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A Physics-Based Tessellation Algorithm for Particle Assemblies on Arbitrary Surfaces Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-12 Shah Wasif Sazzad, Sanjay Dharmavaram, Luigi E. Perotti
Interacting particle assemblies embedded on a surface are often used to model biophysical systems and to study new colloidal materials. The configurations resulting from the particles interacting with each other and with their substrate affect the system's physical properties, which depend on local symmetries and defects. It is therefore important to identify the nature and location of defects in the
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SIMULATeQCD: A simple multi-GPU lattice code for QCD calculations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-08 Lukas Mazur, Dennis Bollweg, David A. Clarke, Luis Altenkort, Olaf Kaczmarek, Rasmus Larsen, Hai-Tao Shu, Jishnu Goswami, Philipp Scior, Hauke Sandmeyer, Marius Neumann, Henrik Dick, Sajid Ali, Jangho Kim, Christian Schmidt, Peter Petreczky, Swagato Mukherjee, (HotQCD collaboration)
The rise of exascale supercomputers has fueled competition among GPU vendors, driving lattice QCD developers to write code that supports multiple APIs. Moreover, new developments in algorithms and physics research require frequent updates to existing software. These challenges have to be balanced against constantly changing personnel. At the same time, there is a wide range of applications for HISQ
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Multipolynomial Monte Carlo for Trace Estimation in Lattice QCD Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-08 Paul Lashomb, Ronald B. Morgan, Travis Whyte, Walter Wilcox
Estimating the trace of the inverse of a large matrix is an important problem in lattice quantum chromodynamics. A multilevel Monte Carlo method is proposed for this problem that uses different degree polynomials for the levels. The polynomials are developed from the GMRES algorithm for solving linear equations. To reduce orthogonalization expense, the highest degree polynomial is a composite or double
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Olsson.wl & ROC2.wl: Mathematica packages for transformations of multivariable hypergeometric functions & regions of convergence for their series representations in the two variables case Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-08 B. Ananthanarayan, Souvik Bera, S. Friot, Tanay Pathak
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Band structure calculations of three-dimensional solid-fluid coupling phononic crystals using dual reciprocity boundary element method and wavelet compression method Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-07 Qi Wei, Jiawei Xiang, Weiping Zhu, Hongjiu Hu
The algorithm for calculating the band structures of two-dimensional phononic crystals (PCs) using the boundary element method (BEM) has been proposed for many years. However, it has not yet been extended to three-dimensional (3D) PCs because the fundamental solutions of 3D dynamics are complex and are related to angular frequency. In this study, the BEM is applied to calculate the band structures
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PolyWeight: A free and open-source program for determination of molecular weight distribution of linear polymers Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-07 Atilio Minotto Neto, Otávio Bianchi, Leonardo Bresciani Canto, Janete Eunice Zorzi, Cláudio Antônio Perottoni
This paper introduces PolyWeight, a Python software featuring a user-friendly graphical user interface (GUI), which offers two distinct approaches for MWD determination: an analytical relation-based method and a parametric model-based method. By utilizing dynamic moduli, users can calculate MWD as well as molecular weight averages such as , , and . The functionality of PolyWeight is validated using
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A class of arbitrarily high-order energy-preserving method for nonlinear Klein–Gordon–Schrödinger equations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-04 Xuelong Gu, Yuezheng Gong, Wenjun Cai, Yushun Wang
In this paper, we develop a class of arbitrarily high-order energy-preserving time integrators for the nonlinear Klein–Gordon–Schrödinger equations. We employ Fourier pseudo-spectral method for spatial discretization, resulting in a semi-discrete system. Subsequently, we employ the Petrov-Galerkin method in time to obtain a fully-discrete system. We rigorously demonstrate that the proposed scheme preserves
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An efficient solution of the multi-term multi-harmonic electron Boltzmann equation for use in global models Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-01 Joel E. Lynch, Travis R. Sippel, Shankar Subramaniam
Solving the electron Boltzmann equation is an essential but costly step in simulating low-temperature plasma kinetics. This work addresses the problem by introducing a solution of the general multi-term multi-harmonic Boltzmann equation (MTMH-BE) optimized for electrons in time-dependent non-equilibrium gases and electric fields. This is accomplished by configuring the numerical Jacobian as the product
