Computer Physics Communications最新文献_第10页

Unsupervised neural-network solvers for multi-material Riemann problems

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-19 DOI: 10.1016/j.cpc.2024.109470

Liang Xu , Ziyan Liu , Yiwei Feng , Tiegang Liu

Machine learning has the potential to provide a non-traditional and feasible approach for solving Riemann problems to model the coupling effects of multi-material flows. However, most recent research on predicting Riemann solutions with neural networks is limited to addressing single-material flows and featured as the supervised learning, or is limited to solving specific problems and difficult to apply to a wide range of initial conditions. In this work, we explore physics-constrained neural networks, termed PCNN-RS, as multi-material Riemann solvers without any labeled data. Based on the frame of a general neural network, physics-constrained functions that conform to the shock/rarefaction relationships between initial states and interfacial states are constructed after the output layer, transforming the unlabeled output into a theoretically zero-valued functional form. This allows training learning models with standard loss functions solely using input data. The interfacial pressure of multi-material Riemann problem is predicted using the surrogate model, and other interfacial states can be directly derived through simple calculations. In addition, the basic principle of scaling of initial conditions and Riemann solutions with general equations of state is established theoretically. Based on this property, a transformation of input and output data is proposed to enhance the wide applicability of the Riemann-solver surrogate model. Furthermore, an optimization of samples is presented to reduce the training dataset and shorten the training time. The PCNN-RS is able to make accurate predictions, even when utilizing a compact neural network architecture with fewer neurons, and it is easily applied to the ghost-fluid-based sharp interface methods. It possesses the ability to simulate various interface evolutions for the interaction between two materials.

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引用次数: 0

An unstructured geometrical un-split VOF method for viscoelastic two-phase flows

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-19 DOI: 10.1016/j.cpc.2024.109475

Matthias Niethammer, Muhammad Hassan Asghar, Dieter Bothe, Tomislav Maric

Since viscoelastic two-phase flows arise in various industrial and natural processes, developing accurate and efficient software for their detailed numerical simulation is a highly relevant and challenging research task. We present a geometrical unstructured Volume-of-Fluid (VOF) method for handling two-phase flows with viscoelastic liquid phase, where the latter is modeled via generic rate-type constitutive equations and a one-field description is derived by conditional volume averaging of the local instantaneous bulk equations and interface jump conditions. The method builds on the plicRDF-isoAdvector geometrical VOF solver that is extended and combined with the modular framework DeboRheo for viscoelastic computational fluid dynamics (CFD). A piecewise-linear geometrical interface reconstruction technique on general unstructured meshes is employed for discretizing the viscoelastic stresses across the fluid interface. DeboRheo facilitates a flexible combination of different rheological models with appropriate stabilization methods to address the high Weissenberg number problem.

Program summary

Program Title: DeboRheo

CPC Library link to program files: https://doi.org/10.17632/gsgdrjm2md.1

Developer's repository link: https://gitlab.com/deborheo/deborheorelease/

Licensing provisions: GPLv3

Programming language: C++

Nature of problem: DNS of viscoelastic two-phase flows encounters major challenges due to abrupt changes of physical properties and rheological behaviors of the two phases at the fluid interface, and viscoelastic flows characterized with high Weissenberg numbers introduce additional numerical challenges.

Solution method: A geometrical unstructured Volume-of-Fluid (VOF) method for handling two-phase flows with a viscoelastic liquid phase, where the latter is modeled by generic rate-type constitutive equations. Appropriate stabilization techniques are included to address the High Weissenberg Number Problem (HWNP).

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引用次数: 0

Fast Brownian cluster dynamics

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-18 DOI: 10.1016/j.cpc.2024.109474

Alexander P. Antonov , Sören Schweers , Artem Ryabov , Philipp Maass

We present an efficient method to perform overdamped Brownian dynamics simulations in external force fields and for particle interactions that include a hardcore part. The method applies to particle motion in one dimension, where it is possible to update particle positions by repositioning particle clusters as a whole. These clusters consist of several particles in contact. They form because particle collisions are treated as completely inelastic rather than elastic ones. Updating of cluster positions in time steps is carried out by cluster fragmentation and merging procedures. The presented method is particularly powerful at high collision rates in densely crowded systems, where collective movements of particle assemblies is governing the dynamics. As an application, we simulate the single-file diffusion of sticky hard spheres in a periodic potential.

