Showing papers in "Computer Physics Communications in 2017"

WannierTools: An open-source software package for novel topological materials

Abstract: We present an open-source software package WannierTools , 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). Program summary Program title: WannierTools Program Files doi: http://dx.doi.org/10.17632/ygsmh4hyh6.1 Licensing provisions: GNU General Public Licence 3.0 Programming language: Fortran 90 External routines/libraries used: • BLAS ( http://www/netlib.org/blas ) • LAPACK ( http://www.netlib.org/lapack ) Nature of problem: Identifying topological classifications of crystalline systems including insulators , semimetals , metals, and studying the electronic properties of the related slab and ribbon systems. Solution method: 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.

Collier: A fortran-based complex one-loop library in extended regularizations

Abstract: We present the library Collier for the numerical evaluation of one-loop scalar and tensor integrals in perturbative relativistic quantum field theories . The code provides numerical results for arbitrary tensor and scalar integrals for scattering processes in general quantum field theories. For tensor integrals either the coefficients in a covariant decomposition or the tensor components themselves are provided. Collier supports complex masses, which are needed in calculations involving unstable particles. Ultraviolet and infrared singularities are treated in dimensional regularization . For soft and collinear singularities mass regularization is available as an alternative. Program summary Program title: Collier Program Files doi: http://dx.doi.org/10.17632/dmdn2ph3x2.1 Licensing provisions: GNU GPL version 3 Programming language: Fortran95 Nature of problem: Evaluation of general one-loop multi-leg scalar and tensor integrals occurring in the calculation of one-loop corrections to scattering amplitudes in relativistic quantum field theories. Solution method: Scalar integrals are evaluated using explicit analytical expressions. Tensor integrals are numerically reduced to scalar integrals via different methods. Depending on the specific kinematical variables, an appropriate method is automatically chosen to optimize the resulting numerical accuracy. Restrictions: real momenta

TikZ-Feynman: Feynman diagrams with TikZ

Abstract: Ti k Z-Feynman is a LaTeX package allowing Feynman diagrams to be easily generated within LaTeX with minimal user instructions and without the need of external programs. It builds upon the Ti k Z package and leverages the graph placement algorithms from Ti k Z in order to automate the placement of many vertices. Ti k Z-Feynman still allows fine-tuned placement of vertices so that even complex diagrams can be generated with ease. Program summary Program title: Ti k Z-Feynman Catalogue identifier: AFBF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AFBF_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU GPL v3 No. of lines in distributed program, including test data, etc.: 6727 No. of bytes in distributed program, including test data, etc.: 413779 Distribution format: tar.gz Programming language: TeX, LaTeX, Lua. Computer: PC’s or workstations. Operating system: Any capable of processing LaTeX. Classification: 4.4. External routines: Ti k Z Nature of problem: Existing methods for drawing Feynman diagrams in LaTeX usually require external programs and are not very user friendly thereby making it difficult and time consuming to generate even simple diagrams. Solution method: Ti k Z-Feynman provides an easier way to draw Feynman diagrams by building on Ti k Z and using graph drawing algorithms to automatically place vertices. This can be combined with some positioning to produce complicated diagrams with relative ease. Running time: Depends on the size

CheckMATE 2: From the model to the limit

Abstract: We present the latest developments to the CheckMATE program that allows models of new physics to be easily tested against the recent LHC data. To achieve this goal, the core of CheckMATE now contains over 60 LHC analyses of which 12 are from the 13 TeV run. The main new feature is that CheckMATE 2 now integrates the Monte Carlo event generation via Madgraph and Pythia 8. This allows users to go directly from a SLHA file or UFO model to the result of whether a model is allowed or not. In addition, the integration of the event generation leads to a significant increase in the speed of the program. Many other improvements have also been made, including the possibility to now combine signal regions to give a total likelihood for a model.

ARC: An open-source library for calculating properties of alkali Rydberg atoms

Abstract: We present an object-oriented Python library for the computation of properties of highly-excited Rydberg states of alkali atoms. These include single-body effects such as dipole matrix elements, excited-state lifetimes (radiative and black-body limited) and Stark maps of atoms in external electric fields, as well as two-atom interaction potentials accounting for dipole and quadrupole coupling effects valid at both long and short range for arbitrary placement of the atomic dipoles. The package is cross-referenced to precise measurements of atomic energy levels and features extensive documentation to facilitate rapid upgrade or expansion by users. This library has direct application in the field of quantum information and quantum optics which exploit the strong Rydberg dipolar interactions for two-qubit gates, robust atom-light interfaces and simulating quantum many-body physics, as well as the field of metrology using Rydberg atoms as precise microwave electrometers. Program summary Program Title: ARC: Alkali Rydberg Calculator Program Files doi: http://dx.doi.org/10.17632/hm5n8w628c.1 Licensing provisions: BSD-3-Clause Programming language: Python 2.7 or 3.5, with C extension External Routines: NumPy [1], SciPy [1], Matplotlib [2] Nature of problem: Calculating atomic properties of alkali atoms including lifetimes, energies, Stark shifts and dipole–dipole interaction strengths using matrix elements evaluated from radial wavefunctions. Solution method: Numerical integration of radial Schrodinger equation to obtain atomic wavefunctions, which are then used to evaluate dipole matrix elements. Properties are calculated using second order perturbation theory or exact diagonalisation of the interaction Hamiltonian, yielding results valid even at large external fields or small interatomic separation. Restrictions: External electric field fixed to be parallel to quantisation axis. Supplementary material: Detailed documentation (.html), and Jupyter notebook with examples and benchmarking runs (.html and .ipynb). [1] T.E. Oliphant, Comput. Sci. Eng. 9, 10 (2007). http://www.scipy.org/ . [2] J.D. Hunter, Comput. Sci. Eng. 9, 90 (2007). http://matplotlib.org/ .

