**Computer Physics Communications**

### 700 datasets for Computer Physics Communications

Contributors: R. Butler, T. Dodwell, Anne Reinarz, A. Sandhu, R. Scheichl, L. Seelinger

Date: 2019-11-14

... The key innovation in this paper is an open-source, high-performance iterative solver for high contrast, strongly anisotropic elliptic partial differential equations implemented within dune-pdelab. The iterative solver exploits a robust, scalable two-level additive Schwarz preconditioner, GenEO (Spillane et al., 2014). The development of this solver has been motivated by the need to overcome the limitations of commercially available modeling tools for solving structural analysis simulations in aerospace composite applications. Our software toolbox dune-composites encapsulates the mathematical complexities of the underlying packages within an efficient C++ framework, providing an application interface to our new high-performance solver. We illustrate its use on a range of industrially motivated examples, which should enable other scientists to build on and extend dune-composites and the GenEO preconditioner for use in their own applications. We demonstrate the scalability of the solver on more than 15,000 cores of the UK national supercomputer Archer, solving an aerospace composite problem with over 200 million degrees of freedom in a few minutes. This scale of computation brings composites problems that would otherwise be unthinkable into the feasible range. To demonstrate the wider applicability of the new solver, we also confirm the robustness and scalability of the solver on SPE10, a challenging benchmark in subsurface flow/reservoir simulation.

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Contributors: Antoni Arbona, A. Artigues, C. Bona-Casas, J. Massó, Borja Miñano, A. Rigo, Miquel Trias, Carles Bona

Date: 2019-11-08

... This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract Simflowny is a software platform which aims to formalize the main elements of a simulation flow. It allows users to manage (i) formal representations of physical models based on Initial Value Problems (hyperbolic, parabolic and mixed-type partial differential equations), (ii) simulation problems based on such models, and (iii) discretization schemes to translate the problem to a finite mesh. Additionally, Simflowny generates automatically code for general-purpose simulation frameworks. This p... Title of program: Simflowny Catalogue Id: AEPL_v1_0 Nature of problem Any problem based on an Initial Value Problem formulation (hyperbolic, parabolic or mixed type partial differential equations). Versions of this program held in the CPC repository in Mendeley Data AEPL_v1_0; Simflowny; 10.1016/j.cpc.2013.04.012

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Contributors: Kuo-Chuan Chang, Chia-Jyi Liu

Date: 2019-10-30

... We develop an algorithm called SPBcal under Java SE runtime environment 1.8.0_131 to calculate transport parameters of thermoelectric materials within the framework of single parabolic band (SPB) model. For calculating Fermi-Dirac integrals, SPBcal is implemented by a double exponential transformation combined with trapezoidal rule to calculate F_1(n) and F_2(n) and the trapezoidal rule with pole correction to calculate F_{-1/2}(n) and F_{1/2}(n), with which good accuracy of the transport parameters as a function of temperature can be obtained with very low execution time of the algorithm as long as the experimentally determined Seebeck coefficients are given. The SPBcal is tested and the results are consistent with the data reported in the literature.

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Contributors: Alexandre Arbey, J. Auffinger, Kevin Hickerson, E.S. Jenssen

Date: 2019-10-30

... We present the version 2 of AlterBBN, an open public code for the calculation of the abundance of the elements from Big-Bang nucleosynthesis. It does not rely on any closed external library or program, aims at being user-friendly and allowing easy modifications, and provides a fast and reliable calculation of the Big-Bang nucleosynthesis constraints in the standard and alternative cosmologies. The previous version of this program (AEMH_v1_0) may be found at http://dx.doi.org/10.1016/j.cpc.2012.03.018.

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Contributors: Jonas Klappert, Fabian Lange

Date: 2019-10-30

... We present the open-source C++ library FireFly for the reconstruction of multivariate rational functions over finite fields. We discuss the involved algorithms and their implementation. As an application, we use FireFly in the context of integration-by-parts reductions and compare runtime and memory consumption to a fully algebraic approach with the program Kira.

