Computer Physics Communications最新文献

{"title":"Scalable, cloud-based simulations of blood flow and targeted drug delivery in retinal capillaries","authors":"Lucas Amoudruz ,&nbsp;Sergey Litvinov ,&nbsp;Riccardo Murri ,&nbsp;Volker Eyrich ,&nbsp;Jens Zudrop ,&nbsp;Costas Bekas ,&nbsp;Petros Koumoutsakos","doi":"10.1016/j.cpc.2025.109967","DOIUrl":"10.1016/j.cpc.2025.109967","url":null,"abstract":"<div><div>We investigate the capabilities of cloud computing for large-scale, tightly-coupled simulations of biological fluids in complex geometries, traditionally performed in supercomputing centers. We demonstrate scalable and efficient simulations in the public cloud. We perform meso-scale simulations of blood flow in image-reconstructed capillaries, and examine targeted drug delivery by artificial bacterial flagella (ABFs). The simulations deploy dissipative particle dynamics (DPD) with two software frameworks, Mirheo(developed by our team) and LAMMPS. Mirheoexhibits remarkable weak scalability for up to 512 GPUs. Similarly, LAMMPS demonstrated excellent weak scalability for pure solvent as well as for blood suspensions and ABFs in reconstructed retinal capillaries. In particular, LAMMPS maintained weak scaling above 90 % on the cloud for up to 2000 cores. Our findings demonstrate that cloud computing can support tightly coupled, large-scale scientific simulations with competitive performance.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109967"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145681671","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}

{"title":"A Memory Reduction Compact Gas Kinetic Scheme on 3D Unstructured Meshes","authors":"Hongyu Liu ,&nbsp;Xing Ji ,&nbsp;Yunpeng Mao ,&nbsp;Zhe Qian ,&nbsp;Kun Xu","doi":"10.1016/j.cpc.2025.109981","DOIUrl":"10.1016/j.cpc.2025.109981","url":null,"abstract":"<div><div>This paper presents a memory-reduction third-order compact gas-kinetic scheme (CGKS) designed to solve compressible Euler and Navier-Stokes equations on 3D unstructured meshes. Utilizing the time-accurate gas distribution function, the gas kinetic solver provides a time-evolution solution at the cell interface, distinguishable from the Riemann solver with a constant solution. With the time evolution solution at the cell interface, evolving both the cell-averaged flow variables and the cell-averaged slopes of flow variables becomes feasible. Therefore, with the cell-averaged flow variables and their slopes inside each cell, the Hermite WENO (HWENO) techniques can be naturally implemented for the compact high-order reconstruction at the beginning of the next time step. However, the HWENO reconstruction method requires the storage of a reconstruction-coefficients matrix for the quadratic polynomial to achieve third-order accuracy, leading to substantial memory consumption. This memory overhead limits both computational efficiency and the scale of simulations.</div><div>A novel reconstruction method, built upon HWENO reconstruction, has been designed to enhance computational efficiency and reduce memory usage compared to the original CGKS. The simple idea is that the first-order and second-order terms of the quadratic polynomials are determined in a two-step way. In the first step, the second-order terms are obtained from the reconstruction of a linear polynomial of the first-order derivatives by only using the cell-averaged slopes, since the second-order derivatives are nothing but the ”derivatives of derivatives”. Subsequently, the first-order terms left can be determined by the linear reconstruction only using cell-averaged values. Thus, we successfully split one quadratic least-square regression into several linear least-square regressions, which are commonly used in a second-order finite volume code. Since only a 3 × 3 matrix inversion is needed in a 3-D linear least-square regression, the computational cost for the new reconstruction is dramatically reduced and the storage of the reconstruction-coefficient matrix is no longer necessary. The proposed memory reduction CGKS is tested for both inviscid and viscous flow at low and high speeds on hybrid unstructured meshes. The proposed new reconstruction technique can reduce the overall computational cost by about 20% to 30%. In the meantime, it also simplifies the algorithm. The challenging large-scale unsteady numerical simulation is performed, which demonstrates that the current improvement brings the CGKS to a new level for industrial applications.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109981"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836434","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}

