## RadLib: A radiative property model library for CFD

1 file (2021)Victoria B. Stephens, Sally Jensen, Isaac Wheeler, David O. Lignell

Computer Physics Communications

Mendeley Data Repository is free-to-use and open access. It enables you to deposit any research data (including raw and processed data, video, code, software, algorithms, protocols, and methods) associated with your research manuscript. Your datasets will also be searchable on Mendeley Data Search, which includes nearly 11 million indexed datasets. For more information, visit Mendeley Data.

## RadLib: A radiative property model library for CFD

1 file (2021)Victoria B. Stephens, Sally Jensen, Isaac Wheeler, David O. Lignell

RadLib is a C++ library of radiation property models that can be applied to variety of systems involving radiative heat transfer, including CFD simulations. RadLib includes three major radiation property models—Planck Mean (PM) absorption coefficients, the weighted sum of gray gases (WSGG) model, and the rank-correlation spectral line weighted-sum-of-gray-gases (RCSLW) model. RadLib includes C++, Python, and Fortran interfaces and can be expanded to include additional models. Several example cases illustrate use of the models with an included ray-tracing solver, compare their accuracy relative to line-by-line (LBL) solutions, and examine their computational costs. Additionally, an integrated CFD example of an ethylene burner configuration using Fire Dynamics Simulator (FDS) is provided. RadLib provides researchers with convenient access to validated radiation property models and a framework for further development.## Analytical formalism for calculations of parameters needed for quantitative analysis by X-ray photoelectron spectroscopy

1 file (2021)Aleksander Jablonski

Quantitative analysis by X-ray photoelectron spectroscopy (XPS) requires knowledge of a theoretical model relating different features of recorded spectra with needed characteristics of a studied sample. An advanced theoretical approach describing an electron transport in condensed matter typically involved Monte Carlo (MC) simulations of electron trajectories since signal electrons undergo multiple interactions in a solid. The relevant algorithms are relatively slow and are burdened with statistical errors; thus they may be inconvenient in certain applications. However, much effort in the past was devoted to create models that describe electron transport by an analytical formalism with similar accuracy as Monte Carlo simulations. There are two major advantages of analytical approaches: (i) the computing time can be much shorter as compared with MC algorithms, and (ii) the relevant software can be easily included in external programs when large number of calculated parameters is needed. In the present work, the analytical formalism derived within the so-called transport approximation (TA) is described in detail, and implemented in the enclosed software TRANS_APPROX (Fortran 90). The formalism of quantitative XPS is based on an expression that provides a probability that a photoelectron emitted at a given depth reaches an analyzer without energy loss (emission depth distribution function – EMDDF). Consequently, the analytical expression for the EMDDF derived from the TA is discussed here. Stress is also put on parameters descending from the EMDDF: (i) the photoelectron signal intensity, (ii) the information depth, (iii) the mean escape depth, and (iv) the attenuation length for overlayer thickness measurements. The input parameters needed for calculations are briefly overviewed, followed by recommendations for use in the proposed program. Finally, it is indicated that the TA formalism requires calculations of numerous integrals with integrable singularities. It was proven here that these singularities do not need to be removed if the quadrature used is based on the so-called double exponential (DE) rule. This approach ensures high accuracy and fast convergence.## LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

1 file (2021)Aidan P. Thompson, H. Metin Aktulga and 13 more

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials.## HTR-1.3 solver: Predicting electrified combustion using the hypersonic task-based research solver

1 file (2021)Mario Di Renzo

This manuscript presents an updated open-source version of the Hypersonics Task-based Research (HTR) solver. The solver, whose main features are presented in Di Renzo et al. (2020) [9] and Di Renzo & Pirozzoli (2021) [10], is designed for direct numerical simulation of reacting flows at high Reynolds numbers. This new version extends the applications of the HTR solver to turbulent combustion in the presence of external electric fields. In particular, a new distributed Poisson solver compatible with heterogeneous architectures has been incorporated in the algorithm to compute the electric potential distribution in bi-periodic configurations. The drift fluxes of the electrically charged species are now included in the transport equations using a targeted essentially non-oscillatory scheme. A verification of these new features of the solver is provided using one-dimensional burner stabilized flames, whereas a three dimensional turbulent flame is utilized to discuss the scalability of the proposed numerical tool.## KLIFF: A framework to develop physics-based and machine learning interatomic potentials

