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Computer Physics Communications

ISSN: 0010-4655

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Datasets associated with articles published in Computer Physics Communications

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1970 2024
5961 results
  • ENDFtk: A robust tool for reading and writing ENDF-formatted nuclear data
    ENDFtk is a recently developed C++ and Python interface to interact with ENDF-6 formatted nuclear data files. It provides a robust and complete interface, allowing the reading and writing of all formats currently part of the ENDF-6 formats manual, as well as some non-ENDF formats used by the NJOY processing code. It provides an interface that mimics the names in the ENDF-6 formats manual as well as an equivalent interface using human-readable attribute names. It is robust and powerful enogh for nuclear data experts to develop complex applications, while also simple enough to be used non-experts to retrieve and manipulate evaluated nuclear data. ENDFtk offers the ability to easily interrogate and manipulate data either in large-scale code projects or in simple Python scripts. In this paper, a brief overview of the interface is given, as well as more substantial examples demonstrating plotting simple data, interacting with more complex data, and writing new data to files. ENDFtk is open source and available for download via GitHub (
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  • Fast-QSGS: A GPU accelerated program for structure generation of granular disordered media
    We present Fast-QSGS, a GPU-accelerated program for granular disordered media generation. Based on vectorization, Fast-QSGS is accelerated by modern GPU thanks to the NumPy-compatible API provided by CuPy. We also introduce a variable growth probability function and seed spacing control to improve the speed and accuracy of the original QSGS method. Computational performance benchmarks are conducted on both consumer-grade and professional-grade GPUs. Generation of disordered media of size 4003 can be completed in 30 s on A100 and 110 s on RTX4060, achieving a speedup of over 400 compared with the serial version. Physical benchmarks on the reconstruction of Fontainebleau sandstone and hydrated cement are conducted. Our results demonstrate that the permeability of the reconstructed Fontainebleau sandstone falls within the range of experimental values. Additionally, the average relative error of the volume fraction of the unhydrated cement and capillary porosity of hydrated cement is 1.9 % and 3.4 % compared with Powers’ law, respectively.
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  • CNUCTRAN: A program for computing final nuclide concentrations using a direct simulation approach
    It is essential to precisely determine the evolving concentrations of radioactive nuclides within transmutation problems. It is also a crucial aspect of nuclear physics with widespread applications in nuclear waste management and energy production. This paper introduces CNUCTRAN, a novel computer program that employs a probabilistic approach to estimate nuclide concentrations in transmutation problems. CNUCTRAN directly simulates nuclei transformations arising from various nuclear reactions, diverging from the traditional deterministic methods that solve the Bateman equation using matrix exponential approximation. This approach effectively addresses numerical challenges associated with solving the Bateman equations, therefore, circumventing the need for matrix exponential approximations that risk producing nonphysical concentrations. Our sample calculations using CNUCTRAN shows that the concentration predictions of CNUCTRAN have a relative error of less than 0.001% compared to the state-of-the-art method, CRAM, in different test cases. This makes CNUCTRAN a valuable alternative tool for transmutation analysis.
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  • Unlocking massively parallel spectral proper orthogonal decompositions in the PySPOD package
    We propose a parallel (distributed) version of the spectral proper orthogonal decomposition (SPOD) technique. The parallel SPOD algorithm distributes the spatial dimension of the dataset preserving time. This approach is adopted to preserve the non-distributed fast Fourier transform of the data in time, thereby avoiding the associated bottlenecks. The parallel SPOD algorithm is implemented in the PySPOD library and makes use of the standard message passing interface (MPI) library, implemented in Python via mpi4py. An extensive performance evaluation of the parallel package is provided, including strong and weak scalability analyses. The open-source library allows the analysis of large datasets of interest across the scientific community. Here, we present applications in fluid dynamics and geophysics, that are extremely difficult (if not impossible) to achieve without a parallel algorithm. This work opens the path toward modal analyses of big quasi-stationary data, helping to uncover new unexplored spatio-temporal patterns.
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  • FIRE 6.5: Feynman integral reduction with new simplification library
    FIRE is a program which performs integration-by-parts (IBP) reductions of Feynman integrals. Originally, the C++ version of FIRE relies on the computer algebra system Fermat by Robert Lewis to simplify rational functions. We present an upgrade of FIRE which incorporates a new library FUEL initially described in a separate publication, which enables a flexible choice of third-party computer algebra systems as simplifiers, as well as efficient communications with some of the simplifiers as C++ libraries rather than through Unix pipes. We achieve significant speedups for IBP reductions of Feynman integrals involving many kinematic variables, when using an open source backend based on FLINT newly added in this work, or the Symbolica backend developed by Ben Ruijl as a potential successor of FORM.
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  • DeHNSSo: The delft harmonic Navier-Stokes solver for nonlinear stability problems with complex geometric features
