Pub Date : 2024-12-17DOI: 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.
{"title":"Data unfolding with mean integrated square error optimization","authors":"Nikolay D. Gagunashvili","doi":"10.1016/j.cpc.2024.109473","DOIUrl":"10.1016/j.cpc.2024.109473","url":null,"abstract":"<div><div>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.</div><div>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.</div><div>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.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109473"},"PeriodicalIF":7.2,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-16DOI: 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.
{"title":"ViTAE-SL: A vision transformer-based autoencoder and spatial interpolation learner for field reconstruction","authors":"Hongwei Fan , Sibo Cheng , Audrey J. de Nazelle , Rossella Arcucci","doi":"10.1016/j.cpc.2024.109464","DOIUrl":"10.1016/j.cpc.2024.109464","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109464"},"PeriodicalIF":7.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-16DOI: 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
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.
{"title":"ADAQ-SYM: Automated symmetry analysis of defect orbitals","authors":"William Stenlund , Joel Davidsson , Rickard Armiento , Viktor Ivády , Igor A. Abrikosov","doi":"10.1016/j.cpc.2024.109468","DOIUrl":"10.1016/j.cpc.2024.109468","url":null,"abstract":"<div><div>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.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> ADAQ-SYM</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/th5362mzxt.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/WSten/ADAQ-SYM</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GNU Affero General Public License Version 3</div><div><em>Programming language:</em> Python 3</div><div><em>Nature of problem:</em> 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.</div><div><em>Solution method:</em> 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.</div><div><em>Additional comments including restrictions and unusual features:</em> Currently the code only works for DFT simulations at the Γ-point.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109468"},"PeriodicalIF":7.2,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162806","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}
Pub Date : 2024-12-14DOI: 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.
{"title":"Efficient multi-GPU implementation of a moving boundary approach in rotor flow simulation using LBM and level-set method","authors":"Xiangcheng Sun, Xian Wang","doi":"10.1016/j.cpc.2024.109469","DOIUrl":"10.1016/j.cpc.2024.109469","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109469"},"PeriodicalIF":7.2,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-13DOI: 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()→ H2() + 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
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 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}
Pub Date : 2024-12-13DOI: 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
{"title":"An OpenFOAM solver incorporating detailed transport model for reacting flow simulations","authors":"Fei Wang, Liang An, Tat Leung Chan","doi":"10.1016/j.cpc.2024.109472","DOIUrl":"10.1016/j.cpc.2024.109472","url":null,"abstract":"<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","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"309 ","pages":"Article 109472"},"PeriodicalIF":7.2,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143127919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-10DOI: 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
{"title":"Corrigendum to “The FLUKA Monte Carlo simulation of the magnetic spectrometer of the FOOT experiment” [Computer physics communications, Volume 307, (2025) 109398]","authors":"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","doi":"10.1016/j.cpc.2024.109466","DOIUrl":"10.1016/j.cpc.2024.109466","url":null,"abstract":"","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109466"},"PeriodicalIF":7.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-09DOI: 10.1016/j.cpc.2024.109467
Andrzej Daniluk, Bartłomiej Daniluk, Grzegorz M. Wójcik
We present a Python-based implementation of a practical procedure of construction of simulation program, which facilitates the calculation of changes to the intensity of RHEED oscillations in the function of the glancing angle of incidence of the electron beam, employing various models of crystal potential for heteroepitaxial structures including the possible existence of various diffuse scattering models through the layer parallel to the surface. The calculations are based on the use of a one-dimensional dynamical diffraction theory. Although this theory has some limitations, in practice it is useful under so-called one-beam condition. Computation performance has been improved by using Numba as an open source, NumPy-aware optimising compiler for Python.
Program Summary
Program Title: PY_RHEED_DIFF
CPC Library link to program files:https://doi.org/10.17632/j6jxt9yr3b.1
Licensing provisions: GNU General Public License 3
Does the new version supersede the previous version?: Yes.
