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The Fortran subroutine package pengeom provides a complete set of tools to handle quadric geometries in Monte Carlo simulations of radiation transport. The material structure where radiation propagates is assumed to consist of homogeneous bodies limited by quadric surfaces. The pengeom subroutines (a subset of the penelope code) track particles through the material structure, independently of the details of the physics models adopted to describe the interactions. Although these subroutines are designed for detailed simulations of photon and electron transport, where all individual interactions are simulated sequentially, they can also be used in mixed (class II) schemes for simulating the transport of high-energy charged particles, where the effect of soft interactions is described by the random-hinge method. The definition of the geometry and the details of the tracking algorithm are tailored to optimize simulation speed. The use of fuzzy quadric surfaces minimizes the impact of round-off errors. The provided software includes a Java graphical user interface for editing and debugging the geometry definition file and for visualizing the material structure. Images of the structure are generated by using the tracking subroutines and, hence, they describe the geometry actually passed to the simulation code. Program summary Program title: Pengeom Catalogue identifier: AEYH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYH_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 89390 No. of bytes in distributed program, including test data, etc.: 5062646 Distribution format: tar.gz Programming language: Fortran, Java. Computer: PC with Java Runtime Environment installed. Operating system: Windows, Linux. RAM: 210 MiB Classification: 21.1, 14. Nature of problem: The Fortran subroutines perform all geometry operations in Monte Carlo simulations of radiation transport with arbitrary interaction models. They track particles through material systems consisting of homogeneous bodies limited by quadric surfaces. Particles are moved in steps (free flights) of a given length, which is dictated by the simulation program, and are halted when they cross an interface between media of different compositions or when they enter selected bodies. Solution method: The pengeom subroutines are tailored to optimize simulation speed and accuracy. Fast tracking is accomplished by the use of quadric surfaces, which facilitate the calculation of ray intersections, and of modules (connected volumes limited by quadric surfaces) organized in a hierarchical structure. Optimal accuracy is obtained by considering fuzzy surfaces, with the aid of a simple algorithm that keeps control of multiple intersections of a ray and a surface. The Java GUI PenGeomJar provides a geometry toolbox; it allows building and debugging the geometry definition file, as well as visualizing the resulting geometry in two and three dimensions. Restrictions: By default pengeom can handle systems with up to 5000 bodies and 10,000 surfaces. These numbers can be increased by editing the Fortran source file. Unusual features: All geometrical operations are performed internally. The connection between the steering main program and the tracking routines is through a Fortran module, which contains the state variables of the transported particle, and the input-output arguments of the subroutine step. Rendering of two- and three-dimensional images is performed by using the pengeom subroutines, so that displayed images correspond to the definitions passed to the simulation program. Additional comments: Java editor and viewer (PenGeomJar), geometry examples, translator to POV-Ray™ format, detailed manual. The Fortran subroutine package pengeom is part of the penelope code system [1]. Running time: The running time much depends on the complexity of the material system. The most complicated example provided, phantom, an anthropomorphic phantom, has 264 surfaces and 169 bodies and modules, with different levels of grouping; the largest module contains 51 daughters. The rendering of a 3D image of phantom with 1680x1050 pixels takes about 25 s (i.e., about 1.5⋅10 −5 seconds per ray) on an Intel Core I7-3520M CPU, with Windows 7 and subroutines compiled with gfortran. References: [1] F. Salvat, PENELOPE-2014: A Code System for Monte Carlo Simulation of Electron and Photon Transport, OECD/NEA Data Bank, Issy-les-Moulineaux, France, 2015. Available from http://www.nea.fr/lists/penelope.html . [ABSTRACT FROM AUTHOR]

