**Computer Physics Communications**

### 3473 datasets for Computer Physics Communications

Contributors: David Moxey, Chris D. Cantwell, Yan Bao, Andrea Cassinelli, Giacomo Castiglioni, Sehun Chun, Emilia Juda, Ehsan Kazemi, Kilian Lackhove, Julian Marcon

Date: 2020-01-10

... Nektar++ is an open-source framework that provides a flexible, high-performance and scalable platform for the development of solvers for partial differential equations using the high-order spectral/hp element method. In particular, Nektar++ aims to overcome the complex implementation challenges that are often associated with high-order methods, thereby allowing them to be more readily used in a wide range of application areas. In this paper, we present the algorithmic, implementation and application developments associated with our Nektar++ version 5.0 release. We describe some of the key software and performance developments, including our strategies on parallel I/O, on in situ processing, the use of collective operations for exploiting current and emerging hardware, and interfaces to enable multi-solver coupling. Furthermore, we provide details on a newly developed Python interface that enables a more rapid introduction for new users unfamiliar with spectral/hp element methods, C++ and/or Nektar++. This release also incorporates a number of numerical method developments – in particular: the method of moving frames (MMF), which provides an additional approach for the simulation of equations on embedded curvilinear manifolds and domains; a means of handling spatially variable polynomial order; and a novel technique for quasi-3D simulations (which combine a 2D spectral element and 1D Fourier spectral method) to permit spatially-varying perturbations to the geometry in the homogeneous direction. Finally, we demonstrate the new application-level features provided in this release, namely: a facility for generating high-order curvilinear meshes called NekMesh; a novel new AcousticSolver for aeroacoustic problems; our development of a ‘thick’ strip model for the modelling of fluid–structure interaction (FSI) problems in the context of vortex-induced vibrations (VIV). We conclude by commenting on some lessons learned and by discussing some directions for future code development and expansion.

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Contributors: Deok-Soo Kim, Joonghyun Ryu, Youngsong Cho, Mokwon Lee, Jehyun Cha, Chanyoung Song, Sang Wha Kim, Roman A. Laskowski, Kokichi Sugihara, Jong Bhak

Date: 2020-01-10

... The geometry of atomic arrangement underpins the structural understanding of molecules in many fields. However, no general framework of mathematical/computational theory for the geometry of atomic arrangement exists. Here we present “Molecular Geometry (MG)” as a theoretical framework accompanied by “MG Operating System (MGOS)” which consists of callable functions implementing the MG theory. MG allows researchers to model complicated molecular structure problems in terms of elementary yet standard notions of volume, area, etc. and MGOS frees them from the hard and tedious task of developing/implementing geometric algorithms so that they can focus more on their primary research issues. MG facilitates simpler modeling of molecular structure problems; MGOS functions can be conveniently embedded in application programs for the efficient and accurate solution of geometric queries involving atomic arrangements. The use of MGOS in problems involving spherical entities is akin to the use of math libraries in general purpose programming languages in science and engineering.

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Contributors: Xavier Gone, Bernard Amadon, Gabriel Antonius, Frédéric Arnardi, Lucas Baguet, Jean-Michel Beuken, Jordan Bieder, François Bottin, Johann Bouchet, Eric Bousquet

Date: 2020-01-09

... Abinit is a material- and nanostructure-oriented package that implements density-functional theory (DFT) and many-body perturbation theory (MBPT) to find, from first principles, numerous properties including total energy, electronic structure, vibrational and thermodynamic properties, different dielectric and non-linear optical properties, and related spectra. In the special issue to celebrate the 40th anniversary of CPC, published in 2009, a detailed account of Abinit was included [Gonze et al. (2009)], and has been amply cited. The present article comes as a follow-up to this 2009 publication. It includes an analysis of the impact that Abinit has had, through for example the bibliometric indicators of the 2009 publication. Links with several other computational materials science projects are described. This article also covers the new capabilities of Abinit that have been implemented during the last three years, complementing a recent update of the 2009 article published in 2016. Physical and technical developments inside the abinit application are covered, as well as developments provided with the Abinit package, such as the multibinit and a-tdep projects, and related Abinit organization developments such as AbiPy . The new developments are described with relevant references, input variables, tests, and tutorials.

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Contributors: Zdeněk Mašín, Jakub Benda, Jimena D. Gorfinkiel, Alex G. Harvey, Jonathan Tennyson

Date: 2020-01-09

... UKRmol+ is a new implementation of the time-independent UK R-matrix electron–molecule scattering code. Key features of the implementation are the use of quantum chemistry codes such as Molpro to provide target molecular orbitals; the optional use of mixed Gaussian — B-spline basis functions to represent the continuum and improved configuration and Hamiltonian generation. The code is described, and examples covering electron collisions from a range of targets, positron collisions and photoionization are presented. The codes are freely available as a tarball from Zenodo.

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Contributors: H. Bahl, T. Hahn, S. Heinemeyer, W. Hollik, S. Paßehr, H. Rzehak, G. Weiglein

Date: 2020-01-09

... We present an overview of the status and recent developments of FeynHiggs (current version: 2.14.3) since version 2.12.2. The main purpose of FeynHiggs is the calculation of the Higgs-boson masses and other physical observables in the MSSM. For a precise prediction of the Higgs-boson masses for low and high SUSY scales, state-of-the-art fixed-order and effective-field-theory calculations are combined. We first discuss improvements of the fixed-order calculation, namely an optional renormalization of the stop sector and a renormalization of the Higgs sector ensuring the chosen input mass to be equivalent with the corresponding physical mass. Second, we describe improvements of the EFT calculation, i.e. an implementation of non-degenerate threshold corrections as well as an interpolation for complex parameters. Lastly, we highlight some improvements of the code structure easing future extensions of FeynHiggs to models beyond the MSSM. The previous version (ADKT_v2_0) of this program may be found at http://dx.doi.org/10.1016/j.cpc.2009.02.014.

