  PROOF Many new features, adding to PROOF?s usability, plus improvements and fixes.

• • 

  PyROOT Support of Python 3 has been added.

• • 

  Tutorials Several new tutorials were provided for above new features (notably RooStats).

A detailed list of all the changes is available at http://root.cern.ch/root/htmldoc/examples/V5.Additional comments: For an up-to-date author list see: http://root.cern.ch/drupal/content/root-development-team and http://root.cern.ch/drupal/content/former-root-developers.The distribution file for this program is over 30 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead a html file giving details of how the program can be obtained is sent.Running time: Depending on the data size and complexity of analysis algorithms.References:

• [1] 

  http://root.cern.ch.

• [2] 

  http://root.cern.ch/drupal/content/production-version-528.

• [3] 

  I. Antcheva, M. Ballintijn, B. Bellenot, M. Biskup, R. Brun, N. Buncic, Ph. Canal, D. Casadei, O. Couet, V. Fine, L. Franco, G. Ganis, A. Gheata, D. Gonzalez Maline, M. Goto, J. Iwaszkiewicz, A. Kreshuk, D. Marcos Segura, R. Maunder, L. Moneta, A. Naumann, E. Offermann, V. Onuchin, S. Panacek, F. Rademakers, P. Russo, M. Tadel, ROOT — A C++ framework for petabyte data storage, statistical analysis and visualization, Comput. Phys. Commun. 180 (2009) 2499.

• [4] 

  http://root.cern.ch/drupal/content/root-version-v5-28-00-patch-release-notes.

     

Indirect search for dark matter with micrOMEGAs_2.4

We present a new module of micrOMEGAs devoted to the computation of indirect signals from dark matter annihilation in any new model with a stable weakly interacting particle. The code provides the mass spectrum, cross-sections, relic density and exotic fluxes of gamma rays, positrons and antiprotons. The propagation of charged particles in the Galactic halo is handled with a new module that allows to easily modify the propagation parameters.

Program summary

Program title: micrOMEGAs2.4Catalogue identifier: ADQR_v2_3Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADQR_v2_3.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.: 401 126No. of bytes in distributed program, including test data, etc.: 6 583 596Distribution format: tar.gzProgramming language: C and FortranComputer: PC, Alpha, Mac, SunOperating system: UNIX (Linux, OSF1, SunOS, Darwin, Cygwin)RAM: 50 MB depending on the number of processes requiredClassification: 1.9, 11.6Catalogue identifier of previous version: ADQR_v2_3Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 747Does the new version supersede the previous version?: YesNature of problem: Calculation of the relic density and detection rates of the lightest stable particle in a generic new model of particle physics.Solution method: In numerically solving the evolution equation for the density of dark matter, relativistic formulas for the thermal average are used. All tree-level processes for annihilation and coannihilation of new particles in the model are included. The cross-sections for all processes are calculated exactly with CalcHEP after definition of a model file. The propagation of the charged cosmic rays is solved within a semi-analytical two-zone model.Reasons for new version: There are many experiments that are currently searching for the remnants of dark matter annihilation. In this version we perform the computation of indirect signals from dark matter annihilation in any new model with a stable weakly interacting particle. We include the propagation of charged particles in the Galactic halo.Summary of revisions:

• • 

  Annihilation cross-sections for all 2-body tree-level processes and for radiative emission of a photon for all models.

• • 

  Annihilation cross-sections into polarised gauge bosons.

• • 

  Annihilation cross-sections for the loop induced processes γγ and γZ0 in the MSSM.

• • 

  Modelling of the DM halo with a general parameterization and with the possibility of including DM clumps.

• • 

  Computation of the propagation of charged particles through the Galaxy, including the possibility of modifying the propagation parameters.

• • 

  Effect of solar modulation on the charged particle spectrum.

• • 

  Model independent predictions of the indirect detection signals.

Unusual features: Depending on the parameters of the model, the program generates additional new code, compiles it and loads it dynamically.Running time: 3 sec     

CIF2Cell: Generating geometries for electronic structure programs

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP.