2 files (2021)Mingjian Wen, Yaser Afshar, Ryan S. Elliott, Ellad B. Tadmor

Interatomic potentials (IPs) are reduced-order models for calculating the potential energy of a system of atoms given their positions in space and species. IPs treat atoms as classical particles without explicitly modeling electrons and thus are computationally far less expensive than first-principles methods, enabling molecular simulations of significantly larger systems over longer times. Developing an IP is a complex iterative process involving multiple steps: assembling a training set, designing a functional form, optimizing the function parameters, testing model quality, and deployment to molecular simulation packages. This paper introduces the KIM-based learning-integrated fitting framework (KLIFF), a package that facilitates the entire IP development process. KLIFF supports both physics-based and machine learning IPs. It adopts a modular approach whereby various components in the fitting process, such as atomic environment descriptors, functional forms, loss functions, optimizers, quality analyzers, and so on, work seamlessly with each other. This provides a flexible framework for the rapid design of new IP forms. Trained IPs are compatible with the Knowledgebase of Interatomic Models (KIM) application programming interface (API) and can be readily used in major materials simulation packages compatible with KIM, including ASE, DL_POLY, GULP, LAMMPS, and QC. KLIFF is written in Python with computationally intensive components implemented in C++. It is parallelized over data and supports both shared-memory multicore desktop machines and high-performance distributed memory computing clusters. We demonstrate the use of KLIFF by fitting a physics-based Stillinger–Weber potential and a machine learning neural network potential for silicon. The KLIFF package, together with its documentation, is publicly available at: https://github.com/openkim/kliff.## CepGen – A generic central exclusive processes event generator for hadron-hadron collisions

1 file (2021)Laurent Forthomme

We present an event generator for the simulation of central exclusive processes in hadron-hadron reactions. Among others, it implements the two-photon production of lepton pairs previously introduced in LPAIR. As a proof of principle, we show that the two approaches are numerically consistent. The k_T-factorized description of this process is also handled, along with the two-photon production of a quark, or a W^+- gauge boson pair. This toolbox may be used as a common framework for the definition of many other processes following this approach. Additionally, photoproduction and other photon induced processes are also considered, or being implemented.## Empathes: A general code for nudged elastic band transition states search

1 file (2021)Marco Bertini, Francesco Ferrante, Dario Duca

An easy and flexible interface, Empathes (Extensible Minimum PATH EStimator), that allows to perform Nudged Elastic Band calculation for the determination of transition states is presented. The code is designed to be easily modified, in order to be associated with the user's preferred calculation software, even with those which implement composite approaches. In particular, the interfaces to Gaussian and Siesta programs are discussed in details, being the former only used for testing purpose, while the latter can be productively employed for transition states search with that commonly used density functional theory software for periodic calculations.## MAELAS 2.0: A new version of a computer program for the calculation of magneto-elastic properties

1 file (2021)P. Nieves, S. Arapan and 4 more

MAELAS is a computer program for the calculation of magnetocrystalline anisotropy energy, anisotropic magnetostrictive coefficients and magnetoelastic constants in an automated way. The method originally implemented in version 1.0 of MAELAS was based on the length optimization of the unit cell, proposed by Wu and Freeman, to calculate the anisotropic magnetostrictive coefficients. We present here a revised and updated version (v2.0) of MAELAS, where we added a new methodology to compute anisotropic magnetoelastic constants from a linear fitting of the energy versus applied strain. We analyze and compare the accuracy of both methods showing that the new approach is more reliable and robust than the one implemented in version 1.0, especially for non-cubic crystal symmetries. This analysis also helps us find that the accuracy of the method implemented in version 1.0 could be improved by using deformation gradients derived from the equilibrium magnetoelastic strain tensor, as well as potential future alternative methods like the strain optimization method. Additionally, we clarify the role of the demagnetized state in the fractional change in length, and derive the expression for saturation magnetostriction for polycrystals with trigonal, tetragonal and orthorhombic crystal symmetry. In this new version, we also fix some issues related to trigonal crystal symmetry found in version 1.0.## PArthENoPE revolutions