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A High-Efficiency Adaptive TENO Scheme with optimal accuracy order for compressible flow simulation Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-01 Shujiang Tang
In this paper, we propose a new adaptive cut-off function and develop a fifth-order targeted ENO scheme that achieves optimal accuracy at any order of critical points, which performs excellently in conventional compressible gas dynamics. The cut-off value is crucial for controlling the dissipation in TENO schemes. Adjusting can improve shock capture and increase dissipation for small-scale features
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Verification of the Fourier-enhanced 3D finite element Poisson solver of the gyrokinetic full-f code PICLS Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-29 A. Stier, A. Bottino, M. Boesl, M. Campos Pinto, T. Hayward-Schneider, D. Coster, A. Bergmann, M. Murugappan, S. Brunner, L. Villard, F. Jenko
We introduce and derive the Fourier-enhanced 3D electrostatic field solver of the gyrokinetic full-f PIC code PICLS. The solver makes use of a Fourier representation in one periodic direction of the domain to make the solving of the system easily parallelizable and thus save run time. The presented solver is then verified using two different approaches of manufactured solutions. The test setup used
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Peridynamic modeling for multiscale heat transport of phonon Boltzmann transport equation Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-29 Weier Liu, Yangde Feng, Ruilin Li, Chenhan Bai, Beifang Niu
Phonons are the main carriers in semiconductor materials, and the Boltzmann transport equation (BTE) can describe the phonon heat transport well. Numerically solving the phonon BTE is a challenging task due to its high dimensionality and nonlinearity. In this work, we develop a Peridynamic model for steady-state phonon heat transport of phonon Boltzmann transport equation based on the Peridynamic differential
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The polarimeter vector for τ → 3πν decays Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-28 Vladimir Cherepanov, Christian Veelken
The polarimeter vector of the represents an optimal observable for the measurement of the spin. In this paper we present an algorithm for the computation of the polarimeter vector for the decay channels and . The algorithm is based on a model for the hadronic current in these decay channels, which was fitted to data recorded by the CLEO experiment . PolarimetricVectorTau2a1, version 1.0.1
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BIMBAMBUM: A potential flow solver for single cavitation bubble dynamics Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-28 Armand Baptiste Sieber, Henri Hugo Sieber, Davide Bernardo Preso, Mohamed Farhat
In the absence of analytical solutions for the dynamics of non-spherical cavitation bubbles, we have implemented a numerical simulation solver based on the boundary integral method (BIM) that models the behavior of a single bubble near an interface between two fluids. The density ratio between the two media can be adjusted to represent different types of boundaries, such as a rigid boundary or a free
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Comparison of effective and stable Langevin dynamics integrators Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-23 Bogdan Tanygin, Simone Melchionna
Langevin and Brownian simulations play a prominent role in computational research, and state of the art integration algorithms provide trajectories with different stability ranges and accuracy in reproducing statistical averages. The practical usability of integrators is an important aspect to allow choosing large time steps while ensuring numerical stability and overall computational efficiency. In
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ERCS24: An updated version of the ERCS08 program for calculations of the cross sections for atomic electron removal based on the ECPSSR theory and its variants Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-23 Vladimir Horvat
ERCS24, an updated version of the ERCS08 program, calculates the atomic lectron emoval ross ections. It is written in FORTRAN in order to make it more portable and easier to customize by a large community of physicists, but it also comes with a separate windows graphics user interface control application ERCS24w that makes it easy to quickly prepare the input file, run the program, as well as view
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Massively parallel implementation of iterative eigensolvers in large-scale plane-wave density functional theory Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-22 Junwei Feng, Lingyun Wan, Jielan Li, Shizhe Jiao, Xinhui Cui, Wei Hu, Jinlong Yang
The Kohn-sham density functional theory (DFT) is a powerful method to describe the electronic structures of molecules and solids in condensed matter physics, computational chemistry and materials science. However, large and accurate DFT calculations within plane waves process a cubic-scaling computational complexity, which is usually limited by expensive computation and communication costs. The rapid