Program summary

Program title: CIF2CellCatalogue identifier: AEIM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU GPL version 3No. of lines in distributed program, including test data, etc.: 12 691No. of bytes in distributed program, including test data, etc.: 74 933Distribution format: tar.gzProgramming language: Python (versions 2.4–2.7)Computer: Any computer that can run Python (versions 2.4–2.7)Operating system: Any operating system that can run Python (versions 2.4–2.7)Classification: 7.3, 7.8, 8External routines: PyCIFRW [1]Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file.Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation.Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13–16].Running time: The examples provided in the distribution take only seconds to run.References:

• [1] 

  J.R. Hester, A validating CIF parser: PyCIFRW, Journal of Applied Crystallography 39 (4) (2006) 621–625, doi:10.1107/S0021889806015627, URL http://dx.doi.org/10.1107/S0021889806015627

• [2] 

  X. Gonze, G.-M. Rignanese, M. Verstraete, J.-M. Beuken, Y. Pouillon, R. Caracas, F. Jollet, M. Torrent, G. Zerah, M. Mikami, P. Ghosez, M. Veithen, J.-Y. Raty, V. Olevano, F. Bruneval, L. Reining, R. Godby, G. Onida, D.R. Hamann, D.C. Allan, A brief introduction to the abinit software package, Zeitschrift für Kristallographie 220 (12) (2005) 558–562.

• [3] 

  X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Ct, T. Deutsch, L. Genovese, P. Ghosez, M. Giantomassi, S. Goedecker, D. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M. Verstraete, G. Zerah, J. Zwanziger, Abinit: First-principles approach to material and nanosystem properties, Computer Physics Communications 180 (12) (2009) 2582–2615 (40 years of CPC: A celebratory issue focused on quality software for high performance, grid and novel computing architectures), doi:10.1016/j.cpc.2009.07.007; http://www.sciencedirect.com/science/article/B6TJ5-4WTRSCM-3/2/20edf8da70cd808f10fe352c45d0c0be.

• [4] 

  S.J. Clark, M.D. Segall, C.J. Pickard, P.J. Hasnip, M.J. Probert, K. Refson, M.C. Payne, First principles methods using CASTEP, Zeitschrift für Kristallographie 220 (12) (2005) 567–570.

• [5] 

  URL http://www.cpmd.org.

• [6] 

  R. Dovesi, R. Orlando, B. Civalleri, C. Roetti, V.R. Saunders, C.M. Zicovich-Wilson, Crystal: a computational tool for the ab initio study of the electronic properties of crystals, Zeitschrift für Kristallographie 220 (2005) 571–573. URL http://dx.doi.org/10.1524/zkri.220.5.571.65065.

• [7] 

  URL http://elk.sourceforge.net.

• [8] 

  URL http://exciting-code.org.

• [9] 

  L. Vitos, Computational Quantum Mechanics for Materials Engineers; The EMTO Method and Applications, Springer, London, 2007, doi:10.1007/978-1-84628-951-4.

• [10] 

  URL http://www.flapw.de.

• [11] 

  J.M. Wills, O. Eriksson, M. Alouani, D.L. Price, Full-potential LMTO total energy and force calculations, in: H. Dreussé (Ed.), Electronic Structure and Physical Properties of Solids; The Uses of the LMTO Method, Springer, 1996, pp. 148–167.

• [12] 

  J.M. Soler, E. Artacho, J.D. Gale, A. García, J. Junquera, P. Ordejón, D. Sánchez-Portal, The siesta method for ab initio order-n materials simulation, Journal of Physics: Condensed Matter 14 (11) (2002) 2745. URL http://stacks.iop.org/0953-8984/14/i=11/a=302

• [13] 

  G. Kresse, J. Hafner, Ab initio molecular dynamics for liquid metals, Phys. Rev. B 47 (1) (1993) 558–561, doi:10.1103/PhysRevB.47.558.

• [14] 

  G. Kresse, J. Hafner, Ab initio molecular-dynamics simulation of the liquid–metal amorphous-semiconductor transition in germanium, Phys. Rev. B 49 (20) (1994) 14251–14269, doi:10.1103/PhysRevB.49.14251.