The interface for VENUS and NWChem, and the resulting software package for direct dynamics simulations are described. The coupling of the two codes is considered to be a tight coupling since the two codes are compiled and linked together and act as one executable with data being passed between the two codes through routine calls. The advantages of this type of coupling are discussed. The interface has been designed to have as little interference as possible with the core codes of both VENUS and NWChem. VENUS is the code that propagates the direct dynamics trajectories and, therefore, is the program that drives the overall execution of VENUS/NWChem. VENUS has remained an essentially sequential code, which uses the highly parallel structure of NWChem. Subroutines of the interface that accomplish the data transmission and communication between the two computer programs are described. Recent examples of the use of VENUS/NWChem for direct dynamics simulations are summarized. Program summary : Program title: VENUS/NWChem Catalogue identifier: AERS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERS_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 10,831,970 No. of bytes in distributed program, including test data, etc.: 77,141,871 Distribution format: tar.gz Programming language: Fortran 77 with some C in NWChem, MPI. Computer: All Linux based workstations and parallel supercomputers. Operating system: Linux. Has the code been vectorized or parallelized?: Venus is a sequential code; NWChem can run in parallel. Classification: 16.8. Nature of problem: Direct dynamics simulations play an important role in investigating and understanding atomic-level chemical dynamics information such as atomistic reaction mechanisms, unimolecular and bimolecular rate constants, intramolecular vibrational energy redistribution rates, etc. The ability to couple direct dynamics with electronic structure methods brings a level of fidelity to the simulations that is important for complex systems. However, a tight coupling between two codes that have their own development teams and schedules can be challenging. Solution method: The VENUS/NWChem interface is designed to link the general electronic structure program (NWChem) and classical chemical dynamics simulation program (VENUS) to perform direct dynamics simulation in which the trajectories “on the fly” with the potential and its derivatives obtained directly from electronic structure theory. One of the design goals is to build interfaces that require as little interference in NWChem and VENUS as possible so that each of the code developments can continue independently. This is especially important since VENUS is currently a sequential code and NWChem is a parallel code and being able to compute the energies, gradients, and Hessian in parallel is an important aspect of making the software useful to users. In this manuscript, the tight coupling interface between the two codes is described and examples of its use are given. In the classical chemical dynamics simulation an ensemble of trajectories is calculated, and the initial sampling represents the conditions of the reactants for the chemical reaction under investigation. Each trajectory is evaluated by numerically integrating either Hamilton’s or Newton’s equations of motion. The Schrödinger equation is solved and the energy and energy gradient are calculated in the electronic structure program (NWChem), and this information is passed to the classical trajectory program (VENUS) to solve the equations of motion. Additional comments: Full documentation is provided in the distribution file. This includes a README file giving the names and brief description of all the files that make up the package and instructions on the installation and execution of the program. Sample input and output data for test run will also be provided. The software is free to download and use once a signed license agreement has been received. The agreement will be displayed when the program is requested. Running time: The running time depends on the size of the chemical system, simulation time, complexity of the ab initio method and number of CPUs. The ab initio method is the most time consuming part of each step in the calculations and scaling for different types of systems and levels of theory is available in Valiev et al. (2010). Again, there are many factors that affect the running time for the full simulation and it can range from several hours for simulations of a few atoms with DFT and a small basis set running on a single compute node to several days for the simulation of tens of heavy atoms with larger basis set running parallel. [ABSTRACT FROM AUTHOR]

The Lambert function and its possible applications in physics are presented. The actual numerical implementation in C++ consists of Halley’s and Fritsch’s iterations with initial approximations based on branch-point expansion, asymptotic series, rational fits, and continued-logarithm recursion. Program summary: Program title: LambertW Catalogue identifier: AENC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AENC_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 1335 No. of bytes in distributed program, including test data, etc.: 25283 Distribution format: tar.gz Programming language: C++ (with suitable wrappers it can be called from C, Fortran etc.), the supplied command-line utility is suitable for other scripting languages like sh, csh, awk, perl etc. Computer: All systems with a C++ compiler. Operating system: All Unix flavors, Windows. It might work with others. RAM: Small memory footprint, less than 1 MB Classification: 1.1, 4.7, 11.3, 11.9. Nature of problem: Find fast and accurate numerical implementation for the Lambert W function. Solution method: Halley’s and Fritsch’s iterations with initial approximations based on branch-point expansion, asymptotic series, rational fits, and continued logarithm recursion. Additional comments: Distribution file contains the command-line utility lambert-w. Doxygen comments, included in the source files. Makefile. Running time: The tests provided take only a few seconds to run. [ABSTRACT FROM AUTHOR]

