The program is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. It contains a library of hard processes, models for initial- and final-state parton showers, matching and merging methods between hard processes and parton showers, multiparton interactions, beam remnants, string fragmentation and particle decays. It also has a set of utilities and several interfaces to external programs. 8.2 is the second main release after the complete rewrite from Fortran to C++, and now has reached such a maturity that it offers a complete replacement for most applications, notably for LHC physics studies. The many new features should allow an improved description of data. Pythia 8.2 ACTU_v4_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public Licence, version 2 478360 14131810 tar.gz C++. Commodity PCs, Macs. Linux, OS X; should also work on other systems. ∼10 megabytes 11.2. Yes ACTU_v3_0 Comput. Phys. Comm. 178 (2008) 852 High-energy collisions between elementary particles normally give rise to complex final states, with large multiplicities of hadrons, leptons, photons and neutrinos. The relation between these final states and the underlying physics description is not a simple one, for two main reasons. Firstly, we do not even in principle have a complete understanding of the physics. Secondly, any analytical approach is made intractable by the large multiplicities. Complete events are generated by Monte Carlo methods. The complexity is mastered by a subdivision of the full problem into a set of simpler separate tasks. All main aspects of the events are simulated, such as hard-process selection, initial- and final-state radiation, beam remnants, fragmentation, decays, and so on. Therefore events should be directly comparable with experimentally observable ones. The programs can be used to extract physics from comparisons with existing data, or to study physics at future experiments. Improved and expanded physics models. Hundreds of new features and bug fixes, allowing improved modelling. Depends on the problem studied. 10–1000 events per second, depending on process studied.
is a -based package which addresses the implementation of particle physics models, which are given in the form of a list of fields, parameters and a Lagrangian, into high-energy physics tools. It calculates the underlying Feynman rules and outputs them to a form appropriate for various programs such as , , , and . Since the original version, many new features have been added: support for two-component fermions, spin-3/2 and spin-2 fields, superspace notation and calculations, automatic mass diagonalization, completely general output, a new universal output interface, a new interface, automatic decay width calculation, improved speed and efficiency, new guidelines for validation and a new web-based validation package. With this feature set, enables models to go from theory to simulation and comparison with experiment quickly, efficiently and accurately. FeynRules 2.0 AEDI_v2_0 CPC Program Library, Queen’s University, Belfast, N. Ireland Standard CPC licence, 51324 455219 tar.gz Mathematica. Platforms on which Mathematica is available. Operating systems on which Mathematica is available. 11.1, 11.6. Yes AEDI_v1_1 Comput. Phys. Comm. 182 (2011) 2404 The program computes the Feynman rules of any quantum field theory, expressed in four-dimensional space–time, directly from the Lagrangian of the model. Various interfaces to Feynman diagram calculators are included that allow the exportation of the interaction vertices in a format readable by different Monte Carlo event generators or symbolic calculation tools. FeynRules works in three steps: Bug fixes. Mathematica version 7.0 or higher. The Lagrangian must fulfill basic quantum field theory requirements, such as locality and Lorentz and gauge invariance. Fields with spin 0, 1/2, 1, 3/2 and 2 are supported. Translation interfaces to various Feynman diagram generators exist. Superfields are also supported and can be expanded in terms of their component fields, which allows the performance of various sets of superspace computations. The computation of the Feynman rules from a Lagrangian varies with the complexity of the model, and runs from a few seconds to several minutes. See Section 7 of the present manuscript for more information.
