The BAGEL assembler generation library

This paper presents two coupled software packages which receive widespread use in the field of numerical simulations of Quantum Chromo-Dynamics. These consist of the BAGEL library and the BAGEL fermion sparse-matrix library, BFM.The Bagel library can generate assembly code for a number of architectures and is configurable – supporting several precision and memory pattern options to allow architecture specific optimisation. It provides high performance on the QCDOC, BlueGene/L and BlueGene/P parallel computer architectures that are popular in the field of lattice QCD. The code includes a complete conjugate gradient implementation for the Wilson and domain wall fermion actions, making it easy to use for third party codes including the Jefferson Laboratory's CHROMA, UKQCD's UKhadron, and the Riken–Brookhaven–Columbia Collaboration's CPS packages.

Program summary

Program title: BagelCatalogue identifier: AEFE_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFE_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: GNU Public License V2No. of lines in distributed program, including test data, etc.: 109 576No. of bytes in distributed program, including test data, etc.: 892 841Distribution format: tar.gzProgramming language: C++, assemblerComputer: Massively parallel message passing. BlueGene/QCDOC/others.Operating system: POSIX, Linux and compatible.Has the code been vectorised or parallelized?: Yes. 16 384 processors used.Classification: 11.5External routines: QMP, QDP++Nature of problem: Quantum Chromo-Dynamics sparse matrix inversion for Wilson and domain wall fermion formulations.Solution method: Optimised Krylov linear solver.Unusual features: Domain specific compiler generates optimised assembly code.Running time: 1 h per matrix inversion; multi-year simulations.     

The program LOPT for least-squares optimization of energy levels

The article describes a program that solves the least-squares optimization problem for finding the energy levels of a quantum-mechanical system based on a set of measured energy separations or wavelengths of transitions between those energy levels, as well as determining the Ritz wavelengths of transitions and their uncertainties. The energy levels are determined by solving the matrix equation of the problem, and the uncertainties of the Ritz wavenumbers are determined from the covariance matrix of the problem.

Program summary

Program title: LOPTCatalogue identifier: AEHM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHM_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.: 19 254No. of bytes in distributed program, including test data, etc.: 427 839Distribution format: tar.gzProgramming language: Perl v.5Computer: PC, Mac, Unix workstationsOperating system: MS Windows (XP, Vista, 7), Mac OS X, Linux, Unix (AIX)RAM: 3 Mwords or moreWord size: 32 or 64Classification: 2.2Nature of problem: The least-squares energy-level optimization problem, i.e., finding a set of energy level values that best fits the given set of transition intervals.Solution method: The solution of the least-squares problem is found by solving the corresponding linear matrix equation, where the matrix is constructed using a new method with variable substitution.Restrictions: A practical limitation on the size of the problem N is imposed by the execution time, which scales as N³ and depends on the computer.Unusual features: Properly rounds the resulting data and formats the output in a format suitable for viewing with spreadsheet editing software. Estimates numerical errors resulting from the limited machine precision.Running time: 1 s for N=100, or 60 s for N=400 on a typical PC.     

An efficient quantum circuit analyser on qubits and qudits

This paper presents a highly efficient decomposition scheme and its associated Mathematica notebook for the analysis of complicated quantum circuits comprised of single/multiple qubit and qudit quantum gates. In particular, this scheme reduces the evaluation of multiple unitary gate operations with many conditionals to just two matrix additions, regardless of the number of conditionals or gate dimensions. This improves significantly the capability of a quantum circuit analyser implemented in a classical computer. This is also the first efficient quantum circuit analyser to include qudit quantum logic gates.