    A nonlinear Harmonic Navier-Stokes (HNS) framework is introduced for simulating instabilities in laminar spanwise-invariant shear layers, featuring sharp and smooth wall surface protuberances. While such cases play a critical role in the process of laminar-to-turbulent transition, classical stability theory analyses such as parabolized or local stability methods fail to provide (accurate) results, due to their underlying assumptions. The generalized incompressible Navier-Stokes (NS) equations are expanded in perturbed form, using a spanwise and temporal Fourier ansatz for flow perturbations. The resulting equations are discretized using spectral collocation in the wall-normal direction and finite-difference methods in the streamwise direction. The equations are then solved using a direct sparse-matrix solver. The nonlinear mode interaction terms are converged iteratively. The solution implementation makes use of a generalized domain transformation to account for geometrical smooth surface features, such as humps. No-slip conditions can be embedded in the interior domain to account for the presence of sharp surface features such as forward- or backward-facing steps. Common difficulties with Navier-Stokes solvers, such as the treatment of the outflow boundary and convergence of nonlinear terms, are considered in detail. The performance of the developed solver is evaluated against several cases of representative boundary layer instability growth, including linear and nonlinear growth of Tollmien-Schlichting waves in a Blasius boundary layer and stationary crossflow instabilities in a swept flat-plate boundary layer. The latter problem is also treated in the presence of a geometrical smooth hump and a sharp forward-facing step at the wall. HNS simulation results, such as perturbation amplitudes, growth rates, and shape functions, are compared to benchmark flow stability analysis methods such as Parabolized Stability Equations (PSE), Adaptive Harmonic Linearized Navier-Stokes (AHLNS), or Direct Numerical Simulations (DNS). Good agreement is observed in all cases. The HNS solver is subjected to a grid convergence study and a simple performance benchmark, namely memory usage and computational cost. The computational cost is found to be considerably lower than high-fidelity DNS at comparable grid resolutions.
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  • Jiezi: an open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism
    We present a Python-based open-source library named Jiezi, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of Jiezi lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET).
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  • MISTER-T: An open-source software package for quantum optimal control of multi-electron systems on arbitrary geometries
    We present an open-source software package, MISTER-T (Manipulating an Interacting System of Total Electrons in Real-Time), for the quantum optimal control of interacting electrons within a time-dependent Kohn-Sham formalism. In contrast to other implementations restricted to simple models on rectangular domains, our method enables quantum optimal control calculations for multi-electron systems (in the effective mass formulation) on nonuniform meshes with arbitrary two-dimensional cross-sectional geometries. Our approach is enabled by forward and backward propagator integration methods to evolve the Kohn-Sham equations with a pseudoskeleton decomposition algorithm for enhanced computational efficiency. We provide several examples of the versatility and efficiency of the MISTER-T code in handling complex geometries and quantum control mechanisms. The capabilities of the MISTER-T code provide insight into the implications of varying propagation times and local control mechanisms to understand a variety of strategies for manipulating electron dynamics in these complex systems.
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  • Improvements in charged lepton and photon propagation for the software PROPOSAL
    Accurate particle simulations are essential for the next generation of experiments in astroparticle physics. The Monte Carlo simulation library PROPOSAL is a flexible tool to efficiently propagate high-energy leptons and photons through large volumes of media, for example in the context of underground observatories. It is written as a C++ library, including a Python interface. In this paper, the most recent updates of PROPOSAL are described, including the addition of electron, positron, and photon propagation, for which new interaction types have been implemented. This allows the usage of PROPOSAL to simulate electromagnetic particle cascades, for example in the context of air shower simulations. The precision of the propagation has been improved by including rare interaction processes, new photonuclear parametrizations, deflections in stochastic interactions, and the possibility of propagating in inhomogeneous density distributions. Additional technical improvements regarding the interpolation routine and the propagation algorithm are described.
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  • CUDA-based focused Gaussian beams second-harmonic generation efficiency calculator
    We present an object-oriented programming (OOP) CUDA-based package for fast and accurate simulation of second-harmonic generation (SHG) efficiency using focused Gaussian beams. The model includes linear as well as two-photon absorption that can ultimately lead to thermal lensing due to self-heating effects. Our approach speeds up calculations by nearly 40x (11x) without (with) temperature profiles with respect to an equivalent implementation using CPU. The package offers a valuable tool for experimental design and study of 3D field propagation in nonlinear three-wave interactions. It is useful for optimization of SHG-based experiments and mitigates undesired thermal effects, enabling improved oven designs and advanced device architectures, leading to stable, efficient high-power SHG.
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