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Quasi-optimal domain decomposition method for neural network-based computation of the time-dependent Schrödinger equation Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-21 Emmanuel Lorin, Xu Yang
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A binary filter inspired from the PIC sparse grid technique – Illustration on the XTOR-K code Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-21 T. Nicolas, V. Dubois, Q. Fang, H. Lütjens
It is known that the sparse grid method for Particle-In-Cell (PIC) solvers acts as a filter to reduce the PIC noise. In this paper, a simple rule to discard or keep modes in Fourier space (a binary filter with values either 0 or 1) is derived using the sparse grid combination formula. Its relation to the standard sparse grid filter, which is characterized quantitatively, is explained. The relations
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ePDFpy: A Python-based interactive GUI tool for electron pair distribution function analysis of amorphous materials Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-19 Minhyo Kim, Pilsung Kim, Riccardo Bassiri, Kiran Prasai, Martin M. Fejer, Kyung-ha Lee
ePDFpy is an interactive analysis program with a graphical user interface (GUI), designed to process the electron Pair Distribution Function (PDF) analysis of diffraction patterns from Transmission Electron Microscope (TEM), to identify the local atomic structure of amorphous materials. The program offers a user-friendly Python-based interface, providing a straightforward and adaptable workflow for
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Attosecond Chemistry Special Issue Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-16 Jimena D. Gorfinkiel, Fernando Martín
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Development of a tokamak magnetohydrodynamic code with the discontinuous Galerkin and Weighted Essentially Non-Oscillatory methods Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 J. Ma, W. Guo, Y. Xie
In this study, we present the development of a new initial-value magnetohydrodynamic (MHD) code for toroidal geometry using discontinuous Galerkin (DG) and Weighted Essentially Non-Oscillatory (WENO) methods. The code utilizes a triangular mesh based on the flux of the fixed boundary equilibrium in the poloidal plane, which is uniformly divided in the toroidal direction. By solving the conservative
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micrOMEGAs 6.0: N-component dark matter Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 G. Alguero, G. Bélanger, F. Boudjema, S. Chakraborti, A. Goudelis, S. Kraml, A. Mjallal, A. Pukhov
is a numerical code to compute dark matter (DM) observables in generic extensions of the Standard Model (SM) of particle physics. We present a new version of that includes a generalization of the Boltzmann equations governing the DM cosmic abundance evolution which can be solved to compute the relic density of N-component DM. The direct and indirect detection rates in such scenarios take into account
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ERSN-OpenMC-Py: A python-based open-source software for OpenMC Monte Carlo code Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 M. Lahdour, T. El Bardouni, O. El Hajjaji, J. EL Bakkali, J. Al-Zain, S. Oulad-Belayachi, H. Ziani, Abdelghani Idrissi, S. El Maliki El Hlaibi
The graphical user interface is a key element in facilitating the use of complex simulation software. This project describes the development of a graphical user interface called “ERSN-OpenMC-Py” for an existing neutron simulation code, OpenMC. The main goal is to make simulation more accessible to a wider audience by providing a user-friendly and intuitive user interface. The process of developing
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Trans-Net: A transferable pretrained neural networks based on temporal domain decomposition for solving partial differential equations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Dinglei Zhang, Ying Li, Shihui Ying
Physics-Informed Neural Networks (PINNs) has provided a novel direction for solving partial differential equations (PDEs) and has achieved significant advancements in the field of scientific computing. PINNs effectively incorporate the physical constraints of equations into the loss function, enabling neural networks to learn and approximate the behavior of physical systems by optimizing the loss function
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A well-balanced all-Mach scheme for compressible two-phase flow Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Sandro Malusà, Alessandro Alaia
We present an implicit-explicit finite volume scheme for the compressible two-phase model in all-Mach number regimes. In order to solve model equations efficiently and accurately in the low Mach regime, the convective term is split in a stiff part associated to fast acoustic waves, and a non-stiff part corresponding to mean flow advection. A Implicit-Explicit Runge-Kutta (IMEX-RK) method is used to
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Evaluation of classical correlation functions from 2/3D images on CPU and GPU architectures: Introducing CorrelationFunctions.jl Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Vasily Postnicov, Aleksei Samarin, Marina V. Karsanina, Mathieu Gravey, Aleksey Khlyupin, Kirill M. Gerke
