**Computer Physics Communications**

### 3485 datasets for Computer Physics Communications

Contributors: M. Blytt, Michael Kachelriess, S. Ostapchenko

Date: 2020-02-06

... The version 3.01 of ELMAG, a Monte Carlo program for the simulation of electromagnetic cascades initiated by high-energy photons and electrons interacting with extragalactic background light (EBL), is presented. Pair production and inverse Compton scattering on EBL photons as well as synchrotron losses are implemented using weighted sampling of the cascade development. New features include, among others, the implementation of turbulent extragalactic magnetic fields and the calculation of three-dimensional electron and positron trajectories, solving the Lorentz force equation. As final result of the three-dimensional simulations, the program provides two-dimensional source images as function of the energy and the time delay of secondary cascade particles.

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Contributors: Dmitry Gulevich

Date: 2020-02-06

... MiTMoJCo (Microscopic Tunneling Model for Josephson Contacts) is C code which aims to assist modeling of superconducting Josephson contacts based on the microscopic tunneling theory. The code offers implementation of a computationally demanding part of this calculation, that is evaluation of superconducting pair and quasiparticle tunnel currents from the given tunnel current amplitudes (TCAs) which characterize the junction material. MiTMoJCo comes with a library of pre-calculated TCAs for frequently used Nb-AlOx-Nb and Nb-AlN-NbN junctions, a Python module for developing custom TCAs, supplementary optimum filtration module for extraction of a constant component of a sinusoidal signal and examples of modeling few common cases of superconducting Josephson contacts.

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Contributors: Philipp Höllmer, Liang Qin, Michael F. Faulkner, A.C. Maggs, Werner Krauth

Date: 2020-02-06

... We present JeLLyFysh-Version1.0, an open-source Python application for event-chain Monte Carlo (ECMC), an event-driven irreversible Markov-chain Monte Carlo algorithm for classical N-body simulations in statistical mechanics, biophysics and electrochemistry. The application’s architecture mirrors the mathematical formulation of ECMC. Local potentials, long-ranged Coulomb interactions and multi-body bending potentials are covered, as well as bounding potentials and cell systems including the cell-veto algorithm. Configuration files illustrate a number of specific implementations for interacting atoms, dipoles, and water molecules.

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Contributors: Rithwik Tom, Timothy Rose, Imanuel Bier, Harriet O’Brien, Álvaro Vázquez-Mayagoitia, Noa Marom

Date: 2020-02-06

... Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine.

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Contributors: E.R. Smith, D.J. Trevelyan, E. Ramos-Fernandez, A. Sufian, C. O’Sullivan, D. Dini

Date: 2020-02-06

... We present an open-source library for coupling particle codes, such as molecular dynamics (MD) or the discrete element method (DEM), and grid based computational fluid dynamics (CFD). The application is focused on domain decomposition coupling, where a particle and continuum software model different parts of a single simulation domain with information exchange. This focus allows a simple library to be developed, with core mapping and communication handled by just four functions. Emphasis is on scaling on supercomputers, a tested cross-language library, deployment with containers and well-documented simple examples. Building on this core, a template is provided to facilitate the user development of common features for coupling, such as averaging routines and functions to apply constraint forces. The interface code for LAMMPS and OpenFOAM is provided to both include molecular detail in a continuum solver and model fluids flowing through a granular system. Two novel development features are highlighted which will be useful in the development of the next generation of multi-scale software: (i) The division of coupled code into a smaller blocks with testing over a range of processor topologies. (ii) The use of coupled mocking to facilitate coverage of various parts of the code and allow rapid prototyping. These two features aim to help users develop coupled models in a test-driven manner and focus on the physics of the problem instead of just software development. All presented code is open-source with detailed documentation on the dedicated website (cpl-library.org) permitting useful aspects to be evaluated and adopted in other projects.

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Contributors: Alexander Semenov, Bikramaditya Mandal, Dmitri Babikov

Date: 2020-02-06

... A program named MQCT is developed for calculations of rotationally and vibrationally inelastic scattering of molecules using the mixed quantum/classical theory approach. Calculations of collisions between two general asymmetric top rotors are now possible, which is a feature unavailable in other existing codes. Vibrational states of diatomic molecules can also be included in the basis set expansion, to carry out calculations of ro-vibrational excitation and quenching. Minimal input for the code assumes several defaults and is very simple, easy to set-up and run by non-experts. Multiple options, available for expert calculations, are listed in the Supplemental Information. The code is parallel and takes advantage of intrinsic massive parallelism of the mixed quantum/classical approach. A Monte-Carlo sampling procedure, implemented as option in the code, enables calculations for complicated systems with many internal states and large number of partial scattering waves. The coupled-states approximation is also implemented as an option. Integral and differential cross sections can be computed for the elastic channel. Rotational symmetry of each molecule, as well as permutation symmetry of two collision partners, are implemented. Potential energy surfaces for H_2 O + He, H_2 O + H_2, and H_2 O + H_2 O are included in the code. Example input files are also provided for these systems.

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Contributors: A. Bjelčić, T. Nikšić

Date: 2020-02-05

... The DIRQFAM code calculates the multipole response of even-even axially symmetric deformed nuclei using the framework of relativistic self-consistent mean-field models. The response is calculated by implementing the finite amplitude method for relativistic quasiparticle random phase approximation.

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Contributors: L. Naterop, A. Signer, Y. Ulrich

Date: 2020-01-30

... Generalised polylogarithms naturally appear in higher-order calculations of quantum field theories. We present handyG, a Fortran 90 library for the evaluation of such functions, by implementing the algorithm proposed by Vollinga and Weinzierl. This allows fast numerical evaluation of generalised polylogarithms with currently relevant weights, suitable for Monte Carlo integration.

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Contributors: M. Broz, J.G. Contreras, J.D. Tapia Takaki

Date: 2020-01-30

... The study of photon-induced reactions in collisions of heavy nuclei at RHIC and the LHC has become an important direction of the research program of these facilities in recent years. In particular, the production of vector mesons in ultra-peripheral collisions (UPC) has been intensively studied. Owing to the intense photon fluxes, the two nuclei participating in such processes undergo electromagnetic dissociation producing neutrons at beam rapidities. Here, we introduce the nOOn (pronounced noon) Monte Carlo program, which generates events containing such neutrons. nOOn is a ROOT based program that can be interfaced with existing generators of vector meson production in UPC or with theoretical calculations of such photonuclear processes. nOOn can also be easily integrated with the simulation programs of the experiments at RHIC and the LHC.

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### Questaal: A package of electronic structure methods based on the linear muffin-tin orbital technique

Contributors: Dimitar Pashov, Swagata Acharya, Walter R. L. Lambrecht, Jerome Jackson, Kirill D. Belashchenko, Athanasios Chantis, Francois Jamet, Mark van Schilfgaarde

Date: 2020-01-23

... This paper summarises the theory and functionality behind Questaal, an open-source suite of codes for calculating the electronic structure and related properties of materials from first principles. The formalism of the linearised muffin-tin orbital (LMTO) method is revisited in detail and developed further by the introduction of short-ranged tight-binding basis functions for full-potential calculations. The LMTO method is presented in both Green’s function and wave function formulations for bulk and layered systems. The suite’s full-potential LMTO code uses a sophisticated basis and augmentation method that allows an efficient and precise solution to the band problem at different levels of theory, most importantly density functional theory, LDA +U, quasi-particle self-consistent GW and combinations of these with dynamical mean field theory. This paper details the technical and theoretical bases of these methods, their implementation in Questaal, and provides an overview of the code’s design and capabilities.

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