**Computer Physics Communications**

### 3459 datasets for Computer Physics Communications

Contributors: Santiago Badia, Alberto F. Martín

Date: 2019-12-13

... This work is a user guide to the FEMPAR scientific software library. FEMPAR is an open-source object-oriented framework for the simulation of partial differential equations (PDEs) using finite element methods on distributed-memory platforms. It provides a rich set of tools for numerical discretization and built-in scalable solvers for the resulting linear systems of equations. An application expert that wants to simulate a PDE-governed problem has to extend the framework with a description of the weak form of the PDE at hand (and additional perturbation terms for non-conforming approximations). We show how to use the library by going through three different tutorials. The first tutorial simulates a linear PDE (Poisson equation) in a serial environment for a structured mesh using both continuous and discontinuous Galerkin finite element methods. The second tutorial extends it with adaptive mesh refinement on octree meshes. The third tutorial is a distributed-memory version of the previous one that combines a scalable octree handler and a scalable domain decomposition solver. The exposition is restricted to linear PDEs and simple geometries to keep it concise. The interested user can dive into more tutorials available in the FEMPAR public repository to learn about further capabilities of the library, e.g., nonlinear PDEs and nonlinear solvers, time integration, multi-field PDEs, block preconditioning, or unstructured mesh handling.

Files:

Contributors: Andrea Martini, Sergey Guda, A.A. Guda, G. Smolentsev, A. Algasov, O. Usoltsev, M.A. Soldatov, A. Bugaev, Yu. Rusalev, C. Lamberti

Date: 2019-12-13

... X-ray absorption near-edge spectroscopy (XANES) is becoming an extremely popular tool for material science thanks to the development of new synchrotron radiation light sources. It provides information about charge state and local geometry around atoms of interest in operando and extreme conditions. However, in contrast to X-ray diffraction, a quantitative analysis of XANES spectra is rarely performed in the research papers. The reason must be found in the larger amount of time required for the calculation of a single spectrum compared to a diffractogram. For such time-consuming calculations, in the space of several structural parameters, we developed an interpolation approach proposed originally by Smolentsev and Soldatov (2007). The current version of this software, named PyFitIt, is a major upgrade version of FitIt and it is based on machine learning algorithms. We have chosen Jupyter Notebook framework to be friendly for users and at the same time being available for remastering. The analytical work is divided into two steps. First, the series of experimental spectra are analyzed statistically and decomposed into principal components. Second, pure spectral profiles, recovered by principal components, are fitted by theoretical interpolated spectra. We implemented different schemes of choice of nodes for approximation and learning algorithms including Gradient Boosting of Random Trees, Radial Basis Functions and Neural Networks. The fitting procedure can be performed both for a XANES spectrum or for a difference spectrum, thus minimizing the systematic errors of theoretical simulations. The problem of several local minima is addressed in the framework of direct and indirect approaches.

Files:

Contributors: Markus Q. Huber, Anton K. Cyrol, Jan M. Pawlowski

Date: 2019-12-13

... We present version 3.0 of the Mathematica package DoFun for the derivation of functional equations. In this version, the derivation of equations for correlation functions of composite operators was added. In the update, the general workflow was slightly modified taking into account experience with the previous version. In addition, various tools were included to improve the usage experience and the code was partially restructured for easier maintenance.

Files:

Contributors: Dongyue Li, Daniele Marchisio, Christian Hasse, Dirk Lucas

Date: 2019-12-13

... twoWayGPBEFoam is an open-source mesoscopic Eulerian QBMM solver for monokinetic bubbly flows. The solver is implemented within the OpenFOAM software framework. Unlike the existing macroscopic two-fluid model (TFM) solver twoPhaseEulerFoam, it can predict the size segregation phenomenon and the size-conditional velocities of the disperse phase, although it will not be able to predict the particle trajectory crossing (PTC). On theoretical grounds, the evolution of the disperse phase in multiphase flows is dictated by the generalized population balance equation (GPBE), which can be transformed into moment transport equations and solved using the finite-volume method with higher-order realizable spatial-discretization schemes and time-integration schemes. In order to address the closure problem of the size-conditional spatial flux, the size-conditional velocities need to be modeled. In many previous works, these are assumed to be identical with the disperse phase velocity predicted by the TFM. In this work, the size-conditional velocities were modeled using the velocity polynomial approximation (VPA), for which the velocity polynomial coefficients (VPCs) can be obtained from the moments themselves. By carrying out several test cases with both one-way and two-way coupling, we show that the results predicted by our solver agree well with the analytical solutions and the existing experimental data.

Files:

Contributors: Andrew C. Brown, Gregory S.J. Armstrong, Jakub Benda, Daniel D.A. Clarke, Jack Wragg, Kathryn R. Hamilton, Zdeněk Mašín, Jimena D. Gorfinkiel, Hugo W. van der Hart

Date: 2019-12-13

... RMT is a program which solves the time-dependent Schrödinger equation for general, multielectron atoms, ions and molecules interacting with laser light. As such it can be used to model ionization (single-photon, multiphoton and strong-field), recollision (high-harmonic generation, strong-field rescattering) and, more generally, absorption or scattering processes with a full account of the multielectron correlation effects in a time-dependent manner. Calculations can be performed for targets interacting with ultrashort, intense laser pulses of long wavelength and arbitrary polarization. Calculations for atoms can optionally include the Breit–Pauli correction terms for the description of relativistic (in particular, spin–orbit) effects.