Program summary

Program title:CUGates.mCatalogue identifier: AEJM_v1_0Program summary: URL: http://cpc.cs.qub.ac.uk/summaries/AEJM_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.: 8168No. of bytes in distributed program, including test data, etc.: 173 899Distribution format: tar.gzProgramming language: MathematicaComputer: Any computer installed with Mathematica 6.0 or higher.Operating system: Any system with a copy of Mathematica 6.0 or higher installed.Classification: 4.15Nature of problem: The CUGates notebook simulates arbitrarily complex quantum circuits comprised of single/multiple qubit and qudit quantum gates.Solution method: It utilizes an irreducible form of matrix decomposition for a general controlled gate with multiple conditionals and is highly efficient in simulating complex quantum circuits.Running time: Details of CPU time usage for various example runs are given in Section 4.     

ALTDSE: An Arnoldi–Lanczos program to solve the time-dependent Schrödinger equation

We describe a general ab initio and non-perturbative method to solve the time-dependent Schrödinger equation (TDSE) for the interaction of a strong attosecond laser pulse with a general atom. While the field-free Hamiltonian and the dipole matrices may be generated using an arbitrary primitive basis, they are assumed to have been transformed to the eigenbasis of the problem before the solution of the TDSE is propagated in time using the Arnoldi–Lanczos method. Probabilities for survival of the ground state, excitation, and single ionization can be extracted from the propagated wavefunction.

Program summary

Program title: ALTDSECatalogue identifier: AEDM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDM_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.: 2154No. of bytes in distributed program, including test data, etc.: 30 827Distribution format: tar.gzProgramming language: Fortran 95. [A Fortran 2003 call to “flush” is used to simplify monitoring the output file during execution. If this function is not available, these statements should be commented out.].Computer: Shared-memory machinesOperating system: Linux, OpenMPHas the code been vectorized or parallelized?: YesRAM: Several Gb, depending on matrix size and number of processorsSupplementary material: To facilitate the execution of the program, Hamiltonian field-free and dipole matrix files are provided.Classification: 2.5External routines: LAPACK, BLASNature of problem: We describe a computer program for a general ab initio and non-perturbative method to solve the time-dependent Schrödinger equation (TDSE) for the interaction of a strong attosecond laser pulse with a general atom [1,2]. The probabilities for survival of the initial state, excitation of discrete states, and single ionization due to multi-photon processes can be obtained.Solution method: The solution of the TDSE is propagated in time using the Arnoldi–Lanczos method. The field-free Hamiltonian and the dipole matrices, originally generated in an arbitrary basis (e.g., the flexible B-spline R-matrix (BSR) method with non-orthogonal orbitals [3]), must be provided in the eigenbasis of the problem as input.Restrictions: The present program is restricted to a ¹S^e initial state and linearly polarized light. This is the most common situation experimentally, but a generalization is straightforward.Running time: Several hours, depending on the number of threads used.References: [1] X. Guan, O. Zatsarinny, K. Bartschat, B.I. Schneider, J. Feist, C.J. Noble, Phys. Rev. A 76 (2007) 053411. [2] X. Guan, C.J. Noble, O. Zatsarinny, K. Bartschat, B.I. Schneider, Phys. Rev. A 78 (2008) 053402. [3] O. Zatsarinny, Comput. Phys. Comm. 174 (2006) 273.     

An object-oriented implementation of a solver of the time-dependent Schrödinger equation using the CUDA technology