Reasons for the new version: Python, as a powerful, accessible and general-purpose programming language, has gained tremendous popularity in recent years. Python is characterised by a remarkable simplicity that makes it an ideal choice for users for whom knowledge of high-level programming techniques is not the most important in research work. According to users’ suggestions we have developed a Python-based implementation of generic computational model for simulations of changes to the intensity of RHEED oscillations in the function of the glancing angle of incidence of the electron beam, employing various models of crystal potential for heteroepitaxial structures including the possible existence of various diffuse scattering models through the layer parallel to the surface. This version implements improvements for ergonomics, computational performances, readability, and code functionality by adding new capabilities which make the output data generation and visualisation process much more efficient compared to the previous version.
{"title":"A Python code for simulations of RHEED intensity oscillations within the one-dimensional dynamical approximation","authors":"Andrzej Daniluk, Bartłomiej Daniluk, Grzegorz M. Wójcik","doi":"10.1016/j.cpc.2024.109467","DOIUrl":"10.1016/j.cpc.2024.109467","url":null,"abstract":"<div><div>We present a Python-based implementation of a practical procedure of construction of simulation program, which facilitates the calculation of changes to the intensity of RHEED oscillations in the function of the glancing angle of incidence of the electron beam, employing various models of crystal potential for heteroepitaxial structures including the possible existence of various diffuse scattering models through the layer parallel to the surface. The calculations are based on the use of a one-dimensional dynamical diffraction theory. Although this theory has some limitations, in practice it is useful under so-called one-beam condition. Computation performance has been improved by using <em>Numba</em> as an open source, <em>NumPy</em>-aware optimising compiler for Python.</div></div><div><h3>Program Summary</h3><div><em>Program Title:</em> PY_RHEED_DIFF</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/j6jxt9yr3b.1</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GNU General Public License 3</div><div><em>Programming language:</em> Python 3.12.7</div><div><em>Journal reference of previous version:</em> Computer Physics Communications 185 (2014) 3001–3009</div><div><em>Does the new version supersede the previous version?:</em> Yes.</div><div><em>Reasons for the new version:</em> Python, as a powerful, accessible and general-purpose programming language, has gained tremendous popularity in recent years. Python is characterised by a remarkable simplicity that makes it an ideal choice for users for whom knowledge of high-level programming techniques is not the most important in research work. According to users’ suggestions we have developed a Python-based implementation of generic computational model for simulations of changes to the intensity of RHEED oscillations in the function of the glancing angle of incidence of the electron beam, employing various models of crystal potential for heteroepitaxial structures including the possible existence of various diffuse scattering models through the layer parallel to the surface. This version implements improvements for ergonomics, computational performances, readability, and code functionality by adding new capabilities which make the output data generation and visualisation process much more efficient compared to the previous version.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109467"},"PeriodicalIF":7.2,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143162807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-07DOI: 10.1016/j.cpc.2024.109465
Tao Sun , Jianmei Yuan
High-throughput screening or generative models rapidly identify crystal structures with the desired properties, but the synthesizable ratio is generally low. Experimentally verifying the synthesizability of individual virtual crystals would entail significant time and resources. Therefore, a method for automatically assessing the synthesizability of virtual crystals is urgently needed. This paper describes an approach that combines contrastive learning and positive unlabeled learning. The resulting contrastive positive unlabeled learning (CPUL) model predicts the crystal-likeness score (CLscore) of virtual materials. The model achieves a true positive (CLscore > 0.5) prediction accuracy of 93.95% on a test set containing 10,000 materials taken from the Materials Project (MP) database. We further validate the model by using all Fe-containing materials from the MP database as the test set, obtaining a true positive rate of 88.89%. This indicates that the CPUL model performs well, even with limited knowledge of the interactions between Fe and the atoms in the crystals. The CPUL model is then used to assess the CLscore of virtual crystals in the MP database and analyze their synthesizability by combining the energy above the hull. Finally, the synthesizability of perovskite materials is predicted using the proposed CPUL model, resulting in seven candidate halide perovskite materials for photovoltaic applications.