Correlation functions are becoming one of the major tools for quantification of structural information that is usually represented as 2D or 3D images of porous material. In this paper we introduce ▪ open-source package developed in Julia and capable of computing all classical correlation functions based on imaging input data. Images include both binary and multi-phase representations. Our code is capable
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Handling shape optimization of superconducting cavities with DNMOGA Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Peilin Wang, Kuangkuang Ye, Xuerui Hao, Jike Wang
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PolyHoop: Soft particle and tissue dynamics with topological transitions Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Roman Vetter, Steve V.M. Runser, Dagmar Iber
We present PolyHoop, a lightweight standalone C++ implementation of a mechanical model to simulate the dynamics of soft particles and cellular tissues in two dimensions. With only few geometrical and physical parameters, PolyHoop is capable of simulating a wide range of particulate soft matter systems: from biological cells and tissues to vesicles, bubbles, foams, emulsions, and other amorphous materials
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A SPIRED code for the reconstruction of spin distribution Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-15 Simon Buchwald, Gabriele Ciaramella, Julien Salomon, Dominique Sugny
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Identification of self-interstitial atoms and vacancies in crystalline materials in atomistic simulation Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-14 Jun Wang, Tao Li, Ziwen Fu, Baoqin Fu, Chengjun Gou
As the most important intrinsic point defects, self-interstitial atoms and vacancies play crucial roles in governing the microstructural evolution in crystalline materials. In atomistic simulation, the self-interstitial atoms and vacancies are identified by various location methods, such as the Wigner-Seitz cell method. Here we reveal that the mobile defects will give rise to the random drift of the
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Linear-scale simulations of quench dynamics Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-13 Niaz Ali Khan, Wen Chen, Munsif Jan, Gao Xianlong
The accurate description and robust computational modeling of the nonequilibrium properties of quantum systems remain a challenge in condensed matter physics. In this work, we develop a linear-scale computational simulation technique for the non-equilibrium dynamics of quantum quench systems. In particular, we report a polynomial-expansion of the Loschmidt echo to describe the dynamical quantum phase
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Optimized parallelization of boundary integral Poisson-Boltzmann solvers Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-12 Xin Yang, Elyssa Sliheet, Reece Iriye, Daniel Reynolds, Weihua Geng
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By considering the advantages of current algorithms and computer hardware, we focus on the parallelization of the treecode-accelerated boundary integral (TABI) PB solver using
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Improved stellarator permanent magnet designs through combined discrete and continuous optimizations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-09 K.C. Hammond, A.A. Kaptanoglu
A common optimization problem in the areas of magnetized plasmas and fusion energy is the design of magnets to produce a given three-dimensional magnetic field distribution to high precision. When designing arrays of permanent magnets for stellarator plasma confinement, such problems have tens of thousands of degrees of freedom whose solutions, for practical reasons, should be constrained to discrete
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Quadrature of functions with endpoint singular and generalised polynomial behaviour in computational physics Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-09 Guido Lombardi, Davide Papapicco
Fast and accurate numerical integration always represented a bottleneck in high-performance computational physics, especially in large and multiscale industrial simulations involving Finite (FEM) and Boundary Element Methods (BEM). The computational demand escalates significantly in problems modelled by irregular or endpoint singular behaviours which can be approximated with generalised polynomials
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Developing performance portable plasma edge simulations: A survey Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-07 Steven A. Wright, Christopher P. Ridgers, Gihan R. Mudalige, Zaman Lantra, Josh Williams, Andrew Sunderland, H. Sue Thorne, Wayne Arter
Heterogeneous architectures are increasingly common in modern High-Performance Computing (HPC) systems. Achieving high-performance on such heterogeneous systems requires new approaches to application development that are able to achieve the three Ps: Performance, Portability, and Productivity.