Abstract: We present a Fortran program package, MSTor, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsional motions by the recently proposed MS-T method. This method interpolates between the local harmonic approximation in the low-temperature limit, and the limit of free internal rotation of all torsions at high temperature. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes six utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Program summary: Program title: MSTor Catalogue identifier: AEMF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMF_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 77 434 No. of bytes in distributed program, including test data, etc.: 3 264 737 Distribution format: tar.gz Programming language: Fortran 90, C, and Perl Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), Elmo (Sun Fire X4600 Linux cluster with AMD Opteron cores), and Mac Pro (two 2.8 GHz Quad-core Intel Xeon processors) Operating system: Linux/Unix/Mac OS RAM: 2 Mbytes Classification: 16.3, 16.12, 23 Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperatures) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation [1]. Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multi-torsional problems for which one can afford to calculate all the conformations and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes and six utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomain defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 24 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 seconds. References: [[1]] J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, D.G. Truhlar, Practical methods for including torsional anharmonicity in thermochemical calculations of complex molecules: The internal-coordinate multi-structural approximation, Phys. Chem. Chem. Phys. 13 (2011) 10885–10907. [Copyright &y& Elsevier]

Abstract: Numerical values of the Chandrasekhar function are needed with high accuracy in evaluations of theoretical models describing electron transport in condensed matter. An algorithm for such calculations should be possibly fast and also accurate, e.g. an accuracy of 10 decimal digits is needed for some applications. Two of the integral representations of the Chandrasekhar function are prospective for constructing such an algorithm, but suitable transformations are needed to obtain a rapidly converging quadrature. A mixed algorithm is proposed in which the Chandrasekhar function is calculated from two algorithms, depending on the value of one of the arguments. Program summary: Program title: CHANDRAS Catalogue identifier: AEMC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMC_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 567 No. of bytes in distributed program, including test data, etc.: 4444 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any computer with a FORTRAN 90 compiler Operating system: Linux, Windows 7, Windows XP RAM: 0.6 Mb Classification: 2.4, 7.2 Nature of problem: An attempt has been made to develop a subroutine that calculates the Chandrasekhar function with high accuracy, of at least 10 decimal places. Simultaneously, this subroutine should be very fast. Both requirements stem from the theory of electron transport in condensed matter. Solution method: Two algorithms were developed, each based on a different integral representation of the Chandrasekhar function. The final algorithm is edited by mixing these two algorithms and by selecting ranges of the argument ω in which performance is the fastest. Restrictions: Two input parameters for the Chandrasekhar function, x and ω (notation used in the code), are restricted to the range: and , which is sufficient in numerous applications. Unusual features: The program uses the Romberg quadrature for integration. This quadrature is applicable to integrands that satisfy several requirements (the integrand does not vary rapidly and does not change sign in the integration interval; furthermore, the integrand is finite at the endpoints). Consequently, the analyzed integrands were transformed so that these requirements were satisfied. In effect, one can conveniently control the accuracy of integration. Although the desired fractional accuracy was set at , the obtained accuracy of the Chandrasekhar function was much higher, typically 13 decimal places. Running time: Between 0.7 and 5 milliseconds for one pair of arguments of the Chandrasekhar function. [Copyright &y& Elsevier]

Abstract: A general and systematic regularization is developed for the exact solitonic form factors of exponential operators in the ()-dimensional sine-Gordon model by analytical continuation of their integral representations. The procedure is implemented in Mathematica. Test results are shown for four- and six-soliton form factors. Program summary: Program title: SGFF Catalogue identifier: AEMG_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMG_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1462 No. of bytes in distributed program, including test data, etc.: 15 488 Distribution format: tar.gz Programming language: Mathematica [1] Computer: PC Operating system: Cross-platform Classification: 7.7, 11.1, 23 Nature of problem: The multi-soliton form factors of the sine-Gordon model (relevant in two-dimensional physics) were given only by highly non-trivial integral representation with a limited domain of convergence. Practical applications of the form factors, e.g. calculation of correlation functions in two-dimensional condensed matter systems, were not possible in general. Solution method: Using analytic continuation techniques an efficient algorithm is found and implemented in Mathematica, which provides a general and systematic way to calculate multi-soliton form factors in the sine-Gordon model. The package contains routines to compute the two-, four- and six-soliton form factors. Running time: Strongly dependent on the desired accuracy and the number of solitons. For physical rapidities after an initialization of about 30 s, the calculation of the two-, four- and six-soliton form factors at a single point takes approximately 0.5 s, 2.5 s and 8 s, respectively. Reference: [[1]] Wolfram Research, Inc., Mathematica Edition: Version 7.0, Wolfram Research, Inc., Champaign, Illinois, 2008. [Copyright &y& Elsevier]