We present a set of C++ classes which allow one to use the graphics card processor?s cores for quantum ab initio simulations, i.e. a direct solving of the time-dependent Schrödinger equation, gaining the benefits from the parallel architecture of the graphical processor units. We use the Chebyshev polynomial and FFT algorithm. The solution is based on NVIDIA CUDA technology. The speed-up factor in the test runs of our classes performed using the graphics card processor can even be of order of 300 in comparison with the test runs using only the single core of CPU. Not only the Schrödinger equation can be integrated using the presented solver. With only small changes it can be used for solving the nonlinear Gross–Pitaevskii equation of BEC?s dynamics, the heat equation, the diffusion equation or other parabolic partial differential equations of second order.¹Program summaryProgram title: QnDynCUDACatalogue identifier: AELE_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELE_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.: 101 359No. of bytes in distributed program, including test data, etc.: 3 165 228Distribution format: tar.gzProgramming language: C++, C for CUDAComputer: Graphics card with CUDA technology recommendedOperating system: No limits (tested on 32-bit and 64-bit Windows and 64-bit Linux)Has the code been vectorized or parallelized?: Yes, number of processors used – one CPU core and all CUDA cores of the selected processor of graphics cardRAM: Dependent on user?s parameters, typically between several tens of megabytes and several gigabytes (this concerns also the graphics card?s memory)Supplementary material: Test input and output files (approx. 3.4 Gigabytes) are availableClassification: 2.7, 6.5Nature of problem: Solving the time-dependent Schrödinger equation.Solution method: FFT and Chebyshev polynomial algorithm, CUDA technology.Running time: Every test example included in the distribution package takes approximately an hour or so if the GPU is engaged and a day or so if only CPU is used.     

Plato: A localised orbital based density functional theory code

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

Program summary

Program title: PlatoCatalogue identifier: AEFC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen's University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 219 974No. of bytes in distributed program, including test data, etc.: 1 821 493Distribution format: tar.gzProgramming language: C/MPI and PERLComputer: Apple Macintosh, PC, Unix machinesOperating system: Unix, Linux and Mac OS XHas the code been vectorised or parallelised?: Yes, up to 256 processors testedRAM: Up to 2 Gbytes per processorClassification: 7.3External routines: LAPACK, BLAS and optionally ScaLAPACK, BLACS, PBLAS, FFTWNature of problem: Density functional theory study of electronic structure and total energies of molecules, crystals and surfaces.Solution method: Localised orbital based density functional theory.Restrictions: Tight-binding and density functional theory only, no exact exchange.Unusual features: Both atom centred and uniform meshes available. Can deal with arbitrary angular momenta for orbitals, whilst still retaining Slater–Koster tables for accuracy.Running time: Test cases will run in a few minutes, large calculations may run for several days.     

HASPRNG: Hardware Accelerated Scalable Parallel Random Number Generators

The Scalable Parallel Random Number Generators library (SPRNG) supports fast and scalable random number generation with good statistical properties for parallel computational science applications. In order to accelerate SPRNG in high performance reconfigurable computing systems, we present the Hardware Accelerated SPRNG library (HASPRNG). Ported to the Xilinx University Program (XUP) and Cray XD1 reconfigurable computing platforms, HASPRNG includes the reconfigurable logic for Field Programmable Gate Arrays (FPGAs) along with a programming interface which performs integer random number generation that produces identical results with SPRNG. This paper describes the reconfigurable logic of HASPRNG exploiting the mathematical properties and data parallelism residing in the SPRNG algorithms to produce high performance and also describes how to use the programming interface to minimize the communication overhead between FPGAs and microprocessors. The programming interface allows a user to be able to use HASPRNG the same way as SPRNG 2.0 on platforms such as the Cray XD1. We also describe how to install HASPRNG and use it. For HASPRNG usage we discuss a FPGA π-estimator for a High Performance Reconfigurable Computer (HPRC) sample application and compare to a software π-estimator. HASPRNG shows 1.7x speedup over SPRNG on the Cray XD1 and is able to obtain substantial speedup for a HPRC application.