• [15] 

  G. Kresse, J. Furthmüller, Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set, Computational Materials Science 6 (1) (1996) 15–50, doi:10.1016/0927-0256(96)00008-0. URL http://www.sciencedirect.com/science/article/B6TWM-3VRVTBF-3/2/88689b1eacfe2b5fe57f09d37eff3b74.

• [16] 

  G. Kresse, J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54 (16) (1996) 11169–11186, doi:10.1103/PhysRevB.54.11169.

     

GeodesicViewer – A tool for exploring geodesics in the theory of relativity

The GeodesicViewer realizes exocentric two- and three-dimensional illustrations of lightlike and timelike geodesics in the general theory of relativity. By means of an intuitive graphical user interface, all parameters of a spacetime as well as the initial conditions of the geodesics can be modified interactively.

New version program summary

Program title: GeodesicViewerCatalogue identifier: AEFP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFP_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.: 76 202No. of bytes in distributed program, including test data, etc.: 1 722 290Distribution format: tar.gzProgramming language: C++, OpenGLComputer: All platforms with a C++ compiler, Qt, OpenGLOperating system: Linux, Mac OS X, WindowsRAM: 24 MBytesClassification: 1.5External routines:

• • 

  Motion4D (included in the package)

• • 

  Gnu Scientific Library (GSL) (http://www.gnu.org/software/gsl/)

• • 

  Qt (http://qt.nokia.com/downloads)

• • 

  OpenGL (http://www.opengl.org/)

Catalogue identifier of previous version: AEFP_v1_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 413Does the new version supersede the previous version?: YesNature of problem: Illustrate geodesics in four-dimensional Lorentzian spacetimes.Solution method: Integration of ordinary differential equations. 3D-Rendering via OpenGL.Reasons for new version: The main reason for the new version was to visualize the parallel transport of the Sachs legs and to show the influence of curved spacetime on a bundle of light rays as is realized in the new version of the Motion4D library (http://cpc.cs.qub.ac.uk/summaries/AEEX_v3_0.html).Summary of revisions:

• • 

  By choosing the new geodesic type “lightlike_sachs”, the parallel transport of the Sachs basis and the integration of the Jacobi equation can be visualized.

• • 

  The 2D representation via Qwt was replaced by an OpenGL 2D implementation to speed up the visualization.

• • 

  Viewing parameters can now be stored in a configuration file (.cfg).

• • 

  Several new objects can be used in 3D and 2D representation.

• • 

  Several predefined local tetrads can be choosen.

• • 

  There are some minor modifications: new mouse control (rotate on sphere); line smoothing; current last point in coordinates is shown; mutual-coordinate representation extended; current cursor position in 2D; colors for 2D view.

Running time: Interactive. The examples given take milliseconds.     

Signal transformation and interpolation based on modified DCT synthesis

This paper proposes a novel signal transformation and interpolation approach based on the modification of DCT (Discrete Cosine Transform). The proposed algorithm can be applied to any periodic or quasi periodic waveform for time scale and/or pitch modification purposes in addition to signal reconstruction, compression, coding and packet lost concealment. The proposed algorithm has two advantages:

• (i) 

  Since DCT does not have the explicit phase information, one does not need the cubic spline interpolation of the phase component of the sinusoidal model.

• (ii) 

  The parameters to be interpolated can be reduced because of the energy packing efficiency of the DCT. This is particularly important if signal synthesis is carried out on a remote location from the transmitted parameters.

The results are presented on periodic waveforms and on speech signal in order to appreciate the fidelity of the proposed algorithm. In addition, the proposed method is compared with TD-PSOLA, sinusoidal model and phase vocoder algorithms. The results are presented in objective PESQ scores for time scale modification and output files are provided as supplementary material,¹ for subjective evaluation, for packet lost concealment. Results prove that the proposed modification of the DCT synthesis provides a favorable algorithm for specialists working in the signal processing area.     

How to market yourself as an ISSO

• 1. 

  1. Prior to being interviewed for TCI's ISSO position, learn all you can about TCI.

• 2. 