Abstract: The computational techniques needed to generate a two-body Generalized Sturmian basis are described. These basis are obtained as a solution of the Schrödinger equation, with two-point boundary conditions. This equation includes two central potentials: A general auxiliary potential and a short-range generating potential. The auxiliary potential is, in general, long-range and it determines the asymptotic behavior of all the basis elements. The short-range generating potential rules the dynamics of the inner region. The energy is considered a fixed parameter, while the eigenvalues are the generalized charges. Although the finite differences scheme leads to a generalized eigenvalue matrix system, it cannot be solved by standard computational linear algebra packages. Therefore, we developed computational routines to calculate the basis with high accuracy and low computational time. The precise charge eigenvalues with more than 12 significant figures along with the corresponding wave functions can be computed on a single processor within seconds. [Copyright &y& Elsevier]

Abstract: The beauty of molecular magnets lies on their simplicity in what concerns quantum description. Zero-dimensional clusters have, due to the well-known Hamiltonians (e.g., Heisenberg, asymmetric, anti-symmetric and others), analytical solution of the thermodynamic quantities (of course, for a reasonable size of the Hilbert space). The aim of this paper is to describe step-by-step of how to develop models to explain the magnetic behavior of these materials. In spite the possibility of hand calculation (that opens doors for mistakes), computational codes can help to optimize this process of modeling; and then we provide a fully automatize computational routine to do the whole process: the CARDAMOMO package. Nine different Hamiltonians are available, as well as three different methods to obtain the eigenvalues. Thermodynamic quantities are obtained automatically and then fitted to the experimental data. At the end of this paper, an appendix support the physical background behind the Hamiltonians. [Copyright &y& Elsevier]

Abstract: The stochastic hyperfine interactions modeling library (SHIML) provides a set of routines to assist in the development and application of stochastic models of hyperfine interactions. The library provides routines written in the C programming language that (1) read a text description of a model for fluctuating hyperfine fields, (2) set up the Blume matrix, upon which the evolution operator of the system depends, and (3) find the eigenvalues and eigenvectors of the Blume matrix so that theoretical spectra of experimental techniques that measure hyperfine interactions can be calculated. The optimized vector and matrix operations of the BLAS and LAPACK libraries are utilized; however, there was a need to develop supplementary code to find an orthonormal set of (left and right) eigenvectors of complex, non-Hermitian matrices. In addition, example code is provided to illustrate the use of SHIML to generate perturbed angular correlation spectra for the special case of polycrystalline samples when anisotropy terms of higher order than can be neglected. Program summary: Program title: SHIML Catalogue identifier: AEIF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIF_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: GNU GPL 3 No. of lines in distributed program, including test data, etc.: 8224 No. of bytes in distributed program, including test data, etc.: 312 348 Distribution format: tar.gz Programming language: C Computer: Any Operating system: LINUX, OS X RAM: Varies Classification: 7.4 External routines: TAPP [1], BLAS [2], a C-interface to BLAS [3], and LAPACK [4] Nature of problem: In condensed matter systems, hyperfine methods such as nuclear magnetic resonance (NMR), Mössbauer effect (ME), muon spin rotation (μSR), and perturbed angular correlation spectroscopy (PAC) measure electronic and magnetic structure within Angstroms of nuclear probes through the hyperfine interaction. When interactions fluctuate at rates comparable to the time scale of a hyperfine method, there is a loss in signal coherence, and spectra are damped. The degree of damping can be used to determine fluctuation rates, provided that theoretical expressions for spectra can be derived for relevant physical models of the fluctuations. SHIML provides routines to help researchers quickly develop code to incorporate stochastic models of fluctuating hyperfine interactions in calculations of hyperfine spectra. Solution method: Calculations are based on the method for modeling stochastic hyperfine interactions for PAC by Winkler and Gerdau [5]. The method is extended to include other hyperfine methods following the work of Dattagupta [6]. The code provides routines for reading model information from text files, allowing researchers to develop new models quickly without the need to modify computer code for each new model to be considered. Restrictions: In the present version of the code, only methods that measure the hyperfine interaction on one probe spin state, such as PAC, μSR, and NMR, are supported. Running time: Varies References: [1] M.O. Zacate, The adjustable parameter package, Technical report 2, CINSAM Grant 2006-R7 (unpublished); available for download at http://tapp.nku.edu/. [2] L.S. Blackford, et al., ACM Trans. Math. Soft. 28 (2) (2002) 135–151; J. Dongarra, International Journal of High Performance Applications and Supercomputing 16 (1–2) (2002) 1–199; http://www.netlib.org/blas/. [3] M. Galassi, et al., GNU Scientific Library Reference Manual, third edition (2009); available for download at http://www.gnu.org/software/gsl/. [4] E. Anderson, et al., LAPACK Users'' Guide, third edition, Society for Industrial and Applied Mathematics, Philadelphia, 1999; http://www.netlib.org/lapack/. [5] H. Winkler, E. Gerdau, Z. Phys. 262 (1973) 363–376. [6] S. Dattagupta, Hyperfine Interactions 11 (1981) 77–126. [Copyright &y& Elsevier]