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field. PLUMED 2 AEEE_v2_0 CPC Program Library, Queen’s University, Belfast, N. Ireland Yes 700646 6618136 tar.gz ANSI-C++. Any computer capable of running an executable produced by a C++ compiler. Linux operating system, Unix OSs. Yes, parallelized using MPI. Depends on the number of atoms, the method chosen and the collective variables used. 3, 7.7, 23. AEEE_v1_0. Comput. Phys. Comm. 180 (2009) 1961. GNU libmatheval, Lapack, Blas, MPI. This version supersedes the previous version for the most part. There are a small number of very specific situations where the previous version is better, due to performance or to non-ported features. We are actively working on porting these last few features into the new code. Calculation of free-energy surfaces for molecular systems of interest in biology, chemistry and materials science, on the fly and analysis of molecular dynamics trajectories using advanced collective variables. Implementations of various collective variables and enhanced sampling techniques. The old version was difficult to maintain and its design was not as flexible as this new version. This lack of flexibility made it difficult to implement a number of novel methods that have emerged since the release of the original code. The new version of the code has a completely redesigned architecture, which allows for several important enhancements. This allows for a much simpler and robust input syntax and for improved performance. In addition, it provides several, more-complex collective variables which could not have been written using the previous implementation. Furthermore, the entire code is fully documented so it is easier to extend. Finally, the code is designed so that users can implement new variables directly in the input files and thus develop bespoke applications of these powerful algorithms. PLUMED 2 can be used either as a standalone program, e.g. for analysis of trajectories, or as a library embedded in a molecular dynamics code (such as GROMACS, NAMD, Quantum ESPRESSO, and LAMMPS). Interfaces with these particular codes are provided in patches, which a simple script will insert into the underlying molecular dynamics codes source code files. For other molecular dynamics codes there is extensive documentation on how to add PLUMED in our manual. The distribution file contains a test suite, user and developer documentation and a collection of patches and utilities. Depends on the number of atoms, the method chosen and the collective variables used. The regression test suite provided takes approximately 1 min to run.
is a software package for computing the lattice thermal conductivity of crystalline bulk materials and nanowires with diffusive boundary conditions. It is based on a full iterative solution to the Boltzmann transport equation. Its main inputs are sets of second- and third-order interatomic force constants, which can be calculated using third-party packages. Dirac delta distributions arising from conservation of energy are approximated by Gaussian functions. A locally adaptive algorithm is used to determine each process-specific broadening parameter, which renders the method fully parameter free. The code is free software, written in Fortran and parallelized using MPI. A complementary Python script to help compute third-order interatomic force constants from a minimum number of calculations, using a real-space finite-difference approach, is also publicly available for download. Here we discuss the design and implementation of both pieces of software and present results for three example systems: Si, InAs and lonsdaleite. ShengBTE AESL_v1_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public License, version 3 292 052 1 989 781 tar.gz Fortran 90, MPI. Non-specific. Unix/Linux. Yes, parallelized using MPI. Up to several GB 7.9. LAPACK, MPI, spglib ( ) Calculation of thermal conductivity and related quantities, determination of scattering rates for allowed three-phonon processes Iterative solution, locally adaptive Gaussian broadening Up to several hours on several tens of processors
We present an open-source software package , a tool for investigation of novel topological materials. This code works in the tight-binding framework, which can be generated by another software package Wannier90 (Mostofi et al., 2008). It can help to classify the topological phase of a given material by calculating the Wilson loop, and can get the surface state spectrum, which is detected by angle resolved photoemission (ARPES) and in scanning tunneling microscopy (STM) experiments. It also identifies positions of Weyl/Dirac points and nodal line structures, calculates the Berry phase around a closed momentum loop and Berry curvature in a part of the Brillouin zone (BZ). GNU General Public Licence 3.0 Fortran 90 Identifying topological classifications of crystalline systems including insulators, semimetals, metals, and studying the electronic properties of the related slab and ribbon systems. Tight-binding method is a good approximation for solid systems. Based on that, Wilson loop is used for topological phase classification. The iterative Green’s function is used for obtaining the surface state spectrum.