Program summary

Program title: HASPRNGCatalogue identifier: AEER_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEER_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.: 594 928No. of bytes in distributed program, including test data, etc.: 6 509 724Distribution format: tar.gzProgramming language: VHDL (XUP and Cray XD1), C++ (XUP), C (Cray XD1)Computer: PowerPC 405 (XUP) / AMD 2.2 GHz Opteron processor (Cray XD1)Operating system: LinuxFile size: 15 MB (XUP) / 22 MB (Cray XD1)Classification: 4.13Nature of problem: Many computational science applications are able to consume large numbers of random numbers. For example, Monte Carlo simulations such as π-estimation are able to consume limitless random numbers forthe computation as long as hardware resources for the computing are supported. Moreover, parallel computational science applications require independent streams of random numbers to attain statistically significant results. The SPRNG library provides this capability, but at a significant computational cost. The library presented here accelerates the generators of independent streams of random numbers.Solution method: Multiple copies of random number generators in FPGAs allow a computational science application to consume large numbers of random numbers from independent, parallel streams. HASPRNG is a random number generators library to allow a computational science application to employ the multiple copies of random number generators to boost performance. Users can interface HASPRNG with software code executing on microprocessors and/or with hardware applications executing on FPGAs.     

PHON: A program to calculate phonons using the small displacement method

The program phon calculates force constant matrices and phonon frequencies in crystals. From the frequencies it also calculates various thermodynamic quantities, like the Helmholtz free energy, the entropy, the specific heat and the internal energy of the harmonic crystal. The procedure is based on the small displacement method, and can be used in combination with any program capable to calculate forces on the atoms of the crystal. In order to examine the usability of the method, I present here two examples: metallic Al and insulating MgO. The phonons of these two materials are calculated using density functional theory. The small displacement method results are compared with those obtained using the linear response method. In the case of Al the method provides accurate phonon frequencies everywhere in the Brillouin Zone (BZ). In the case of MgO the longitudinal branch of the optical phonons near the centre of the BZ is incorrectly described as degenerate with the two transverse branches, because the non-analytical part of the dynamical matrix is ignored here; however, thermodynamic properties like the Helmholtz free are essentially unaffected.

Program summary

Program title: PHONCatalogue identifier: AEDP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDP_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.: 19 580No. of bytes in distributed program, including test data, etc.: 612 193Distribution format: tar.gzProgramming language: Fortran 90Computer: Any Unix, LinuxOperating system: UnixRAM: Depends on super-cell size, but usually negligibleClassification: 7.8External routines: Subprograms ZHEEV and DSYEV (Lapack); needs BLAS. A tutorial is provided with the distribution which requires the installation of the quantum-espresso package (http://www.quantum-espresso.org)Nature of problem: Stable crystals at low temperature can be well described by expanding the potential energy around the atomic equilibrium positions. The movements of the atoms around their equilibrium positions can then be described using harmonic theory, and is characterised by global vibrations called phonons, which can be identified by vectors in the Brillouin zone of the crystal, and there are 3 phonon branches for each atom in the primitive cell. The problem is to calculate the frequencies of these phonons for any arbitrary choice of q-vector in the Brillouin zone.Solution method: The small displacement method: each atom in the primitive cell is displaced by a small amount, and the forces induced on all the other atoms in the crystal are calculated and used to construct the force constant matrix. Supercells of ∼100 atoms are usually large enough to describe the force constant matrix up to the range where its elements have fallen to negligibly small values. The force constant matrix is then used to compute the dynamical matrix at any chosen q-vector in the Brillouin zone, and the diagonalisation of the dynamical matrix provides the squares of the phonon frequencies. The PHON code needs external programs to calculate these forces, and it can be used with any program capable of calculating forces in crystals. The most useful applications are obtained with codes based on density functional theory, but there is no restriction on what can be used.Running time: Negligible, typically a few seconds (or at most a few minutes) on a PC. It can take longer if very dense meshes of q-points are needed, for example, to compute very accurate phonon density of states.     

HidSecSOFTSUSY: Incorporating effects from hidden sectors in the numerical computation of the MSSM spectrum

SOFTSUSY is a software designed to solve the RG equations of the MSSM and compute its low energy spectrum. HidSecSOFTSUSY is an extension of the SOFTSUSY package which modifies the beta functions to include contributions from light dynamic fields in the hidden sector.