Abstract: EPW (Electron–Phonon coupling using Wannier functions) is a program written in Fortran90 for calculating the electron–phonon coupling in periodic systems using density-functional perturbation theory and maximally localized Wannier functions. EPW can calculate electron–phonon interaction self-energies, electron–phonon spectral functions, and total as well as mode-resolved electron–phonon coupling strengths. The calculation of the electron–phonon coupling requires a very accurate sampling of electron–phonon scattering processes throughout the Brillouin zone, hence reliable calculations can be prohibitively time-consuming. EPW combines the Kohn–Sham electronic eigenstates and the vibrational eigenmodes provided by the Quantum ESPRESSO package (see Giannozzi et al., 2009 ) with the maximally localized Wannier functions provided by the wannier90 package (see Mostofi et al., 2008 ) in order to generate electron–phonon matrix elements on arbitrarily dense Brillouin zone grids using a generalized Fourier interpolation. This feature of EPW leads to fast and accurate calculations of the electron–phonon coupling, and enables the study of the electron–phonon coupling in large and complex systems. Program summary: Program title: EPW Catalogue identifier: AEHA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHA_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: GNU Public License No. of lines in distributed program, including test data, etc.: 304 443 No. of bytes in distributed program, including test data, etc.: 1 487 466 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any architecture with a Fortran 90 compiler Operating system: Any environment with a Fortran 90 compiler Has the code been vectorized or parallelized?: Yes, optimized for 1 to 64 processors RAM: Heavily system dependent, as small as a few MB Supplementary material: A copy of the “EPW/examples” directory containing the phonon binary files can be downloaded Classification: 7 External routines: MPI, Quantum-ESPRESSO package [1], BLAS, LAPACK, FFTW. (The necessary Blas, Lapack and FFTW routines are included in the Quantum-ESPRESSO package [1].) Nature of problem: The calculation of the electron–phonon coupling from first-principles requires a very accurate sampling of electron–phonon scattering processes throughout the Brillouin zone; hence reliable calculations can be prohibitively timeconsuming. Solution method: EPW makes use of a real-space formulation and combines the Kohn–Sham electronic eigenstates and the vibrational eigenmodes provided by the Quantum-ESPRESSO package with the maximally localized Wannier functions provided by the wannier90 package in order to generate electron–phonon matrix elements on arbitrarily dense Brillouin zone grids using a generalized Fourier interpolation. Running time: Single processor examples typically take 5–10 minutes. References: [[1]] P. Giannozzi, et al., J. Phys. Condens. Matter 21 (2009), 395502, http://www.quantum-espresso.org/. [Copyright &y& Elsevier]