1 file (2021)S. Gariazzo, P. F. de Salas, O. Pisanti, R. Consiglio

This paper presents the main features of a new and updated version of the program PArthENoPE, which the community has been using for many years for computing the abundances of light elements produced during Big Bang Nucleosynthesis. This is the third release of the PArthENoPE code, after the 2008 and the 2018 ones, and will be distributed from the code's website, http://parthenope.na.infn.it. Apart from minor changes, the main improvements in this new version include a revisited implementation of the nuclear rates for the most important reactions of deuterium destruction, 2H(p,γ)^3 He, 2H(d, n)^3 He and 2H(d, p)^3 H, and a re-designed GUI, which extends the functionality of the previous one. The new GUI, in particular, supersedes the previous tools for running over grids of parameters with a better management of parallel runs, and it offers a brand-new set of functions for plotting the results.## Migration of hyper-fractal analysis from visual basic 6 to C# .Net

2 files (2021)Ioan Valeriu Grossu

In Grossu et al. (Comput. Phys. Commun. 184 (2013) 1812–1813) we presented Hyper-Fractal Analysis, a visual tool for estimating the fuzzy fractal dimension of images and 4D objects. As Visual Basic 6 could be considered an outdated language, with limited Object-Oriented Programming capabilities, migrating the application to C# .Net was treated in high priority. Following the goal of creating a highly reusable fractal analysis library, the code was also refactored to SOLID. Together with various improvements, the.Net version is also providing new tools for iso-fractal areas identification. The project success was confirmed by a comparative old/new version study. On the other hand, the most relevant functionalities were covered by unit tests.## UnDiFi-2D: An unstructured discontinuity fitting code for 2D grids

1 file (2021)Lorenzo Campoli, A. Assonitis and 4 more

UnDiFi-2D, an open source (free software) Unstructured-grid, Discontinuity Fitting code, is presented. The aim of UnDiFi-2D is to model gas-dynamic discontinuities in two-dimensional (2D) flows as if they were true discontinuities of null thickness that bound regions of the flow-field where a smooth solution to the governing PDEs exists. UnDiFi-2D therefore needs to be coupled with an unstructured CFD solver that is used to discretize the governing PDEs within the smooth regions of the flow-field. Two different, in-house developed, CFD solvers are also included in the current distribution. The main features of the UnDiFi-2D software can be summarized as follows: Programming language UnDiFi-2D is written in standard Fortran 77/95; its design is highly modular in order to enhance simplicity of use, maintenance and allow coupling with virtually any existing CFD solver; Usability, maintenance and enhancement In order to improve the usability, maintenance and enhancement of the code also the documentation has been carefully taken into account. The git distributed versioning system has been adopted to facilitate collaborative maintenance and code development; Copyrights UnDiFi-2D is a free software that anyone can use, copy, distribute, change and improve under the GNU Public License version 3. The present paper is a manifesto of the first public release of the UnDiFi-2D code. It describes the currently implemented features, which are the result of more than a decade of still ongoing CFD developments. This work is focused on the computational techniques adopted and a detailed description of the main characteristics is reported. UnDiFi-2D capabilities are demonstrated by means of examples test cases. The design of the code allows to easily include existing CFD codes and is aimed at ease code reuse and readability.## A practical guide to writing a radiative transfer code

