COMPUTER PHYSICS COMMUNICATIONS计算机物理通讯
COMPUTER PHYSICS COMMUNICATIONS(英文缩写 COMPUT PHYS COMMUN),ISSN 0010-4655,eISSN 1879-2944,中文译名:计算机物理通讯 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-11-01 至 2026-10-31，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 4.717 | Q1 |
| 2022 | 6.300 | Q1 |
| 2023 | 7.200 | Q1 |
| 2024 | 3.400 | Q1 |
| 2025 | 3.900 | Q1 |
COMPUTER PHYSICS COMMUNICATIONS 最新收录文献
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1. Bloch-state optimal basis sets: An efficient approach for electronic structure interpolation.
PMID:日期:2025-08We present an efficient implementation of the -space interpolation for electronic structure based on the optimal basis method originally proposed by Shirley [Phys. Rev. B , 16464 (1996)] The method allows interpolation onto any -point from a minimal set of input density functional theory (DFT) wavefunctions. Numerically interpolated eigenvalues have an accuracy within 0.01 eV with very small computational cost. The interpolated wavefunctions were used in the Bethe-Salpeter equation to simulate x-ray absorption spectra of different systems, ranging from small bulk crystals to large intermetallic supercells. The method is extensively tested in terms of verification and accuracy for best practices. The approach is shown to be robust and will greatly help accelerate high-throughput DFT studies.
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2. Time-domain event detection using single-instruction, multiple-thread gpGPU architectures in single-molecule biophysical data.
PMID:日期:2024-03-28Discrete amplitude levels in ordered, time-domain data often represent different underlying latent states of the system that is being interrogated. Analysis and feature extraction from these data sets generally require considering the order of each individual point; this approach cannot take advantage of contemporary general-purpose graphics processing units (gpGPU) and single-instruction multiple-data (SIMD) instruction set architectures. Two sources of such data from single-molecule biological measurements are nanopores and single-molecule field effect transistor (smFET) nanotube devices; both generate streams of time-ordered current or voltage data, typically sampled near 1 MS/s, with run times of minutes, yielding terabyte-scale datasets. Here, we present three gpGPU-based algorithms to overcome limitations associated with serial event detection in time series data, resulting in a 250× improvement in the rate with which we can detect salient features in nanopore and smFET datasets. The code is freely available.
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3. MCGPU-PET: An Open-Source Real-Time Monte Carlo PET Simulator.
PMID:日期:2023-11-13Monte Carlo (MC) simulations are commonly used to model the emission, transmission, and/or detection of radiation in Positron Emission Tomography (PET). In this work, we introduce a new open-source MC software for PET simulation, MCGPU-PET, which has been designed to fully exploit the computing capabilities of modern GPUs to simulate the acquisition of more than 100 million coincidences per second from voxelized sources and material distributions. The new simulator is an extension of the PENELOPE-based MCGPU code previously used in cone-beam CT and mammography applications. We validated the accuracy of the accelerated code by comparing it to GATE and PeneloPET simulations achieving an agreement within 10 percent approximately. As an example application of the code for fast estimation of PET coincidences, a scan of the NEMA IQ phantom was simulated. A fully 3D sinogram with 6382 million true coincidences and 731 million scatter coincidences was generated in 54 seconds in one GPU. MCGPU-PET provides an estimation of true and scatter coincidences and spurious background (for positron-gamma emitters such as I) at a rate 3 orders of magnitude faster than CPU-based MC simulators. This significant speed-up enables the use of the code for accurate scatter and prompt-gamma background estimations within an iterative image reconstruction process.
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4. {"_":": A program for combined quantum mechanical and molecular mechanical modeling and simulations.","i":["QMMM 2023"]}
PMID:日期:2023-10-26Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. is a general-purpose program for single-point calculations, geometry optimizations, transition state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. supports GAMESS-US, , and ORCA as QM packages and TINKER as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC, balanced-RCD, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM-MM boundary. Geometry optimization can be done using the optimizer implemented in or the Berny optimizer in through external calls to . Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. The adaptive-partitioning treatments permit on-the-fly relocation of the QM-MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.
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5. Electrical impulse characterization along actin filaments in pathological conditions.
PMID:日期:2022-02-22We present an interactive Mathematica notebook that characterizes the electrical impulses along actin filaments in both muscle and non-muscle cells for a wide range of physiological and pathological conditions. The simplicity of the theoretical formulation, and high performance of the Mathematica software, enable the analysis of multiple conditions without computational restrictions. The program is based on a multi-scale (atomic → monomer → filament) approach capable of accounting for the atomistic details of a protein molecular structure, its biological environment, and their impact on the travel distance, velocity, and attenuation of monovalent ionic wave packets propagating along microfilaments. The interactive component allows investigators to choose the experimental conditions (intracellular Vs in vitro), nucleotide state (ATP Vs ADP), actin isoform (alpha, gamma, beta, and muscle or non-muscle cell), as well as a conformation model that covers a variety of mutants and wild-type (the control) actin filament. We used the computational tool to analyze environmental changes such as temperature effects and pH changes of the surrounding solutions, as well as structural changes to an actin monomer due to radius changes. Additionally, we investigated for the first time the electrostatic consequences of actin mutations from different disease conditions. These studies may provide an unprecedented molecular understanding of why and how age, inheritance, and disease conditions induce dysfunctions in the biophysical mechanisms underlying the propagation of electrical signals along actin filaments.
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6. Full 3D position reconstruction of a radioactive source based on a novel hyperbolic geometrical algorithm.