Abstract: A previous subroutine, LSFBTR, for computing numerical spherical Bessel (Hankel) transforms is updated with several improvements and modifications. The procedure is applicable if the input radial function and the output transform are defined on logarithmic meshes and if the input function satisfies reasonable smoothness conditions. Important aspects of the procedure are that it is simply implemented with two successive applications of the fast Fourier transform, and it yields accurate results at very large values of the transform variable. Applications to the evaluation of overlap integrals and the Coulomb potential of multipolar charge distributions are described. Program summary: Program title: NumSBT Catalogue identifier: AANZ_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AANZ_v2_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 476 No. of bytes in distributed program, including test data, etc.: 4451 Distribution format: tar.gz Programming language: Fortran 90 Computer: Generic Operating system: Linux Classification: 4.6 Catalogue identifier of previous version: AANZ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 30 (1983) 93 Does the new version supersede the previous version?: No Nature of problem: This program is a subroutine which, for a function defined numerically on a logarithmic mesh in the radial coordinate, generates the spherical Bessel, or Hankel, transform on a logarithmic mesh in the transform variable. Accurate results for large values of the transform variable are obtained, that would not be otherwise obtainable. Solution method: The program applies a procedure proposed by the author [1] that treats the problem as a convolution. The calculation then requires two applications of the fast Fourier transform method. Reasons for new version: The method of computing the transform at small values of the transform variable has been substantially changed and the whole procedure simplified. In addition, the possibility of computing the transform for a single transform variable value has been incorporated. The code has also been converted to Fortran 90 from Fortran 77. Restrictions: The procedure is most applicable to smooth functions defined on with a limited number of nodes. Running time: The example provided with the distribution takes a few seconds to execute. References: [1] J.D. Talman, J. Comp. Phys. 29 (1978) 35. [Copyright &y& Elsevier]

We present in this work a new computational code for the quantum calculation of integral cross sections for atom–molecule (linear) scattering processes. The atom is taken to be structureless while the molecule can be in its singlet, doublet, or triplet spin states and can be treated as either a rigid rotor or a rovibrational target. All the relevant state-to-state integral cross sections, and their sums over final states, can be calculated with the present code, for which we also describe in detail the various component routines. Program summary: Program title: ASPIN Catalogue identifier: AEBO_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBO_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 99 596 No. of bytes in distributed program, including test data, etc.: 1 267 615 Distribution format: tar.gz Programming language: Fortran/MPI Computer: AMD OPTERON COMPUTING SYSTEMS, model TYAN GX28 (B2882) Operating system: SuSE LINUX Professional 9 RAM: 128 GB Classification: 2.6 External routines: LAPACK/BLAS Nature of problem: Scattering of a diatomic molecule in its , , or spin states with an atom in its state. Partial and integral cross sections. Solution method: The coupled channel equations that describe the scattering process are solved through the propagation of the reactance K matrix employing a modification of the Variable Phase Method [1–3]. Restrictions: Depending on the vib-rotational base used the problem may or may not fit into available RAM memory because all the runtime relevant quantities are stored on RAM memory instead of on disk. Additional comments: Both serial and parallel implementations of the program are provided. The CPC Librarian was not able to successfully run the parallel version. Running time: For simple and converged calculations a usual running time is in the order of a few minutes in the computer mentioned above, being shorter for the singlet and longer for the triplet. References: [1] F. Calogero, Variable Phase Approach to Potential Scattering, New York, 1967. [2] A. Degasperis, Il Nuovo Cimento 34 (1964) 1667. [3] C. Zemach, Il Nuovo Cimento 33 (1964) 939. [Copyright &y& Elsevier]

