Monte Carlo event generator for black hole production and decay in proton-proton collisions - QBH version 1.02

We describe the Monte Carlo event generator for black hole production and decay in proton-proton collisions - QBH version 1.02. The generator implements a model for quantum black hole production and decay based on the conservation of local gauge symmetries and democratic decays. The code in written entirely in C++ and interfaces to the PYTHIA 8 Monte Carlo code for fragmentation and decays.

Program summary

Program title: QBHCatalogue identifier: AEGU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGU_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 048No. of bytes in distributed program, including test data, etc.: 118 420Distribution format: tar.gzProgramming language: C++Computer: x86Operating system: Scientific Linux, Mac OS XRAM: 1 GBClassification: 11.6External routines: PYTHIA 8130 (http://home.thep.lu.se/~torbjorn/pythiaaux/present.html) and LHAPDF (http://projects.hepforge.org/lhapdf/)Nature of problem: Simulate black hole production and decay in proton-proton collision.Solution method: Monte Carlo simulation using importance sampling.Running time: Eight events per second.     

CPsuperH2.0: An improved computational tool for Higgs phenomenology in the MSSM with explicit CP violation

We describe the Fortran code CPsuperH2.0, which contains several improvements and extensions of its predecessor CPsuperH. It implements improved calculations of the Higgs-boson pole masses, notably a full treatment of the 4×4 neutral Higgs propagator matrix including the Goldstone boson and a more complete treatment of threshold effects in self-energies and Yukawa couplings, improved treatments of two-body Higgs decays, some important three-body decays, and two-loop Higgs-mediated contributions to electric dipole moments. CPsuperH2.0 also implements an integrated treatment of several B-meson observables, including the branching ratios of Bs→μ⁺μ⁻, Bd→τ⁺τ⁻, Bu→τν, B→Xsγ and the latter's CP-violating asymmetry ACP, and the supersymmetric contributions to the mass differences. These additions make CPsuperH2.0 an attractive integrated tool for analyzing supersymmetric CP and flavour physics as well as searches for new physics at high-energy colliders such as the Tevatron, LHC and linear colliders.¹

Program summary

Program title: CPsuperH2.0Catalogue identifier: ADSR_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSR_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.: 13 290No. of bytes in distributed program, including test data, etc.: 89 540Distribution format: tar.gzProgramming language: Fortran 77Computer: PC running under Linux and computers in Unix environmentOperating system: LinuxRAM: 32 MbytesClassification: 11.1Catalogue identifier of the previous version: ADSR_v1_0Journal reference of the previous version: CPC 156 (2004) 283Does the new version supersede the previous version?: YesNature of problem: The calculations of mass spectrum, decay widths and branching ratios of the neutral and charged Higgs bosons in the Minimal Supersymmetric Standard Model with explicit CP violation have been improved. The program is based on recent renormalization-group-improved diagrammatic calculations that include dominant higher-order logarithmic and threshold corrections, b-quark Yukawa-coupling resummation effects and improved treatment of Higgs-boson pole-mass shifts. The couplings of the Higgs bosons to the Standard Model gauge bosons and fermions, to their supersymmetric partners and all the trilinear and quartic Higgs-boson self-couplings are also calculated. The new implementations include a full treatment of the 4×4(2×2) neutral (charged) Higgs propagator matrix together with the center-of-mass dependent Higgs-boson couplings to gluons and photons, two-loop Higgs-mediated contributions to electric dipole moments, and an integrated treatment of several B-meson observables.Solution method: One-dimensional numerical integration for several Higgs-decay modes, iterative treatment of the threshold corrections and Higgs-boson pole masses, and the numerical diagonalization of the neutralino mass matrix.Reasons for new version: Mainly to provide a coherent numerical framework which calculates consistently observables for both low- and high-energy experiments.Summary of revisions: Improved treatment of Higgs-boson masses and propagators. Improved treatment of Higgs-boson couplings and decays. Higgs-mediated two-loop electric dipole moments. B-meson observables.Running time: Less than 0.1 seconds.     

