GNU General Public License Research Articles

Does GPLv2 Include an ‘Installation Information’ Obligation? A Textual & Historical Analysis

One of the features included in version 3 of the GNU General Public License (GPLv3) was a requirement, in certain circumstances, to provide ‘Installation Information.’ This was a new addition to the licence to address a ‘loophole’ that existed in version 2 of the licence (GPLv2); a loophole that was perceived as being exploited, at the time, by certain device vendors. Recently, it has been asserted that this requirement was inherent, or explicitly called for, in GPLv2. This paper examines the historical record around the time that the ‘Installation Information’ requirement was proposed, and eventually ratified, in GPLv3, to show that this requirement was understood to be both new, and not a part of GPLv2. A textual analysis of GPLv2 yields an identical result.

GroupMath: A Mathematica package for group theory calculations

GroupMath is a Mathematica package which performs several calculations related to semi-simple Lie algebras and the permutation groups, both of which are important in various areas of physics. Having in mind the specific needs of theoretical particle physicists, the program computes several basis-independent quantities (such as roots, weights, decomposition of products of representations, branching rules) as well as basis-dependent ones (including explicit representation matrices and Clebsch-Gordon coefficients). Program summaryProgram Title: GroupMath: A Mathematica package for group theory calculationsCPC Library link to program files:https://doi.org/10.17632/hdkksr6v7t.1Developer's repository link:renatofonseca.net/groupmathLicensing provisions: GNU General Public License 3Programming language: MathematicaNature of problem: Computations involving semi-simple Lie algebras are commonplace in several areas of research, such as particle physics. Indeed model builders trying to extend the Standard Model often need to consider new fields which transform as irreducible representations of these algebras. It is therefore convenient to have a computer program which can perform these calculations systematically. Such code might be used directly by the user, or be incorporated in a longer chain of programs. The permutation groups Sm are also important, both by themselves and also as a tool to better describe the properties of the representations of semi-simple Lie algebras.Solution method: GroupMath performs several computations related to semi-simple Lie algebras which are important in high energy physics: Cartan matrices, roots, weights, Weyl reflections, decomposition of products of representations, subgroups, branching rules, and others. Algorithms available in the literature are used to efficiently perform some of these calculations. The program also computes basis-dependent quantities such as representation matrices and Clebsch-Gordon coefficients. Several elements of the theory of finite permutation groups have also been implemented, including Young diagrams and tableaux, the decomposition of products of representations, branching rules, and explicit representation matrices.Additional comments including restrictions and unusual features: Most of GroupMath's functions can handle arbitrary representations of any semi-simple Lie algebra and any permutation group. However, memory and time constraints are important when considering large and/or numerous representations. This is particularly true for the functions which perform basis-dependent computations.

SpectrumSDT: A program for parallel calculation of coupled rotational-vibrational energies and lifetimes of bound states and scattering resonances in triatomic systems

We present SpectrumSDT – a program for calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems. Large-amplitude vibrational motion is treated explicitly using hyper-spherical coordinates. Three options for the rotational-vibrational interaction are supported: uncoupled (symmetric top rotor), partially coupled (to include interaction between several nearest states only) and full-coupled (vibrating asymmetric-top rotor). In addition to energies and lifetimes, SpectrumSDT is able to integrate ro-vibrational wave functions over the user-defined regions of potential energy surface, which helps to classify these states. In this release of the code, SpectrumSDT is limited to ABA-type molecules with wave functions that do not extend into the regions near Eckart singularities. Program summaryProgram title: SpectrumSDTCPC Library link to program files:https://doi.org/10.17632/9gftxjs4yk.1Developer's repository link:https://github.com/IgorGayday/SpectrumSDTLicensing provisions: GNU General Public License 3 (GPL)Programming language: FortranNature of problem: Calculations of energies and lifetimes of bound rotational-vibrational states below and scattering resonances above the dissociation threshold on a global potential energy surface of a triatomic system, which may include stable molecules, weekly-bound van-der-Waals complexes, and unbound atom + diatom scattering systems.Solution method: A Hamiltonian matrix is built in APH coordinates using an optimal 2D basis set, adjusted for a given problem. A complex absorbing potential (CAP) is added to define a boundary condition for calculation of scattering resonances above the dissociation threshold. The eigenstates of the Hamiltonain matrix are found using a state-of-the-art iterative eigensolver.Restrictions: The present version is restricted to ABA-molecules and wave functions that do not extend into linear and equilateral triangle configurations.Additional comments including restriction and unusual features: Probabilities and lifetimes of the wave functions can be calculated in user-defined regions on the PES, which allows to analyze their localization properties (i.e. automatic isotopomer assignment) and obtain channel-specific lifetimes for scattering resonances.