引用次数: 0

Data unfolding with mean integrated square error optimization

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-17 DOI: 10.1016/j.cpc.2024.109473

Nikolay D. Gagunashvili

Experimental data in Particle and Nuclear physics, Particle Astrophysics and Radiation Protection Dosimetry are obtained from experimental facilities comprising a complex array of sensors, electronics and software. Computer simulation is used to study the measurement process. Probability Density Functions (PDFs) of measured physical parameters deviate from true PDFs due to resolution, bias, and efficiency effects. Good estimates of the true PDF are necessary for testing theoretical models, comparing results from different experiments, and combining results from various research endeavors.

In the article, the histogram method is employed to estimate both the measured and true PDFs. The binning of histograms is determined using the K-means clustering algorithm. The true PDF is estimated through the maximization of the likelihood function with entropy regularization, utilizing a non-linear optimization algorithm specially designed for this purpose. The accuracy of the results is assessed using the Mean Integrated Square Error.

To determine the optimal value for the regularization parameter, a bootstrap method is applied. Additionally, a mathematical model of the measurement system is formulated using system identification methods. This approach enhances the robustness and precision of the estimation process, providing a more reliable analysis of the system's characteristics.

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引用次数: 0

ViTAE-SL: A vision transformer-based autoencoder and spatial interpolation learner for field reconstruction

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-16 DOI: 10.1016/j.cpc.2024.109464

Hongwei Fan , Sibo Cheng , Audrey J. de Nazelle , Rossella Arcucci

Reliable and accurate reconstruction for large-scale and complex physical fields in real-time from limited observations has been a longstanding challenge. In recent years, sensors have been increasingly deployed in numerous physical systems. However, the locations of these sensors can shift over time, such as with mobile sensors, or when sensors are deployed and removed. These sparse and randomly located sensors further exacerbate the difficulty of reconstructing the physical field. In this paper, we present a new deep learning model called Vision Transformer-based Autoencoder (ViTAE) for reconstructing large-scale and complex fields. The proposed network structure is based on a novel core design: vision transformer encoder and Convolutional Neural Network (CNN) decoder. First, we split a two-dimensional field into patches and developed a vision transformer encoder to transfer patches into latent representations. We then reshape the linear latent representations to patches before concatenation, along with a CNN decoder, to reconstruct the field. The proposed model is tested in four different numerical experiments, using generated synthetic data, spatially distributed PM2.5 data, Computational Fluid Dynamics (CFD) simulation data and National Oceanic and Atmospheric Administration (NOAA) sea surface temperature data. The numerical results highlight the strength of ViTAE-SL compared to Kriging and state-of-the-art deep-learning models with significantly higher reconstruction accuracy, computational efficiency, and robust scaling behavior.

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引用次数: 0

ADAQ-SYM: Automated symmetry analysis of defect orbitals

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-16 DOI: 10.1016/j.cpc.2024.109468

William Stenlund , Joel Davidsson , Rickard Armiento , Viktor Ivády , Igor A. Abrikosov

Quantum technologies like single photon emitters and qubits can be enabled by point defects in semiconductors, with the NV-center in diamond being the most prominent example. There are many different semiconductors, each potentially hosting interesting defects. The symmetry properties of the point defect orbitals can yield useful information about the behavior of the system, such as the interaction with polarized light. We have developed a tool to perform symmetry analysis of point defect orbitals obtained by plane-wave density functional theory simulations. The software tool, named ADAQ-SYM, calculates the characters for each orbital, finds the irreducible representations, and uses selection rules to find which optical transitions are allowed. The capabilities of ADAQ-SYM are demonstrated on several defects in diamond and 4H-SiC. The symmetry analysis explains the different zero phonon line (ZPL) polarization of the hk and kh divacancies in 4H-SiC.

Program summary

Program Title: ADAQ-SYM

CPC Library link to program files: https://doi.org/10.17632/th5362mzxt.1

Developer's repository link: https://github.com/WSten/ADAQ-SYM

Licensing provisions: GNU Affero General Public License Version 3

Programming language: Python 3

Nature of problem: Point defects in semiconductors can have localized orbitals in the band gap, these can be simulated with density functional theory (DFT). Automatically finding the symmetry properties (character and irreducible representation) of these orbitals would reduce manual work, and make the inclusion of symmetry properties in high-throughput screenings possible.

Solution method: ADAQ-SYM addresses this problem by calculating symmetry operator expectation values of orbitals computed with DFT, and translating these to characters and irreducible representation. The code also finds the symmetry allowed optical transitions.

Additional comments including restrictions and unusual features: Currently the code only works for DFT simulations at the Γ-point.