We present the program for the numerical evaluation of the total inclusive cross-section for producing top quark pairs at hadron colliders. The program calculates the cross-section in (a) fixed order approach with exact next-to-next-to leading order (NNLO) accuracy and (b) by including soft-gluon resummation for the hadronic cross-section in Mellin space with full next-to-next-to-leading logarithmic (NNLL) accuracy. The program offers the user significant flexibility through the large number (29) of available options. is written in C++. It has a very simple to use interface that is intuitive and directly reflects the physics. The running of the program requires no programming experience from the user. Top++ (ver. 2.0) AETR_v1_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public License 15 896 695 919 tar.gz C++. any running a unix operating system. Program was developed and tested with GNU Compiler Collection, C++ compiler. Linux; Mac OS X; can be adapted for other unix systems. typically less than 200 MB. 11.1. GNU Scientific Library (GSL); the Les Houches Accord pdf Interface (LHAPDF). computation of the total cross-section in perturbative QCD. numerical integration of the product of hard partonic cross-section (with or without soft gluon resummation) with two parton distribution functions. sub per-mill accuracy achievable in realistic time (program does not employ Monte Carlo methods). depending on the options. The program is optimized for speed.
We present the program Top++ for the numerical evaluation of the total inclusive cross-section for producing top quark pairs at hadron colliders. The program calculates the cross-section in (a) fixed order approach with exact next-to-next-to leading order (NNLO) accuracy and (b) by including soft-gluon resummation for the hadronic cross-section in Mellin space with full next-to-next-to-leading logarithmic (NNLL) accuracy. The program offers the user significant flexibility through the large number (29) of available options. Top++ is written in C++. It has a very simple to use interface that is intuitive and directly reflects the physics. The running of the program requires no programming experience from the user. Program summary Program summary Program title: Top++ (ver. 2.0) Catalogue identifier: AETR_v1_0 Program summary UAL: http://cpc.cs.qub.ac.uk/summaries/AETR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 15 896 No. of bytes in distributed program, including test data, etc.: 695 919 Distribution format: tar.gz Programming language: C++. Computer: any running a unix operating system. Program was developed and tested with GNU Compiler Collection, C++ compiler. Operating system: Linux; Mac OS X; can be adapted for other unix systems. RAM: typically less than 200 MB. Classification: 11.1. External routines: GNU Scientific Library (GSL); the Les Houches Accord pdf Interface (LHAPDF). Nature of problem: computation of the total cross-section in perturbative QCD. Solution method: numerical integration of the product of hard partonic cross-section (with or without soft gluon resummation) with two parton distribution functions. Additional comments: sub per-mill accuracy achievable in realistic time (program does not employ Monte Carlo methods). Running time: depending on the options. The program is optimized for speed. (C) 2014 Elsevier B.V. All rights reserved.
We have developed a software package CALYPSO ( ) to predict the energetically stable/metastable crystal structures of materials at given chemical compositions and external conditions (e.g., pressure). The CALYPSO method is based on several major techniques (e.g. particle-swarm optimization algorithm, symmetry constraints on structural generation, bond characterization matrix on elimination of similar structures, partial random structures per generation on enhancing structural diversity, and penalty function, etc.) for global structural minimization from scratch. All of these techniques have been demonstrated to be critical to the prediction of global stable structure. We have implemented these techniques into the CALYPSO code. Testing of the code on many known and unknown systems shows high efficiency and the highly successful rate of this CALYPSO method [Y. Wang, J. Lv, L. Zhu, Y. Ma, Phys. Rev. B 82 (2010) 094116] . In this paper, we focus on descriptions of the implementation of CALYPSO code and why it works.