Cij: A Python code for quasiharmonic thermoelasticity

The Wu-Wentzcovitch semi-analytical method (SAM) is a concise and predictive formalism to calculate the high-pressure and high-temperature (high-PT) thermoelastic tensor (Cij) of crystalline materials. This method has been successfully applied to materials across different crystal systems in conjunction with ab initio calculations of static elastic coefficients and phonon frequencies. Such results have offered first-hand insights into the composition and structure of the Earth's mantle.Here we introduce the cij package, a Python implementation of the SAM-Cij formalism. It enables a thermoelasticity calculation to be initiated from a single command and fully configurable from a calculation settings file to work with solids within any crystalline system. These features allow SAM-Cij calculations to work on a personal computer and to be easily integrated as a part of high-throughput workflows. Here we show the performance of this code for three minerals from different crystal systems at their relevant PTs: diopside (monoclinic), akimotoite (trigonal), and bridgmanite (orthorhombic). Program summaryProgram title:cijCPC Library link to program files:https://doi.org/10.17632/b8xf5jh5s8.1Developer's repository link:https://github.com/MineralsCloud/cijLicensing provisions: GNU General Public License 3Programming language: Python 3Nature of problem: Experimental measurements of full elastic tensor coefficients under high-pressure and high-temperature conditions are challenging and susceptible to uncertainties. Computations of thermoelastic coefficients based on the conventional density functional theory (DFT) plus quasiharmonic approximation (QHA) or ab initio molecular dynamics (AIMD) methods are computationally extremely demanding, especially for materials with low symmetries because of the revaluation of free energy for strained configurations.Solution method: Based on a semi-analytical method proposed by Wu and Wentzcovitch [1], we developed a handy code that only needs static-state elastic coefficients and phonon vibrational density of states for several equilibrium configurations at different pressure points as input to calculate the thermal elasticity. This method avoids the reevaluation of free energy for strained configurations and can be applied to all crystal systems. Reference[1]Z. Wu, R.M. Wentzcovitch, Phys. Rev. B 83 (2011) 184115.

Multiple-Scattering $T$-Matrix Simulations for Nanophotonics: Symmetries and Periodic Lattices

The multiple scattering method T-matrix (MSTMM) can be used to solve the electromagnetic response of systems consisting of many compact scatterers, retaining a good level of accuracy while using relatively few degrees of freedom, largely surpassing other methods in the number of scatterers it can deal with. Here we extend the method to infinite periodic structures using Ewald-type lattice summation, and we exploit the possible symmetries of the structure to further improve its efficiency, so that systems containing tens of thousands of particles can be studied with relative ease. We release a modern implementation of the method, including the theoretical improvements presented here, under GNU General Public Licence.

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph

Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as rmapper, and compare its performance against the assembler of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) and Solve by Bionano Genomics on data from three genomes: E. coli, human, and climbing perch fish (Anabas Testudineus). Our method was able to successfully run on all three genomes. The method of Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006) only successfully ran on E. coli. Moreover, on the human genome rmapper was at least 130 times faster than Bionano Solve, used five times less memory and produced the highest genome fraction with zero mis-assemblies. Our software, rmapper is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/Rmapper.