STARlight: A Monte Carlo simulation program for ultra-peripheral collisions of relativistic ions

Abstract: Ultra-peripheral collisions (UPCs) have been a significant source of study at RHIC and the LHC. In these collisions, the two colliding nuclei interact electromagnetically, via two-photon or photonuclear interactions, but not hadronically; they effectively miss each other. Photonuclear interactions produce vector meson states or more general photonuclear final states, while two-photon interactions can produce lepton or meson pairs, or single mesons. In these interactions, the collision geometry plays a major role. We present a program, STARlight, that calculates the cross-sections for a variety of UPC final states and also creates, via Monte Carlo simulation, events for use in determining detector efficiency.

Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

Abstract: We present novel methods implemented within the non-equilibrium Green function code (NEGF) transiesta based on density functional theory (DFT). Our flexible, next-generation DFT–NEGF code handles devices with one or multiple electrodes ( N e ≥ 1 ) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization . Additionally, a generic NEGF “post-processing” code ( tbtrans / phtrans ) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, N e ≥ 1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 10 6 atoms on workstation computers . The new features of both codes are demonstrated and bench-marked for relevant test systems.

Recola2: REcursive Computation of One-Loop Amplitudes 2

Abstract: We present the Fortran95 program Recola2 for the perturbative computation of next-to-leading-order transition amplitudes in the Standard Model of particle physics and extended Higgs sectors. New theories are implemented via model files in the ’t Hooft–Feynman gauge in the conventional formulation of quantum field theory and in the Background-Field method. The present version includes model files for Two-Higgs-Doublet Model and the Higgs-Singlet Extension of the Standard Model. We support standard renormalization schemes for the Standard Model as well as many commonly used renormalization schemes in extended Higgs sectors. Within these models the computation of next-to-leading-order polarized amplitudes and squared amplitudes, optionally summed over spin and colour, is fully automated for any process. Recola2 allows the computation of colour- and spin-correlated leading-order squared amplitudes that are needed in the dipole subtraction formalism. Recola2 is publicly available for download at http://recola.hepforge.org . Program summary Program Title: Recola2 Program Files doi: http://dx.doi.org/10.17632/sn4wvmkd9k.1 Licensing provisions: GNU GPL version 3 Programming language: Fortran95 Nature of problem: Evaluation of general tree-level and one-loop scattering amplitudes occurring in the calculation of observables in relativistic quantum field theories. Solution method: Tree-level and one-loop amplitudes are numerically calculated using a recursive algorithm. For one-loop amplitudes numerical results for tensor integrals are needed as input. These are provided by the Collier library. In addition, contributions of counterterms and rational terms are determined via dedicated Feynman rules. Restrictions: The code has been used for processes with up to 9 external particles at one-loop level and up to 10 external particles at tree level. For large multiplicities available internal storage may cause limitations. Presently besides the Standard Model, the Two-Higgs-Doublet Model and the Higgs-singlet extension of the Standard Model are supported.

Version 3 of RunDec and CRunDec

Abstract: We present new versions of the packages RunDec and CRunDec which can be used for the running and decoupling of the strong coupling constant and quark masses. Furthermore several conversion formulae for heavy quark masses are implemented. The new versions include five-loop corrections of the QCD beta function and four-loop decoupling effects. Furthermore, various relations between the heavy quark mass defined in the MS ¯ and other short-distance schemes are implemented to next-to-next-to-next-to-leading order. We discuss in detail the improvements and provide several examples which show how RunDec and CRunDec can be used in frequently occurring situations. Program summary Program title: RunDec , CRunDec Program Files doi: http://dx.doi.org/10.17632/4gsm8tmjtj.1 Licensing provisions: GPLv3 Programming language: The procedures are implemented both in Mathematica (RunDec) and in C++11 (CRundec). Nature of problem: The value for the coupling constant of Quantum Chromodynamics, α s ( n f ) ( μ ) , depends on the considered energy scale, μ , and the number of active quark flavours, n f . The same applies to light quark masses, m q ( n f ) ( μ ) , if they are, e.g., evaluated in the MS ¯ scheme. In the programs RunDec and CRunDec all relevant formulae are collected and various procedures are provided which allow for a convenient evaluation of α s ( n f ) ( μ ) and m q ( n f ) ( μ ) using the state-of-the-art correction terms. Furthermore, the programs contain several conversion formulae which allow to transform the MS ¯ value of a heavy quark into other short-distance values or the on-shell definition. Solution method: CRunDec is implemented in C++ . For the solution of the differential equations an adaptive Runge–Kutta procedure has been implemented. The Mathematica version RunDec uses function provided by Mathematica to solve the differential equations. Additional comments including restrictions: It could be that for an unphysical choice of the input parameters the results are nonsensical.

almaBTE : A solver of the space–time dependent Boltzmann transport equation for phonons in structured materials

Abstract: almaBTE is a software package that solves the space- and time-dependent Boltzmann transport equation for phonons , using only ab-initio calculated quantities as inputs. The program can predictively tackle phonon transport in bulk crystals and alloys, thin films , superlattices , and multiscale structures with size features in the nm – μ m range. Among many other quantities, the program can output thermal conductances and effective thermal conductivities , space-resolved average temperature profiles, and heat-current distributions resolved in frequency and space. Its first-principles character makes almaBTE especially well suited to investigate novel materials and structures. This article gives an overview of the program structure and presents illustrative examples for some of its uses. PROGRAM SUMMARY Program Title: almaBTE Program Files doi: http://dx.doi.org/10.17632/8tfzwgtp73.1 Licensing provisions: Apache License, version 2.0 Programming language: C++ External routines/libraries: BOOST, MPI, Eigen, HDF5, spglib Nature of problem: Calculation of temperature profiles, thermal flux distributions and effective thermal conductivities in structured systems where heat is carried by phonons Solution method: Solution of linearized phonon Boltzmann transport equation, Variance-reduced Monte Carlo