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Gradient-enhanced stochastic optimization of high-fidelity simulations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-06 Alejandro Quirós Rodríguez, Miguel Fosas de Pando, Taraneh Sayadi
Optimization and control of complex unsteady flows remains an important challenge due to the large cost of performing a function evaluation, i.e. a full computational fluid dynamics (CFD) simulation. Reducing the number of required function evaluations would help to decrease the computational cost of the overall optimization procedure. In this article, we consider the stochastic derivative-free surrogate-model
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High-degree polynomial noise subtraction for disconnected loops Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-05 Paul Lashomb, Ronald B. Morgan, Travis Whyte, Walter Wilcox
In lattice QCD, the calculation of physical quantities from disconnected quark loop calculations have large variance due to the use of Monte Carlo methods for the estimation of the trace of the inverse lattice Dirac operator. In this work, we build upon our POLY and HFPOLY variance reduction methods by using high-degree polynomials. Previously, the GMRES polynomials used were only stable for low-degree
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A highly-efficient locally encoded boundary scheme for lattice Boltzmann method on GPU Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-05 Zehua Zhang, Cheng Peng, Chengxiang Li, Hua Zhang, Tao Xian, Lian-Ping Wang
The lattice Boltzmann method (LBM) is an algorithm to simulate fluid flows with the advantage of locality and simplicity, which is suitable for GPU acceleration and simulation of complex flows. However, LBM simulations involving complex solid boundaries require each boundary node to be aware of the types of all its neighbor nodes, i.e., fluid or solid, during the execution of boundary conditions, which
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TokaMaker: An open-source time-dependent Grad-Shafranov tool for the design and modeling of axisymmetric fusion devices Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-29 C. Hansen, I.G. Stewart, D. Burgess, M. Pharr, S. Guizzo, F. Logak, A.O. Nelson, C. Paz-Soldan
In this paper, we present a new static and time-dependent MagnetoHydroDynamic (MHD) equilibrium code, TokaMaker, for axisymmetric configurations of magnetized plasmas, based on the well-known Grad-Shafranov equation. This code utilizes finite element methods on an unstructured triangular grid to enable capturing accurate machine geometry and simple mesh generation from engineering-like descriptions
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Conservative discontinuous Galerkin interpolation: Sheared boundary conditions Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-29 Manaure Francisquez, Noah R. Mandell, Ammar Hakim, Gregory W. Hammett
Local studies of accretion disks and laboratory magnetized plasmas employ analytical coordinate mappings that introduce sheared boundary conditions (BCs). We present a discontinuous Galerkin (DG) algorithm to apply such BCs based on projections and quadrature-free integration. The procedure is high-order accurate, preserves moments exactly and works in multiple dimensions. Tests of increasing complexity
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UKRmol-scripts: A Perl-based system for the automated operation of the photoionization and electron/positron scattering suite UKRmol+ Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-02 Karel Houfek, Jakub Benda, Zdeněk Mašín, Alex Harvey, Thomas Meltzer, Vincent Graves, Jimena D. Gorfinkiel
UKRmol-scripts is a set of Perl scripts to automatically run the UKRmol+ codes, a complex software suite based on the R-matrix method to calculate fixed-nuclei photoionization and electron- and positron-scattering for polyatomic molecules. Starting with several basic parameters, the scripts operatively produce all necessary input files and run all codes for electronic structure and scattering calculations
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Adaptive moving window technique for SPH simulation of stationary shock waves Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-02 S.A. Murzov, S.A. Dyachkov, V.V. Zhakhovsky
A novel adaptive moving window (AMW) technique is developed for simulating stationary shock waves in a moving coordinate system associated with a simulation box. The velocity of this system is adjusted by an iterative feedback algorithm with the purpose of establishing a desirable position of shock front. Galilean transformations are iteratively used to maintain the shape of the flow profile. The moving
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A lubrication model with slope-dependent disjoining pressure for modeling wettability alteration Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-01 Mojtaba Norouzisadeh, Philippe Leroy, Cyprien Soulaine