  2. Read articles about how to prepare and dress for interviews.

• 3. 

  3. Prepare answers for the typical questions you will probably be asked and practice the interview process so your answers come across naturally, and not as memorized, rehearsed answers.

• 4. 

  4. Develop an ISSO portfolio to be used during the interview.

• 5. 

  5. During the interview, refer the interviewers to the portfolio.

• 6. 

  6. During the interview, use “we” and “our” as if you already worked at TCI.

     

QCDMAPT_F: Fortran version of QCDMAPT package

The QCDMAPT program package facilitates computations in the framework of dispersive approach to Quantum Chromodynamics. The QCDMAPT_F version of this package enables one to perform such computations with Fortran, whereas the previous version was developed for use with Maple system. The QCDMAPT_F package possesses the same basic features as its previous version. Namely, it embodies the calculated explicit expressions for relevant spectral functions up to the four–loop level and the subroutines for necessary integrals.

New version program summary

Program title: QCDMAPT_FCatalogue identifier: AEGP_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGP_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.: 10 786No. of bytes in distributed program, including test data, etc.: 332 329Distribution format: tar.gzProgramming language: Fortran 77 and higherComputer: Any which supports Fortran 77Operating system: Any which supports Fortran 77Classification: 11.1, 11.5, 11.6External routines: MATHLIB routine RADAPT (D102) from CERNLIB Program Library [1]Catalogue identifier of previous version: AEGP_v1_0Journal reference of previous version: Comput. Phys. Comm. 181 (2010) 1769Does the new version supersede the previous version?: No. This version provides an alternative to the previous, Maple, version.Nature of problem: A central object of the dispersive (or “analytic”) approach to Quantum Chromodynamics [2,3] is the so-called spectral function, which can be calculated by making use of the strong running coupling. At the one-loop level the latter has a quite simple form and the relevant spectral function can easily be calculated. However, at the higher loop levels the strong running coupling has a rather cumbersome structure. Here, the explicit calculation of corresponding spectral functions represents a somewhat complicated task (see Section 3 and Appendix B of Ref. [4]), whereas their numerical evaluation requires a lot of computational resources and essentially slows down the overall computation process.Solution method: The developed package includes the calculated explicit expressions for relevant spectral functions up to the four-loop level and the subroutines for necessary integrals.Reasons for new version: The previous version of the package (Ref. [4]) was developed for use with Maple system. The new version is developed for Fortran programming language.Summary of revisions: The QCDMAPT_F package consists of the main program (QCDMAPT_F.f) and two samples of the file containing the values of input parameters (QCDMAPT_F.i1 and QCDMAPT_F.i2). The main program includes the definitions of relevant spectral functions and subroutines for necessary integrals. The main program also provides an example of computation of the values of (M)APT spacelike/timelike expansion functions for the specified set of input parameters and (as an option) generates the output data files with values of these functions over the given kinematic intervals.Additional comments: For the proper functioning of QCDMAPT_F package, the “MATHLIB” CERNLIB library [1] has to be installed.Running time: The running time of the main program with sample set of input parameters specified in the file QCDMAPT_F.i2 is about a minute (depends on CPU).References:

• [1] 

  Subroutine D102 of the “MATHLIB” CERNLIB library, URL addresses: http://cernlib.web.cern.ch/cernlib/mathlib.html, http://wwwasdoc.web.cern.ch/wwwasdoc/shortwrupsdir/d102/top.html.

• [2] 

  D.V. Shirkov, I.L. Solovtsov, Phys. Rev. Lett. 79 (1997) 1209;   K.A. Milton, I.L. Solovtsov, Phys. Rev. D 55 (1997) 5295;   K.A. Milton, I.L. Solovtsov, Phys. Rev. D 59 (1999) 107701;   I.L. Solovtsov, D.V. Shirkov, Theor. Math. Phys. 120 (1999) 1220;   D.V. Shirkov, I.L. Solovtsov, Theor. Math. Phys. 150 (2007) 132.