MOCOKI: A Monte Carlo approach for optimal control in the force of a linear kinetic model

A Monte Carlo framework for solving optimal control problems governed by kinetic models is presented. The focus is on a kinetic model with Keilson-Storer linear collision term and the control mechanism is an external space-dependent force. The purpose of this control is to drive an ensemble of particles to acquire a desired mean velocity and position and to reach a desired final configuration in phase space. For this purpose, a gradient-based computational strategy in the framework of Monte Carlo methods is developed. Results of numerical experiments successfully validate the proposed control framework. Program summaryProgram title: MOCOKICPC Library link to program files:https://doi.org/10.17632/6cb8fggwm2.1Licensing provisions: GNU General Public License 3Programming language: C/C++/PythonNature of problem: In many applications involving gases or plasma, it is not possible to assume a continuum and therefore models and methods that work at the mesoscopic level are needed. In this framework, kinetic models and Monte Carlo techniques play a central role. On the other hand, many present and envisioned application require to design control strategies by external forces that drive the evolution of these systems. For this purpose, it is necessary to implement optimal control techniques consistent with kinetic structures and Monte Carlo schemes. The novel methodology presented in this paper, although focusing on a linear kinetic model and a low-dimensional setting, can be extended in principle to nonlinear models and high-dimensional problems.Solution method: The proposed computational framework solves ensemble optimal control problems governed by linear kinetic models with a control-in-the-force mechanism. This framework combines transport techniques and Monte Carlo schemes for collision with numerical optimization methods.

Bathometer: lightning fast depth-of-reads query.

MotivationThe query for the number of reads overlapping a given region is a common step in the analysis of Illumina sequencing data. Sometimes, these queries are not conveniently precomputable. It seems beneficial to make this kind of arbitrary query as fast and convenient as possible.ResultsWe present Bathometer, a tool that indexes BAM files in a space efficient way, which allows ad hoc queries for the number of reads overlapping any given genomic region to be answered much more quickly than by counting with common tools such as Samtools, while incurring much less disk I/O.Availabilityand implementationBathometer is implemented in C, licensed under the GNU General Public License version 3+ and freely downloadable from Bitbucket (https://bitbucket.org/ustenzel/bathometer)Supplementary informationSupplementary data are available at Bioinformatics online.

NeoFox: annotating neoantigen candidates with neoantigen features.

SummaryThe detection and prediction of true neoantigens is of great importance for the field of cancer immunotherapy. Wesearched the literature for proposed neoantigen features and integrated them into a toolbox called NEOantigen Feature toolbOX (NeoFox). NeoFox is an easy-to-use Python package that enables the annotation of neoantigen candidates with 16 neoantigen features.Availability and implementationNeoFox is freely available as an open source Python package released under the GNU General Public License (GPL) v3 license at https://github.com/TRON-Bioinformatics/neofox.Supplementary information Supplementary data are available at Bioinformatics online.

Integral reduction with Kira 2.0 and finite field methods

We present the new version 2.0 of the Feynman integral reduction program Kira and describe the new features. The primary new feature is the reconstruction of the final coefficients in integration-by-parts reductions by means of finite field methods with the help of FireFly. This procedure can be parallelized on computer clusters with MPI. Furthermore, the support for user-provided systems of equations has been significantly improved. This mode provides the flexibility to integrate Kira into projects that employ specialized reduction formulas, direct reduction of amplitudes, or to problems involving linear system of equations not limited to relations among standard Feynman integrals. We show examples from state-of-the-art Feynman integral reduction problems and provide benchmarks of the new features, demonstrating significantly reduced main memory usage and improved performance w.r.t. previous versions of Kira. New version program summaryProgram title:KiraCPC Library link to program files:https://doi.org/10.17632/v3cmsnfrnn.2Developer's repository link:https://gitlab.com/kira-pyred/kiraLicensing provisions: GNU General Public License 3 (GPL)Programming language:C++Journal Reference of previous version: P. Maierhöfer, J. Usovitsch and P. Uwer, Kira—A Feynman integral reduction program, Comput. Phys. Commun.230 (2018) 99 [1705.05610].Does the new version supersede the previous version?: Yes.Reasons for the new version: Implementation of new features, some of which improve the performance significantly for many problems.Summary of revisions: The primary new feature is the reconstruction of the final coefficients in integration-by-parts reductions by means of finite field methods with the help of FireFly [1,2]. This procedure can be parallelized on computer clusters with MPI. Further improvements include the expanded support for user-provided systems of equations as well as a new feature to reduce the main memory usage when generating the system of equations.Nature of problem: The reduction of Feynman integrals to a smaller set of master integrals is a central strategy for high precision calculations in theoretical particle physics, e.g. for cross sections. Furthermore, the reduction is a key ingredient in many methods to calculate the master integrals themselves.Solution method:Kira generates a system of equations employing integration-by-parts [3,4] and Lorentz-invariance identities [5] as well as symmetry relations. Linearly dependent equations are removed and master integrals are identified by solving the system over a finite field. The resulting system can be solved with two methods: Since version 1.0, Kira can solve the system algebraically with the help of Fermat [6]. New in this version is the strategy of solving the system many times over finite fields and reconstructing the master integral coefficients with the help of FireFly [1,2]. Both strategies can also be applied to arbitrary homogeneous linear systems of equations.

