Computer Physics Communications

ISSN: 0010-4655
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  • Here we present a new code for modelling electron kinetics in the tokamak Scrape-Off Layer (SOL). SOL-KiT (Scrape-Off Layer Kinetic Transport) is a fully implicit 1D code with kinetic (or fluid) electrons, fluid (or stationary) ions, and diffusive neutrals. The code is designed for fundamental exploration of non-local physics in the SOL and utilizes an arbitrary degree Legendre polynomial decomposition of the electron distribution function, treating both electron–ion and electron–atom collisions. We present a novel method for ensuring particle and energy conservation in inelastic and superelastic collisions, as well as the first full treatment of the logical boundary condition in the Legendre polynomial formalism. To our knowledge, SOL-KiT is the first fully implicit arbitrary degree harmonic kinetic code, offering a conservative and self-consistent approach to fluid–kinetic comparison with its integrated fluid electron mode. In this paper we give the model equations and their discretizations, as well as showing the results of a number of verification/benchmarking simulations.
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  • A general program to fit global adiabatic potential energy surfaces of up to tetratomic molecules to ab initio points and available spectroscopic data for simple diatomics is reported. It is based on the Combined-Hyperbolic-Inverse-Power-Representation (CHIPR) method. The final form describes all dissociating fragments and long-range/valence interactions, while obeying the system permutational symmetry. The code yields as output a Fortran 90 subroutine that readily evaluates the potential and gradient at any arbitrary geometry.
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  • Inclusive Monte-Carlo samples are indispensable for signal selection and background suppression in many high energy physics experiments. A clear knowledge of the physics processes involved in the samples, including the types of processes and the number of processes in each type, is a great help to investigating signals and backgrounds. To help analysts obtain the physics process information from the truth information of the samples, we develop a physics process analysis program, TopoAna, with C++, ROOT, and LaTeX. The program implements the functionalities of component analysis and signal identification with many kinds of fine, customizable classification and matching algorithms. It tags physics processes in individual events accurately in the output root files, and exports the physics process information at the sample level clearly to the output plain text, tex source, and pdf files. Independent of specific software frameworks, the program is applicable to many experiments. At present, it has come into use in three e^+ e^- colliding experiments: the BESIII, Belle, and Belle II experiments. The use of the program in other similar experiments is also prospective.
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  • In this paper, we present the basic routines of the C++-program Matslise 3.0, an updated but yet restricted version of the matlab package Matslise 2.0. Matslise 3.0 currently allows the accurate, but in comparison to Matslise 2.0, faster computation of eigenvalues and eigenfunctions of one dimensional time-independent Schrödinger problems. The numerical examples show that speed up factors up to 20 (for the eigenvalues) and 200 (for the eigenfunctions) are obtained. These highly optimized routines will enable us, in the near future, to extend Matslise 3.0 to solve time-independent 2D and 3D as well as time-dependent 1D problems.
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  • We present SimpleBounce, a C++ package for finding the bounce solution for the false vacuum decay. This package is based on a flow equation which is proposed by the author R. Sato (2020) and solves Coleman–Glaser–Martin’s reduced problem (S. R. Coleman et al. 1978): the minimization problem of the kinetic energy while fixing the potential energy. The bounce configuration is obtained by a scale transformation of the solution of this problem. For models with 1–8 scalar field(s), the bounce action can be calculated with O(0.1) % accuracy in O(0.1) s. This package is available at http://github.com/rsato64/SimpleBounce.
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  • We develop Kω, an open-source linear algebra library for the shifted Krylov subspace methods. The methods solve a set of shifted linear equations (z_k I - H)x^(k) = b (k = 0, 1, 2, ...) for a given matrix H and a vector b, simultaneously. The leading order of the operational cost is the same as that for a single equation. The shift invariance of the Krylov subspace is the mathematical foundation of the shifted Krylov subspace methods. Applications in materials science are presented to demonstrate the advantages of the algorithm over the standard Krylov subspace methods such as the Lanczos method. We introduce benchmark calculations of (i) an excited (optical) spectrum and (ii) intermediate eigenvalues by the contour integral on the complex plane. In combination with the quantum lattice solver HΦ, Kω can realize parallel computation of excitation spectra and intermediate eigenvalues for various quantum lattice models.