PMID:日期:2020-07A new method to locate, with millimetre uncertainty, in 3D, a -ray source emitting multiple -rays in a cascade, employing conventional LaBr(Ce) scintillation detectors, has been developed. Using 16 detectors in a symmetrical configuration the detector energy and time signals, resulting from the -ray interactions, are fed into a new source position reconstruction algorithm. The Monte-Carlo based Geant4 framework has been used to simulate the detector array and a Co source located at two positions within the spectrometer central volume. For a source located at (0,0,0) the algorithm reports X, Y, Z values of -0.3 ± 2.5, -0.4 ± 2.4, and -0.6 ± 2.5 mm, respectively. For a source located at (20,20,20) mm, with respect to the array centre, the algorithm reports X, Y, Z values of 20.2 ± 1.0, 20.2 ± 0.9, and 20.1 ± 1.2 mm. The resulting precision of the reconstruction means that this technique could find application in a number of areas including nuclear medicine, national security, radioactive waste assay and proton beam therapy.
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7. MFC: An open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver.
PMID:日期:2020-05-23MFC is an open-source tool for solving multi-component, multi-phase, and bubbly compressible flows. It is capable of efficiently solving a wide range of flows, including droplet atomization, shock-bubble interaction, and bubble dynamics. We present the 5- and 6-equation thermodynamically-consistent diffuse-interface models we use to handle such flows, which are coupled to high-order interface-capturing methods, HLL-type Riemann solvers, and TVD time-integration schemes that are capable of simulating unsteady flows with strong shocks. The numerical methods are implemented in a flexible, modular framework that is amenable to future development. The methods we employ are validated via comparisons to experimental results for shock-bubble, shock-droplet, and shock-water-cylinder interaction problems and verified to be free of spurious oscillations for material-interface advection and gas-liquid Riemann problems. For smooth solutions, such as the advection of an isentropic vortex, the methods are verified to be high-order accurate. Illustrative examples involving shock-bubble-vessel-wall and acoustic-bubble-net interactions are used to demonstrate the full capabilities of MFC.
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8. Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis.
PMID:日期:2020-04-17Inverse Ising inference is a method for inferring the coupling parameters of a Potts/Ising model based on observed site-covariation, which has found important applications in protein physics for detecting interactions between residues in protein families. We introduce Mi3-GPU ("mee-three", for CMC nverse sing nference) software for solving the inverse Ising problem for protein-sequence datasets with few analytic approximations, by parallel Markov-Chain Monte-Carlo sampling on GPUs. We also provide tools for analysis and preparation of protein-family Multiple Sequence Alignments (MSAs) to account for finite-sampling issues, which are a major source of error or bias in inverse Ising inference. Our method is "generative" in the sense that the inferred model can be used to generate synthetic MSAs whose mutational statistics (marginals) can be verified to match the dataset MSA statistics up to the limits imposed by the effects of finite sampling. Our GPU implementation enables the construction of models which reproduce the covariation patterns of the observed MSA with a precision that is not possible with more approximate methods. The main components of our method are a GPU-optimized algorithm to greatly accelerate MCMC sampling, combined with a multi-step Quasi-Newton parameter-update scheme using a "Zwanzig reweighting" technique. We demonstrate the ability of this software to produce generative models on typical protein family datasets for sequence lengths ~ 300 with 21 residue types with tens of millions of inferred parameters in short running times.
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9. PyLCP: A Python package for computing laser cooling physics.
PMID:日期:2020-01We present a Python object-oriented computer program for simulating various aspects of laser cooling physics. Our software is designed to be both easy to use and adaptable, allowing the user to specify the level structure, magnetic field profile, or the laser beams' geometry, detuning, and intensity. The program contains three levels of approximation for the motion of the atom, applicable in different regimes offering cross checks for calculations and computational efficiency depending on the physical situation. We test the software by reproducing well-known phenomena, such as damped Rabi flopping, electromagnetically induced transparency, stimulated Raman adiabatic passage, and optical molasses. We also use our software package to quantitatively simulate recoil-limited magneto-optical traps, like those formed on the narrow S → P transition in Sr and Sr.
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10. A comparison of numerical approaches to the solution of the time-dependent Schrödinger equation in one dimension.
PMID:日期:2020We present a simple, one-dimensional model of an atom exposed to a time-dependent intense, short-pulse EM field with the objective of teaching undergraduates how to apply various numerical methods to study the behavior of this system as it evolves in time using several time propagation schemes.In this model, the exact Coulomb potential is replaced by a soft-core interaction to avoid the singularity at the origin. While the model has some drawbacks, it has been shown to be a reasonable representation of what occurs in the fully three-dimensional hydrogen atom.The model can be used as a tool to train undergraduate physics majors in the art of computation and software development. 1d hydrogen light interaction http://dx.doi.org/10.17632/2275fmvdzc.1 https://doi.org/10.24433/CO.1476487.v1 MIT license FORTRAN90 The one dimensional time dependent Schrödinger equation has been shown to be quite useful as a model to study the Hydrogen atom exposed to an intense, short pulse, electromagnetic field. We use a model potential that is cut-off near = 0 and avoids the singularity of the true 1-D potential, but retains the characteristic Rydberg series and continuum to study excitation and ionization of the true H atom. The code employs a number of numerical methods to understand and compare the efficacy and accuracy when applied to this model problem. The program uses and contrasts a number of approaches; the Crank-Nicolson, Short Iterative Lanczos, various incarnations of the split-operator and the Chebychev method have been programmed. These methods have been compared using a 3-point finite difference (FD) discretization of the space coordinate. For completeness, some attention has also been given to using 5-9 FD formulas in order to show how higher order discretization affects the accuracy and efficiency of the methods but the primary focus of the method is the time propagation. The main purpose of this code is as a teaching tool for undergraduates interested in acquiring knowledge of numerical methods and programming skills useful to a practicing computational physicist.