{"title":"Crystal synthesizability prediction using contrastive positive unlabeled learning","authors":"Tao Sun , Jianmei Yuan","doi":"10.1016/j.cpc.2024.109465","DOIUrl":"10.1016/j.cpc.2024.109465","url":null,"abstract":"<div><div>High-throughput screening or generative models rapidly identify crystal structures with the desired properties, but the synthesizable ratio is generally low. Experimentally verifying the synthesizability of individual virtual crystals would entail significant time and resources. Therefore, a method for automatically assessing the synthesizability of virtual crystals is urgently needed. This paper describes an approach that combines contrastive learning and positive unlabeled learning. The resulting contrastive positive unlabeled learning (CPUL) model predicts the crystal-likeness score (CLscore) of virtual materials. The model achieves a true positive (CLscore > 0.5) prediction accuracy of 93.95% on a test set containing 10,000 materials taken from the Materials Project (MP) database. We further validate the model by using all Fe-containing materials from the MP database as the test set, obtaining a true positive rate of 88.89%. This indicates that the CPUL model performs well, even with limited knowledge of the interactions between Fe and the atoms in the crystals. The CPUL model is then used to assess the CLscore of virtual crystals in the MP database and analyze their synthesizability by combining the energy above the hull. Finally, the synthesizability of perovskite materials is predicted using the proposed CPUL model, resulting in seven candidate halide perovskite materials for photovoltaic applications.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"308 ","pages":"Article 109465"},"PeriodicalIF":7.2,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-06DOI: 10.1016/j.cpc.2024.109463
Charles Cheung , Mikhail G. Kozlov , Sergey G. Porsev , Marianna S. Safronova , Ilya I. Tupitsyn , Andrey I. Bondarev
<div><div>We introduce the pCI software package for high-precision atomic structure calculations. The standard method of calculation is based on the configuration interaction (CI) method to describe valence correlations, but can be extended to attain better accuracy by including core correlations via many-body perturbation theory (CI+MBPT) or the all-order (CI+all-order) method. The software package enables calculations of atomic properties, including energy levels, <em>g</em>-factors, hyperfine structure constants, multipole transition matrix elements, polarizabilities, and isotope shifts. It also features modern high-performance computing paradigms, including dynamic memory allocations and large-scale parallelization via the message-passing interface, to optimize and accelerate computations. To improve accuracy of the calculations, we include a supplementary program package to calculate QED corrections via a variant of QEDMOD, as well as a package to include core correlations.</div></div><div><h3>Program summary</h3><div><em>Program Title:</em> pCI</div><div><em>CPC Library link to program files:</em> <span><span>https://doi.org/10.17632/2kn5npnxj7.1</span><svg><path></path></svg></span></div><div><em>Developer's repository link:</em> <span><span>https://github.com/ud-pci/pCI</span><svg><path></path></svg></span></div><div><em>Licensing provisions:</em> GPLv3</div><div><em>Programming language:</em> Fortran</div><div><em>Supplementary material:</em> Documentation available at <span><span>https://pci.readthedocs.io</span><svg><path></path></svg></span></div><div><em>Nature of problem:</em> Calculation of atomic and ionic properties, including energy levels, hyperfine structure constants, multipole transition matrix elements, and polarizabilities.</div><div><em>Solution method:</em> The software package calculates energies and associated wave functions for the desired atomic states using the configuration interaction method. Using calculated wave functions, different atomic properties can be obtained, including <em>g</em>-factors, hyperfine structure constants, multipole transition amplitudes, polarizabilities, and others.</div><div><em>Additional comments including restrictions and unusual features:</em> All serial programs have been compiled and tested with the freely available Intel Fortran compilers “ifx” and “ifort”, and all parallel programs with the OpenMPI wrapper “mpifort” for Intel Fortran compilers.</div><div>One-electron orbitals outside the nucleus are defined on the radial grid points. Inside the nucleus, they are described in a Taylor expansion over <span><math><mi>r</mi><mo>/</mo><mi>R</mi></math></span>, where <em>R</em> is the nuclear radius.</div><div>This software package is not designed for calculations of high Rydberg states and continuous spectrum. The parallel programs are intended to be run on large computing clusters.</div></div><div><h3>References</h3><div><ul><li><span>[1]</span><span><div>M.G. Kozlov et al., Comput. P
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