• [3] 

  A.V. Nesterenko, Phys. Rev. D 62 (2000) 094028;   A.V. Nesterenko, Phys. Rev. D 64 (2001) 116009;   A.V. Nesterenko, Int. J. Mod. Phys. A 18 (2003) 5475;   A.V. Nesterenko, J. Papavassiliou, J. Phys. G 32 (2006) 1025;   A.V. Nesterenko, Nucl. Phys. B (Proc. Suppl.) 186 (2009) 207.

• [4] 

  A.V. Nesterenko, C. Simolo, Comput. Phys. Comm. 181 (2010) 1769.

     

Fast computation of close-coupling exchange integrals using polynomials in a tree representation

The semi-classical atomic-orbital close-coupling method is a well-known approach for the calculation of cross sections in ion–atom collisions. It strongly relies on the fast and stable computation of exchange integrals. We present an upgrade to earlier implementations of the Fourier-transform method.For this purpose, we implement an extensive library for symbolic storage of polynomials, relying on sophisticated tree structures to allow fast manipulation and numerically stable evaluation. Using this library, we considerably speed up creation and computation of exchange integrals. This enables us to compute cross sections for more complex collision systems.

Program summary

Program title: TXINTCatalogue identifier: AEHS_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHS_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.: 12 332No. of bytes in distributed program, including test data, etc.: 157 086Distribution format: tar.gzProgramming language: Fortran 95Computer: All with a Fortran 95 compilerOperating system: All with a Fortran 95 compilerRAM: Depends heavily on input, usually less than 100 MiBClassification: 16.10Nature of problem: Analytical calculation of one- and two-center exchange matrix elements for the close-coupling method in the impact parameter model.Solution method: Similar to the code of Hansen and Dubois [1], we use the Fourier-transform method suggested by Shakeshaft [2] to compute the integrals. However, we heavily speed up the calculation using a library for symbolic manipulation of polynomials.Restrictions: We restrict ourselves to a defined collision system in the impact parameter model.Unusual features: A library for symbolic manipulation of polynomials, where polynomials are stored in a space-saving left-child right-sibling binary tree. This provides stable numerical evaluation and fast mutation while maintaining full compatibility with the original code.Additional comments: This program makes heavy use of the new features provided by the Fortran 90 standard, most prominently pointers, derived types and allocatable structures and a small portion of Fortran 95. Only newer compilers support these features. Following compilers support all features needed by the program.

• • 

  GNU Fortran Compiler “gfortran” from version 4.3.0

• • 

  GNU Fortran 95 Compiler “g95” from version 4.2.0

• • 

  Intel Fortran Compiler “ifort” from version 11.0

Running time: Heavily dependent on input, usually less than one CPU second.References:

• [1] 

  J.-P. Hansen, A. Dubois, Comput. Phys. Commun. 67 (1992) 456.

• [2] 

  R. Shakeshaft, J. Phys. B: At. Mol. Opt. Phys. 8 (1975) L134.

     

Spanners in sparse graphs

A t-spanner of a graph G is a spanning subgraph S in which the distance between every pair of vertices is at most t times their distance in G. If S is required to be a tree then S is called a tree t-spanner of G. In 1998, Fekete and Kremer showed that on unweighted planar graphs deciding whether G admits a tree t-spanner is polynomial time solvable for t?3 and is NP-complete when t is part of the input. They also left as an open problem if the problem is polynomial time solvable for every fixed t?4. In this work we resolve the open question of Fekete and Kremer by proving much more general results:

• • 

  The problem of finding a t-spanner of treewidth at most k in a given planar graph G is fixed parameter tractable parameterized by k and t. Moreover, for every fixed t and k, the running time of our algorithm is linear.

• • 

  Our technique allows to extend the result from planar graphs to much more general classes of graphs. An apex graph is a graph that can be made planar by the removal of a single vertex. We prove that the problem of finding a t-spanner of treewidth k is fixed parameter tractable on graphs that do not contain some fixed apex graph as a minor, i.e. on apex-minor-free graphs. The class of apex-minor-free graphs contains planar graphs and graphs of bounded genus.