Universal interface of TAUOLA: Technical and physics documentation

Because of their narrow width, τ decays can be well separated from their production process. Only spin degrees of freedom connect these two parts of the physics process of interest for high energy collision experiments. In the following, we present a Monte Carlo algorithm which is based on that property. The interface supplements events generated by other programs, with τ decays. Effects of spin, including transverse degrees of freedom, genuine weak corrections or of new physics may be taken into account at the time when a τ decay is generated and written into an event record. The physics content of the C++ interface is already now richer than its FORTRAN predecessor.Program summaryProgram title: TAUOLA++, versions 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6Catalogue identifier: AELH_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELH_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.: 649 068No. of bytes in distributed program, including test data, etc.: 6 544 479Distribution format: tar.gzProgramming language: C++, FORTRAN77Computer: PCs, workstationsOperating system: Linux, MacOSRAM: $<10\text{MB}$Classification: 11.2External routines: HepMC (http://lcgapp.cern.ch/project/simu/HepMC/), optional; PYTHIA8 (http://home.thep.lu.se/~torbjorn/Pythia.html)Subprograms used:     

4.

NMSDECAY: A Fortran code for supersymmetric particle decays in the Next-to-Minimal Supersymmetric Standard Model     

Debottam Das  Ulrich Ellwanger  Ana M. Teixeira 《Computer Physics Communications》2012,183(3):774-779

     

5.

The Fedosov ∗-product in Mathematica     

Jaromir Tosiek 《Computer Physics Communications》2010,181(3):704

The computer program ‘Fecom.nb’ implementing the Fedosov ∗-product in Darboux coordinates is presented. It has been written in Mathematica 6.0 but it can be easily modified to be run in some earlier version of Mathematica. To optimize computations elements of the Weyl algebra are treated as polynomials. Several procedures which order the terms are included.

New version program summary

Program title: Fecom.nbCatalogue identifier: AEBU_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBU_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.: 8107No. of bytes in distributed program, including test data, etc.: 42 175Distribution format: tar.gzProgramming language: Mathematica v.6.0Computer: AllOperating system: AllRAM: Sufficient for installation of MathematicaClassification: 17.16Catalogue identifier of previous version: AEBU_v1_0Journal reference of previous version: Comput. Phys. Comm. 179 (2008) 924Does the new version supersede the previous version?: YesNature of problem: Computing the ∗-product of the Weyl type in the Fedosov formalism in a Darboux chart.Solution method: Inputting the dimension of the phase space, coefficients of the symplectic connection, the range of approximation and the functions to be multiplied; computing the Abelian connection and the flat sections of the Weyl bundle representing the multiplied functions; calculating the projection of the ○-product of these flat sections on the phase space.Reasons for new version: Optimization and including the trivial cases - deformations of the 0th and the 1st order.Summary of revisions: In case we calculate the ∗-product up to the odd power hk, it is necessary to know the Abelian connection and the flat sections up to the degree 2k−1. But for the even power hk, it is sufficient to know the Abelian connection and the flat sections up to the degree 2k−2. In the new version of the program we use this observation. Now the running time of the program for even powers hk is shorter than in the previous version. The 0th and the 1st order of the deformation are trivial - the pointwise product of functions and the Poisson bracket of them respectively. But to make the program complete we added the possibility of calculating also these trivial situations. The new version of the program works then also for the maximal power of h equal 0 and 1.Running time: The test run, provided with the distribution, took approximately 2 minutes to run using Mathematica 7.0 on a Windows XP machine.     

6.

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations     

S. Jadach  M. Skrzypek 《Computer Physics Communications》2010,181(2):393-412

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 5×¹⁰−4. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods.

New version program summary

Program title: EvolFMC v.2Catalogue identifier: AEFN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFN_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 binary test data, etc.: 66 456 (7407 lines of C++ code)No. of bytes in distributed program, including test data, etc.: 412 752Distribution format: tar.gzProgramming language: C++Computer: PC, MacOperating system: Linux, Mac OS XRAM: Less than 256 MBClassification: 11.5External routines: ROOT (http://root.cern.ch/drupal/)Nature of problem: Solution of the QCD evolution equations for the parton momentum distributions of the DGLAP- and modified-DGLAP-type in the LO and NLO approximations.Solution method: Monte Carlo simulation of the Markovian process of a multiple emission of partons.Restrictions:

1.