We present the algorithm and the source code of our numerical model to characterize the wettability of a three-phase system. Wettability is imperative in describing two-phase flow in subsurface geo-environmental applications, including storage of carbon dioxide in deep saline aquifers and groundwater remediation. Although the concept of contact angle is widely used to characterize the affinity of a
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Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-01 Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Paweł Czarnul
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Two-dimensional helium-like atom in a homogeneous magnetic field: Numerically exact solutions Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-01 Duy-Nhat Ly, Duong D. Hoang-Trong, Ngoc-Hung Phan, Duy-Anh P. Nguyen, Van-Hoang Le
A two-dimensional helium atom (2D-helium) is a real subject for current studies, particularly regarding a hot topic of negatively charged excitons (trions) in semiconducting monolayers. The present study considers a 2D-helium-like atom in a homogeneous magnetic field. We are able to rewrite its Schrödinger equation into a polynomial form concerning dynamic variables. This form is useful for utilizing
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On the one-point quadrature discretization in peridynamics: A novel perspective from Monte Carlo integration Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-30 Hengjie Liu, Ziguang Chen
One-point quadrature discretization is one of the most popular discretizations for peridynamic simulation, but it suffers from poor accuracy. Employing smoothly decaying influence functions or precise volume correction can address this, but the former applies only to specific materials, and the latter may be computationally expensive and limited to square or cubic meshes. This paper discusses one-point
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New Orthogonality Relationships of the Gaunt Coefficients Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-30 S. Özay, S. Akdemir, E. Öztekin
A new analytical formula for the Gaunt coefficients is derived using expressions of Clebsch Gordan coefficients in terms of the generalized hypergeometric functions of unit argument and binomial coefficients. In addition, new sum expressions and orthogonality relations containing the Gaunt coefficients are written. These expressions are used to test the accuracy of the numerical calculation for the
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Variational Quantum Eigenvalue Solver Algorithm Utilizing Bridge-inspired Quantum Circuits and a Gradient Filter Module Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-30 Guojian Wu, Dejian Huang, Feng Shuang, Fang Gao
The complexity of theoretical simulation for drug molecule synthesis increases exponentially with the growth in system dimensions, posing a challenging task for precise solutions. Currently, the quantum algorithm capable of accurately simulating chemical molecule properties in the era of Noisy Intermediate-Scale Quantum (NISQ) devices is the Variational Quantum Eigensolver (VQE) algorithm. This paper
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RI−Calc: A user friendly software and web server for refractive index calculation Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-24 Leandro Benatto, Omar Mesquita, Lucimara S. Roman, Marlus Koehler, Rodrigo B. Capaz, Graziâni Candiotto
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Enabling particle transport on CAD-based geometries for radiation simulations with penRed Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-22 S. Oliver, S. Rodriguez Bosca, V. Giménez-Alventosa
Geometry construction is a fundamental aspect of any radiation transport simulation, regardless of the Monte Carlo code being used. Typically, this process is tedious, time-consuming, and error-prone. The conventional approach involves defining geometries using mathematical objects or surfaces. However, this method comes with several limitations, especially when dealing with complex models, particularly
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The QISG suite: High-performance codes for studying quantum Ising spin glasses Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-26 Massimo Bernaschi, Isidoro González-Adalid Pemartín, Víctor Martín-Mayor, Giorgio Parisi
We release a set of GPU programs for the study of the Quantum (S=1/2) Spin Glass on a square lattice, with binary couplings. The library contains two main codes: MCQSG (that carries out Monte Carlo simulations using both the Metropolis and the Parallel Tempering algorithms, for the problem formulated in the Trotter-Suzuki approximation), and EDQSG (that obtains the extremal eigenvalues of the Transfer
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openFuelCell2: A New Computational Tool for Fuel Cells, Electrolyzers, and Other Electrochemical Devices and Processes Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-19 Shidong Zhang, Steffen Hess, Holger Marschall, Uwe Reimer, Steven Beale, Werner Lehnert