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引用次数: 0

Efficient multi-GPU implementation of a moving boundary approach in rotor flow simulation using LBM and level-set method

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-14 DOI: 10.1016/j.cpc.2024.109469

Xiangcheng Sun, Xian Wang

Moving boundary recognition exists widely in the numerical simulation of motion problems in fluid mechanics engineering. Particularly, in rotating machinery flows simulations, a method for handling moving boundaries with high-resolution grids, high computational performance, and efficient implementation on high-performance computing systems is crucial. Based on an in-house lattice Boltzmann method (LBM) solver, this study has developed a moving boundary approach suitable for simulating three-dimensional rotating flows. This method couples a multi-block grid method for local grid refinement and utilizes the level-set method for accurately capturing moving solid boundaries. Moreover, the implementation has been successfully carried out on a desktop-level multi-graphics processing unit (GPU) parallel system. The results show that adjusting the number of GPUs enables flexible scaling of the computational domain size, making this method particularly well-suited for large computational domains in rotating flow problems. Furthermore, the detailed evaluation of parallel GPU performance reveals that the computational performance with nine GPUs in parallel at maximum grid size is 2.33 times greater than that with three GPUs in parallel. Additionally, when the grid size per GPU varies, both kernel functions time and communication time significantly impact performance. The optimized data transfer strategy helps to minimize interpolation overhead and avoid additional communication overhead associated with multi-block grid refinement. The test results show a maximum MLUPS performance of 3074.85 with three V100 GPUs in parallel. Finally, the simulations of flow over three rotor configurations indicate that the proposed implementation accurately identifies rotating motion boundaries and can be applied in real-world rotor flow simulations.

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引用次数: 0

MADWAVE3: A quantum time dependent wave packet code for nonadiabatic state-to-state reaction dynamics of triatomic systems

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-13 DOI: 10.1016/j.cpc.2024.109471

Octavio Roncero , Pablo del Mazo-Sevillano

We present MADWAVE3, a FORTRAN90 code designed for quantum time-dependent wave packet propagation in triatomic systems. This program allows the calculation of state-to-state probabilities for inelastic and reactive collisions, as well as photodissociation processes, over one or multiple coupled diabatic electronic states. The code is highly parallelized using MPI and OpenMP. The execution requires the potential energy surfaces of the different electronic states involved, as well as the transition dipole moments for photodissociation processes. The formalism underlying the code is presented in section 2, together with the modular structure of the code. This is followed by the installation procedures and a comprehensive list and explanation of the parameters that control the code, organized within their respective namelists.

Finally, a case study is presented, focusing on the prototypical reactive collision H+DH(

v, j

)→ H₂(

v^{'}, j^{'}

) + D. Both the potential energy surface and the input files required to reproduce the calculation are provided and are available on the repository's main page. This example is used to study the parallelization speedup of the code.

Program summary

Program Title: MADWAVE3

CPC Library link to program files: https://doi.org/10.17632/jv4wj2w23x.1

Developer's repository link: https://github.com/qmolastro/madwave3

Licensing provisions: GPLv3

Programming language: Fortran 90

External libraries: FFTW3, MPI

Nature of problem: Quantum time propagation of a wave packet describing a reactive process in a triatomic systems, for collisions (inelastic and reactive) and photodissociation processes, and considering several coupled diabatic electronic state

Solution method: A modified Chebyshev propagator is used, keeping the real Chebyshev components, which are represented in grids for the internal Jacobi coordinates

r, R

and γ and in a basis for electronic and helicity components. The potential represented in a grid as well as the reactants and products wave functions are previously calculated in a preparatory stage.