Limited to the case of massless partons.

2.

Implemented in the LO and NLO approximations only.

3.

Weighted events only.

Unusual features: Modified-DGLAP evolutions included up to the NLO level.Additional comments: Technical precision established at 5×¹⁰−4.Running time: For the 10⁶ events at 100 GeV: DGLAP NLO: 27s; C^′-type modified DGLAP NLO: 150s (MacBook Pro with Mac OS X v.10.5.5, 2.4 GHz Intel Core 2 Duo, gcc 4.2.4, single thread).     

7.

A brief introduction to PYTHIA 8.1     

Torbjörn Sjöstrand  Stephen Mrenna 《Computer Physics Communications》2008,178(11):852-867

     

8.

LIBERI: Library for numerical evaluation of electron-repulsion integrals     

Masayuki Toyoda  Taisuke Ozaki 《Computer Physics Communications》2010,181(8):1455-1463

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.     

9.

HypExp 2, Expanding hypergeometric functions about half-integer parameters     

Tobias Huber 《Computer Physics Communications》2008,178(10):755-776

In this article, we describe a new algorithm for the expansion of hypergeometric functions about half-integer parameters. The implementation of this algorithm for certain classes of hypergeometric functions in the already existing Mathematica package HypExp is described. Examples of applications in Feynman diagrams with up to four loops are given.

New version program summary

Program title:HypExp 2Catalogue identifier:ADXF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXF_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.:106 401No. of bytes in distributed program, including test data, etc.:2 668 729Distribution format:tar.gzProgramming language:MathematicaComputer:Computers running MathematicaOperating system:Linux, Windows, MacRAM:Depending on the complexity of the problemSupplementary material:Library files which contain the expansion of certain hypergeometric functions around their parameters are availableClassification:4.7, 5Does the new version supersede the previous version?:YesNature of problem:Expansion of hypergeometric functions about parameters that are integer and/or half-integer valued.Solution method:New algorithm implemented in Mathematica.Reasons for new version:Expansion about half-integer parameters.Summary of revisions:Ability to expand about half-integer valued parameters added.Restrictions:The classes of hypergeometric functions with half-integer parameters that can be expanded are listed below.Additional comments:The package uses the package HPL included in the distribution.Running time:Depending on the expansion.     

10.

SMMP v. 3.0—Simulating proteins and protein interactions in Python and Fortran     

Jan H. Meinke  Sandipan Mohanty 《Computer Physics Communications》2008,178(6):459-470

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more.

Program summary

Title of program:SMMPCatalogue identifier:ADOJ_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.htmlProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlProgramming language used:FORTRAN, PythonNo. of lines in distributed program, including test data, etc.:52 105No. of bytes in distributed program, including test data, etc.:599 150Distribution format:tar.gzComputer:Platform independentOperating system:OS independentRAM:2 MbytesClassification:3Does the new version supersede the previous version?:YesNature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins.Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles.Reasons for new version:API changes and increased functionality.Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings.Restrictions:The consumed CPU time increases with the size of protein molecule.Running time:Depends on the size of the simulated molecule.     

11.

JJGEN: A flexible program for generating lists of jj-coupled configuration state functions     

L. Sturesson  C. Froese Fischer 《Computer Physics Communications》2007,177(6):539-550

The success of large scale relativistic multiconfiguration Dirac-Hartree-Fock calculations for atomic systems rely on judiciously chosen configuration expansions. Dependent on the atomic system as well as on the studied properties, various correlation effects need to be considered. Based on the active set approach, this program allows the user to generate general lists of jj-coupled configuration state functions to be used as input to the grasp2K multiconfiguration Dirac-Hartree-Fock package [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. (2007), in press].

Program summary

Program title: JJGENCatalogue identifier: ADZG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZG_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 673No. of bytes in distributed program, including test data, etc.: 430 543Distribution format: tar.gzProgramming language: FortranComputer: Intel compatible PCOperating system: Linux, UnixWord size: 32 bitsClassification: 7.3Nature of problem: Generation of lists of jj-coupled configuration state functions to describe different electron correlation effects in many-electron atoms.Solution method: From a set of reference configurations a list of jj-coupled configuration state functions is generated by excitations to an active set of orbitals. Imposing restrictions on the allowed excitations the configuration expansion can be targeted to describe different correlation effects.Restrictions: The complexity of the cases that can be handled is entirely determined by the grasp2K package [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. (2007), in press] used for the generation of the electronic wave-functions.Running time: CPU time required to execute test cases: few seconds.     