1 file (2021)Sergey Korkin, A.M. Sayer, A. Ibrahim, A. Lyapustin

Using our decades-long experience in radiative transfer (RT) code development for Earth science, we endeavor to reduce the knowledge gap of bringing RT from theory to code quickly. Despite numerous classic and recent literature, it is still hard to develop an RT code from scratch within a few weeks. It is equally hard to understand, not to mention modify, an existing “monster” RT code, for which the developer is either located remotely or has retired. Following the format of “Numerical Recipes” by Press et al., we collocate in this paper small pieces of necessary theory with corresponding small pieces of RT code. These are arranged in an order that is natural for code development, which is often opposite of the natural order for laying out the theoretical basis. We focus on the transfer of unpolarized monochromatic solar radiation in a plane-parallel atmosphere over a reflecting surface. Both the surface and the atmosphere are homogeneous (uniform) at all directions. The multiple scattering is numerically solved using the deterministic method of Gauss-Seidel iterations. Except for the presented Python-Numba open-source RT code gsit, the paper does not report any new scientific results, but rather serves as an academic demonstration. If development time is an issue or the reader is familiar with basic concepts of RT theory, we recommend proceeding directly to Sec. 3 “RT code development”.## Complete Lagrangian and set of Feynman rules for scalar leptoquarks

1 file (2021)Andreas Crivellin, Luc Schnell

Leptoquarks (LQs) have attracted increasing attention within recent years, mainly since they can explain the flavor anomalies found in $R(D^{(*)})$, $b \rightarrow s \ell^+ \ell^-$ transitions and the anomalous magnetic moment of the muon. In this article, we lay the groundwork for further automated analyses by presenting the complete Lagrangian and the corresponding set of Feynman rules for scalar leptoquarks. This means we consider the five representations $\Phi_1, \Phi_{\tilde1}, \Phi_2, \Phi_{\tilde2}$ and $\Phi_3$ and include the triple and quartic self-interactions, as well as couplings to the Standard Model (SM) fermions, gauge bosons and the Higgs. The calculations are performed using FeynRules and all model files are publicly available online at https://gitlab.com/lucschnell/SLQrules.## Merlin++, a flexible and feature-rich accelerator physics and particle tracking library

1 file (2021)Robert B. Appleby, Roger J. Barlow and 7 more

Merlin++ is a C++ charged-particle tracking library developed for the simulation and analysis of complex beam dynamics within high energy particle accelerators. Accurate simulation and analysis of particle dynamics is an essential part of the design of new particle accelerators, and for the optimization of existing ones. Merlin++ is a feature-full library with focus on long-term tracking studies. A user may simulate distributions of protons or electrons in either single particle or sliced macro-particle bunches. The tracking code includes both straight and curvilinear coordinate systems allowing for the simulation of either linear or circular accelerator lattice designs, and uses a fast and accurate explicit symplectic integrator. Physics processes for common design studies have been implemented, including RF cavity acceleration, synchrotron radiation damping, on-line physical aperture checks and collimation, proton scattering, wakefield simulation, and spin-tracking. Merlin++ was written using C++ object orientated design practices and has been optimized for speed using multicore processors. This article presents an account of the program, including its functionality and guidance for use.## WannSymm: A symmetry analysis code for Wannier orbitals

1 file (2021)Guo-Xiang Zhi, Chenchao Xu and 3 more

We derived explicit expressions of symmetry operators on Wannier basis, and implemented these operators in WannSymm software. Based on this implementation, WannSymm can i) symmetrize the real-space Hamiltonian output from Wannier90 code, ii) generate symmetry operators of the little group at a specific k-point, and iii) perform symmetry analysis for Wannier band structure. In general, symmetrized Hamiltonians yield improved results compared with the original ones when they are employed for nodal structure searching, surface Green's function calculations, and other model calculations.## Twister: Construction and structural relaxation of commensurate moiré superlattices

1 file (2021)Saismit Naik, Mit H. Naik, Indrajit Maity, Manish Jain

Introduction of a twist between layers of two-dimensional materials which leads to the formation of a moiré pattern is an emerging pathway to tune the electronic, vibrational and optical properties. The fascinating properties of these systems are often linked to large-scale structural reconstruction of the moiré pattern. Hence, an essential first step in the theoretical study of these systems is the construction and structural relaxation of the atoms in the moiré superlattice. We present the Twister package, a collection of tools that constructs commensurate superlattices for any combination of 2D materials and also helps perform structural relaxations of the moiré superlattice. Twister constructs commensurate moiré superlattices using the coincidence lattice method and provides an interface to perform structural relaxations using classical forcefields.## MultivariateApart: Generalized partial fractions