{"title":"MADWAVE3: A quantum time dependent wave packet code for nonadiabatic state-to-state reaction dynamics of triatomic systems","authors":"Octavio Roncero , Pablo del Mazo-Sevillano","doi":"10.1016/j.cpc.2024.109471","DOIUrl":"10.1016/j.cpc.2024.109471","url":null,"abstract":"<div><div>We present MADWAVE3, a FORTRAN90 code designed for quantum time-dependent wave packet propagation in triatomic systems. This program allows the calculation of state-to-state probabilities for inelastic and reactive collisions, as well as photodissociation processes, over one or multiple coupled diabatic electronic states. The code is highly parallelized using MPI and OpenMP. The execution requires the potential energy surfaces of the different electronic states involved, as well as the transition dipole moments for photodissociation processes. The formalism underlying the code is presented in section <span><span>2</span></span>, together with the modular structure of the code. This is followed by the installation procedures and a comprehensive list and explanation of the parameters that control the code, organized within their respective namelists.</div><div>Finally, a case study is presented, focusing on the prototypical reactive collision H+DH(<span><math><mi>v</mi><mo>,</mo><mi>j</mi></math></span>)→ H<sub>2</sub>(<span><math><msup><mrow><mi>v</mi></mrow><mrow><mo>′</mo></mrow></msup><mo>,</mo><msup><mrow><mi>j</mi></mrow><mrow><mo>′</mo></mrow></msup></math></span>) + D. Both the potential energy surface and the input files required to reproduce the calculation are provided and are available on the repository's main page. This example is used to study the parallelization speedup of the code.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> MADWAVE3</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/jv4wj2w23x.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/qmolastro/madwave3</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GPLv3</div><div><em>Programming language:</em> Fortran 90</div><div><em>External libraries:</em> FFTW3, MPI</div><div><em>Nature of problem:</em> Quantum time propagation of a wave packet describing a reactive process in a triatomic systems, for collisions (inelastic and reactive) and photodissociation processes, and considering several coupled diabatic electronic state</div><div><em>Solution method:</em> A modified Chebyshev propagator is used, keeping the real Chebyshev components, which are represented in grids for the internal Jacobi coordinates <span><math><mi>r</mi><mo>,</mo><mi>R</mi></math></span> and <em>γ</em> and in a basis for electronic and helicity components. The potential represented in a grid as well as the reactants and products wave functions are previously calculated in a preparatory stage.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109471"},"PeriodicalIF":7.2,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An OpenFOAM solver incorporating detailed transport model for reacting flow simulations

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-13 DOI: 10.1016/j.cpc.2024.109472

Fei Wang, Liang An, Tat Leung Chan

<div><div>OpenFOAM (Open-source Field Operation and Manipulation) has become an important scientific tool for solving computational fluid dynamics due to its free and open-source nature, but its application in reacting flows may be restricted due to either the use of a simplified transport model or the requirement for pre-specified species (binary) mass diffusion coefficients as well as the use of Sutherland's formula. To fill this gap, a detailed transport model using a mixture-averaged formulation based on the standard kinetic theory of gases is newly incorporated into combustion solvers for dealing with reacting flow simulations in OpenFOAM. This is achieved by developing a new utility to input molecular transport parameters and a new library to calculate transport properties. All the codes are completely written under the code framework of OpenFOAM, making them very easy to read, use, maintain, enhance and extend. The developed utility and library are then coupled with a new reacting flow solver developed for the governing equations in terms of mass, momentum, species and energy by configurating an interface. In the present study, the function of the new utility is firstly examined and then a new solver (i.e., <em>standardReactingFoam</em>) is developed for solving reacting flows. A systematical validation and assessment in different flame configurations with detailed chemical kinetics is studied to evaluate the computational performance of these new solvers. A zero-dimensional auto ignition, one-dimensional premixed flame and two-dimensional non-premixed counterflow flame are selected to validate the solvers against Cantera and CHEMKIN, while a realistic combustion simulation of a two-dimensional partially premixed coflow flame is also verified. Numerical simulation results show that very good agreements with the benchmark data are obtained for all studied flames, which demonstrates the high computational accuracy of the developed combustion solvers incorporating a detailed transport model.</div></div><div><h3>Program summary</h3><div><em>Program title:</em> standardReactingFoam.</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/rbm3cjk8rr.1</span><svg><path></path></svg></span>.</div><div><em>Licensing provisions:</em> GPLv3.</div><div><em>Programming language:</em> C++.</div><div><em>Nature of problem:</em> The performance of OpenFOAM solvers for reacting flow simulations is greatly limited by a simplified transport model or the requirement for pre-specified species (binary) mass diffusion coefficients as well as the use of Sutherland's formula, leading to incorrect numerical calculation of the critical transport properties. Developing an interface between OpenFOAM and Cantera can achieve the evaluation of transport properties, which makes it difficult to be widely used and conveniently maintained. Developing a separate package to obtain transport properties results in a very complicated operation w

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引用次数: 0

Corrigendum to “The FLUKA Monte Carlo simulation of the magnetic spectrometer of the FOOT experiment” [Computer physics communications, Volume 307, (2025) 109398]

IF 7.2 2区物理与天体物理 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer Physics Communications

Pub Date : 2024-12-10 DOI: 10.1016/j.cpc.2024.109466

Y. Dong , S.M. Valle , G. Battistoni , I. Mattei , C. Finck , V. Patera , A. Alexandrov , B. Alpat , G. Ambrosi , S. Argiro , M. Barbanera , N. Bartosik , M.G. Bisogni , V. Boccia , F. Cavanna , P. Cerello , E. Ciarrocchi , A. De Gregorio , G. De Lellis , A. Di Crescenzo , S. Muraro

引用次数: 0