• • 

  Finally, we show that the tractability border of the t-spanner problem cannot be extended beyond the class of apex-minor-free graphs and in this sense our results are tight. In particular, for every t?4, the problem of finding a tree t-spanner is NP-complete on K6-minor-free graphs.

     

FARM_2DRMP: A version of FARM for use with 2DRMP

To complete the 2DRMP package an asymptotic program, such as FARM, is needed. The original version of FARM is designed to construct the physical R-matrix, R, from surface amplitudes contained in the H-file. However, in 2DRMP, R has already been constructed for each scattering energy during propagation. Therefore, this modified version of FARM, known as FARM_2DRMP, has been developed solely for use with 2DRMP.

New version program summary

Program title: FARM_2DRMPCatalogue identifier: ADAZ_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADAZ_v1_1.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 806No. of bytes in distributed program, including test data, etc.: 134 462Distribution format: tar.gzProgramming language: Fortran 95 and MPIComputer: Tested on CRAY XT4 [1]; IBM eServer 575 [2]; Itanium II cluster [3]Operating system: Tested on UNICOS/lc [1]; IBM AIX [2]; Red Hat Linux Enterprise AS [3]Has the code been vectorized or parallelized?: Yes. 16 cores were used for the small test runClassification: 2.4External routines: BLAS, LAPACKDoes the new version supersede the previous version?: NoNature of problem: The program solves the scattering problem in the asymptotic region of R-matrix theory where exchange is negligible.Solution method: A radius is determined at which the wave function, calculated as a Gailitis expansion [4] with accelerated summing [5] over terms, converges. The R-matrix is propagated from the boundary of the internal region to this radius and the K-matrix calculated. Collision strengths or cross sections may be calculated.Reasons for new version: To complete the 2DRMP package [6] an asymptotic program, such as FARM [7], is needed. The original version of FARM is designed to construct the physical R-matrix, R, from surface amplitudes contained in the H-file. However, in 2DRMP, R, has already been constructed for each scattering energy during propagation and each R is stored in one of the RmatT files described in Fig. 8 of [6]. Therefore, this modified version of FARM, known as FARM_2DRMP, has been developed solely for use with 2DRMP. Instructions on its use and corresponding test data is provided with 2DRMP [6].Summary of revisions: FARM_2DRMP contains two codes, farm.f and farm_par.f90. The former is a serial code while the latter is a parallel F95 code that employs an MPI harness to enable the nenergy energies to be computed simultaneously across ncore cores, with each core processing either ⌊nenergy/ncore⌋ or ⌈nenergy/ncore⌉ energies. The input files, input.d and H, and the output file farm.out are as described in [7]. Both codes read R directly from RmatT.Restrictions: FARM_2DRMP is for use solely with 2DRMP and for a specified L,S and Π combination. The energy range specified in input.d must match that specified in energies.data.Running time: The wall clock running time for the small test run using 16 cores and performed on [3] is 9 secs.References:

• [1] 

  HECToR, CRAY XT4 running UNICOS/lc, http://www.hector.ac.uk/, visited 22 July, 2009.

• [2] 

  HPCx, IBM eServer 575 running IBM AIX, http://www.hpcx.ac.uk/, visited 22 July, 2009.

• [3] 

  HP Cluster, Itanium II cluster running Red Hat Linux Enterprise AS, Queen's University Belfast, http://www.qub.ac.uk/directorates/InformationServices/Research/HighPerformanceComputing/Services/Hardware/HPResearch/, visited 22 July, 2009.

• [4] 

  M. Gailitis, J. Phys. B 9 (1976) 843.

• [5] 

  C.J. Noble, R.K. Nesbet, Comput. Phys. Comm. 33 (1984) 399.

• [6] 

  N.S. Scott, M.P. Scott, P.G. Burke, T. Stitt, V. Faro-Maza, C. Denis, A. Maniopoulou, Comput. Phys. Comm. 180 (12) (2009) 2424–2449, this issue.

• [7] 

  V.M. Burke, C.J. Noble, Comput. Phys. Comm. 85 (1995) 471.