Numerical evaluation of iterated integrals related to elliptic Feynman integrals

We report on an implementation within GiNaC to evaluate iterated integrals related to elliptic Feynman integrals numerically to arbitrary precision within the region of convergence of the series expansion of the integrand. The implementation includes iterated integrals of modular forms as well as iterated integrals involving the Kronecker coefficient functions g(k)(z,τ). For the Kronecker coefficient functions iterated integrals in dτ and dz are implemented. This includes elliptic multiple polylogarithms. Program summaryNote: The program uploaded to the CPC Library is the full GiNaC program, original authors C. Bauer, A. Frink and R. Kreckel. The algorithms described in this article are integrated into GiNaC.Program title:GiNaC_elipticFeynmanCPC Library link to program files:https://doi.org/10.17632/8vyydbc7zw.1Developer's repository link:https://www.ginac.de/Licensing provisions: GNU General Public License version 2Programming language:C++Other programs called: CLN library, available from https://www.ginac.de/CLN.Nature of problem: Numerical evaluation of iterated integrals related to elliptic Feynman integrals.Solution method: Removal of trailing zeros followed by series expansion.

Calculation of five-particle harmonic-oscillator transformation brackets

In this work we present a FORTRAN code for the calculation of the matrix of the orbital fractional parentage coefficients for five particles (5HOB) in a translationally invariant basis. Our code calculates the 5HOB eigenvector matrix M and the diagonal eigenvalue matrix F. The full 5HOB matrix is obtained from these matrices. Program summaryProgram title: 5hob_serialCPC Library link to program files:https://doi.org/10.17632/fb737j8xnt.1Licensing provisions: GNU General Public License version 3Programming language: FORTRAN 90Nature of problem: Calculation of five-particle harmonic-oscillator transformation brackets matrix.Solution method: The method is based on compact expressions of the five-particle harmonics oscillator brackets (5HOB), presented in [1].Additional comments including restrictions and unusual features: For theoretical issues of revision see section ‘Theoretical aspects’ and for more detailed information see [1]. Restrictions: the 5HOB matrices up to E=28.

Adaptive third order Adams-Bashforth time integration for extended Boussinesq equations