{"title":"RelExt: A new dark matter tool for the exploration of dark matter models","authors":"Rodrigo Capucha ,&nbsp;Karim Elyaouti ,&nbsp;Margarete Mühlleitner ,&nbsp;Johann Plotnikov ,&nbsp;Rui Santos","doi":"10.1016/j.cpc.2025.109968","DOIUrl":"10.1016/j.cpc.2025.109968","url":null,"abstract":"<div><div>We present the <span>C++</span> program <span><math><mi>RelExt</mi></math></span> for Standard Model (SM) extensions that feature a Dark Matter (DM) candidate. The tool allows to efficiently scan the parameter spaces of these models to find parameter combinations that lead to relic density values which are compatible with the measured value within the uncertainty specified by the user. The code computes the relic density for freeze-out (co-)annihilation processes. The user can choose between several pre-installed models or any arbitrary other model featuring a discrete <span><math><msub><mi>Z</mi><mn>2</mn></msub></math></span> symmetry, by solely providing the corresponding <span>FeynRules</span> model files. The code automatically generates the required (co-)annihilation amplitudes and thermally averaged cross sections, including the total widths in the <em>s</em>-channel mediators, and solves the Boltzmann equation to determine the relic density. It can easily be linked to other tools like e.g. <span>ScannerS</span> to check for the relevant theoretical and experimental constraints, or to <span>BSMPT</span> to investigate the phase history of the model and possibly related gravitational waves signals.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109968"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145836599","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}

{"title":"MHIT36: Extension to wall-bounded turbulence and scalar transport equation","authors":"Alessio Roccon","doi":"10.1016/j.cpc.2025.109956","DOIUrl":"10.1016/j.cpc.2025.109956","url":null,"abstract":"<div><div>We present an extended version of MHIT36, a GPU-tailored solver for interface-resolved simulations of multiphase turbulence. The framework couples direct numerical simulation (DNS) of the Navier–Stokes equations, which describe the flow field, with a phase-field method to capture interfacial phenomena. In addition, the transport equation for a scalar can also be solved. The governing equations are discretized using a second-order finite difference scheme. The Navier–Stokes equations are time advanced with an explicit fractional-step method, and the resulting pressure Poisson equation is solved using a FFT-based method. The accurate conservative diffuse interface (ACDI) formulation is used to describe the transport of the phase-field variable. Simulations can be performed in two configurations: a triply-periodic cubic domain or a rectangular domain of arbitrary dimensions bounded by two walls. From a computational standpoint, MHIT36 employs a two-dimensional domain decomposition to distribute the workload across MPI tasks. The cuDecomp library is used to perform pencil transpositions and halo updates, while the cuFFT library and OpenACC directives are leveraged to offload the remaining computational kernels to the GPU. MHIT36 is developed using the managed memory feature and it provides a baseline code that is easy to further extend and modify. MHIT36 is released open source under the MIT license.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109956"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616112","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}

{"title":"Numerical implementation of the partial secular approximation and unified master equation in structured open quantum systems","authors":"Antti Vaaranta ,&nbsp;Marco Cattaneo","doi":"10.1016/j.cpc.2025.109948","DOIUrl":"10.1016/j.cpc.2025.109948","url":null,"abstract":"<div><div>The Markovian dynamics of open quantum systems is typically described through Lindblad equations, which are derived from the Redfield equation via the <em>full</em> secular approximation. The latter neglects the rotating terms in the master equation corresponding to pairs of jump operators with different Bohr frequencies. However, for many physical systems this approximation breaks down, and thus a more accurate treatment of the slowly rotating terms is required. Indeed, more precise physical results can be obtained by performing the <em>partial</em> secular approximation, which takes into account the relevant time scale associated with each pair of jump operators and compares it with the time scale arising from the system-environment coupling. In this work, we introduce a general code for performing the partial secular approximation in the Redfield equation for structured open quantum systems. The code can be applied to a generic Hamiltonian of any multipartite system coupled to bosonic baths. Moreover, it can also reproduce the <em>unified master equation</em>, which captures the same physical behavior as the Redfield equation under the partial secular approximation, but is mathematically guaranteed to generate a completely positive dynamical map. Finally, the code can compute both the local and global version of the master equation for the same physical problem. We illustrate the code by studying the steady-state heat flow in a structured open quantum system composed of two superconducting qubits, each coupled to a bosonic mode, which in turn interacts with a thermal bath. The results in this work can be employed for the numerical study of a wide range of complex open quantum systems.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109948"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616216","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}