is a program for calculating maximally-localised Wannier functions (MLWFs) from a set of Bloch energy bands that may or may not be attached to or mixed with other bands. The formalism works by minimising the total spread of the MLWFs in real space. This is done in the space of unitary matrices that describe rotations of the Bloch bands at each k-point. As a result, is independent of the basis set used in the underlying calculation to obtain the Bloch states. Therefore, it may be interfaced straightforwardly to any electronic structure code. The locality of MLWFs can be exploited to compute band-structure, density of states and Fermi surfaces at modest computational cost. Furthermore, is able to output MLWFs for visualisation and other post-processing purposes. Wannier functions are already used in a wide variety of applications. These include analysis of chemical bonding in real space; calculation of dielectric properties via the modern theory of polarisation; and as an accurate and minimal basis set in the construction of model Hamiltonians for large-scale systems, in linear-scaling quantum Monte Carlo calculations, and for efficient computation of material properties, such as the anomalous Hall coefficient. We present here an updated version of , 2.0, including minor bug fixes and parallel (MPI) execution for band-structure interpolation and the calculation of properties such as density of states, Berry curvature and orbital magnetisation. is freely available under the GNU General Public License from . wannier90 AEAK_v2_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public License, version 2 930 386 47 939 902 tar.gz Fortran90, perl. Any architecture with a Fortran 90 compiler. Linux, Windows, Solaris, AIX, Tru64 Unix, OSX. Yes, parallelized using MPI. 10 Mb 7.3. AEAK_v1_0 Comput. Phys. Comm. 178(2008)685 Yes Obtaining maximally-localised Wannier functions  from a set of Bloch energy bands that may or may not be entangled, and using these Wannier functions to calculate electronic properties of materials. In the case of entangled bands, the optimally-connected subspace of interest is determined by minimising a functional which measures the subspace dispersion across the Brillouin zone. The maximally-localised Wannier functions within this subspace are obtained by subsequent minimisation of a functional that represents the total spread of the Wannier functions in real space. For the case of isolated energy bands only the second step of the procedure is required [3, 4]. Addition of new functionality, minor bug fixes, and parallel (MPI) execution for parts of the code. Full details are given in the CHANGE.log file, which can be found in the root directory of the distribution. The distribution file for this program is over 47 MB and therefore is not delivered directly when Download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Example calculations run in a few minutes.
is a code to compute dark matter observables in generic extensions of the standard model. This new version of is a major update which includes a generalization of the Boltzmann equations to accommodate models with asymmetric dark matter or with semi-annihilation and a first approach to a generalization of the thermodynamics of the Universe in the relic density computation. Furthermore a switch to include virtual vector bosons in the final states in the annihilation cross sections or relic density computations is added. Effective operators to describe loop-induced couplings of Higgses to two-photons or two-gluons are introduced and reduced couplings of the Higgs are provided allowing for a direct comparison with recent LHC results. A module that computes the signature of DM captured in celestial bodies in neutrino telescopes is also provided. Moreover the direct detection module has been improved as concerns the implementation of the strange “content” of the nucleon. New extensions of the standard model are included in the distribution. micrOMEGAs3. PC, Mac UNIX (Linux, Darwin) C and Fortran 50 MB depending on the number of processes required. 1 no 70736 kB no CalcHEP, SuSpect, NMSSMTools, CPSuperH, LoopTools, HiggsBounds ADQR_v1_3 Comput. Phys. Comm. 182 (2011) 842 yes Calculation of the relic density and direct and indirect detection rates of the lightest stable particle in a generic new model of particle physics. In numerically solving the evolution equation for the density of dark matter, relativistic formulae for the thermal average are used. All tree-level processes for annihilation and coannihilation of new particles in the model are included as well as some 3-body final states. The cross-sections for all processes are calculated exactly with CalcHEP after definition of a model file. The propagation of the charged cosmic rays is solved within a semi-analytical two-zone model. There are many experiments that are currently searching for the remnants of dark matter annihilation and the relic density is determined precisely from cosmological measurements. In this version we add the computation of dark matter signals in neutrino telescopes, we generalize the Boltzmann equations so as to take into account a larger class of dark matter models and improve the precision in the prediction of the relic density for DM masses that are below the W mass. We compute the signal strength for Higgs production in different channels to compare with the results of the LHC. 4 s Depending on the parameters of the model, the program generates additional new code, compiles it and loads it dynamically.