We develop the third-order adaptive Adams-Bashforth time integration and the second-order finite difference equation for variable time steps. We incorporate these schemes in the Celeris Advent software to discretize and solve the 2D extended Boussinesq equations. This software uses a hybrid finite volume – finite difference scheme and leverages the GPU to solve the equations faster than real-time while concurrently visualizing them. The newly added adaptive scheme significantly improves the robustness of the model while providing faster computational performance. We simulate several benchmarks using the adaptive time stepping scheme of Celeris Advent and demonstrate the capability of the software in modeling wave-breaking, wave runup, irregular waves, and rip currents. Program SummaryProgram title: Celeris Advent (v.1.3.4)CPC Library link to program files:https://doi.org/10.17632/pwsjdsgz89.1Licensing provisions: GNU General Public License 3Programming language: C++, HLSLNature of problem: Celeris Advent started a new paradigm in nearshore wave simulations and enabled researchers and engineers to run a Boussinesq-type model, faster than real-time and in an interactive environment. For simplicity, we assumed a fixed time step in our first implementation of Celeris Advent. This fixed time step often needs to be chosen conservatively such that the model can resolve the most extreme cases during the experiment. In practical simulations, such as simulating coastal fields, the superposition of boundary and initial conditions may cause rare but extreme conditions, requiring a very small time step that is too conservative during most of the simulation.Solution method: We developed adaptive third order Adams-Bashforth time integration to let Celeris Advent solve the extended Boussinesq equations with a variable time step, allowing it to decrease the time step only when necessary. The adaptive equations are presented in a generic format and therefore can be used for solving other equations as well.Additional comments including restrictions and unusual features: The new version of the Celeris Advent with the adaptive time integration runs ∼3 times faster for the standard conical island benchmark, allowing Celeris Advent simulate this benchmark on a 200×200 grid an order of magnitude faster than real-time on a consumer-level gaming laptop. For a field simulation benchmark, with rare but extreme events, the new version runs ∼25 times faster.

NanoTox: Development of a Parsimonious In Silico Model for Toxicity Assessment of Metal-Oxide Nanoparticles Using Physicochemical Features.

Metal-oxide nanoparticles find widespread applications in mundane life today, and cost-effective evaluation of their cytotoxicity and ecotoxicity is essential for sustainable progress. Machine learning models use existing experimental data and learn quantitative feature–toxicity relationships to yield predictive models. In this work, we adopted a principled approach to this problem by formulating a novel feature space based on intrinsic and extrinsic physicochemical properties, including periodic table properties but exclusive of in vitro characteristics such as cell line, cell type, and assay method. An optimal hypothesis space was developed by applying variance inflation analysis to the correlation structure of the features. Consequent to a stratified train-test split, the training dataset was balanced for the toxic outcomes and a mapping was then achieved from the normalized feature space to the toxicity class using various hyperparameter-tuned machine learning models, namely, logistic regression, random forest, support vector machines, and neural networks. Evaluation on an unseen test set yielded >96% balanced accuracy for the random forest, and neural network with one-hidden-layer models. The obtained cytotoxicity models are parsimonious, with intelligible inputs, and an embedded applicability check. Interpretability investigations of the models identified the key predictor variables of metal-oxide nanoparticle cytotoxicity. Our models could be applied on new, untested oxides, using a majority-voting ensemble classifier, NanoTox, that incorporates the best of the above models. NanoTox is the first open-source nanotoxicology pipeline, freely available under the GNU General Public License (https://github.com/NanoTox).