1 file (2021)Matthias Heller, Andreas von Manteuffel

We present a package to perform partial fraction decompositions of multivariate rational functions. The algorithm allows to systematically avoid spurious denominator factors and is capable of producing unique results also when being applied to terms of a sum separately. The package is designed to work in Mathematica, but also provides interfaces to the Form and Singular computer algebra systems.## RichardsFoam3: A new version of RichardsFoam for continental surfaces hydrogeology modelling

1 file (2021)laurent orgogozo

RichardsFoam3 is an updated version of the OpenFOAM® solver RichardsFoam, previously presented in “An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale” by L. Orgogozo, N. Renon, C. Soulaine, F. Hénon, S.K. Tomer, D. Labat, O.S. Pokrovsky, M. Sekhar, R. Ababou, M. Quintard (Comput. Phys. Commun. 185 (2014) 3358-3371, https://doi.org/10.1016/j.cpc.2014.08.004), and in the new version announcement “RichardsFOAM2: a new version of RichardsFOAM devoted to the modelling of the vadose zone” by L. Orgogozo (Comput. Phys. Commun. 196 (2015) 619-620, https://doi.org/10.1016/j.cpc.2015.07.009). This new version includes improvements of memory handling and of on-the-fly control of computations, a better integration in the OpenFOAM® framework, simplifications of the coding of some expressions, as well as new advanced boundary conditions. All together these developments allow to enhance the ease of application of the code to continental surfaces hydrogeology modelling, its computational performances and its readability. The description of the elements contained in this release may be found in the readMe file. Please note that you may also find RichardsFoam3 on the hydrology page of the develop.openfoam.com interface: https://develop.openfoam.com/Community/hydrology/ The previous version of this program (AEUF_v2_0) may be found at https://doi.org/10.1016/j.cpc.2015.07.009.## FourPhonon: An extension module to ShengBTE for computing four-phonon scattering rates and thermal conductivity

1 file (2021)Zherui Han, Xiaolong Yang and 3 more

FourPhonon is a computational package that can calculate four-phonon scattering rates in crystals. It is built within ShengBTE framework, which is a well-recognized lattice thermal conductivity solver based on Boltzmann transport equation. An adaptive energy broadening scheme is implemented for the calculation of four-phonon scattering rates. In analogy with thirdorder.py in ShengBTE, we also provide a separate python script, Fourthorder.py, to calculate fourth-order interatomic force constants. The extension module preserves all the nice features of the well-recognized lattice thermal conductivity solver ShengBTE, including good parallelism and straightforward workflow. In this paper, we discuss the general theory, program design, and example calculations on Si, BAs and LiCoO_2.## MTASpec software for calculating the vibrational IR and Raman spectra of large molecules at ab initio level

2 files (2021)Subodh S. Khire, Nityananda Sahu, Shridhar R. Gadre

Fragmentation-based (FB) methods have been developed for enabling ab initio calculations on large molecules and clusters. However, a well-benchmarked FB-based utility, for calculating the vibrational spectra is not available. The present article reports a software package MTASpec, based on the FB-molecular tailoring approach (MTA), for computing the single point energy followed by vibrational IR and Raman spectra for spatially extended molecular systems. Accuracy and efficiency of MTASpec are assessed vis-à-vis their full calculation counterparts for some medium- to large-sized molecular systems using HF, DFT and MP2 theory employing large basis sets. The code is fully automated for use on linux platform, with the Gaussian suite of software at the back-end. It is envisaged that the MTASpec package would enable spectral studies of molecular systems containing ∼100 atoms and/or ∼10000 basis functions employing correlated theories with computational economy.## Principles of modeling the fluorescence spectral dynamics of dye molecules in solutions