ABINIT is a package whose main program allows one to find the total energy, charge density, electronic structure and many other properties of systems made of electrons and nuclei, (molecules and periodic solids) within Density Functional Theory (DFT), Many-Body Perturbation Theory (GW approximation and Bethe–Salpeter equation) and Dynamical Mean Field Theory (DMFT). ABINIT also allows to optimize the geometry according to the DFT forces and stresses, to perform molecular dynamics simulations using these forces, and to generate dynamical matrices, Born effective charges and dielectric tensors. The present paper aims to describe the new capabilities of ABINIT that have been developed since 2009. It covers both physical and technical developments inside the ABINIT code, as well as developments provided within the ABINIT package. The developments are described with relevant references, input variables, tests and tutorials. ABINIT AEEU_v2_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public License, version 3 4845789 71340403 tar.gz Fortran2003, PERL scripts, Python scripts. 7.3, 7.8. (all optional) BigDFT , ETSF_IO , libxc , NetCDF , MPI , Wannier90 , FFTW . AEEU_v1_0 Comput. Phys. Comm. 180 (2009) 2582 Yes. The abinit-7.10.5 version is now the up to date stable version of ABINIT This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and vibrational life-times, and others. Software application based on Density Functional Theory, Many-Body Perturbation Theory and Dynamical Mean Field Theory, pseudopotentials, with plane waves or wavelets as basis functions. Since 2009, the abinit-5.7.4 version of the code has considerably evolved and is not yet up to date. The abinit- 7.10.5 version contains new physical and technical features that allow electronic structure calculations impossible to carry out in the previous versions. It is difficult to answer to the question as the use of ABINIT is very large. On one hand, ABINIT can run on 10,000 processors for hours to perform quantum molecular dynamics on large systems. On the other hand, tutorials for students can be performed on a laptop within a few minutes.
We present version 3.4 of the CalcHEP software package which is designed for effective evaluation and simulation of high energy physics collider processes at parton level. The main features of CalcHEP are the computation of Feynman diagrams, integration over multi-particle phase space and event simulation at parton level. The principle attractive key-points along these lines are that it has: (a) an easy startup and usage even for those who are not familiar with CalcHEP and programming; (b) a friendly and convenient graphical user interface (GUI); (c) the option for the user to easily modify a model or introduce a new model by either using the graphical interface or by using an external package with the possibility of cross checking the results in different gauges; (d) a batch interface which allows to perform very complicated and tedious calculations connecting production and decay modes for processes with many particles in the final state. With this features set, CalcHEP can efficiently perform calculations with a high level of automation from a theory in the form of a Lagrangian down to phenomenology in the form of cross sections, parton level event simulation and various kinematical distributions. In this paper we report on the new features of CalcHEP 3.4 which improves the power of our package to be an effective tool for the study of modern collider phenomenology. CalcHEP AEOV_v1_0 CPC Program Library, Queen’s University, Belfast, N. Ireland Standard CPC licence, 78535 818061 tar.gz C. PC, MAC, Unix Workstations. Unix. Depends on process under study 4.4, 5. X11 Up to production ( decay) processes are realistic on typical computers. Higher multiplicities sometimes possible for specific and processes. Graphical user interface, symbolic algebra calculation of squared matrix element, parallelization on a pbs cluster. Depends strongly on the process. For a typical process it takes seconds. For processes the typical running time is of the order of minutes. For higher multiplicities it could take much longer.
The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. NWChem AEGI_v1_0 CPC Program Library, Queen's University, Belfast, N. Ireland Open Source Educational Community License 11 709 543 680 696 106 tar.gz Fortran 77, C all Linux based workstations and parallel supercomputers, Windows and Apple machines Linux, OS X, Windows Code is parallelized 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Full documentation is provided in the distribution file. This includes an file giving details of how to build the package. A set of test runs is provided in the directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or molecular dynamics simulation on hundreds of atoms.
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, 2013). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of .