SpaceGroupIrep: A package for irreducible representations of space group

We have developed a Mathematica program package SpaceGroupIrep which is a database and tool set for irreducible representations (IRs) of space group in BC convention, i.e. the convention used in the famous book “The mathematical theory of symmetry in solids” by C.J. Bradley & A.P. Cracknell. Using this package, elements of any space group, little group, Herring little group, or central extension of little co-group can be easily obtained. This package can give not only little-group (LG) IRs for any k-point but also space-group (SG) IRs for any k-stars in intuitive table form, and both single-valued and double-valued IRs are supported. This package can calculate the decomposition of the direct product of SG IRs for any two k-stars. This package can determine the LG IRs of Bloch states in energy bands in BC convention and this works for any input primitive cell thanks to its ability to convert any input cell to a cell in BC convention. This package can also provide the correspondence of k-points and LG IR labels between BCS (Bilbao Crystallographic Server) and BC conventions. In a word, the package SpaceGroupIrep is very useful for both study and research, e.g. for analyzing band topology or determining selection rules. Program summaryProgram title:SpaceGroupIrepCPC Library link to program files:https://doi.org/10.17632/3vm4g32t4d.1Developer's repository link:https://github.com/goodluck1982/SpaceGroupIrepLicensing provisions: GNU General Public Licence 3.0Programming language: MathematicaExternal routines/libraries used:spglib (http://spglib.github.io/spglib)Nature of problem: Space groups and their representations are important mathematical language to describe symmetry in crystals. The book—“The mathematical theory of symmetry in solids” by C.J. Bradley & A.P. Cracknell (called the BC book)—is highly influential because it contains not only systematic theory but also detailed complete data of space groups and their representations. The package SpaceGroupIrep digitizes these data in the BC book and provides tens of functions to manipulate them, such as obtaining group elements and calculating their multiplications, identifying k-points, showing the character table of any little group, determining the little-group (LG) irreducible representations (IRs) of energy bands, and calculating the direct product of space-group (SG) IRs. This package is a useful database and tool set for space groups and their representations in BC convention.Solution method: The direct data in the BC book is used to calculate the LG IRs for standard k-points defined in the book. For a non-standard k-point, we first relate it to a standard k-point by an element which makes the space group self-conjugate and then calculate the LG IRs through the element. SG IRs are obtained by calculating the induced representations of the corresponding LG IRs. The full-group method based on double coset is used to calculate the direct products of SG IRs. In addition, an external package spglib is utilized to help convert any input cell to a cell in BC convention.

Finite difference magnetoelastic simulator.

We describe an extension of the micromagnetic finite difference simulation software MuMax3 to solve elasto-magneto-dynamical problems. The new module allows for numerical simulations of magnetization and displacement dynamics in magnetostrictive materials and structures, including both direct and inverse magnetostriction. The theoretical background is introduced, and the implementation of the extension is discussed. The magnetoelastic extension of MuMax3 is freely available under the GNU General Public License v3.

Equivalent finite difference and partial differential equations for the lattice Boltzmann method

A general method for the derivation of equivalent finite difference equations (EFDEs) and subsequent equivalent partial differential equations (EPDEs) is presented for a general matrix lattice Boltzmann method (LBM). The method can be used for both the advection diffusion equations and Navier–Stokes equations in all dimensions.In principle, the EFDEs are derived using a recurrence formula. A computational algorithm is proposed for generating sequences of matrices and vectors that are used to obtain EFDEs coefficients. For all DdQq velocity models, the algorithm is proven to be finite and all coefficients are obtained after q iterations. The resulting EFDEs and EPDEs are derived for selected velocity models and include the single relaxation time, multiple relaxation times, and cascaded LBM collision operators.The algorithm for the derivation of EFDEs and EPDEs is implemented in C++ using the GiNaC library for symbolic algebraic computations. Its implementation is available under the terms and conditions of the GNU general public license (GPL).

Interpolation of dense and sparse rational functions and other improvements in FireFly

We present the main improvements and new features in version 2.0 of the open-source C++ library FireFly for the interpolation of rational functions. This includes algorithmic improvements, e.g. a hybrid algorithm for dense and sparse rational functions and an algorithm to identify and remove univariate factors. The new version is applied to a Feynman-integral reduction to showcase the runtime improvements achieved. Moreover, FireFly now supports parallelization with MPI and offers new tools like a parser for expressions or an executable for the insertion of replacement tables. New version program summaryProgram title:FireFlyCPC Library link to program files:https://doi.org/10.17632/nzgxdwwt8k.2Code Ocean capsule:https://codeocean.com/capsule/4860843/tree/v1Licensing provisions: GNU General Public License 3Programming language:C++Journal reference of previous version: J. Klappert, F. Lange, Comp. Phys. Commun. 247 (2020) 106951, , arXiv:1904.00009.Does the new version supersede the previous version?: YesReasons for the new version: Significant performance improvements and new featuresSummary of revisions: We implemented new algorithms: The racing algorithm of Ref.[1] for univariate polynomials, a dense and sparse hybrid algorithm for rational functions, and an algorithm to search for univariate factors which can be removed in the actual interpolation. In addition, we changed the interface to allow for an overhead reduction inspired by vectorization and implemented the parallelization with MPI. Moreover, we include some new tools, e.g. a parser for expressions and an executable for the insertion of replacement tables.Nature of problem: The interpolation of an unknown rational function, called black box, from only its evaluations can be used in many physical contexts where algebraic calculations fail due to memory and runtime restrictions.Solution method: The black-box function is evaluated at different points over a finite field. These points are then used by interpolation algorithms[1-4] to obtain the analytic form of the function. The elements of a finite field are promoted to Q using rational reconstruction algorithms[5,6].Additional comments including restrictions and unusual features: For better performance, we advise to use FLINT[7] for the finite-field arithmetics and an improved memory allocator like jemalloc[8].