1 file (2021)Alexey E. Nazarov, Anatoly I. Ivanov

FSDS is Fluorescence Spectral Dynamics Simulator, designed to investigate photoinduced charge transfer and its manifestations in time-resolved fluorescence spectra of a dye in a solvent. The project is implemented in C, using the MPI library. The computer model simulates stationary absorption and fluorescence spectra, as well as the time evolution of population distributions along the solvent reaction coordinate, to calculate spectral dynamics. Excitation and relaxation of intramolecular high-frequency vibrations are described at the quantum level. FSDS can fit the physical parameters of the dyes to experimental data. The dye excitation is consistently described accounting for the finite duration of the pump pulse. The program code implements two evolutionary models: a spin-boson model within the harmonic potential and a stochastic model based on the Smoluchowski diffusion operator for an arbitrary free energy surface. Computer simulation shows the numerical coincidence of the calculations performed in the framework of these models for the harmonic free energy surface. The detail description of the code and numerical schemes are presented.## TPMD toolkit: A toolkit for studying rate processes using molecular dynamics trajectories and performing temperature programmed molecular dynamics calculations

1 file (2021)Saurabh Shivpuje, Abhijit Chatterjee

A set of basic components needed for the analysis of state-to-state transitions in molecular dynamics (MD) trajectories is provided in the form of a toolkit. The toolkit can be used to (a) determine long-lived states of the system, (b) identify mechanism for transition from one state to another by listing atoms that participate in the transition, and (c) calculate kinetic parameters associated with the rate process, e.g., rate constants and Arrhenius parameters. Additionally, the toolkit enables the study of rare kinetic events using the temperature programmed MD (TPMD) method. Results obtained with two prototype systems, namely, Ag trimer diffusion, and Li diffusion in LiFePO_4, are discussed to illustrate the application of the toolkit.## Parallel time integration using Batched BLAS (Basic Linear Algebra Subprograms) routines

1 file (2021)Konstantin Herb, Pol Welter

We present an approach for integrating the time evolution of quantum systems. We leverage the computation power of graphics processing units (GPUs) to perform the integration of all time steps in parallel. The performance boost is especially prominent for small to medium-sized quantum systems. The devised algorithm can largely be implemented using the recently-specified batched versions of the BLAS routines, and can therefore be easily ported to a variety of platforms. Our PARAllelized Matrix Exponentiation for Numerical Time evolution (PARAMENT) implementation runs on CUDA-enabled graphics processing units.## ElasTool: An automated toolkit for elastic constants calculation

1 file (2021)Zhongli Liu, C.E. Ekuma and 3 more

We present the ElasTool package, an automated toolkit for calculating the second-order elastic constants (SOECs) of any two- (2D) and three-dimensional (3D) crystal systems. ElasTool uses three kinds of strain-matrix sets, i.e., the high-efficiency strain-matrix sets (OHESS), the universal linear-independent coupling strains (ULICS), and the all-single-element strain-matrix sets (ASESS), to calculate the SOECs automatically. ElasTool can efficiently compute both zero- and high-temperature elastic constants. We describe in detail the theoretical background and computational method of elastic constants, the package structure, the installation, and run, the input/output files, the controlling parameters, and two representative examples of how to use the ElasTool package. ElasTool is useful for either the exploration of materials' elastic properties or high-throughput new materials screening and design. ElasTool is freely available on GitHub: https://github.com/elastool## Efficient generation of self-avoiding, semiflexible rotational isomeric chain ensembles in bulk, in confined geometries, and on surfaces

1 file (2021)Oliver Weismantel, Aikaterini A. Galata and 3 more

We provide an efficient ready-to-run code gensaw that generates single or large ensembles of self-avoiding, flexible, semiflexible, rotationally isometric or helical chains in the bulk or subject to arbitrary confinement and tethering conditions, where we allow for arbitrary intramolecular bending and dihedral energy functions. The resulting configuration files are provided in various common formats and can be immediately used to do molecular simulations or statistical analysis. We work out analytic expressions for the mean squared end-to-end distance and gyration radius of the semiflexible, helical and rotational isomeric state models with a finite number of bonds and arbitrary interaction potentials for direct comparison and testing of the code in the limiting case of unconfined phantom chains. In addition to the graphics-free linux standalone batch version gensaw that creates configuration and other files for high throughput applications from the command line, we provide an interactive online version gensaw-visualization that serves as platform-independent graphical user interface, and animates the resulting conformations using a remote gensaw server.