Fuel cells/electrolyzers are efficient and clean electrochemical devices that convert chemical energy directly into electricity and vice versa. They have attracted sustainable attention over the past decade from multiple experimental and numerical studies. However, detailed experimental investigations are typically expensive and challenging for providing a number of operating conditions and designs
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Update of HΦ: Newly added functions and methods in versions 2 and 3 Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-19 Kota Ido, Mitsuaki Kawamura, Yuichi Motoyama, Kazuyoshi Yoshimi, Youhei Yamaji, Synge Todo, Naoki Kawashima, Takahiro Misawa
HΦ [aitch-phi] is an open-source software package of numerically exact and stochastic calculations for a wide range of quantum many-body systems. In this paper, we present the newly added functions and the implemented methods in vers. 2 and 3. In ver. 2, we implement spectrum calculations by the shifted Krylov method, and low-energy excited state calculations by the locally optimal block preconditioned
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Multilevel Monte Carlo methods for the Grad-Shafranov free boundary problem Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-19 Howard C. Elman, Jiaxing Liang, Tonatiuh Sánchez-Vizuet
The equilibrium configuration of a plasma in an axially symmetric reactor is described mathematically by a free boundary problem associated with the celebrated Grad-Shafranov equation. The presence of uncertainty in the model parameters introduces the need to quantify the variability in the predictions. This is often done by computing a large number of model solutions on a computational grid for an
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NekMesh: An open-source high-order mesh generation framework Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-19 M.D. Green, K.S. Kirilov, M. Turner, J. Marcon, J. Eichstädt, E. Laughton, C.D. Cantwell, S.J. Sherwin, J. Peiró, D. Moxey
High-order spectral element simulations are now becoming increasingly popular within the computational modelling community, as they offer the potential to deliver increased accuracy at reduced cost compared to traditional low-order codes. However, to support accurate, high-fidelity simulations in complex industrial applications, there is a need to generate curvilinear meshes which robustly and accurately
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Training normalizing flows with computationally intensive target probability distributions Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-18 Piotr Białas, Piotr Korcyl, Tomasz Stebel
Machine learning techniques, in particular the so-called normalizing flows, are becoming increasingly popular in the context of Monte Carlo simulations as they can effectively approximate target probability distributions. In the case of lattice field theories (LFT) the target distribution is given by the exponential of the action. The common loss function's gradient estimator based on the “reparametrization
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Analytic pulse technique for computational electromagnetics Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-18 K. Weichman, K.G. Miller, B. Malaca, W.B. Mori, J.R. Pierce, D. Ramsey, J. Vieira, M. Vranic, J.P. Palastro
Numerical modeling of electromagnetic waves is an important tool for understanding the interaction of light and matter, and lies at the core of computational electromagnetics. Traditional approaches to injecting and evolving electromagnetic waves, however, can be prohibitively expensive and complex for emerging problems of interest and can restrict the comparisons that can be made between simulation
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Tau lepton identification and reconstruction: A new frontier for jet-tagging ML algorithms Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-18 Torben Lange, Saswati Nandan, Joosep Pata, Laurits Tani, Christian Veelken
Identifying and reconstructing hadronic τ decays (τh) is an important task at current and future high-energy physics experiments, as τh represent an important tool to analyze the production of Higgs and electroweak bosons as well as to search for physics beyond the Standard Model. The identification of τh can be viewed as a generalization and extension of jet-flavour tagging, which has in the recent
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A GPU accelerated three-dimensional ghost cell method with an improved implicit surface representation for complex rigid or flexible boundary flows Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-01-17 Fulong Shi, Jianjian Xin, Pandeng Yin, Yehong Dong
This paper presents an efficient and reliable three-dimensional (3D) ghost cell method for complex rigid or flexible boundary flows. An improved implicit interface representation method is developed to treat the arbitrary complex interfaces including the thin or sharp boundaries. This method is robust and avoids the solving of a large dense matrix, and thus the computational efficiency is greatly enhanced