We present a very fast implementation of the Butler–Portugal algorithm for index canonicalization with respect to permutation symmetries. It is called xPerm, and has been written as a combination of a Mathematica package and a C subroutine. The latter performs the most demanding parts of the computations and can be linked from any other program or computer algebra system. We demonstrate with tests and timings the effectively polynomial performance of the Butler–Portugal algorithm with respect to the number of indices, though we also show a case in which it is exponential. Our implementation handles generic tensorial expressions with several dozen indices in hundredths of a second, or one hundred indices in a few seconds, clearly outperforming all other current canonicalizers. The code has been already under intensive testing for several years and has been essential in recent investigations in large-scale tensor computer algebra. Program summary: Program title: xPerm Catalogue identifier: AEBH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEBH_v1_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 93 582 No. of bytes in distributed program, including test data, etc.: 1 537 832 Distribution format: tar.gz Programming language: C and Mathematica (version 5.0 or higher) Computer: Any computer running C and Mathematica (version 5.0 or higher) Operating system: Linux, Unix, Windows XP, MacOS RAM:: 20 Mbyte Word size: 64 or 32 bits Classification: 1.5, 5 Nature of problem: Canonicalization of indexed expressions with respect to permutation symmetries. Solution method: The Butler–Portugal algorithm. Restrictions: Multiterm symmetries are not considered. Running time: A few seconds with generic expressions of up to 100 indices. The xPermDoc.nb notebook supplied with the distribution takes approximately one and a half hours to execute in full. [Copyright &y& Elsevier]

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 V3.0 Catalogue identifier:AEAZ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEAZ_v1_0.html Program obtainable from:CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions:Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.:5683 No. of bytes in distributed program, including test data, etc.: 37 061 Distribution format:tar.gz Programming language:MATLAB 6.5; runs also on Octave Computer:Any which supports MATLAB 6.5 Operating system:Any which supports MATLAB 6.5; e.g., Microsoft Windows XP, Linux Classification:4.15 Nature 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 [Copyright &y& Elsevier]

We replace the old PACIAE 2.1 and PACIAE 2.2 program series with new ones, respectively. In the new program series, the method of creation of the partonic initial state is changed, an option for calling PYEVNT or PYEVNW in PYTHIA is added, and the few bugs in the calculation for the reduction of strange quark suppression are corrected. New version program summary Program Title: PACIAE version 2.1 & 2.2 Program Files doi: http://dx.doi.org/10.17632/w3g68dj4d9.1 Licensing provisions: CC By 4.0 Programming language: FORTRAN 77 Journal reference of previous version: Comput. Phys. Comm. 184 (2013) 1476, 193 (2015) 89. Does the new version supersede the previous version?: Yes Nature of problem: PYEVNT is the subroutine in PYTHIA to administer the generation of a high-pT event via calls a number of subroutines. PYEVNW is the new subroutine in PYTHIA to administer the generation of an event for new multiple interactions scenario. In previous PACIAE versions only PYEVNT is called, while both PYEVNT and PYEVNW can be called in this new version. Solution method: There has been added a parameter of mstp81 in PACIAE programs and input files of usux.dat (for 21a or 22a) and usu.dat (for 21b, 21c ,22b and 22c). The PACIAE will call PYEVNT when mstp81=1( default) and call PYEVNW when mstp81=21. Reasons for the new version: The method of creation of the partonic initial state is changed, an option for calling PYEVNT or PYEVNW in PYTHIA is added, and the few bugs in the calculation for the reduction of strange quark suppression are corrected in the new version. Summary of revisions: The PACIAE model [1] is a parton and hadron cascade model based on PYTHIA [2]. PACIAE model consists of four stages of the parton initiation, the parton evolution (rescattering), the hadronization, and the hadron evolution (rescattering). The stage of parton initiation is just by means of PYTHIA model and the rest are modeled by us [1]. PYTHIA model is for the high energy elementary particle collisions such as hadron–hadron and lepton–hadron collisions, but PACIAE model is also for high energy lepton–nucleus, hadron–nucleus and nucleus–nucleus collisions. So far, the PACIAE model has three series of PACIAE 2.0 (catalogue identifier: AEKI_v1_0) [1], PACIAE 2.1 (AEKI_v2_0) [3], and PACIAE 2.2 (AEKI_v2_2) [4]. The discrepancy between PACIAE 2.0 and PACIAE 2.1 is just the sampling of momentum x and y components at fixed p T . In the PACIAE 2.0 it is sampled on the circle with radius of p T , but on the circumference of ellipse with half major and minor axes of p T ( 1 + δ p ) and p T ( 1 − δ p ) , respectively in PACIAE 2.1. Including the reaction of lepton–nucleon and lepton–nucleus is the distinction of PACIAE 2.2 series from the PACIAE 2.1. Each series of PACIAE 2.0, PACIAE 2.1 and PACIAE 2.2 consists of a, b, and c packages. The package of PACIAE 2.1a, for instance, is for the high energy elementary collisions, while the PACIAE 2.1b as well as PACIAE 2.1c for the high energy hadron–nucleus and nucleus–nucleus collisions. We refer to [1] for the difference between PACIAE 2.0b and PACIAE 2.0c (PACIAE 2.1b and PACIAE 2.1c as well as PACIAE 2.2b and PACIAE 2.2c). In this replacement the modifications are as follows: 1. The method of creation of a partonic initial state is changed from setting mstj(1)=0 (or mstp(111)=0) before “CALL PYINIT” to adding a “RETURN” statement before the statement of “CALL PYEXEC” in subroutine PYEVNT (PYEVNW) in p21b.f. 2. Correcting the mistakes in the calculation for the mechanism of reduction of strange quark suppression. 3. Calling PYEVNT or PYEVNW is controlled by mstp(81) (=1 or 21) instead of calling PYEVNT only originally. References [1] Ben-Hao Sa, Dai-Mei Zhou, Yu-Liang Yan, Xiao-Mei Li, Sheng-Qin Feng, Bao-Guo Dong, and Xu Cai, Comput. Phys. Comm. 183 (2012) 333. [2] Sjöstrand T, Mrenna S, Skands P, J. High Energy Phys., 05 (2006) 026, arXiv:hep-ph/0603175. [3] Ben-Hao Sa, Dai-Mei Zhou, Yu-Liang Yan, Bao-Guo Dong, and Xu Cai, Comput. Phys. Comm. 184 (2013) 1476. [4] Dai-Mei Zhou, Yu-Liang Yan, Xing-Long Li, Xiao-Mei Li, Bao-Guo Dong, Xu Cai, and Ben-Hao Sa, Comput. Phys. Comm. 193 (2015) 89. [ABSTRACT FROM AUTHOR]