We present the new version of the package which provides the same features for a non-supersymmetric model as previous versions for supersymmetric models. This includes an easy and straightforward definition of the model, the calculation of all vertices, mass matrices, tadpole equations, and self-energies. Also the two-loop renormalization group equations for a general gauge theory are now included and have been validated with the independent code . Model files for , / , and in the format can be written, and source code for for the calculation of the mass spectrum, a set of precision observables, and the decay widths and branching ratios of all states can be generated. Furthermore, the new version includes routines to output model files for for both, supersymmetric and non-supersymmetric, models. Global symmetries are also supported with this version and by linking the handling of Lie groups has been improved and extended. SARAH AEIB_v3_0 CPC Program Library, Queen’s University, Belfast, N. Ireland Standard CPC licence, 271 795 2 612 867 tar.gz Mathematica. All for which Mathematica is available. All for which Mathematica is available. 11.1, 11.6. AEIB_v2_1 Comput. Phys. Commun. 184 (2013) 2604 Yes, the new version includes all known features of the previous versions but also provides the new features mentioned below. A supersymmetric model is usually characterized by the particle content, the gauge sector and the superpotential. It is a time consuming process to obtain all necessary information for phenomenological studies from these basic ingredients. Non-supersymmetric models are supported by the new possibility to define not only chiral superfields but also component fields. The renormalization group equations (RGEs) for a non-supersymmetric models are calculated by using the generic formulae for a general quantum field theory. New features in the definition of models and a full support of non-supersymmetric models. New output for Vevacious. Support of non-supersymmetric models; calculation of renormalization group equations for a general gauge theory; link to Susyno for handling of non-SU(N) gauge groups; support of global symmetries; output of model files for Vevacious; support of aligned VEVs; calculation of gauge dependent parts of RGEs for VEVs in running of supersymmetric and non-supersymmetric models. Only renormalizable terms in the Lagrangian are supported. No support of fields with spin 2 or 3/2. Calculation of non-supersymmetric RGEs includes effects of kinetic mixing as well as gauge dependence of running vacuum expectation values. SARAH is the first tool which can automatically create model files for Vevacious. Fully automatized derivation of all terms in the Lagrangian which are fixed by gauge invariance. Loading the Standard Model: 1.6 s; calculation of all vertices: 11.8 s; calculation of all RGEs: 130.2 s; output for Vevacious model files: 0.1 s; output of model files in UFO format: 0.8 s; output of model files for FeynArts: 0.1 s; output of model files for CalcHep: 0.8 s; output of model files for WHIZARD: 3.5 s; writing of source code for SPheno: 34.5 s. All times measured on Lenovo X220 with Intel(R) Core(TM) i7-2620M CPU @ 2.70 GHz.
We present new developments of the evolutionary algorithm USPEX for crystal structure prediction and its adaptation to cluster structure prediction. We show how to generate randomly symmetric structures, and how to introduce ‘smart’ variation operators, learning about preferable local environments. These and other developments substantially improve the efficiency of the algorithm and allow reliable prediction of structures with up to ∼200 atoms in the unit cell. We show that an advanced version of the Particle Swarm Optimization (PSO) can be created on the basis of our method, but PSO is strongly outperformed by USPEX. We also show how ideas from metadynamics can be used in the context of evolutionary structure prediction for escaping from local minima. Our cluster structure prediction algorithm, using the ideas initially developed for crystals, also shows excellent performance and outperforms other state-of-the-art algorithms.
We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760.], we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch–Redfield and Floquet–Markov master equations. Here we introduce these new features, demonstrate their use, and give a summary of the important backward-incompatible API changes introduced in this version. QuTiP: The Quantum Toolbox in Python AEMB_v2_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU General Public License, version 3 33625 410064 tar.gz Python. i386, x86-64. Linux, Mac OSX. 2+ Gigabytes 7. NumPy, SciPy, Matplotlib, Cython AEMB_v1_0 Comput. Phys. Comm. 183 (2012) 1760 Yes Dynamics of open quantum systems Numerical solutions to Lindblad, Floquet–Markov, and Bloch–Redfield master equations, as well as the Monte Carlo wave function method. Compared to the preceding version we have introduced numerous new features, enhanced performance, and made changes in the Application Programming Interface (API) for improved functionality and consistency within the package, as well as increased compatibility with existing conventions used in other scientific software packages for Python. The most significant new features include efficient solvers for arbitrary time-dependent Hamiltonians and collapse operators, support for the Floquet formalism, and new solvers for Bloch–Redfield and Floquet–Markov master equations. Problems must meet the criteria for using the master equation in Lindblad, Floquet–Markov, or Bloch–Redfield form. A few seconds up to several tens of hours, depending on size of the underlying Hilbert space.