     

tmLQCD: A program suite to simulate Wilson twisted mass lattice QCD

We discuss a program suite for simulating Quantum Chromodynamics on a 4-dimensional space–time lattice. The basic Hybrid Monte Carlo algorithm is introduced and a number of algorithmic improvements are explained. We then discuss the implementations of these concepts as well as our parallelisation strategy in the actual simulation code. Finally, we provide a user guide to compile and run the program.

Program summary

Program title: tmLQCDCatalogue identifier: AEEH_v1_0Program summary URL::http://cpc.cs.qub.ac.uk/summaries/AEEH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence (GPL)No. of lines in distributed program, including test data, etc.: 122 768No. of bytes in distributed program, including test data, etc.: 931 042Distribution format: tar.gzProgramming language: C and MPIComputer: anyOperating system: any with a standard C compilerHas the code been vectorised or parallelised?: Yes. One or optionally any even number of processors may be used. Tested with up to 32 768 processorsRAM: no typical values availableClassification: 11.5External routines: LAPACK [1] and LIME [2] libraryNature of problem: Quantum ChromodynamicsSolution method: Markov Chain Monte Carlo using the Hybrid Monte Carlo algorithm with mass preconditioning and multiple time scales [3]. Iterative solver for large systems of linear equations.Restrictions: Restricted to an even number of (not necessarily mass degenerate) quark flavours in the Wilson or Wilson twisted mass formulation of lattice QCD.Running time: Depending on the problem size, the architecture and the input parameters from a few minutes to weeks.References:

• [1] 

  http://www.netlib.org/lapack/.

• [2] 

  USQCD, http://usqcd.jlab.org/usqcd-docs/c-lime/.

• [3] 

  C. Urbach, K. Jansen, A. Shindler, U. Wenger, Comput. Phys. Commun. 174 (2006) 87, hep-lat/0506011.

     

An improved version of the Green's function molecular dynamics method

This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer.

New version program summary

Program title: FixGFC/FixGFMD v1.12Catalogue identifier: AECW_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.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.: 206 436No. of bytes in distributed program, including test data, etc.: 4 314 850Distribution format: tar.gzProgramming language: C++Computer: AllOperating system: LinuxHas the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives.RAM: Depends on the problemClassification: 7.7External routines: LAMMPS (http://lammps.sandia.gov/), MPI (http://www.mcs.anl.gov/research/projects/mpi/), FFT (http://www.fftw.org/)Catalogue identifier of previous version: AECW_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1004Does the new version supersede the previous version?: YesNature of problem: Green's function molecular dynamics (GFMD) is a coarse-graining method that enables one to investigate the full elastic response of an interface between a semi-infinite solid and a contact while taking only the surface atoms in the solid into consideration. The effect of long-range elastic deformations on the surface atoms from the semi-infinite solid is replaced by effective elastic interactions, thus reducing the problem from three dimensions to two dimensions without compromising the physical essence of the problem.Solution method: See “Nature of problem”.Reasons for new version: The basic theory underlying the new version is essentially the same as the previous one, while the special treatment to reduce the finite size effect on effective elastic coefficients at the Γ-point is now realized in a physically meaningful manner. Finite size effects are an important issue in molecular dynamics simulations, particularly for GFMD, they result in a violation of the acoustic sum rule (ASR) for the effective elastic coefficients measured at the Γ-point (ΦΓ). In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered by setting their eigenvalues corresponding to the acoustic modes to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. We therefore adopt a new algorithm to enforce the ASR for ΦΓ (Kong, 2010 [3]) which is implemented in this revision.Summary of revisions: Assuming the lattice under study consists of surface unit cells with n basis atoms labeled by k=1,2,…,n. When all atoms in the lattice are moved by the same amount, i.e., the crystal is rigidly translated, the force on any atom must be zero. This is known as the translational invariance, leading to the so-called acoustic sum rule: k^′_∑Φkα,k^′β(Γ)=0 where Φkα,k^′β(Γ) is the kα,k^′β component of the effective elastic coefficients at the Γ-point; we will denote it as ΦΓ hereafter. α and β enumerate the Cartesian directions. In addition, ΦΓ should be Hermitian (or symmetric, since at the Γ-point, the imaginary part of ΦΓ is zero.) because of the commutative nature of the force constants: . These two properties are expected for ΦΓ, yet the ASR is not satisfied during the measurement (done by FixGFC) because of the finite size effect. A scheme is therefore needed to enforce ASR on ΦΓ afterwards, while the symmetric nature of ΦΓ should be retained.We list below the detailed scheme adopted to enforce ASR implemented in the improved version of GFMD together with some other revisions to the code after the previous release.