Program summary

Program title: HidSecSOFTSUSYCatalogue identifier: AEHP_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHP_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.: 4167No. of bytes in distributed program, including test data, etc.: 141 411Distribution format: tar.gzProgramming language: C++, FortranComputer: Personal computerOperating system: Tested on GNU/LinuxWord size: 32 bitsClassification: 11.6External routines: Requires an installed version of SOFTSUSY (http://projects.hepforge.org/softsusy/)Nature of problem: Calculating supersymmetric particle spectrum and mixing parameters while incorporating dynamic modes from the hidden sector into the renormalization group equations. The solution to the equations must be consistent with a high-scale boundary condition on supersymmetry breaking parameters, as well as a weak-scale boundary condition on gauge couplings, Yukawa couplings and the Higgs potential parameters.Solution method: Nested iterative algorithm.Running time: A few seconds per parameter point.     

2DRMP: A suite of two-dimensional R-matrix propagation codes

The R-matrix method has proved to be a remarkably stable, robust and efficient technique for solving the close-coupling equations that arise in electron and photon collisions with atoms, ions and molecules. During the last thirty-four years a series of related R-matrix program packages have been published periodically in CPC. These packages are primarily concerned with low-energy scattering where the incident energy is insufficient to ionise the target. In this paper we describe 2DRMP, a suite of two-dimensional R-matrix propagation programs aimed at creating virtual experiments on high performance and grid architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies.

Program summary

Program title: 2DRMPCatalogue identifier: AEEA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEA_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.: 196 717No. of bytes in distributed program, including test data, etc.: 3 819 727Distribution format: tar.gzProgramming language: Fortran 95, 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 vectorised or parallelised?: Yes. 16 cores were used for small test runClassification: 2.4External routines: BLAS, LAPACK, PBLAS, ScaLAPACKSubprograms used: ADAZ_v1_1Nature of problem: 2DRMP is a suite of programs aimed at creating virtual experiments on high performance architectures to enable the study of electron scattering from H-like atoms and ions at intermediate energies.Solution method: Two-dimensional R-matrix propagation theory. The (r₁,r₂) space of the internal region is subdivided into a number of subregions. Local R-matrices are constructed within each subregion and used to propagate a global R-matrix, ℜ, across the internal region. On the boundary of the internal region ℜ is transformed onto the IERM target state basis. Thus, the two-dimensional R-matrix propagation technique transforms an intractable problem into a series of tractable problems enabling the internal region to be extended far beyond that which is possible with the standard one-sector codes. A distinctive feature of the method is that both electrons are treated identically and the R-matrix basis states are constructed to allow for both electrons to be in the continuum. The subregion size is flexible and can be adjusted to accommodate the number of cores available.Restrictions: The implementation is currently restricted to electron scattering from H-like atoms and ions.Additional comments: The programs have been designed to operate on serial computers and to exploit the distributed memory parallelism found on tightly coupled high performance clusters and supercomputers. 2DRMP has been systematically and comprehensively documented using ROBODoc [4] which is an API documentation tool that works by extracting specially formatted headers from the program source code and writing them to documentation files.Running time: The wall clock running time for the small test run using 16 cores and performed on [3] is as follows: bp (7 s); rint2 (34 s); newrd (32 s); diag (21 s); amps (11 s); prop (24 s).References:

• [1] 

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

• [2] 

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

• [4] 

  Automating Software Documentation with ROBODoc, http://www.xs4all.nl/~rfsber/Robo/, accessed 22 July, 2009.

     

A cascadic monotonic time-discretized algorithm for finite-level quantum control computation

A computer package (CNMS) is presented aimed at the solution of finite-level quantum optimal control problems. This package is based on a recently developed computational strategy known as monotonic schemes.Quantum optimal control problems arise in particular in quantum optics where the optimization of a control representing laser pulses is required. The purpose of the external control field is to channel the system's wavefunction between given states in its most efficient way. Physically motivated constraints, such as limited laser resources, are accommodated through appropriately chosen cost functionals.