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Contributors: Vasily Tulsky, Dieter Bauer

Date: 2020-01-09

... The calculation of accurate photoelectron spectra (PES) for strong-field laser-atom experiments is a demanding computational task, even in single-active-electron approximation. The Qprop code, published in 2006, has been extended in 2016 in order to provide the possibility to calculate PES using the so-called t-SURFF approach [Tao and Scrinzi (2012)]. In t-SURFF, the flux through a surface while the laser is on is monitored. Calculating PES from this flux through a surface enclosing a relatively small computational grid is much more efficient than calculating it from the widely spread wavefunction at the end of the laser pulse on a much larger grid. However, the smaller the minimum photoelectron energy of interest is, the more post-propagation after the actual laser pulse is necessary. This drawback of t-SURFF has been overcome by Morales et al. [Morales et al. (2016)] by noticing that the propagation of the wavefunction from the end of the laser pulse to infinity can be performed very efficiently in a single step. In this work, we introduce Qprop 3.0, in which this single-step post-propagation (dubbed i-SURFV) is added. Examples, illustrating the new feature, are discussed. A few other improvements, concerning mainly the parameter files, are also explained.

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Contributors: Evgueni Ovtchinnikov, Richard Brown, Christoph Kolbitsch, Edoardo Pasca, Casper da Costa-Luis, Ashley G. Gillman, Benjamin A. Thomas, Nikos Efthimiou, Johannes Mayer, Palak Wadhwa

Date: 2020-01-09

... The combination of positron emission tomography (PET) with magnetic resonance (MR) imaging opens the way to more accurate diagnosis and improved patient management. At present, the data acquired by PET-MR scanners are essentially processed separately, but the opportunity to improve accuracy of the tomographic reconstruction via synergy of the two imaging techniques is an active area of research. In this paper, we present Release 2.1.0 of the CCP-PETMR Synergistic Image Reconstruction Framework (SIRF) software suite, providing an open-source software platform for efficient implementation and validation of novel reconstruction algorithms. SIRF provides user-friendly Python and MATLAB interfaces built on top of C++ libraries. SIRF uses advanced PET and MR reconstruction software packages and tools. Currently, for PET this is Software for Tomographic Image Reconstruction (STIR); for MR, Gadgetron and ISMRMRD; and for image registration tools, NiftyReg. The software aims to be capable of reconstructing images from acquired scanner data, whilst being simple enough to be used for educational purposes. The most recent version of the software can be downloaded from http://www.ccppetmr.ac.uk/downloads and https://github.com/CCPPETMR/.

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Contributors: Kevin Schmidmayer, Fabien Petitpas, Sébastien Le Martelot, eric daniel

Date: 2020-01-09

... ECOGEN, a new open-source computational fluid dynamics code is presented. It is a multi-model tool devoted to the simulation of compressible flows. A large range of problems can be solved, from single-phase gas dynamics to multiphase, multiphysics flows including interface problems between pure fluids. This code is suited for strongly unsteady flows. The numerical solver of ECOGEN is implemented in a flexible structure making the code able to compute such complex flows on different kinds of discretization grids. The implemented hyperbolic solver is able to deal with Cartesian geometries as well as unstructured grids. A recent adaptive mesh refinement method is also implemented. Its numerical implementation is presented in detail to help the enthusiastic developer to contribute to this open-source project. Representative test cases are presented to show the tool abilities and to open the gate for future developments.

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Contributors: D.T. Waide, D.G. Green, G.F. Gribakin

Date: 2020-01-09

... BSHF solves the Hartree–Fock equations in a B-spline basis for atoms, negatively charged ions, and systems of N electrons in arbitrary central potentials. In the B-spline basis the Hartree–Fock integro-differential equations are reduced to a computationally simpler eigenvalue problem. As well as solving this for the ground-state electronic structure self-consistently, the program can calculate discrete and/or continuum excited states of an additional electron or positron in the field of the frozen-target N-electron ground state. It thus provides an effectively complete orthonormal basis that can be used for higher-order many-body theory calculations. Robust and efficient convergence in the self-consistent iterations is achieved by a number of strategies, including by gradually increasing the strength of the electron–electron interaction by scaling the electron charge from a reduced value to its true value. The functionality and operation of the program is described in a tutorial style example.

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Contributors: Ben Palmer, Brian Connolly, Mark Read

Date: 2019-12-19

... A computer program, Activity, was developed to predict the activity and gamma lines of materials irradiated with an ion beam. It uses the TENDL (Koning and Rochman, 2012) proton reaction cross section database, the Stopping and Range of Ions in Matter (SRIM) (Biersack et al., 2010) code, a Nuclear Data Services (NDS) radioactive decay database (Sonzogni, 2006) and an ENDF gamma decay database (Herman and Chadwick, 2006). An extended version of Bateman’s equation is used to calculate the activity at time t, and this equation is solved analytically, with the option to also solve by numeric inverse Laplace Transform as a failsafe. The program outputs the expected activity and gamma lines of the activated material.

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