• 1. 

  In FixGFMD, the previously employed method to rescale the effective elastic coefficients at Γ is obsoleted. Instead, an iterative procedure is adopted to enforce the acoustic sum rule on ΦΓ (Kong, 2010 [3]). (i)  k′∑Φkα,k′β=0 is enforced by subtracting each element involved by a constant term; this procedure removes the violation of the acoustic sum rule, while in turn, usually destroys the symmetry of the force constant matrix. (ii)  Symmetry is restored by replacing Φkα,k′β and Φk′β,kα with their average value; this will ensure the symmetry of the matrix, however, it will break the acoustic sum rule slightly. (iii)  The above steps are repeated for several iterations, followed by a “symmetric ASR”: similar to step (i), k′∑Φkα,k′β=0 is enforced but only elements with k′?k are subtracted by a constant value, while setting Φk′β,kα=Φkα,k′β.

• 2. 

  In FixGFC, the surface lattice vectors and the relative positions of each atom in the surface unit cell are also computed and written to the binary file, which can be used in FixGFMD to set the equilibrium positions in the Green's function slab based on their lattice indices.

• 3. 

  In FixGFMD, it is now possible to output the total forces applied on atoms in the Green's function slab before applying the elastic forces as a thermal quantity for LAMMPS (http://lammps.sandia.gov [6]). It is also possible to reset these forces to zero before applying the elastic forces.

• 4. 

  In both FixGFC and FixGFMD, the dependence on MPI-enabled FFTW 2.1.5 was lifted. The Fourier transformations are now accomplished by calling the FFT3d wrapper from standard package “kspace” of LAMMPS (Plimpton, 1995; Plimpton et al., 1997; http://lammps.sandia.gov [4,5,6]).

Restrictions: By adopting the new method to enforce the acoustic sum rule, the restriction that atoms in the Green's function slab must be in the same layer is lifted, while it is still necessary to ensure that the mean equilibrium positions of atoms in the Green's function slab satisfy the Born–von Karman boundary condition. In addition, only deformations within the harmonic regime are expected in the slab during Green's function molecular dynamics simulations.Additional comments: The new version is not compatible with the previous one: the contents in the binary file are different and therefore the effective elastic coefficients measured by the previous version of FixGFC cannot be used by the current version of FixGFMD.Running time: FixGFC varies from minutes to days, like a typical molecular dynamics simulation, depending on the system size, the number of processors used, and the complexity of the force field. FixGFMD varies from seconds to hours, depending on the system size and the number of processors used.References:

• [1] 

  L.T. Kong, G. Bartels, C. Campañá, C. Denniston, M.H. Müser, Implementation of Green's function molecular dynamics: An extension to LAMMPS, Computer Physics Communications 180 (6) (2009) 1004–1010.

• [2] 

  C. Campañá, M.H. Müser, Practical Green's function approach to the simulation of elastic semi-infinite solids, Physical Review B (Condensed Matter and Materials Physics) 74 (7) (2006) 075420.

• [3] 

  L.T. Kong, Phonon dispersion measured directly from molecular dynamics simulations, Computer Physics Communications (2010), submitted for publication.

• [4] 

  S.J. Plimpton, Fast parallel algorithms for short-range molecular dynamics, J. Comp. Phys. 117 (1995) 1–19.

• [5] 

  S.J. Plimpton, R. Pollock, M. Stevens, Particle-mesh Ewald and RRESPA for parallel molecular dynamics simulation, in: Proc. of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN, 1997.

• [6] 

  Large-scale Atomic/Molecular Massively Parallel Simulator, LAMMPS, available at: http://lammps.sandia.gov.