is a code to compute dark matter observables in generic extensions of the standard model. This version of includes a generalization of the Boltzmann equations to take into account the possibility of two dark matter candidates. The modification of the relic density calculation to include interactions between the two dark matter sectors as well as semi-annihilation is presented. Both dark matter signals in direct and indirect detection are computed as well. An extension of the standard model with two scalar doublets and a singlet is used as an example. MicrOMEGAs4.1 ADQR_v4_0 CPC Program Library, Queen’s University, Belfast, N. Ireland Standard CPC licence, 738425 9807620 tar.gz C and Fortran. PC, Mac. UNIX (Linux, Darwin). 50MB depending on the number of processes required. 1.9, 11.6. ADQR_v3.0 Comput. Phys. Comm. 185 (2014) 960 CalcHEP, SuSpect, NMSSMTools, CPSuperH, LoopTools, HiggsBounds Yes Calculation of the relic density and direct and indirect detection rates of the lightest stable particle in particle physics models with at most two stable dark matter candidates. In the case where the two dark matter particles have very different masses, we find that the equations for the evolution of the density of dark matter behave as stiff equations. To solve these we use the backward scheme and the Rosenbrock algorithm. The standard solution based on the Runge–Kutta method is still used for models with only one dark matter candidate. There are many experiments that are currently searching for the remnants of dark matter annihilation and the relic density is determined precisely from cosmological measurements. In this version we generalize the Boltzmann equations to take into account the possibility of two dark matter candidates. Thus, in solving for the relic density we include interactions between the two dark matter sectors as well as semi-annihilation. The dark matter signals in direct and indirect detection are computed as well. Depending on the parameters of the model, the program generates additional new code, compiles it and loads it dynamically. 4 sec
gprMax is open source software that simulates electromagnetic wave propagation, using the Finite-Difference Time-Domain (FDTD) method, for the numerical modelling of Ground Penetrating Radar (GPR). gprMax was originally developed in 1996 when numerical modelling using the FDTD method and, in general, the numerical modelling of GPR were in their infancy. Current computing resources offer the opportunity to build detailed and complex FDTD models of GPR to an extent that was not previously possible. To enable these types of simulations to be more easily realised, and also to facilitate the addition of more advanced features, gprMax has been redeveloped and significantly modernised. The original C-based code has been completely rewritten using a combination of Python and Cython programming languages. Standard and robust file formats have been chosen for geometry and field output files. New advanced modelling features have been added including: an unsplit implementation of higher order Perfectly Matched Layers (PMLs) using a recursive integration approach; diagonally anisotropic materials; dispersive media using multi-pole Debye, Drude or Lorenz expressions; soil modelling using a semi-empirical formulation for dielectric properties and fractals for geometric characteristics; rough surface generation; and the ability to embed complex transducers and targets. gprMax AFBG_v1_0 CPC Program Library, Queen’s University, Belfast, N. Ireland GNU GPL v3 627180 26762280 tar.gz Python. Any computer with a Python interpreter and a C compiler. Microsoft Windows, Mac OS X, and Linux. Problem dependent 10. Cython, h5py, matplotlib, NumPy, mpi4py Classical electrodynamics Finite-Difference Time-Domain (FDTD) Problem dependent
ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, the RooFit package allows the user to perform complex data modeling and fitting while the RooStats library provides abstractions and implementations for advanced statistical tools. Multivariate classification methods based on machine learning techniques are available via the TMVA package. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks — e.g. data mining in HEP — by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way. ROOT AEFA_v1_0 CPC Program Library, Queen's University, Belfast, N. Ireland LGPL 3 044 581 36 325 133 tar.gz C++ Intel i386, Intel x86-64, Motorola PPC, Sun Sparc, HP PA-RISC GNU/Linux, Windows XP/Vista, Mac OS X, FreeBSD, OpenBSD, Solaris, HP-UX, AIX Yes 4, 9, 11.9, 14 Storage, analysis and visualization of scientific data Object store, wide range of analysis algorithms and visualization methods For an up-to-date author list see: and Depending on the data size and complexity of analysis algorithms