{"title":"Physics-based super-resolved simulation of 3D elastic wave propagation adopting scalable diffusion transformer","authors":"Hugo Gabrielidis ,&nbsp;Filippo Gatti ,&nbsp;Stéphane Vialle","doi":"10.1016/j.cpc.2025.109930","DOIUrl":"10.1016/j.cpc.2025.109930","url":null,"abstract":"<div><div>In this study, we develop a Diffusion Transformer (referred as to DiT1D) for synthesizing realistic earthquake time histories. The DiT1D generates realistic broadband accelerograms (0–30Hz resolution), constrained at low frequency by 3-dimensional (3D) elastodynamics numerical simulations, ensuring the fulfillment of the minimum observable physics. The DiT1D architecture, successfully adopted in super-resolution image generation, is trained on recorded single-station 3-components (3C) accelerograms. Thanks to Multi-Head Cross-Attention (MHCA) layers, we guide the DiT1D inference by enforcing the low-frequency part of the accelerogram spectrum into it. The DiT1D learns the low-to-high frequency map from the recorded accelerograms, duly normalized, and successfully transfer it to synthetic time histories. The latter are low-frequency by nature, because of the lack of knowledge on the underground structure of the Earth, demanded to fully calibrate the numerical model. We developed a CNN-LSTM lightweight network in conjunction with the DiT1D, so to predict the peak amplitude of the broadband signal from its low-pass-filtered counterpart, and rescale the normalized accelerograms rendered by the DiT1D. Despite the DiT1D being agnostic to any earthquake event peculiarities (magnitude, site conditions, etc.), it showcases remarkable zero-shot prediction realism when applied to the output of validated earthquake simulations. The generated time histories are viable input accelerograms for earthquake-resistant structural design and the pre-trained DiT1D holds a huge potential to integrate full-scale fault-to-structure digital twins of earthquake-prone regions. The pretrained DiT1D is available at <span><span>https://github.com/HugoGabrielidis16/Seismic_DiT1D</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109930"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616213","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}

{"title":"Hybrid spectral semi-Lagrangian method for electromagnetic gyrokinetic simulations of Tokamak plasma","authors":"Pengfei Zhao,&nbsp;Lei Ye,&nbsp;Xiaotao Xiao","doi":"10.1016/j.cpc.2025.109953","DOIUrl":"10.1016/j.cpc.2025.109953","url":null,"abstract":"<div><div>The Numerical Lie Transform approach for gyrokinetic simulation has been extended to the electromagnetic model through integration with the mixed-variable and pull-back scheme. We developed a hybrid spectral semi-Lagrangian method for solving the gyrokinetic equation in toroidal geometry. The nonlinear Vlasov equation is expressed in a convective formalism aligned with unperturbed gyrocenter trajectories. Combined with toroidal spectral decomposition, this reformulation enables efficient semi-Lagrangian solutions through fixed-point interpolation method with 3D B-splines. The implemented algorithm in the NLT code facilitates electromagnetic turbulence simulations in tokamak plasmas. Verification was achieved through systematic benchmarking against electromagnetic instabilities including ion temperature gradient (ITG) modes, trapped electron modes (TEM), kinetic ballooning modes (KBM), toroidal Alfvén eigenmodes (TAE), and energetic particle-driven modes (EPM).</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109953"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145571121","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}

{"title":"Semiconductor Bloch equations in Wannier gauge with well-behaved dephasing","authors":"Martin Thümmler ,&nbsp;Thomas Lettau ,&nbsp;Alexander Croy ,&nbsp;Ulf Peschel ,&nbsp;Stefanie Gräfe","doi":"10.1016/j.cpc.2025.109958","DOIUrl":"10.1016/j.cpc.2025.109958","url":null,"abstract":"<div><div>The semiconductor Bloch equations (SBEs) with a dephasing operator for the microscopic polarizations are a well established approach to simulate high-harmonic spectra in solids. We discuss the impact of the dephasing operator on the stability of the numerical integration of the SBEs in the Wannier gauge. It is shown that the commonly used phenomenological approach to apply dephasing is ill-defined in the presence of band crossings and leads to artifacts in the carrier distribution. They are caused by rapid changes of the dephasing operator matrix elements in the Wannier gauge, which render the convergence of the simulation in the stationary basis infeasible. In the comoving basis, also called Houston basis, these rapid changes can be resolved, but only at the cost of a largely increased computation time. As a remedy, we propose a modification of the dephasing operator with reduced magnitude in energetically close subspaces. This approach removes the artifacts in the carrier distribution and significantly speeds up the calculations, while affecting the high-harmonic spectrum only marginally. To foster further development, we provide our parallelized source code.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109958"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616215","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}