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  • We present and distribute a FreeFem++ Toolbox for the parallel computing of two- or three-dimensional liquid–solid phase-change systems involving natural convection. FreeFem++ (www.freefem.org) is a free finite-element software available for all existing operating systems. We use the recent library ffddm that makes available in FreeFem++ state-of-the-art scalable Schwarz domain decomposition methods (DDM). The single domain approach used in our previous contribution (Rakotondrandisa et al., 2020) is adapted for the use of the DDM method. As a result, the computational time is considerably reduced for 2D configurations and furthermore 3D problems become affordable. The numerical method is based on an enthalpy-porosity model. The same set of equations is solved in both liquid and solid phases: the incompressible Navier–Stokes equations with Boussinesq approximation for thermal effects. A Carman-Kozeny-type penalty term is added to the momentum equations to bring progressively the velocity to zero into the solid. Model equations are discretized using Galerkin triangular or tetrahedral finite elements. The coupled system of equations is integrated in time using a second-order Gear implicit scheme. The resulting discrete equations are solved using a Newton algorithm. The DDM approach is based on an overlapping Schwarz method. The mesh is first split in subdomains using Scotch or Metis libraries. The final linear system is then solved in parallel using a GMRES Krylov method, with a Restricted Additive Schwarz (RAS) preconditioner. The mesh is adapted during the computation using metrics control. The 3D-mesh adaptivity uses the mmg (www.mmgtools.org) open source library. Parallel 2D and 3D computations of benchmark cases of increasing difficulty are presented: natural convection of air, natural convection of water, melting or solidification of a phase-change material, and, finally, a water freezing case. For each case, careful validations are provided and the performance of the code is assessed. The robustness of the Toolbox in 3D is also demonstrated by adapting the number of processors to the number of tetrahedra, which can considerably vary after the mesh adaptation.
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  • Nonequispaced discrete Fourier transformation (NDFT) is widely applied in all aspects of computational science and engineering. The computational efficiency and accuracy of NDFT has always been a critical issue in hindering its comprehensive applications both in intensive and in extensive aspects of scientific computing. In our previous work Yang et al. (2018), a CUNFFT method was proposed and it shown outstanding performance in handling NDFT at intermediate scale based on CUDA (Compute Unified Device Architecture) technology. In the current work, we further improved the computational efficiency of the CUNTTF method using an efficient MPI-CUDA hybrid parallelization (HP) scheme of NFFT to achieve a cutting-edge treatment of NDFT at super extended scale. Within this HP-NFFT method, the spatial domain of NDFT is decomposed into several parts according to the accumulative feature of NDFT and the detailed number of CPU and GPU nodes. These decomposed NDFT subcells are independently calculated on different CPU nodes using a MPI process-level parallelization mode, and on different GPU nodes using a CUDA thread-level parallelization mode and CUNFFT algorithm. A massive benchmarking of the HP-NFFT method indicates that this method exhibit a dramatic improvement in computational efficiency for handling NDFT at super extended scale without loss of computational precision. Furthermore, the HP-NFFT method is validated via the calculation of Madelung constant of fluorite crystal structure, and thereafter verified that this method is robust for the calculation of electrostatic interactions between charged ions in molecular dynamics simulation systems.
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  • MITNS (Multiple-Ion Transport Numerical Solver) is a new numerical tool designed to perform 1D simulations of classical cross-field transport in magnetized plasmas. Its detailed treatment of multi-species effects makes it a unique tool in the field. We describe the physical model it simulates, as well as its numerical implementation and performance.
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  • I present a Mathematica package designed for manipulations and evaluations of triple-K integrals and conformal correlation functions in momentum space. Additionally, the program provides tools for evaluation of a large class of 2- and 3-point massless multi-loop Feynman integrals with generalized propagators. The package is accompanied by five Mathematica notebooks containing detailed calculations of numerous conformal 3-point functions in momentum space.
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