Program summary

Program title: CNMSCatalogue identifier: ADEB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADEB_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.: 770No. of bytes in distributed program, including test data, etc.: 7098Distribution format: tar.gzProgramming language: MATLAB 6Computer: AMD Athlon 64 × 2 Dual, 2:21 GHz, 1:5 GB RAMOperating system: Microsoft Windows XPWord size: 32Classification: 4.9Nature of problem: Quantum controlSolution method: IterativeRunning time: 60-600 sec     

An object-oriented C++ implementation of Davidson method for finding a few selected extreme eigenpairs of a large, sparse, real, symmetric matrix

A C++ class named Davidson is presented for determining a few eigenpairs with lowest or alternatively highest values of a large, real, symmetric matrix. The algorithm described by Stathopoulos and Fischer is used. The exception mechanism is involved to report the errors. The class is written in ANSI C++, so it is fully portable. In addition a console program as well as a program with graphical user interface for Microsoft Windows is attached, which allow one to calculate the lowest eigenstates of time-independent Schrödinger equation for a given binding potential in one, two or three spatial dimensions. The package contains the classes providing often used potential functions (model atom potential, Coulomb potential, square well potential and Kramers-Henneberger well potential) as well as a possibility to use any potential stored in a file (then any dimensionality of the problem is allowed).The described code is the subject of M.Sc. thesis of T.D. prepared under the supervision of J.M.

Program summary

Program title: DavidsonCatalogue identifier: ADZM_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZM_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.: 3 037 055No. of bytes in distributed program, including test data, etc.: 20 002 609Distribution format: tar.gzProgramming language: C++Computer: AllOperating system: AnyRAM: User's parameters dependentWord size: 32 and 64 bitsSupplementary material: Test results for the 2D and 3D cases is availableClassification: 4, 4.8Nature of problem: Finding a few extreme eigenpairs of a real, symmetric, sparse matrix. Examples in quantum optics (interaction of matter with a laser field).Solution method: Davidson algorithmRunning time: The test example included in the distribution package (1D matrix) takes approximately 30 minutes to run. 2D matrix calculations can take hours and 3D, days, to run.     

SLHAplus: A library for implementing extensions of the standard model

We provide a library to facilitate the implementation of new models in codes such as matrix element and event generators or codes for computing dark matter observables. The library contains an SLHA reader routine as well as diagonalisation routines. This library is available in CalcHEP and micrOMEGAs. The implementation of models based on this library is supported by LanHEP and FeynRules.

Program summary

Program title: SLHAplus_1.3Catalogue identifier: AEHX_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHX_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.: 6283No. of bytes in distributed program, including test data, etc.: 52 119Distribution format: tar.gzProgramming language: CComputer: IBM PC, MACOperating system: UNIX (Linux, Darwin, Cygwin)RAM: 2000 MBClassification: 11.1Nature of problem: Implementation of extensions of the standard model in matrix element and event generators and codes for dark matter observables.Solution method: For generic extensions of the standard model we provide routines for reading files that adopt the standard format of the SUSY Les Houches Accord (SLHA) file. The procedure has been generalized to take into account an arbitrary number of blocks so that the reader can be used in generic models including non-supersymmetric ones. The library also contains routines to diagonalize real and complex mass matrices with either unitary or bi-unitary transformations as well as routines for evaluating the running strong coupling constant, running quark masses and effective quark masses.Running time: 0.001 sec     

REACH: A program for coarse-grained biomolecular simulation

REACH (Realistic Extension Algorithm viaCovariance Hessian) is a program package for residue-scale coarse-grained biomolecular simulation. The program calculates the force constants of a residue-scale elastic network model in single-domain proteins using the variance-covariance matrix obtained from atomistic molecular dynamics simulation. Secondary-structure dependence of the force constants is integrated. The method involves self-consistent, direct mapping of atomistic simulation results onto a coarse-grained force field in an efficient automated procedure without requiring iterative fits and avoiding system dependence.

