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A custom detector construction pattern for Geant4 applications Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-25 Mustafa Kandemir
Geant4 Detector Construction Pattern (G4DCP) is a template developed to flexibly construct complex detectors in Geant4 applications. The elements of G4DCP, including , form an elegant template for detector setups. We construct a sample detector geometry utilizing this template and make the developed code available to the public. G4DCP
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Stokes-Einstein relation for binary mixtures Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-24 Yang Liu, Dietmar Block
The applicability of the Stokes-Einstein (SE) relation in two-dimensional finite binary mixtures is tested using the Langevin simulation method. Calculations of viscosity and self-diffusion coefficients are compared between monodisperse and binary systems. It is shown that adapted definitions of coupling strength Γ and screening parameter allow to describe the transport properties for both monodisperse
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Local discontinuous Galerkin for the functional renormalisation group Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-24 Friederike Ihssen, Jan M. Pawlowski, Franz R. Sattler, Nicolas Wink
We apply a Local Discontinuous Galerkin discretisation to flow equations of the O(N)-model in the Local Potential Approximation. The improved stability is directly observed by solving the flow equation for various and space-time dimensions . A particular focus of this work is the numerical discretisation and its implementation. It is realised as a module within the high performance PDE framework DUNE
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Arbitrary controlled re-orientation of a spinning body by evolving its tensor of inertia Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-21 Igor A. Ostanin, Matthias Sperl
Bodies with the nonspherical tensor of inertia (TOI) exhibit a variety of rotational motion patterns, including chaotic motion, stable periodic (quasi-periodic) rotation, unstable rotation around the direction close to the body's second principal axis, featuring a well-known tennis-racket (also known as Garriott-Dzhanibekov ) effect – series of seemingly spontaneous 180 degrees flips. These patterns
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mqdtfit: A collection of Python functions for empirical multichannel quantum defect calculations Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-20 R.M. Potvliege
The Python functions distributed with this article can be used for calculating the parameters of multichannel quantum defect theory models describing excited bound states of complex atoms. These parameters are obtained by fitting a model to experimental data provided by the user. The two main formulations of the theory are supported, namely the one in which the parameters of the model are a set of
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FiniteFieldSolve: Exactly solving large linear systems in high-energy theory Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-20 James Mangan
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Simulating CDT quantum gravity Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-19 Joren Brunekreef, Renate Loll, Andrzej Görlich
We provide a hands-on introduction to Monte Carlo simulations in nonperturbative lattice quantum gravity, formulated in terms of Causal Dynamical Triangulations (CDT). We describe explicitly the implementation of Monte Carlo moves and the associated detailed-balance equations in two and three spacetime dimensions. We discuss how to optimize data storage and retrieval, which are nontrivial due to the
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Supervised training of neural-network quantum states for the next-nearest neighbor Ising model Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-19 Zheyu Wu, Remmy Zen, Heitor P. Casagrande, Dario Poletti, Stéphane Bressan
Different neural network architectures can be unsupervisedly or supervisedly trained to represent quantum states. We explore and compare different strategies for the supervised training of feed forward neural network quantum states. We empirically and comparatively evaluate the performance of feed forward neural network quantum states in different phases of matter for variants of the architecture,
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An improved methodology for modeling short pulse buried layer x-ray emission spectra Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-15 D.T. Cliche, M.E. Martin, R.A. London, H.A. Scott, M.V. Patel
Radiation-hydrodynamic and spectroscopic modeling are important aspects of high energy density experimental design. In this paper, we improve the performance and capabilities over those obtainable with a previous methodology used for simulating x-ray emission spectra from buried layer targets heated by short pulse lasers. The improvement incorporates post-processing HYDRA radiation-hydrodynamic output
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On polytope intersection by half-spaces and hyperplanes for unsplit geometric volume of fluid methods on arbitrary grids Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-13 Joaquín López, Julio Hernández
Several tools with improved accuracy and computational efficiency, along with added capabilities, are presented for performing analytic and geometric operations involving intersections between half-spaces or hyperplanes and 2- or 3-polytopes (polygons or polyhedra, either convex or non-convex) that typically arise in advanced volume of fluid (VOF) methods on arbitrary grids. In particular, tools for
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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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ElasTool v3.0: Efficient computational and visualization toolkit for elastic and mechanical properties of materials Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-03-07 C.E. Ekuma, Z.-L. Liu
Efficient computation and visualization of elastic and mechanical properties are crucial in the selection of materials and the design of new materials. The toolkit marks a significant advancement in the computational analysis and visualization of elastic and mechanical properties of materials, essential in material selection and design. This enhanced version extends beyond standard calculations like
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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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Neutrinos from muon-rich ultra high energy electromagnetic cascades: The MUNHECA code Comput. Phys. Commun. (IF 6.3) Pub Date : 2024-02-29 AmirFarzan Esmaeili, Arman Esmaili, Pasquale Dario Serpico
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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 → 3πντ 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
In this paper, we derive and analyze the performance of optimal/quasi-optimal Schwarz Waveform Relaxation (SWR) domain decomposition methods (DDM) for the time-dependent Schrödinger equation when implement with neural network-based Partial Differential Equations (PDE) solvers. Optimal SWR methods, which are based on Dirichlet-to-Neumann operators, are known to have a higher convergence rate than classical
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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. 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 of evaluating
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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
Radiofrequency (RF) cavities hold immense importance in various accelerator applications, but their optimization poses significant challenges due to complex situations involved. In this study, a recently proposed multi-objective optimization algorithm is utilized to optimize the 325 MHz double spoke cavity, which is characterized by 38 geometric parameters and is one of the most complex cavities commonly
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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