SusHi Bento: Beyond NNLO and the heavy-top limit

Abstract: Version 1.6.0 of the code SusHi is presented. Concerning inclusive CP-even Higgs production in gluon fusion, the following new features with respect to previous versions have been implemented: expansion of the partonic cross section in the soft limit, i.e. around x = M H 2 ∕ s ˆ → 1 ; N 3 LO QCD corrections in terms of the soft expansion; top-quark mass suppressed terms through NNLO; matching to the cross section at x → 0 through N 3 LO. For CP-even and -odd scalars, an efficient evaluation of the renormalization-scale dependence is included, and effects of dimension-5 operators can be studied, which we demonstrate for the SM Higgs boson and for a CP-even scalar with a mass of 750 GeV . In addition, as a generalization of the previously available b b → H cross section, SusHi_1.6.0 provides the cross section for charged and neutral Higgs production in the annihilation of arbitrary heavy quarks. At fixed order in perturbation theory, SusHi thus allows to obtain Higgs cross-section predictions in different models to the highest precision known today. For the SM Higgs boson of M H = 125 GeV , SusHi yields 48.28 pb for the gluon-fusion cross section at the LHC at 13 TeV . Simultaneously, SusHi provides the renormalization-scale uncertainty of ± 1 . 97 pb. New version program summary Program title: SusHi . Program Files doi: http://dx.doi.org/10.17632/3bb3z4k9hp.1 Licensing provisions: GNU General Public License 3 (GPL). Programming language: Fortran 77. Journal Reference of previous version: Comp. Phys. Comm. 184, Issue 6 (2013) 1605–1617 Does the new version supersede the previous version?: Yes. The new version also includes all features of previous versions. Reasons for the new version: Compared to version 1.0.0 the newest SusHi version 1.6.0 now supports the 2-Higgs-Doublet-Model (2HDM) and the next-to-minimal supersymmetric standard model (NMSSM). The effects of dimension-5 operators in the calculation of the gluon-fusion cross section can be studied. It allows to calculate the Higgs production cross section from the annihilation of heavy quarks and includes various new features which improve the gluon-fusion cross-section prediction and the associated uncertainty estimate. Links to external codes 2HDMC , MoRe-SusHi and MadGraph5_aMC@NLO can be established. Summary of revisions: Inclusion of 2HDM, NMSSM; Improvements in the prediction of the gluon-fusion cross section: Top-quark mass terms up to next-to-next-to leading order, soft expansion and next-to-next-to-next-to leading order corrections in the heavy top-quark effective theory, top squark corrections up to next-to-next-to leading order; dimension-5 operators; analytic determination of the renormalization scale dependence. Inclusion of heavy-quark annihilation cross sections. Link to MoRe-SusHi for the calculation of resummed transverse-momentum distributions. Nature of problem: Calculation of inclusive and exclusive Higgs production cross sections in gluon fusion and heavy-quark annihilation in the SM and extended Higgs sectors through next-to-leading order QCD, including (next-to-)next-to-next-to-leading order top-(s)quark contributions and electroweak effects. Solution method: Numerical Monte Carlo integration. References: http://sushi.hepforge.org

Fuchsia : A tool for reducing differential equations for Feynman master integrals to epsilon form ☆

Abstract: We present Fuchsia — an implementation of the Lee algorithm, which for a given system of ordinary differential equations with rational coefficients ∂ x J ( x , ϵ ) = A ( x , ϵ ) J ( x , ϵ ) finds a basis transformation T ( x , ϵ ) , i.e., J ( x , ϵ ) = T ( x , ϵ ) J ′ ( x , ϵ ) , such that the system turns into the epsilon form : ∂ x J ′ ( x , ϵ ) = ϵ S ( x ) J ′ ( x , ϵ ) , where S ( x ) is a Fuchsian matrix. A system of this form can be trivially solved in terms of polylogarithms as a Laurent series in the dimensional regulator ϵ . That makes the construction of the transformation T ( x , ϵ ) crucial for obtaining solutions of the initial system. In principle, Fuchsia can deal with any regular systems, however its primary task is to reduce differential equations for Feynman master integrals. It ensures that solutions contain only regular singularities due to the properties of Feynman integrals. Program summary Program Title: Fuchsia Program Files doi: http://dx.doi.org/10.17632/zj6zn9vfkh.1 Licensing provisions: MIT Programming language: Python 2.7 Nature of problem: Feynman master integrals may be calculated from solutions of a linear system of differential equations with rational coefficients. Such a system can be easily solved as an ϵ -series when its epsilon form is known. Hence, a tool which is able to find the epsilon form transformations can be used to evaluate Feynman master integrals. Solution method: The solution method is based on the Lee algorithm (Lee, 2015) which consists of three main steps: fuchsification, normalization, and factorization. During the fuchsification step a given system of differential equations is transformed into the Fuchsian form with the help of the Moser method (Moser, 1959). Next, during the normalization step the system is transformed to the form where eigenvalues of all residues are proportional to the dimensional regulator ϵ . Finally, the system is factorized to the epsilon form by finding an unknown transformation which satisfies a system of linear equations. Additional comments including Restrictions and Unusual features: Systems of single-variable differential equations are considered. A system needs to be reducible to Fuchsian form and eigenvalues of its residues must be of the form n + m ϵ , where n is integer. Performance depends upon the input matrix, its size, number of singular points and their degrees. It takes around an hour to reduce an example 74 × 74 matrix with 20 singular points on a PC with a 1.7 GHz Intel Core i5 CPU. An additional slowdown is to be expected for matrices with complex and/or irrational singular point locations, as these are particularly difficult for symbolic algebra software to handle.