Program summary

Program title: REACHCatalogue identifier: AEDA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDA_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.: 42 244No. of bytes in distributed program, including test data, etc.: 3 682 118Distribution format: tar.gzProgramming language: FORTRAN 77Computer: x86 PCOperating system: GNU/Linux, SUSE and Red HatRAM: Depends on the system size to be calculatedWord size: 32 or 64 bitsClassification: 3External routines: LAPACK, BLASNature of problem: A direct calculation of force field for residue-scale coarse-grained biomolecular simulation derived from atomistic molecular dynamics trajectory.Solution method: A variance-covariance matrix and the associated Hessian (second-derivative) matrix are calculated from an atomistic molecular dynamics trajectory of single-domain protein internal motion and the off-diagonal Hessian matrix is fitted to that of a residue-scale elastic network model. The resulting force constants for the residue pair interactions are expressed as model functions as a function of pairwise distance.Running time: Depends on the system size and the number of MD trajectory frames used. The test run provided with the distribution takes only a few seconds to execute.     

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios.

Program summary

Program title: edgecountCatalogue identifier: AEIA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIA_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.: 66 685No. of bytes in distributed program, including test data, etc.: 485 381Distribution format: tar.gzProgramming language:Fortran 90/95Computer: Most UNIX-based platformsOperating system: Linux, Mac OSClassification: 16.1, 7.8Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice.Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern.Running time: Typically ∼second(s) for all examples.     

QUBIT4MATLAB V3.0: A program package for quantum information science and quantum optics for MATLAB

A program package for MATLAB is introduced that helps calculations in quantum information science and quantum optics. It has commands for the following operations: (i) Reordering the qudits of a quantum register, computing the reduced state of a quantum register. (ii) Defining important quantum states easily. (iii) Formatted input and output for quantum states and operators. (iv) Constructing operators acting on given qudits of a quantum register and constructing spin chain Hamiltonians. (v) Partial transposition, matrix realignment and other operations related to the detection of quantum entanglement. (vi) Generating random state vectors, random density matrices and random unitaries.

Program summary

Program title:QUBIT4MATLAB V3.0Catalogue identifier:AEAZ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAZ_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.:5683No. of bytes in distributed program, including test data, etc.: 37 061Distribution format:tar.gzProgramming language:MATLAB 6.5; runs also on OctaveComputer:Any which supports MATLAB 6.5Operating system:Any which supports MATLAB 6.5; e.g., Microsoft Windows XP, LinuxClassification:4.15Nature of problem: Subroutines helping calculations in quantum information science and quantum optics.Solution method: A program package, that is, a set of commands is provided for MATLAB. One can use these commands interactively or they can also be used within a program.Running time:10 seconds-1 minute     

Generating and using truly random quantum states in Mathematica

The problem of generating random quantum states is of a great interest from the quantum information theory point of view. In this paper we present a package for Mathematica computing system harnessing a specific piece of hardware, namely Quantis quantum random number generator (QRNG), for investigating statistical properties of quantum states. The described package implements a number of functions for generating random states, which use Quantis QRNG as a source of randomness. It also provides procedures which can be used in simulations not related directly to quantum information processing.Program summaryProgram title: TRQSCatalogue identifier: AEKA_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKA_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.: 7924No. of bytes in distributed program, including test data, etc.: 88 651Distribution format: tar.gzProgramming language: Mathematica, CComputer: Requires a Quantis quantum random number generator (QRNG, http://www.idquantique.com/true-random-number-generator/products-overview.html) and supporting a recent version of MathematicaOperating system: Any platform supporting Mathematica; tested with GNU/Linux (32 and 64 bit)RAM: Case dependentClassification: 4.15Nature of problem: Generation of random density matrices.Solution method: Use of a physical quantum random number generator.Running time: Generating 100 random numbers takes about 1 second, generating 1000 random density matrices takes more than a minute.