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Contributors: Phani Motamarri, Sambit Das, Shiva Rudraraju, Krishnendu Ghosh, Denis Davydov, Vikram Gavini

Date: 2019-10-30

... We present an accurate, efficient and massively parallel finite-element code, DFT-FE, for large-scale ab-initio calculations (reaching ~100,000 electrons) using Kohn–Sham density functional theory (DFT). DFT-FE is based on a local real-space variational formulation of the Kohn–Sham DFT energy functional that is discretized using a higher-order adaptive spectral finite-element (FE) basis, and treats pseudopotential and all-electron calculations in the same framework, while accommodating non-periodic, semi-periodic and periodic boundary conditions. We discuss the main aspects of the code, which include, the various strategies of adaptive FE basis generation, and the different approaches employed in the numerical implementation of the solution of the discrete Kohn–Sham problem that are focused on significantly reducing the floating point operations, communication costs and latency. We demonstrate the accuracy of DFT-FE by comparing the energies, ionic forces and periodic cell stresses on a wide range of problems with popularly used DFT codes. Further, we demonstrate that DFT-FE significantly outperforms widely used plane-wave codes—both in CPU-times and wall-times, and on both non-periodic and periodic systems—at systems sizes beyond a few thousand electrons, with over 5-10 fold speedups in systems with more than 10,000 electrons. The benchmark studies also highlight the excellent parallel scalability of DFT-FE, with strong scaling demonstrated on up to 192,000 MPI tasks.

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Contributors: Marco Caliari, Stefan Rainer

Date: 2019-10-19

... GSGPEs is a MATLAB/GNU Octave suite of programs for the computation of the ground state of systems of Gross–Pitaevskii equations. It can compute the ground state in the defocusing case, for any number of equations with harmonic or quasi-harmonic trapping potentials, in spatial dimension one, two or three. The computation is based on a spectral decomposition of the solution into Hermite functions and direct minimization of the energy functional through a Newton-like method with an approximate line-search strategy. This new version is due to a change in the function eig of Matlab® which requires a new way to compute Gauss–Hermite quadrature nodes and weights. The previous version of this program (AENT_v1_0) may be found at http://dx.doi.org/10.1016/j.cpc.2012.10.007.

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Contributors: N. Sanna, G. Morelli, S. Orlandini, M. Tacconi, I. Baccarelli

Date: 2019-10-10

... SCELib is a computer program which implements the Single Center Expansion (SCE) method to describe molecular electronic densities and the interaction potentials between a charged projectile (electron or positron) and a target molecular system. The first version (CPC Catalog identifier ADMG_v1_0) was submitted to the CPC Program Library in 2000, version 2.0 (ADMG_v2_0) was submitted in 2004 and version 3.0 (ADMG_v3_0) was submitted in 2009. We here announce the new release 4.0 which presents additional features with respect to the previous versions aiming at a significant enhancement of its capabilities to deal with larger molecular systems. In SCELib 4.0 we implemented an automatic R grid generator based on a screened nuclear potential. By coupling the R generator with a parametric θ, ϕ definition of the angular grid, one is then able to define the 3D grid which best follows the molecular shape of systems as large as nucleotides and DNA fragments. The list of supported architectures has been updated and the code already ported in v3.0 to hybrid platforms based on NVIDIA GPU, has now been fully ported in double precision arithmetic and parallelized with MPI under either Linux or Microsoft Windows operating systems. The resulting benchmarks of the new code will be discussed in details and for the first time we present the performance test on a system as large as the Cytidine Mono Phosphate (CMP) which at present is the largest system ever simulated with this and related kind of codes.

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Contributors: Carl-Martin Pfeiler, Michele Ruggeri, Bernhard Stiftner, Lukas Exl, Matthias Hochsteger, Gino Hrkac, Joachim Schöberl, Norbert J. Mauser, Dirk Praetorius

Date: 2019-10-10

... We present our open-source Python module Commics for the study of the magnetization dynamics in ferromagnetic materials via micromagnetic simulations. It implements state-of-the-art unconditionally convergent finite element methods for the numerical integration of the Landau–Lifshitz–Gilbert equation. The implementation is based on the multiphysics finite element software Netgen/NGSolve. The simulation scripts are written in Python, which leads to very readable code and direct access to extensive post-processing. Together with documentation and example scripts, the code is freely available on GitLab.

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Contributors: L.Y. Jia

Date: 2019-10-10

... Recently Jia (2019) proposed a new scheme that applies the variational principle directly to a coherent-pair condensate. This work publishes its computer code. The result is equivalent to that of the so-called variation after particle-number projection in the BCS case, but the new code always conserves the particle number and avoids the time-consuming projection. Specifically, the variational principle is solved by iterating the coherent-pair-structure expression at the energy minimum. We publish the code together with a semirealistic example that uses the realistic V_{low -k} interaction and large model spaces (up to 15 harmonic-oscillator major shells). The average energy can be minimized to practically arbitrary precision. We also test the code under the pairing Hamiltonian.

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