Multi-resolution Delta-plus-SPH with tensile instability control: Towards high Reynolds number flows

Abstract: It is well known that the use of SPH models in simulating flow at high Reynolds numbers is limited because of the tensile instability inception in the fluid region characterized by high vorticity and negative pressure. In order to overcome this issue, the δ + -SPH scheme is modified by implementing a Tensile Instability Control (TIC). The latter consists of switching the momentum equation to a non-conservative formulation in the unstable flow regions. The loss of conservation properties is shown to induce small errors, provided that the particle distribution is regular. The latter condition can be ensured thanks to the implementation of a Particle Shifting Technique (PST). The novel variant of the δ + -SPH is proved to be effective in preventing the onset of tensile instability. Several challenging benchmark tests involving flows past bodies at large Reynolds numbers have been used. Within this a simulation characterized by a deforming foil that resembles a fish-like swimming body is used as a practical application of the δ + -SPH model in biological fluid mechanics.

epsilon: A tool to find a canonical basis of master integrals

Abstract: In 2013, Henn proposed a special basis for a certain class of master integrals, which are expressible in terms of iterated integrals. In this basis, the master integrals obey a differential equation, where the right hand side is proportional to ϵ in d = 4 − 2 ϵ space–time dimensions. An algorithmic approach to find such a basis was found by Lee. We present the tool epsilon , an efficient implementation of Lee’s algorithm based on the Fermat computer algebra system as computational back end. Program summary Program Title: epsilon Program Files doi: http://dx.doi.org/10.17632/j59sy5n729.1 Licensing provisions: GPLv3 Programming language: C++ Nature of problem: For a certain class of master integrals, a canonical basis can be found in which they fulfill a differential equation with the right hand side proportional to ϵ . In such a basis the solution of the master integrals in an ϵ -expansion becomes trivial. Unfortunately, the problem of finding a canonical basis is challenging. Solution method: Algorithm by Lee [1] Restrictions: The normalization step of Lee’s algorithm will fail if the eigenvalues of the matrix residues are not of the form a + b ϵ with a , b ∈ Z . Multi-scale problems are not supported. [1] R.N. Lee, JHEP 1504 (2015) 108 [ arXiv:1411.0911 [hep-ph]].

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Abstract: Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

AZURITE : An algebraic geometry based package for finding bases of loop integrals

Abstract: For any given Feynman graph, the set of integrals with all possible powers of the propagators spans a vector space of finite dimension. We introduce the package Azurite (A ZUR ich-bred method for finding master I nTE grals), which efficiently finds a basis of this vector space. It constructs the needed integration-by-parts (IBP) identities on a set of generalized-unitarity cuts. It is based on syzygy computations and analyses of the symmetries of the involved Feynman diagrams and is powered by the computer algebra systems Singular and Mathematica . It can moreover analytically calculate the part of the IBP identities that is supported on the cuts. In some cases, the basis obtained by Azurite may be slightly overcomplete. Program summary Program Title: Azurite Program Files doi: http://dx.doi.org/10.17632/g7p7z3w9dj.1 Licensing provisions: GNU General Public License (GPL) Programming language: Wolfram Mathematica version 10.0 or higher Supplementary material: A manual in the form of a Mathematica notebook Nature of problem: Determination of a basis of the space of loop integrals spanned by a given Feynman diagram and all of its subdiagrams Solution method: Mathematica implementation

An efficient FSI coupling strategy between Smoothed Particle Hydrodynamics and Finite Element methods

Abstract: An efficient coupling between Smoothed Particle Hydrodynamics (SPH) and Finite Element (FE) methods dedicated to violent fluid–structure interaction (FSI) modeling is proposed in this study. The use of a Lagrangian meshless method for the fluid reduces the complexity of fluid–structure interface handling, especially in presence of complex free surface flows. The paper details the discrete SPH equations and the FSI coupling strategy adopted. Both convergence and robustness of the SPH-FE coupling are performed and discussed. More particularly, the loss and gain in stability is studied according to various coupling parameters, and different coupling algorithms are considered. Investigations are performed on 2D academic and experimental test cases in the order of increasing complexity.

dsmcFoam+: An OpenFOAM based direct simulation Monte Carlo solver

Abstract: dsmcFoam+ is a direct simulation Monte Carlo (DSMC) solver for rarefied gas dynamics, implemented within the OpenFOAM software framework, and parallelised with MPI. It is open-source and released under the GNU General Public License in a publicly available software repository that includes detailed documentation and tutorial DSMC gas flow cases. This release of the code includes many features not found in standard dsmcFoam, such as molecular vibrational and electronic energy modes, chemical reactions, and subsonic pressure boundary conditions. Since dsmcFoam+ is designed entirely within OpenFOAM’s C++ object-oriented framework, it benefits from a number of key features: the code emphasises extensibility and flexibility so it is aimed first and foremost as a research tool for DSMC, allowing new models and test cases to be developed and tested rapidly. All DSMC cases are as straightforward as setting up any standard OpenFOAM case, as dsmcFoam+ relies upon the standard OpenFOAM dictionary based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of a DSMC simulation is not typical of most OpenFOAM applications. We show that dsmcFoam+ compares well to other well-known DSMC codes and to analytical solutions in terms of benchmark results.

ManeParse : A Mathematica reader for Parton Distribution Functions

Abstract: Parton Distribution Functions (PDFs) are essential non-perturbative inputs for calculation of any observable with hadronic initial states. These PDFs are released by individual groups as discrete grids as a function of the Bjorken- x and energy scale Q . The LHAPDF project maintains a repository of PDFs from various groups in a new standardized LHAPDF6 format, additionally older formats such as the CTEQ PDS grid format are still in use. ManeParse is a package that provides access to PDFs within Mathematica to facilitate calculation and plotting. The program is self-contained so there are no external links to any FORTRAN , C or C++ programs. The package includes the option to use the built-in Mathematica interpolation or a custom cubic Lagrange interpolation routine which allows for flexibility in the extrapolation (particularly at small x -values). ManeParse is fast enough to enable simple calculations (involving even one or two integrations) in the Mathematica framework. Program summary Program Title: ManeParse Program Files doi: http://dx.doi.org/10.17632/knbsccggg4.1 Licensing provisions: MIT Programming language: Mathematica Nature of problem: PDFs are currently read and interpolated via a FORTRAN or C++ interface. No method exist to read the LHAPDF6 or CTEQ PDFs directly in Mathematica . Solution method: A Mathematica package reads in LHAPDF6 and CTEQ PDF files. The PDFs are parsed into a three-dimensional array in Bjorken- x , scattering energy Q , and parton flavor, and are stored in memory. Provided functions give access to the PDF, the PDF uncertainty, the PDF correlations, and the parton–parton Luminosities. The LHAPDF6 info files are converted from YAML format into Mathematica rules.

SPARC: Accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory: Extended systems

Abstract: As the first component of SPARC (Simulation Package for Ab-initio Real-space Calculations), we present an accurate and efficient finite-difference formulation and parallel implementation of Density Functional Theory (DFT) for isolated clusters. Specifically, utilizing a local reformulation of the electrostatics, the Chebyshev polynomial filtered self-consistent field iteration, and a reformulation of the non-local component of the force, we develop a framework using the finite-difference representation that enables the efficient evaluation of energies and atomic forces to within the desired accuracies in DFT. Through selected examples consisting of a variety of elements, we demonstrate that SPARC obtains exponential convergence in energy and forces with domain size; systematic convergence in the energy and forces with mesh-size to reference plane-wave result at comparably high rates; forces that are consistent with the energy, both free from any noticeable ‘egg-box’ effect; and accurate ground-state properties including equilibrium geometries and vibrational spectra. In addition, for systems consisting up to thousands of electrons, SPARC displays weak and strong parallel scaling behavior that is similar to well-established and optimized plane-wave implementations, but with a significantly reduced prefactor. Overall, SPARC represents an attractive alternative to plane-wave codes for practical DFT simulations of isolated clusters. Program summary Program title: SPARC Catalogue identifier: AFBL_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AFBL_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU GPL v3 No. of lines in distributed program, including test data, etc.: 47525 No. of bytes in distributed program, including test data, etc.: 826436 Distribution format: tar.gz Programming language: C/C++. Computer: Any system with C/C++ compiler. Operating system: Linux. RAM: Problem dependent. Ranges from 80 GB to 800 GB for a system with 2500 electrons. Classification: 7.3. External routines: PETSc 3.5.3 ( http://www.mcs.anl.gov/petsc ), MKL 11.2 ( https://software.intel.com/en-us/intel-mkl ), and MVAPICH2 2.1 ( http://mvapich.cse.ohio-state.edu/ ). Nature of problem: Calculation of the electronic and structural ground-states for isolated clusters in the framework of Kohn–Sham Density Functional Theory (DFT). Solution method: High-order finite-difference discretization. Local reformulation of the electrostatics in terms of the electrostatic potential and pseudocharge densities. Calculation of the electronic ground-state using the Chebyshev polynomial filtered Self-Consistent Field (SCF) iteration in conjunction with Anderson extrapolation/mixing. Evaluation of boundary conditions for the electrostatic potential through a truncated multipole expansion. Reformulation of the non-local component of the force. Geometry optimization using the Polak–Ribiere variant of non-linear conjugate gradients with secant line search. Restrictions: System size less than ∼4000 electrons. Local Density Approximation (LDA). Troullier–Martins pseudopotentials without relativistic or non-linear core corrections. Running time: Problem dependent. Timing results for selected examples provided in the paper.

Updated core libraries of the ALPS project

Abstract: The open source ALPS (Algorithms and Libraries for Physics Simulations) project provides a collection of physics libraries and applications, with a focus on simulations of lattice models and strongly correlated systems. The libraries provide a convenient set of well-documented and reusable components for developing condensed matter physics simulation code, and the applications strive to make commonly used and proven computational algorithms available to a non-expert community. In this paper we present an updated and refactored version of the core ALPS libraries geared at the computational physics software development community, rewritten with focus on documentation, ease of installation, and software maintainability. Program summary Program Title: ALPS Core libraries Program Files doi: http://dx.doi.org/10.17632/fckj5d7wtr.1 Programming language: C++ Licensing provisions: GNU GPLv3 Nature of problem: Need for modern, lightweight, tested and documented libraries covering the basic requirements of rapid development of efficient physics simulation codes, especially for modeling strongly correlated electron systems. Solution method: We present a C++ open source computational library that provides a convenient set of components for developing parallel physics simulation code. The library features a short development cycle and up-to-date user documentation. External routines/libraries: CMake , MPI , Boost , HDF5 .

KaTie: For parton-level event generation with kT-dependent initial states

Abstract: KaTie is a parton-level event generator for hadron scattering processes that can deal with partonic initial-state momenta with an explicit transverse momentum dependence causing them to be space-like. Provided with the necessary transverse momentum dependent parton density functions, it calculates the tree-level off-shell matrix elements and performs the phase space importance sampling to produce weighted events, for example in the Les Houches Event File format. It can deal with arbitrary processes within the Standard Model, for up to at least four final-state particles. Furthermore, it can produce events for single-parton scattering as well as for multi-parton scattering. Program summary Program Title: KaTie Program Files doi: http://dx.doi.org/10.17632/yrtgg8w9k8.1 Licensing provisions: GPLv3 Programming language: Fortran 2003 (implemented at least as far as in for example gfortran-4.6), Python (2.x with x ≥ 6 or 3.x), Bash External routines/libraries: Requires avhlib [1] and LHAPDF-6.x [2] Nature of problem: Factorization prescriptions for the cross section calculation of hadron scattering processes that allow for non-vanishing transverse momentum components for the initial-state partons require matrix elements with off-shell initial-state partons. Furthermore, the calculation of such cross sections requires the integration over these initial-state degrees of freedom, besides the components along the colliding hadrons and the final-state phase space degrees of freedom. Solution method: The Monte Carlo method is applied to create event files with which distributions for arbitrary observables can be evaluated. Tree-level off-shell matrix elements are defined as proposed in [3] and evaluated using Dyson–Schwinger recursion [4]. The whole procedure is automated for any process within the Standard Model, including the full particle content with all mass and coupling dependencies except the CKM matrix, but including the Higgs–gluon and Higgs–photon effective interactions. Restrictions: The matrix elements are tree-level matrix elements, and the maximal number of final-state particles is 9. The maximal number (initial plus final) of color pairs (gluons and/or quark–antiquark-pairs) for reasonable execution time is 6. Processes are restricted to the Standard Model, including the Higgs–gluon and Higgs–photon effective interactions. [1] M. Bury and A. van Hameren, Numerical evaluation of multi-gluon amplitudes for High Energy Factorization, Comput. Phys. Commun 196 (2015) 592. http://bitbucket.org/hameren/avhlib [2] A. Buckley, J. Ferrando, S. Lloyd, K. Nordstrom, B. Page, M. Rufenacht, M. Schonherr and G. Watt, LHAPDF6: parton density access in the LHC precision era, Eur. Phys. J. C 75 (2015) 132. http://lhapdf.hepforge.org/ [3] A. van Hameren, P. Kotko, and K. Kutak, Helicity amplitudes for high-energy scattering, JHEP 01 (2013) 078. [4] F. Caravaglios and M. Moretti, An algorithm to compute Born scattering amplitudes without Feynman graphs, Phys. Lett. B 358 (1995) 332. A. Kanaki, C.G. Papadopoulos, HELAC: A Package to compute electroweak helicity amplitudes, Comput. Phys. Commun. 132 (2000) 306.

DynaPhoPy: A code for extracting phonon quasiparticles from molecular dynamics simulations

Abstract: We have developed a computational code, DynaPhoPy , that allows us to extract the microscopic anharmonic phonon properties from molecular dynamics (MD) simulations using the normal-mode-decomposition technique as presented by Sun et al. (2014). Using this code we calculated the quasiparticle phonon frequencies and linewidths of crystalline silicon at different temperatures using both of first-principles and the Tersoff empirical potential approaches. In this work we show the dependence of these properties on the temperature using both approaches and compare them with reported experimental data obtained by Raman spectroscopy (Balkanski et al., 1983; Tsu and Hernandez, 1982). Program summary Program Title: DynaPhoPy Program Files doi: http://dx.doi.org/10.17632/v493dkxk8r.1 Licensing provisions: MIT License Programming language: Python and C External routines/libraries: phonopy, numpy, matplotlib, scipy and h5py python modules. Optional: FFTW and Cuda Nature of problem: Increasing temperature, a crystal potential starts to deviate from the harmonic regime and anharmonicity is getting to be evident (M. T. Dove, Introduction to lattice dynamics, Vol. 4, Cambridge university press, 1993). To treat anharmonicity, perturbation approach often describes successfully phenomena such as phonon lifetime and lattice thermal conductivity. However it fails when the system contains large atomic displacements. Solution method: Extracting the phonon quasiparticles from molecular dynamics (MD) simulations using the normal-mode-decomposition technique. Restrictions: Quantum effects of lattice dynamics are not considered.

Implementation of the maximum entropy method for analytic continuation

Abstract: We present Maxent , a tool for performing analytic continuation of spectral functions using the maximum entropy method. The code operates on discrete imaginary axis datasets (values with uncertainties) and transforms this input to the real axis. The code works for imaginary time and Matsubara frequency data and implements the ‘Legendre’ representation of finite temperature Green’s functions. It implements a variety of kernels, default models, and grids for continuing bosonic, fermionic, anomalous, and other data. Our implementation is licensed under GPLv3 and extensively documented. This paper shows the use of the programs in detail. Program summary Program Title: maxent Program Files doi: http://dx.doi.org/10.17632/rf3p4psdhs.1 Licensing provisions: GPLv3 Programming language: C++ Nature of problem: The analytic continuation of imaginary axis correlation functions to real frequency/time variables is an ill-posed problem which has an infinite number of solutions. Solution method: The maximum entropy method obtains a possible solution that maximizes entropy, enforces sum rules, and otherwise produces ‘smooth’ curves. Our implementation allows for input in Matsubara frequencies, imaginary time, or a Legendre expansion. It implements a range of bosonic, fermionic and generalized kernels for normal and anomalous Green’s functions, self-energies , and two-particle response functions. External routines/libraries: ALPSCore [1][2], GSL, HDF5 [1] B. Bauer, et al., The ALPS project release 2.0: open source software for strongly correlated systems, J. Stat. Mech. Theor. Exp. 2011 (05) (2011) P05001. arXiv:1101.2646, doi:10.1088/17425468/2011/ 05/P05001. [2] A. Gaenko, E. Gull, A.E. Antipov, L. Gamper, G. Carcassi, J. Paki, R. Levy, M. Dolfi, J. Greitemann, J.P.F. LeBlanc, Alpscore: Version 0.5.4doi: 10.5281/zenodo.50203.