A new version of the “MinFinder” program is presented that offers an augmented linking procedure for Fortran-77 subprograms, two additional stopping rules and a new start-point rejection mechanism that saves a significant portion of gradient and function evaluations. The method is applied on a set of standard test functions and the results are reported. New version program summary: Program title: MinFinder v2.0 Catalogue identifier: ADWU_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADWU_v2_0.html Program obtainable from: CPC Program Library, Queen''s University, Belfast, N. Ireland Licensing provisions: Standard CPC Licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 14 150 No. of bytes in distributed program, including test data, etc.: 218 144 Distribution format: tar.gz Programming language used: GNU C++, GNU FORTRAN, GNU C Computer: The program is designed to be portable in all systems running the GNU C++ compiler Operating system: Linux, Solaris, FreeBSD RAM: 200 000 bytes Classification: 4.9 Catalogue identifier of previous version: ADWU_v1_0 Journal reference of previous version: Computer Physics Communications 174 (2006) 166–179 Does the new version supersede the previous version?: Yes Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be trapped in any local minimum. Global optimization is then the appropriate tool. For example, solving a non-linear system of equations via optimization, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zero. Solution method: Using a uniform pdf, points are sampled from a rectangular domain. A clustering technique, based on a typical distance and a gradient criterion, is used to decide from which points a local search should be started. Further searching is terminated when all the local minima inside the search domain are thought to be found. This is accomplished via three stopping rules: the “double-box” stopping rule, the “observables” stopping rule and the “expected minimizers” stopping rule. Reasons for the new version: The link procedure for source code in Fortran 77 is enhanced, two additional stopping rules are implemented and a new criterion for accepting-start points, that economizes on function and gradient calls, is introduced. Summary of revisions: [1.] Addition of command line parameters to the utility program make_program. [2.] Augmentation of the link process for Fortran 77 subprograms, by linking the final executable with the g2c library. [3.] Addition of two probabilistic stopping rules. [4.] Introduction of a rejection mechanism to the Checking step of the original method, that reduces the number of gradient evaluations. Additional comments: A technical report describing the revisions, experiments and test runs is packaged with the source code. Running time: Depending on the objective function. [Copyright &y& Elsevier]

Abstract: The subroutine FANCDEF3 in the code FaCE published as ADTW in CPC 161 (2004) 87, is corrected. [Copyright &y& Elsevier]