{"title":"ggxy: A flexible library to compute gluon-induced cross sections","authors":"Joshua Davies ,&nbsp;Kay Schönwald ,&nbsp;Matthias Steinhauser ,&nbsp;Daniel Stremmer","doi":"10.1016/j.cpc.2025.109933","DOIUrl":"10.1016/j.cpc.2025.109933","url":null,"abstract":"<div><div>We present the library <span>ggxy</span>, written in <span>C++</span>, which can be used to compute partonic and hadronic cross sections for gluon-induced processes with at least one closed heavy quark loop. It is based on analytic ingredients which avoids, to a large extent, expensive numerical integration. This results in significantly shorter run-times than other similar tools. Modifying input parameters, changing the renormalization scheme and varying renormalization and factorization scales is straightforward. In Version 1 of <span>ggxy</span> we implement all routines which are needed to compute partonic and hadronic cross sections for Higgs boson pair production up to next-to-leading order in QCD. We provide flexible interfaces and allow the user to interact with the built-in amplitudes at various levels. <strong>PROGRAM SUMMARY</strong> <em>Program title:</em> <span>ggxy</span> <em>Developer’s repository link:</em> <span><span>https://gitlab.com/ggxy/ggxy-release</span><svg><path></path></svg></span> <em>Licensing provisions:</em> GNU General Public License Version 3 <em>Programming language:</em> C++ and Fortran <em>External routines/libraries used:</em> <span>avhlib</span>, <span>boost</span>, <span>Collier</span>, <span>CuTtools</span>, <span>eigen</span>, <span>LHAPDF</span>, <span>lievaluate</span>, <span>OneLOop</span>, <span>Recola</span>, <span>CRunDec</span> <em>Nature of problem:</em> The computation of partonic and hadronic cross sections for gluon-induced processes. In Version 1, the Higgs boson pair production process is implemented at next-to-leading order in Quantum Chromodynamics. <em>Solution method:</em> For the virtual corrections, deep expansions around the forward and high energy limit are used. <em>Restrictions:</em> The run-times depend crucially on the requested precision. Results at the per-mille level can be obtained in about 30 minutes using a single core on a AMD Ryzen Threadripper PRO 3955WX processor. <em>References and Links:</em> are provided in the paper</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109933"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555178","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}

{"title":"A Wigner matrix based convolution algorithm for matrix elements in the LCAO method","authors":"Tyler C. Sterling","doi":"10.1016/j.cpc.2025.109950","DOIUrl":"10.1016/j.cpc.2025.109950","url":null,"abstract":"<div><div>The linear combination of atomic orbitals (LCAO) method uses a small basis set in exchange for expensive matrix element calculations. The most efficient approximation for the matrix element calculations is the two-center approximation (2CA) in tight binding (TB). In the 2CA, a variety of matrix elements are neglected with only “two-center integrals” (2CI) remaining. The 2CI are calculated efficiently by rotating to symmetrical coordinates where the integral is parameterized. This makes TB fast in exchange for diminished transferability. An ideal electronic structure method has both the efficiency of TB and the transferability of ab-initio methods. In this work, I expand the full crystal potential into multipoles where the resulting matrix elements are transformed into the form of 2CI between high angular momentum functions. The usual Slater-Koster formulae for TB are limited to <em>l</em> ≤ 3; to enable efficient evaluation of the full crystal potential 2CI, I derive a Wigner matrix based convolution algorithm (WMCA) that works for arbitrary angular momentum. Given a suitable method for generating a local ab-initio Kohn-Sham potential, the algorithm for calculating matrix elements is applicable to fully ab-initio LCAO methods (this is the subject of forthcoming work). In this paper, I apply the WMCA to silicon using a model crystal potential.</div></div>","PeriodicalId":285,"journal":{"name":"Computer Physics Communications","volume":"320 ","pages":"Article 109950"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555177","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}