Quantum lattice model solver HΦ

Abstract: H Φ [aitch-phi ] is a program package based on the Lanczos-type eigenvalue solution applicable to a broad range of quantum lattice models , i.e., arbitrary quantum lattice models with two-body interactions, including the Heisenberg model , the Kitaev model, the Hubbard model and the Kondo-lattice model. While it works well on PCs and PC-clusters, H Φ also runs efficiently on massively parallel computers, which considerably extends the tractable range of the system size. In addition, unlike most existing packages, H Φ supports finite-temperature calculations through the method of thermal pure quantum (TPQ) states. In this paper, we explain theoretical background and user-interface of H Φ . We also show the benchmark results of H Φ on supercomputers such as the K computer at RIKEN Advanced Institute for Computational Science (AICS) and SGI ICE XA (Sekirei) at the Institute for the Solid State Physics (ISSP). Program summary Program Title: H Φ Program Files doi: http://dx.doi.org/10.17632/vnfthtyctm.1 Licensing provisions: GNU General Public License , version 3 or later Programming language: C External routines/libraries: MPI, BLAS, LAPACK Nature of problem: Physical properties (such as the magnetic moment , the specific heat, the spin susceptibility) of strongly correlated electrons at zero- and finite-temperature. Solution method: Application software based on the full diagonalization method, the exact diagonalization using the Lanczos method, and the microcanonical thermal pure quantum state for quantum lattice model such as the Hubbard model, the Heisenberg model and the Kondo model. Restrictions: System size less than about 20 sites for an itinerant electronic system and 40 site for a local spin system. Unusual features: Finite-temperature calculation of the strongly correlated electronic system based on the iterative scheme to construct the thermal pure quantum state. This method is efficient for highly frustrated system which is difficult to treat with other methods such as the unbiased quantum Monte Carlo.

FeynHelpers: Connecting FeynCalc to FIRE and Package-X

Abstract: We present a new interface called FeynHelpers that connects FeynCalc , a Mathematica package for symbolic semi-automatic evaluation of Feynman diagrams and calculations in quantum field theory (QFT) to Package-X and FIRE . The former provides a library of analytic results for scalar 1-loop integrals with up to 4 legs, while the latter is a general-purpose tool for reduction of multi-loop scalar integrals using Integration-by-Parts (IBP) identities. Program summary Program Title: FeynHelpers Program Files doi: http://dx.doi.org/10.17632/h5cfbhbbnc.1 Licensing provisions: GNU Public License 3 Programming language: Wolfram Mathematica 8 and higher External routines/libraries: FeynCalc [1,2], FeynArts [3], FeynRules [4], Package-X [5], FIRE [6] Nature of problem: FeynCalc is missing built-in capabilities to provide analytic results for scalar 1-loop integrals and to reduce multi-loop integrals using Integration-by-Parts (IBP) identities. These short-comings limit the usefulness of the package for the fully analytic evaluation of Feynman diagrams. Solution method: An easy-to-use interface implemented in Wolfram Mathematica seamlessly integrates two other Mathematica packages (Package-X and FIRE) into FeynCalc. Restrictions: The interface to FIRE currently misses the ability to recognize loop integrals that belong to the same topology, which means that each integral is processed separately. Furthermore, starting and stopping parallel kernels requires around 1.5 seconds per integral, which can be too slow, when hundreds of integrals are involved. [1] R. Mertig, M. Bohm, and A. Denner, Feyn Calc - Computer-algebraic calculation of Feynman amplitudes, Comput. Phys. Commun., 64, 345–359, (1991). [2] V. Shtabovenko, R. Mertig, and F. Orellana, New Developments in FeynCalc 9.0, Comput. Phys. Commun., 207, 432–444, (2016), arXiv:1601.01167 . [3] T. Hahn, Generating Feynman Diagrams and Amplitudes with FeynArts 3, Comput. Phys. Commun., 140, 418–431, (2001), arXiv:hep-ph/0012260 . [4] N. D. Christensen and C. Duhr, FeynRules - Feynman rules made easy, Comput. Phys. Commun., 180, 1614–1641, (2008), arXiv:0806.4194 . [5] H. H. Patel, Package-X: A Mathematica package for the analytic calculation of one-loop integrals, Comput. Phys. Commun., 197, 276–290, (2015), arXiv:1503.01469 . [6] A. V. Smirnov and V. A. Smirnov, FIRE4, LiteRed and accompanying tools to solve integration by parts relations, Comput. Phys. Commun., 184, 2820–2827, (2013), arXiv:1302.5885 .

The Möbius domain wall fermion algorithm

Abstract: We present a review of the properties of generalized domain wall Fermions, based on a (real) Mobius transformation on the Wilson overlap kernel, discussing their algorithmic efficiency, the degree of explicit chiral violations measured by the residual mass ( m r e s ) and the Ward–Takahashi identities. The Mobius class interpolates between Shamir’s domain wall operator and Borici’s domain wall implementation of Neuberger’s overlap operator without increasing the number of Dirac applications per conjugate gradient iteration. A new scaling parameter ( α ) reduces chiral violations at finite fifth dimension ( L s ) but yields exactly the same overlap action in the limit L s → ∞ . Through the use of 4d Red/Black preconditioning and optimal tuning for the scaling α ( L s ) , we show that chiral symmetry violations are typically reduced by an order of magnitude at fixed L s . We argue that the residual mass for a tuned Mobius algorithm with α = O ( 1 ∕ L s γ ) for γ 1 will eventually fall asymptotically as m r e s = O ( 1 ∕ L s 1 + γ ) in the case of a 5D Hamiltonian with out a spectral gap.