Perturbo: A software package for ab initio electron–phonon interactions, charge transport and ultrafast dynamics

Perturbo is a software package for first-principles calculations of charge transport and ultrafast carrier dynamics in materials. The current version focuses on electron–phonon interactions and can compute phonon-limited transport properties such as the conductivity, carrier mobility and Seebeck coefficient. It can also simulate the ultrafast nonequilibrium electron dynamics in the presence of electron–phonon scattering. Perturbo uses results from density functional theory and density functional perturbation theory calculations as input, and employs Wannier interpolation to reduce the computational cost. It supports norm-conserving and ultrasoft pseudopotentials, spin–orbit coupling, and polar electron–phonon interactions for bulk and 2D materials. Hybrid MPI plus OpenMP parallelization is implemented to enable efficient calculations on large systems (up to at least 50 atoms) using high-performance computing. Taken together, Perturbo provides efficient and broadly applicable ab initio tools to investigate electron–phonon interactions and carrier dynamics quantitatively in metals, semiconductors, insulators, and 2D materials. Program summaryProgram Title:PerturboCPC Library link to program files:https://doi.org/10.17632/34m2p6v79t.1Developer’s repository link:https://perturbo-code.github.ioLicensing provisions: GNU General Public Licence 3.0Programming language:Fortran, PythonExternal routines/libraries:LAPACK, HDF5, MPI, OpenMP, FFTW, Quantum-ESPRESSO, Wannier90Nature of problem: Computing transport properties from first-principles in materials, including the electrical conductivity, carrier mobility and Seebeck coefficient; Simulating ultrafast nonequilibrium electron dynamics, such as the relaxation of excited carriers via interactions with phonons.Solution method: We implement the first-principles Boltzmann transport equation, which employs materials properties such as the electronic structure, lattice dynamics, and electron–phonon collision terms computed with density functional theory and density functional perturbation theory. The Boltzmann transport equation is solved numerically to compute charge transport and simulate ultrafast carrier dynamics. Wannier interpolation is employed to reduce the computational cost.Additional comments: Hybrid MPI plus OpenMP parallelization is implemented to run large calculations and take advantage of high-performance computing. Most results are output to HDF5 file format, which is portable and convenient for post-processing using high-level languages such as Python and Julia.

DSQSS: Discrete Space Quantum Systems Solver

The Discrete Space Quantum Systems Solver (DSQSS) is a program package for solving quantum many-body problems defined on lattices. The DSQSS is based on the quantum Monte Carlo method in Feynman’s path integral representation and covers a broad range of problems using flexible input files that define arbitrary unit cells in arbitrary dimensions and arbitrary matrix elements representing the interactions among an arbitrary number of degrees of freedom. Finite temperature calculations of quantum spin and the Bose–Hubbard models can be performed by specifying parameters such as the number of dimensions, the lattice size, coupling constants, and temperature. The present paper details the use of DSQSS and presents a number of applications thereof. Program summaryProgram Title: DSQSSCPC Library link to program files:https://doi.org/10.17632/pxngkh7krj.1Licensing provisions: GNU General Public License version 3Programming language:C++ and pythonExternal routines/libraries: MPI, NumPy, SciPyNature of problem: Finite temperature calculation of quantum spin model and Bose–Hubbard model.Solution method: Path-integral Monte Carlo method with the directed-loop algorithm.