Files:

Contributors: D. Schick, A. Bojahr, M. Herzog, R. Shayduk, C. von Korff Schmising, M. Bargheer

Date: 2019-12-09

... This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract The udkm1Dsim toolbox is a collection of matlab (MathWorks Inc.) classes and routines to simulate the structural dynamics and the according X-ray diffraction response in one-dimensional crystalline sample structures upon an arbitrary time-dependent external stimulus, e.g. an ultrashort laser pulse. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of corresponding element-specific physical properties. The excitation of ultrafast dynamics is represented by an -temperature model which is commonly applied for ultrafast optical excitations. Structural dynamics due to thermal stress are calculated by a linear-chain model of masses and springs. The resulting X-ray diffraction response is computed by dynamical X-ray theory. The udkm1Dsim toolbox is highly modular and allows for introducing user-defined results at any step in the simulation procedure. Title of program: dkm1Dsim Catalogue Id: AERH_v1_0 Nature of problem Simulate the lattice dynamics of 1D crystalline sample structures due to an ultrafast excitation including thermal transport and compute the corresponding transient X-ray diffraction pattern. Versions of this program held in the CPC repository in Mendeley Data AERH_v1_0; dkm1Dsim; 10.1016/j.cpc.2013.10.009

Files:

Contributors: V. Riccardo, G.G.M. Coppa, G. Lapenta

Date: 2019-12-05

... Abstract Spices1 (Smart Particle In Cell ElectroStatic 1D) simulates 1D plasmas governed by the Vlasov equation. A linear Fokker—Planck operator can be used to represent collisions between plasma species and a given background. The electrostatic approximation is used and no magnetic field is present. Spices1 uses computational particles with internal degrees of freedom (smart particles) to represent better the evolution of the many physical particles allocated to one single computational particle, emp... Title of program: SPICES1 Catalogue Id: ADIQ_v1_0 Nature of problem The computer code simulates electrostatic processes in plasmas using a kinetic model based on the Vlasov equation and on the Fokker-Planck approximation. One-dimensional problems are considered with either open or periodic boundary conditions. Versions of this program held in the CPC repository in Mendeley Data ADIQ_v1_0; SPICES1; 10.1016/S0010-4655(98)00075-7 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)

Files:

Contributors: C.T.K. Kuo, T.W. Cadman, R.J. Arsenault

Date: 2019-12-05

... Title of program: SRNG Catalogue Id: ACIE_v1_0 Nature of problem An algorithm to generate a subset of random integers from a larger set of integers has been developed to minimize both the computing time and the memory space. The algorithm deals with the whole array at the same time, generates a subset of random integers for a given percentage of the range, and the generated subset of random integers is obtained as sequentially increasing numbers. Such random integers are used to specify thepositions of randomly dispersed impurity atoms or solute atoms in many ... Versions of this program held in the CPC repository in Mendeley Data ACIE_v1_0; SRNG; 10.1016/0010-4655(76)90065-5 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Files:

Contributors: K.A. Berrington, P.G. Burke, M. Le Dourneuf, W.D. Robb, K.T. Taylor, Vo Ky Lan

Date: 2019-12-05

... Title of program: A NEW VERSION OF RMATRX STG2 Catalogue Id: AAHG_v1_0 Nature of problem This program reads the radial integrals stored on a magnetic tape or disc file by A NEW VERSION of RMATRX STG1. It then calculates the hamiltonian matrix elements, the asymptotic potential coefficients, and the dipole length and velocity matrix elements from a given initial state to the final state specified by L,S and the channel quantum numbers. These quantities are stored on a magnetic tape or disc file for use by A NEW VERSION of RMATRX STG3. Versions of this program held in the CPC repository in Mendeley Data AAHG_v1_0; A NEW VERSION OF RMATRX STG2; 10.1016/0010-4655(78)90004-8 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Files:

Contributors: Axel Arnold, Christian Holm

Date: 2019-12-05

... Abstract We present a new method to accurately calculate the electrostatic energy and forces on charges being distributed in a two-dimensional periodic array of finite thickness. It is not based on an Ewald summation method and as such does not require any fine-tuning of an Ewald parameter for convergence. We transform the Coulomb sum via a convergence factor into a series of fast decaying functions which can be easily evaluated. Rigorous error bounds for the energies and the forces are derived and nu... Title of program: MMM2D Catalogue Id: ADQM_v1_0 Nature of problem Fast computation of the Coulomb sum in slab geometries. Useful for Molecular Dynamics or Monte Carlo simulations of surfaces or membranes involving charges. Versions of this program held in the CPC repository in Mendeley Data ADQM_v1_0; MMM2D; 10.1016/S0010-4655(02)00586-6 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Files: