# Computer Physics Communications

ISSN: 0010-4655

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Datasets associated with articles published in Computer Physics Communications

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• Point defects in semiconductor crystals provide a means for carriers to recombine nonradiatively. This recombination process impacts the performance of devices. We present the Nonrad code that implements the first-principles approach of Alkauskas et al. (2014) [8] for the evaluation of nonradiative capture coefficients based on a quantum-mechanical description of the capture process. An approach for evaluating electron-phonon coupling within the projector augmented wave formalism is presented. We also show that the common procedure of replacing Dirac delta functions with Gaussians can introduce errors into the resulting capture rate, and implement an alternative scheme to properly account for vibrational broadening. Lastly, we assess the accuracy of using an analytic approximation to the Sommerfeld parameter by comparing with direct numerical evaluation.
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• OpenSBLI is an open-source code-generation system for compressible fluid dynamics (CFD) on heterogeneous computing architectures. Written in Python, OpenSBLI is an explicit high-order finite-difference solver on structured curvilinear meshes. Shock-capturing is performed by a choice of high-order Weighted Essentially Non-Oscillatory (WENO) or Targeted Essentially Non-Oscillatory (TENO) schemes. OpenSBLI generates a complete CFD solver in the Oxford Parallel Structured (OPS) domain specific language. The OPS library is embedded in C code, enabling massively-parallel execution of the code on a variety of high-performance-computing architectures, including GPUs. The present paper presents a code base that has been completely rewritten from the earlier proof of concept Jacobs et al. (2017) [7], allowing shock capturing, coordinate transformations for complex geometries, and a wide range of boundary conditions, including solid walls with and without heat transfer. A suite of validation and verification cases are presented, plus demonstration of a large-scale Direct Numerical Simulation (DNS) of a transitional Shockwave Boundary Layer Interaction (SBLI). The code is shown to have good weak and strong scaling on multi-GPU clusters. We demonstrate that code-generation and domain specific languages are suitable for performing efficient large-scale simulations of complex fluid flows on emerging computing architectures.
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• The REGINA code calculates the São Paulo potential version 2 (SPP2) and the Brazilian nuclear potential (BNP). The code also provides nuclear densities obtained from the Dirac-Hartree-Bogoliubov model, which are used to calculate the nuclear potentials. Elastic scattering cross sections are obtained within the context of the optical model, with different options for the real and imaginary parts of the optical potential. In this manuscript, we provide a summary of the theoretical framework and information about the use of the code.
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• We present an open-source code for the simulation of electron and ion transport for user-defined gas mixtures with static uniform electric and magnetic fields. The program provides microscopic interaction simulation and is interfaced with cross-section tables published by LXCat[1]. The framework was validated against drift velocity tables available in literature obtaining an acceptable match for atomic and non-polar molecular gases with spherical symmetry. The code is written in C++17 and is available as a shared library for easy integration into other simulation applications.
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• Given a value of the Fermi-Dirac integral $\displaystyle \int_0^{\infty}\frac{t^j\,dt}{e^{t-\eta}+1}$, this routine returns the value of the parameter η for a given j with a relative error less than 10^{-13}. The inversion is provided for η ∈ [-30,100] and for the following set of j values, { -1/2, 1/2, 3/2, 5/2, 1, 2 }. For η ∈ [-30,-2], an iterative method involving the McDougall and Stoner series is used. For the rest of the region of interest, a rational fit is employed.
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• We present a new package for Mathematica system, called Libra. Its purpose is to provide convenient tools for the transformation of the first-order differential systems ∂_i j = M_i j for one or several variables. In particular, Libra is designed for the reduction to ϵ-form of the differential systems which appear in multiloop calculations. The package also contains some tools for the construction of general solution: both via perturbative expansion of path-ordered exponent and via generalized power series expansion near regular singular points. Libra also has tools to determine the minimal list of coefficients in the asymptotics of the original master integrals, sufficient for fixing the boundary conditions.
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• Efficient numerical simulations of fluid flow on the pore scale allow for the numerical estimation of effective material properties of porous media like effective permeability or tortuosity, among others. In contrast to time-consuming and often expensive laboratory tests, pore scale-resolved numerical simulations further enable the computational quantification of anisotropy of inherent material properties and the estimation of representative sample domains. Numerically calculated quantities are valuable in several fields, such as carbon dioxide sequestration, geothermal energy production and groundwater contamination remediation. Our specific pore scale-resolved simulation method directly based on images obtained from Micro X-Ray Computed Tomography (μXRCT) is based on the weakly compressible Smoothed Particle Hydrodynamics (SPH) approach. SPH is a meshless Lagrangian method, highly suitable for modeling complex geometries and flow at moderate Reynolds numbers. Low Reynolds number flow, also denoted as creeping flow, is a typical scenario present in the above mentioned applications. However, SPH is computationally demanding, especially in simulations of large domains. To overcome these difficulties, we have designed a specific SPH module for the highly optimized HOOMD-blue Molecular Dynamics software. Our implementation supports single-phase flow, and targets both CPU and GPU clusters. Due to the high computational demands, scalability is essential to make the software practically usable, and our tests indicate that our implementation can scale almost ideally. We study a wide variety of test cases, which are not only representative for XRCT-based geometries, but for pore scale-resolved flow simulations in general. Additionally, we present a large-scale simulation investigating an unconventional high porous volcanic rock sample (Reticulite).
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• Characterization of structural information at the atomistic level in molecular dynamics (MD) simulations is a necessary task for researchers in the fields of materials modeling and simulation. Visualization of the density distribution is typically one of the most important properties in structural characterization. Visual Molecular Dynamics (VMD) is a widely used molecular visualization package that can not only visualize complex molecular systems but also perform analysis by integrating special plugins or by running in-house generated TCL scripts. However, a density analysis is still not an in-built feature of VMD. This work presents a flexible and easy-to-use TCL code to be used in VMD, that can perform both 1D and 2D density calculations over any specified local areas of a given system. By using the built-in commands of VMD, the code can access and process trajectory files in any formats that are supported by VMD, as produced by mainstream simulation packages, i.e., LAMMPS, GROMACS, NAMD, and CHARMM, etc. This work introduces the calculation method, code, and usages in detail to provide a quick start for users in their density analysis work.
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• We present the VASPKIT, a command-line program that aims at providing a robust and user-friendly interface to perform high-throughput analysis of a variety of material properties from the raw data produced by the VASP code. It consists of mainly the pre- and post-processing modules. The former module is designed to prepare and manipulate input files such as the necessary input files generation, symmetry analysis, supercell transformation, k-path generation for a given crystal structure. The latter module is designed to extract and analyze the raw data about elastic mechanics, electronic structure, charge density, electrostatic potential, linear optical coefficients, wave function plots in real space, etc. This program can run conveniently in either interactive user interface or command line mode. The command-line options allow the user to perform high-throughput calculations together with bash scripts. This article gives an overview of the program structure and presents illustrative examples for some of its usages. The program can run on Linux, macOS, and Windows platforms. The executable versions of VASPKIT and the related examples and tutorials are available on its official website vaspkit.com.
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• The udkm1Dsim toolbox is a collection of Python classes and routines to simulate the thermal, structural, and magnetic dynamics after laser excitation as well as the corresponding X-ray scattering response in one-dimensional samples, such as multilayers. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of element-specific physical properties. The excitation of dynamics is represented by an N-temperature-model which is commonly applied in ultrafast physics. Structural dynamics due to thermal stresses are calculated by a linear-chain model of masses and springs. The implementation of specific magnetic dynamics can be easily accomplished by the user employing a generalized magnetization interface class. The resulting X-ray diffraction response is computed by kinematical or dynamical X-ray theory which can also include polarization-dependent magnetic scattering. The udkm1Dsim toolbox is highly modular and allows for injecting user-defined inputs at any step within the simulation procedure. The previous version of this program (AERH_v1_0) can be found at https://doi.org/10.1016/j.cpc.2013.10.009.
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