12.

FDCSUSYDecay: An MSSM decay package     

Wei Qi  Jian-xiong Wang 《Computer Physics Communications》2007,177(4):378-390

     

13.

A program to compute exact hydrogenic radial integrals and Einstein coefficients     

Hoang-Binh Dy 《Computer Physics Communications》2009,180(10):2020

An exact expression for the dipole radial integral of hydrogen has been given by Gordon [Ann. Phys. 2 (1929) 1031]. It contains two hypergeometric functions F(a,b;c;x), which are difficult to calculate directly, when the (negative) integers a, b are large, as in the case of high Rydberg states of hydrogenic ions. We have derived a simple method [D. Hoang-Binh, Astron. Astrophys. 238 (1990) 449], using a recurrence relation to calculate exactly F, starting from two initial values, which are very easy to compute. We present here a numerical code using this method. The code computes exact hydrogenic radial integrals, oscillator strengths, Einstein coefficients, and lifetimes, for principal quantum numbers up to 1000.

Program summary

Program title: ba5.2Catalogue identifier: ADUU_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUU_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.: 1400No. of bytes in distributed program, including test data, etc.: 11 737Distribution format: tar.gzProgramming language: Fortran 77Computer: PC, iMacOperating system: Linux/Unix, MacOS 9.0RAM: Less than 1 MBClassification: 2, 2.2Catalogue identifier of previous version: ADUU_v1_0Journal reference of previous version: Comput. Phys. Comm. 166 (2005) 191Does the new version supersede the previous version?: YesNature of problem: Exact calculation of atomic data.Solution method: Use of a recurrence relation to compute hypergeometric functions.Reasons for new version: This new version computes additional important related data, namely, the total Einstein coefficients, and radiative lifetimes.Summary of revisions: Values of the total Einstein transition probability from an upper level n to a lower level n^′ are computed, as well as the radiative lifetime of a level n.Running time: About 2 seconds     

14.

An improved version of ISICS: A program for calculating K-, L- and M-shell cross sections from PWBA and ECPSSR theory using a personal computer     

Sam J. Cipolla 《Computer Physics Communications》2008,179(8):616

The formatting of the M-shell atomic parameters imbedded in file XCSC.H in ISICS has been corrected. The problem only affected cross section calculations for Uranium and heavier elements. The corrected version of ISICS has been re-compiled and is now available.

New version program summary

Program title: ISICSCatalogue identifier: ADDS_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADDS_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.: 4645No. of bytes in distributed program, including test data, etc.: 106 731Distribution format: tar.gzProgramming language: C++Computer: 80486 or higher-level PCsOperating system: WINDOWS 98 through WINDOWS XPClassification: 16.7Does the new version supersede the previous version?: YesNature of problem: Ionization and X-ray production cross section calculations for ion-atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Reasons for new version: The formatting of the M-shell atomic parameters involving cross section calculations for Uranium and heavier elements needed to be corrected.Summary of revisions: The affected file XCSC.H in ISICS has been corrected and ISICS has been recompiled.Restrictions: The consumed CPU time increases with the atomic shell (K, L, M), but execution is still very fast.Running time: This depends on which shell and the number of different energies to be used in the calculation. For example, to calculate K-shell cross sections for protons striking carbon for 19 different proton energies it took less than 10 s; to calculate M-shell cross sections for protons on gold for 21 proton energies it took 4.2 min.     

15.

TiReX: Replica-exchange molecular dynamics using Tinker     

Evgeni S. Penev  Sotiria Lampoudi  Joan-Emma Shea 《Computer Physics Communications》2009,180(10):2013-4886

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.     

16.

QDENSITY—A Mathematica quantum computer simulation     

Bruno Juliá-Díaz 《Computer Physics Communications》2009,180(3):440

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc.

New version program summary

Program title: QDENSITY 2.0Catalogue identifier: ADXH_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_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.: 26 055No. of bytes in distributed program, including test data, etc.: 227 540Distribution format: tar.gzProgramming language: Mathematica 6.0Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Catalogue identifier of previous version: ADXH_v1_0Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914Classification: 4.15Does the new version supersede the previous version?: Offers an alternative, more up to date, implementationNature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters.Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.     

17.

Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at NLO     

B. Gebremariam  S.K. Bogner  T. Duguet 《Computer Physics Communications》2010,181(6):1167-1177

We present the first of a two-part Mathematica notebook collection that implements a symbolic approach for the application of the density matrix expansion (DME) to the Hartree-Fock (HF) energy from a chiral effective field theory (EFT) three-nucleon interaction at N²LO. The final output from the notebooks is a Skyrme-like energy density functional that provides a quasi-local approximation to the non-local HF energy. In this paper, we discuss the derivation of the HF energy and its simplification in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Furthermore, a set of steps is described and illustrated on how to extend the approach to other three-nucleon interactions.

Program summary

Program title: SymbHFNNNCatalogue identifier: AEGC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGC_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.: 96 666No. of bytes in distributed program, including test data, etc.: 378 083Distribution format: tar.gzProgramming language: Mathematica 7.1Computer: Any computer running Mathematica 6.0 and later versionsOperating system: Windows Xp, Linux/UnixRAM: 256 MbClassification: 5, 17.16, 17.22Nature of problem: The calculation of the HF energy from the chiral EFT three-nucleon interaction at N²LO involves tremendous spin-isospin algebra. The problem is compounded by the need to eventually obtain a quasi-local approximation to the HF energy, which requires the HF energy to be expressed in terms of scalar/vector-isoscalar/isovector parts of the one-body density matrix. The Mathematica notebooks discussed in this paper solve the latter issue.Solution method: The HF energy from the chiral EFT three-nucleon interaction at N²LO is cast into a form suitable for an automatic simplification of the spin-isospin traces. Several Mathematica functions and symbolic manipulation techniques are used to obtain the result in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix.Running time: Several hours     

18.

SPheno 3.1: extensions including flavour,CP-phases and models beyond the MSSM     

W. Porod  F. Staub 《Computer Physics Communications》2012,183(11):2458-2469

     

19.

SANCscope—v.1.00     

A. Andonov  D. Bardin  S. Bondarenko  L. Kalinovskaya  W. von Schlippe 《Computer Physics Communications》2006,174(6):481-517

     

20.

Precision studies of the NNLO DGLAP evolution at the LHC with Candia     

Alessandro Cafarella  Claudio Corianò  Marco Guzzi 《Computer Physics Communications》2008,179(9):665-684

     

The Fedosov ∗-product in Mathematica

The computer program ‘Fecom.nb’ implementing the Fedosov ∗-product in Darboux coordinates is presented. It has been written in Mathematica 6.0 but it can be easily modified to be run in some earlier version of Mathematica. To optimize computations elements of the Weyl algebra are treated as polynomials. Several procedures which order the terms are included.

New version program summary

Program title: Fecom.nbCatalogue identifier: AEBU_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBU_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.: 8107No. of bytes in distributed program, including test data, etc.: 42 175Distribution format: tar.gzProgramming language: Mathematica v.6.0Computer: AllOperating system: AllRAM: Sufficient for installation of MathematicaClassification: 17.16Catalogue identifier of previous version: AEBU_v1_0Journal reference of previous version: Comput. Phys. Comm. 179 (2008) 924Does the new version supersede the previous version?: YesNature of problem: Computing the ∗-product of the Weyl type in the Fedosov formalism in a Darboux chart.Solution method: Inputting the dimension of the phase space, coefficients of the symplectic connection, the range of approximation and the functions to be multiplied; computing the Abelian connection and the flat sections of the Weyl bundle representing the multiplied functions; calculating the projection of the ○-product of these flat sections on the phase space.Reasons for new version: Optimization and including the trivial cases - deformations of the 0th and the 1st order.Summary of revisions: In case we calculate the ∗-product up to the odd power hk, it is necessary to know the Abelian connection and the flat sections up to the degree 2k−1. But for the even power hk, it is sufficient to know the Abelian connection and the flat sections up to the degree 2k−2. In the new version of the program we use this observation. Now the running time of the program for even powers hk is shorter than in the previous version. The 0th and the 1st order of the deformation are trivial - the pointwise product of functions and the Poisson bracket of them respectively. But to make the program complete we added the possibility of calculating also these trivial situations. The new version of the program works then also for the maximal power of h equal 0 and 1.Running time: The test run, provided with the distribution, took approximately 2 minutes to run using Mathematica 7.0 on a Windows XP machine.     

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 5×¹⁰−4. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods.

New version program summary

Program title: EvolFMC v.2Catalogue identifier: AEFN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFN_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 binary test data, etc.: 66 456 (7407 lines of C++ code)No. of bytes in distributed program, including test data, etc.: 412 752Distribution format: tar.gzProgramming language: C++Computer: PC, MacOperating system: Linux, Mac OS XRAM: Less than 256 MBClassification: 11.5External routines: ROOT (http://root.cern.ch/drupal/)Nature of problem: Solution of the QCD evolution equations for the parton momentum distributions of the DGLAP- and modified-DGLAP-type in the LO and NLO approximations.Solution method: Monte Carlo simulation of the Markovian process of a multiple emission of partons.Restrictions:

1.

Limited to the case of massless partons.

2.

Implemented in the LO and NLO approximations only.

3.

Weighted events only.

Unusual features: Modified-DGLAP evolutions included up to the NLO level.Additional comments: Technical precision established at 5×¹⁰−4.Running time: For the 10⁶ events at 100 GeV: DGLAP NLO: 27s; C^′-type modified DGLAP NLO: 150s (MacBook Pro with Mac OS X v.10.5.5, 2.4 GHz Intel Core 2 Duo, gcc 4.2.4, single thread).     

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.     

HypExp 2, Expanding hypergeometric functions about half-integer parameters

In this article, we describe a new algorithm for the expansion of hypergeometric functions about half-integer parameters. The implementation of this algorithm for certain classes of hypergeometric functions in the already existing Mathematica package HypExp is described. Examples of applications in Feynman diagrams with up to four loops are given.

New version program summary

Program title:HypExp 2Catalogue identifier:ADXF_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXF_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.:106 401No. of bytes in distributed program, including test data, etc.:2 668 729Distribution format:tar.gzProgramming language:MathematicaComputer:Computers running MathematicaOperating system:Linux, Windows, MacRAM:Depending on the complexity of the problemSupplementary material:Library files which contain the expansion of certain hypergeometric functions around their parameters are availableClassification:4.7, 5Does the new version supersede the previous version?:YesNature of problem:Expansion of hypergeometric functions about parameters that are integer and/or half-integer valued.Solution method:New algorithm implemented in Mathematica.Reasons for new version:Expansion about half-integer parameters.Summary of revisions:Ability to expand about half-integer valued parameters added.Restrictions:The classes of hypergeometric functions with half-integer parameters that can be expanded are listed below.Additional comments:The package uses the package HPL included in the distribution.Running time:Depending on the expansion.     

SMMP v. 3.0—Simulating proteins and protein interactions in Python and Fortran

We describe a revised and updated version of the program package SMMP. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques. SMMP 3.0 sports a revised API increasing its flexibility, an implementation of the Lund force field, multi-molecule simulations, a parallel implementation of the energy function, Python bindings, and more.

Program summary

Title of program:SMMPCatalogue identifier:ADOJ_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADOJ_v3_0.htmlProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlProgramming language used:FORTRAN, PythonNo. of lines in distributed program, including test data, etc.:52 105No. of bytes in distributed program, including test data, etc.:599 150Distribution format:tar.gzComputer:Platform independentOperating system:OS independentRAM:2 MbytesClassification:3Does the new version supersede the previous version?:YesNature of problem:Molecular mechanics computations and Monte Carlo simulation of proteins.Solution method:Utilizes ECEPP2/3, FLEX, and Lund potentials. Includes Monte Carlo simulation algorithms for canonical, as well as for generalized ensembles.Reasons for new version:API changes and increased functionality.Summary of revisions:Added Lund potential; parameters used in subroutines are now passed as arguments; multi-molecule simulations; parallelized energy calculation for ECEPP; Python bindings.Restrictions:The consumed CPU time increases with the size of protein molecule.Running time:Depends on the size of the simulated molecule.     

JJGEN: A flexible program for generating lists of jj-coupled configuration state functions

The success of large scale relativistic multiconfiguration Dirac-Hartree-Fock calculations for atomic systems rely on judiciously chosen configuration expansions. Dependent on the atomic system as well as on the studied properties, various correlation effects need to be considered. Based on the active set approach, this program allows the user to generate general lists of jj-coupled configuration state functions to be used as input to the grasp2K multiconfiguration Dirac-Hartree-Fock package [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. (2007), in press].

Program summary

Program title: JJGENCatalogue identifier: ADZG_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZG_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 673No. of bytes in distributed program, including test data, etc.: 430 543Distribution format: tar.gzProgramming language: FortranComputer: Intel compatible PCOperating system: Linux, UnixWord size: 32 bitsClassification: 7.3Nature of problem: Generation of lists of jj-coupled configuration state functions to describe different electron correlation effects in many-electron atoms.Solution method: From a set of reference configurations a list of jj-coupled configuration state functions is generated by excitations to an active set of orbitals. Imposing restrictions on the allowed excitations the configuration expansion can be targeted to describe different correlation effects.Restrictions: The complexity of the cases that can be handled is entirely determined by the grasp2K package [P. Jönsson, X. He, C. Froese Fischer, I.P. Grant, Comput. Phys. Comm. (2007), in press] used for the generation of the electronic wave-functions.Running time: CPU time required to execute test cases: few seconds.     

A program to compute exact hydrogenic radial integrals and Einstein coefficients

An exact expression for the dipole radial integral of hydrogen has been given by Gordon [Ann. Phys. 2 (1929) 1031]. It contains two hypergeometric functions F(a,b;c;x), which are difficult to calculate directly, when the (negative) integers a, b are large, as in the case of high Rydberg states of hydrogenic ions. We have derived a simple method [D. Hoang-Binh, Astron. Astrophys. 238 (1990) 449], using a recurrence relation to calculate exactly F, starting from two initial values, which are very easy to compute. We present here a numerical code using this method. The code computes exact hydrogenic radial integrals, oscillator strengths, Einstein coefficients, and lifetimes, for principal quantum numbers up to 1000.

Program summary

Program title: ba5.2Catalogue identifier: ADUU_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUU_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.: 1400No. of bytes in distributed program, including test data, etc.: 11 737Distribution format: tar.gzProgramming language: Fortran 77Computer: PC, iMacOperating system: Linux/Unix, MacOS 9.0RAM: Less than 1 MBClassification: 2, 2.2Catalogue identifier of previous version: ADUU_v1_0Journal reference of previous version: Comput. Phys. Comm. 166 (2005) 191Does the new version supersede the previous version?: YesNature of problem: Exact calculation of atomic data.Solution method: Use of a recurrence relation to compute hypergeometric functions.Reasons for new version: This new version computes additional important related data, namely, the total Einstein coefficients, and radiative lifetimes.Summary of revisions: Values of the total Einstein transition probability from an upper level n to a lower level n^′ are computed, as well as the radiative lifetime of a level n.Running time: About 2 seconds     

An improved version of ISICS: A program for calculating K-, L- and M-shell cross sections from PWBA and ECPSSR theory using a personal computer

The formatting of the M-shell atomic parameters imbedded in file XCSC.H in ISICS has been corrected. The problem only affected cross section calculations for Uranium and heavier elements. The corrected version of ISICS has been re-compiled and is now available.