AELAS: Automatic ELAStic property derivations via high-throughput first-principles computation

Abstract: The elastic properties are fundamental and important for crystalline materials as they relate to other mechanical properties, various thermodynamic qualities as well as some critical physical properties. However, a complete set of experimentally determined elastic properties is only available for a small subset of known materials, and an automatic scheme for the derivations of elastic properties that is adapted to high-throughput computation is much demanding. In this paper, we present the AELAS code, an automated program for calculating second-order elastic constants of both two-dimensional and three-dimensional single crystal materials with any symmetry, which is designed mainly for high-throughput first-principles computation. Other derivations of general elastic properties such as Young’s, bulk and shear moduli as well as Poisson’s ratio of polycrystal materials, Pugh ratio, Cauchy pressure, elastic anisotropy and elastic stability criterion, are also implemented in this code. The implementation of the code has been critically validated by a lot of evaluations and tests on a broad class of materials including two-dimensional and three-dimensional materials, providing its efficiency and capability for high-throughput screening of specific materials with targeted mechanical properties. Program summary Program title: AELAS Program Files doi: http://dx.doi.org/10.17632/f8fwg4j9tw.1 Licensing provisions: BSD 3-Clause Programming language: Fortran Nature of problem: To automate the calculations of second-order elastic constants and the derivations of other elastic properties for two-dimensional and three-dimensional materials with any symmetry via high-throughput first-principles computation. Solution method: The space-group number is firstly determined by the SPGLIB code [1] and the structure is then redefined to unit cell with IEEE-format [2]. Secondly, based on the determined space group number, a set of distortion modes is automatically specified and the distorted structure files are generated. Afterwards, the total energy for each distorted structure is calculated by the first-principles codes, e.g. VASP [3]. Finally, the second-order elastic constants are determined from the quadratic coefficients of the polynomial fitting of the energies vs strain relationships and other elastic properties are accordingly derived. References [1] http://atztogo.github.io/spglib/ . [2] A. Meitzler, H.F. Tiersten, A.W. Warner, D. Berlincourt, G.A. Couqin, F.S. Welsh III, IEEE standard on piezoelectricity, Society, 1988. [3] G. Kresse, J. Furthmuller, Phys. Rev. B 54 (1996) 11169.

APFELgrid : A high performance tool for parton density determinations

Abstract: We present a new software package designed to reduce the computational burden of hadron collider measurements in Parton Distribution Function (PDF) fits. The APFELgrid package converts interpolated weight tables provided by APPLgrid files into a more efficient format for PDF fitting by the combination with PDF and α s evolution factors provided by APFEL . This combination significantly reduces the number of operations required to perform the calculation of hadronic observables in PDF fits and simplifies the structure of the calculation into a readily optimised scalar product. We demonstrate that our technique can lead to a substantial speed improvement when compared to existing methods without any reduction in numerical accuracy. Program Summary Program Title: APFELgrid Program Files doi: http://dx.doi.org/10.17632/mhwjt5nsg7.1 Licensing provisions: MIT license Programming language: C++ Nature of problem: Fast computation of hadronic observables under the variation of parton distribution functions. Solution method: Combination of interpolated weight grids from APPLgrid files and evolution factors from APFEL into efficient FastKernel tables. External routines/libraries: APPLgrid , APFEL

ms2: A molecular simulation tool for thermodynamic properties, release 3.0

Abstract: A new version release (4.0) of the molecular simulation tool ms2 (Deublein et al. 2011; Glass et al. 2014; Rutkai et al. 2017) is presented. Version 4.0 of ms2 features two additional potential functions to address the repulsive and dispersive interactions in a more versatile way, i.e. the Mie potential and the Tang–Toennies potential. This version further introduces Kirkwood–Buff integrals based on radial distribution functions, which allow the sampling of the thermodynamic factor of mixtures with up to four components, orientational distribution functions to elucidate mutual configurations of neighboring molecules, thermal diffusion coefficients of binary mixtures for heat, mass as well as coupled heat and mass transport, Einstein relations to sample transport properties with an alternative to the Green–Kubo formalism, dielectric constant of non-polarizable fluid models, vapor–liquid equilibria relying on the second virial coefficient and cluster criteria to identify nucleation. New version programm summary Program Title: ms2 Program Files doi: http://dx.doi.org/10.17632/nsfj67wydx.3 Licensing provisions: CC by NC 3.0 Programming language: Fortran95 Supplemental material: A detailed description of the parameter setup for the introduced methods, properties, functionalities etc. is given in the supplemental material. Furthermore, all molecular force field models developed by our group are provided by the MolMod Database: Stephan et al., Mol. Sim. 45 (2019) 806 Journal reference of previous version: Deublein et al., Comput. Phys. Commun. 182 (2011) 2350 and Glass et al., Comput. Phys. Commun. 185 (2014) 3302 and Rutkai et al., Comput. Phys. Commun. 221 (2017) 343 Does the new version supersede the previous version?: Yes Reasons for the new version: Introduction of new features as well as enhancement of computational efficiency Summary of revisions: Two new potential functions to address repulsive and dispersive interactions (Mie and Tang–Toennies potential), new properties (Helmholtz energy, Kirkwood–Buff integrals, thermodynamic factor, thermal diffusion coefficients, dielectric constant, mean squared displacement and non-Gaussian parameter), new functionalities (Kirkwood–Buff integration with extrapolation to the thermodynamic limit, van der Vegt correction for the radial distribution function, orientational distribution function, Einstein relations, vapor–liquid equilibria estimations, cluster criteria to identify nucleation). Nature of problem: Calculation of application-oriented thermodynamic properties: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal, caloric and entropic data as well as transport properties and data on microscopic structure Solution method: Molecular dynamics, Monte Carlo, various ensembles, Grand equilibrium method, Green–Kubo formalism, Einstein formalism, Lustig formalism, OPAS method, smooth-particle mesh Ewald summation.