New version program summary

Program title: ISICSCatalogue identifier: ADDS_v3_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADDS_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.: 4645No. of bytes in distributed program, including test data, etc.: 106 731Distribution format: tar.gzProgramming language: C++Computer: 80486 or higher-level PCsOperating system: WINDOWS 98 through WINDOWS XPClassification: 16.7Does the new version supersede the previous version?: YesNature of problem: Ionization and X-ray production cross section calculations for ion-atom collisions.Solution method: Numerical integration of form factor using a logarithmic transform and Gaussian quadrature, plus exact integration limits.Reasons for new version: The formatting of the M-shell atomic parameters involving cross section calculations for Uranium and heavier elements needed to be corrected.Summary of revisions: The affected file XCSC.H in ISICS has been corrected and ISICS has been recompiled.Restrictions: The consumed CPU time increases with the atomic shell (K, L, M), but execution is still very fast.Running time: This depends on which shell and the number of different energies to be used in the calculation. For example, to calculate K-shell cross sections for protons striking carbon for 19 different proton energies it took less than 10 s; to calculate M-shell cross sections for protons on gold for 21 proton energies it took 4.2 min.     

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.     

QDENSITY—A Mathematica quantum computer simulation

This Mathematica 6.0 package is a simulation of a Quantum Computer. The program provides a modular, instructive approach for generating the basic elements that make up a quantum circuit. The main emphasis is on using the density matrix, although an approach using state vectors is also implemented in the package. The package commands are defined in Qdensity.m which contains the tools needed in quantum circuits, e.g., multiqubit kets, projectors, gates, etc.

New version program summary

Program title: QDENSITY 2.0Catalogue identifier: ADXH_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXH_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.: 26 055No. of bytes in distributed program, including test data, etc.: 227 540Distribution format: tar.gzProgramming language: Mathematica 6.0Operating system: Any which supports Mathematica; tested under Microsoft Windows XP, Macintosh OS X, and Linux FC4Catalogue identifier of previous version: ADXH_v1_0Journal reference of previous version: Comput. Phys. Comm. 174 (2006) 914Classification: 4.15Does the new version supersede the previous version?: Offers an alternative, more up to date, implementationNature of problem: Analysis and design of quantum circuits, quantum algorithms and quantum clusters.Solution method: A Mathematica package is provided which contains commands to create and analyze quantum circuits. Several Mathematica notebooks containing relevant examples: Teleportation, Shor's Algorithm and Grover's search are explained in detail. A tutorial, Tutorial.nb is also enclosed.Reasons for new version: The package has been updated to make it fully compatible with Mathematica 6.0Summary of revisions: The package has been updated to make it fully compatible with Mathematica 6.0Running time: Most examples included in the package, e.g., the tutorial, Shor's examples, Teleportation examples and Grover's search, run in less than a minute on a Pentium 4 processor (2.6 GHz). The running time for a quantum computation depends crucially on the number of qubits employed.     

Symbolic computation of the Hartree-Fock energy from a chiral EFT three-nucleon interaction at NLO

We present the first of a two-part Mathematica notebook collection that implements a symbolic approach for the application of the density matrix expansion (DME) to the Hartree-Fock (HF) energy from a chiral effective field theory (EFT) three-nucleon interaction at N²LO. The final output from the notebooks is a Skyrme-like energy density functional that provides a quasi-local approximation to the non-local HF energy. In this paper, we discuss the derivation of the HF energy and its simplification in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix. Furthermore, a set of steps is described and illustrated on how to extend the approach to other three-nucleon interactions.

Program summary

Program title: SymbHFNNNCatalogue identifier: AEGC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGC_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.: 96 666No. of bytes in distributed program, including test data, etc.: 378 083Distribution format: tar.gzProgramming language: Mathematica 7.1Computer: Any computer running Mathematica 6.0 and later versionsOperating system: Windows Xp, Linux/UnixRAM: 256 MbClassification: 5, 17.16, 17.22Nature of problem: The calculation of the HF energy from the chiral EFT three-nucleon interaction at N²LO involves tremendous spin-isospin algebra. The problem is compounded by the need to eventually obtain a quasi-local approximation to the HF energy, which requires the HF energy to be expressed in terms of scalar/vector-isoscalar/isovector parts of the one-body density matrix. The Mathematica notebooks discussed in this paper solve the latter issue.Solution method: The HF energy from the chiral EFT three-nucleon interaction at N²LO is cast into a form suitable for an automatic simplification of the spin-isospin traces. Several Mathematica functions and symbolic manipulation techniques are used to obtain the result in terms of the scalar/vector-isoscalar/isovector parts of the one-body density matrix.Running time: Several hours