Computer Physics Communications

The Neoclassical Toroidal Viscosity (NTV) torque is a crucial source of toroidal momentum in tokamaks, exerting significant influence on plasma instability and performance. Accurate numerical modeling of NTV torque is essential for experimental design and operation, as well as for gaining insight into the relevant physical processes. However, the time-consuming nature of NTV torque calculation poses challenges for its practical application in experiment analysis and physical investigations. In this study, we have developed NTVTOK-ML, a surrogate model for NTV torque calculation that combines the expressive power and fast inference of machine learning methods to achieve simultaneous accuracy and time efficiency. To obtain datasets for NTV torque, extensive numerical calculations using NTVTOK and MARS-F codes were performed under various plasma conditions of Experimental Advanced Superconducting Tokamak (EAST), covering a wide range of experimentally relevant parameter regimes and incorporating rich physical effects such as pitch angle scattering, full toroidal geometry, resonances, etc. For fixed magnetic perturbation case, NTVTOK-ML employs Multi-Layer Perceptron (MLP) deep neural network and eXtreme Gradient Boosting (XGBoost) ensemble learning techniques respectively. Furthermore, when considering linear plasma response effect, Convolutional Neural Network (CNN) is utilized to process two-dimensional magnetic perturbation data. The prediction accuracy of NTVTOK-ML is evaluated based on statistical metrics including coefficient of determination (R^2), mean squared error (MSE), and relative error; single sample prediction ability; and generalization ability - demonstrating its reliability in NTV torque prediction tasks. Importantly, the computational time required for predicting NTV torque using our proposed approach is significantly reduced compared to the original numerical code by several orders of magnitude. Additionally, the flexibility offered by the NTVTOK-ML framework allows users to optimize model performance under specific circumstances. Overall, our developed method provides an accessible solution for rapid yet accurate prediction of NTV torque while incorporating essential physical effects - thereby facilitating real-time or inter-shot analysis in experiments as well as comprehensive multi-scale nonlinear time evolution modeling.

The Fluid Properties module within the Multiphysics Object-Oriented Simulation Environment (MOOSE) is used to compute fluid properties for numerous applications, ranging from nuclear reactor thermal hydraulics to geothermal energy. Those applications drove the development of the module to enable numerous different fluid equations of states, property lookups with primitive and conserved flow variable to cater to pressure and density-driven solvers, and an object-oriented design facilitating expansion and maintenance. Each fluid property is implemented in its own class but inherits capabilities such as automatic differentiation, automated out-of-bounds handling or variable conversion capabilities. This paper presents the module, its design, its user and developer interface, its content in terms of fluids and properties, and several of its applications showing its major role in the MOOSE simulation ecosystem.

The software MCEND (Multi-Configuration Electron-Nuclear Dynamics) is a free open-source program package which simulates the quantum dynamics of electron-nuclei simultaneously for diatomic molecules. Its formulation, implementation, and usage are described in detail. MCEND uses a grid-based basis representation for the nuclei, and the electronic basis is derived from standard electronic structure basis sets on the nuclear grid. The wave function is represented as a sum over products of electronic and nuclear wave functions, thus capturing correlation effects between electrons, nuclei, and electrons and nuclei. The LiH molecule was used as an example for simulating the molecular properties such as the dipole moment and absorption spectrum.

GHW is a gyrofluid code for computation of quasi-two-dimensional turbulence with consistent finite Larmor radius (FLR) effects in magnetized plasmas. The simulation setup allows for fundamental studies of FLR effects on isothermal resistive drift waves and turbulence, and contains the standard Hasegawa-Wakatani model in the limit of cold ions.

This paper presents an enhanced version of the well-known SPH (Smoothed Particle Hydrodynamics) open-source code DualSPHysics for the simulation of free-surface fluid flows, leading to the DualSPHysics+ code. The enhancements are made through incorporation of several schemes with respect to stability, accuracy and energy/volume conservation issues in simulating incompressible free-surface fluid flows within the weakly compressible SPH formalism. The Optimized Particle Shifting (OPS) scheme is implemented to improve the accuracy of particle shifting vectors in the free-surface region. To mitigate energy dissipation and maintain consistency, the artificial viscosity in δ-SPH is substituted with a Riemann stabilization term, leading to the δR-SPH. The Velocity divergence Error Mitigating (VEM) and Volume Conservation Shifting (VCS) schemes are adopted in DualSPHysics+ to mitigate the velocity divergence error and improve the volume conservation, and hence to enhance the resolution of the continuity equation. To further reduce both the instantaneous and accumulated errors in velocity divergence, a Hyperbolic/Parabolic Divergence Cleaning (HPDC) scheme is incorporated in addition to the VEM scheme. The implementations of the introduced schemes on both CPU and GPU-based versions of the DualSPHysics+ code along with details on the compilation, running and computational performance are presented. Validations in terms of accuracy, energy conservation and convergence of DualSPHysics+ are shown via several relevant benchmarks. It is demonstrated that a better velocity divergence error cleaning in both instantaneous and accumulated errors can be achieved by the combination of VEM and HPDC. Meanwhile, the excessive energy dissipation by the artificial viscosity is shown to be suppressed by adopting the Riemann stabilization term. Enhanced resolution of the continuity equation along with improved energy conservation of DualSPHysics+ advance the SPH-based simulation of incompressible free-surface fluid flows.

We present LinApart, a routine designed for efficiently performing the univariate partial fraction decomposition of large symbolic expressions. Our method is based on an explicit closed formula for the decomposition of rational functions with fully factorized denominators. We provide an implementation in the Wolfram Mathematica language, which can lead to very significant performance gains over the built-in Apart command. Furthermore, a C language library implementing the core functionality and suitable for interfacing with other software is also provided. Both codes are made available at https://github.com/fekeshazy/LinApart.

OpenSBLI is an automatic code-generation framework for compressible Computational Fluid Dynamics (CFD) simulations on heterogeneous computing architectures (previous release: Lusher et al. (2021) [4]). OpenSBLI is coupled to the Oxford Parallel Structured (OPS) Domain Specific Language (DSL), which uses source-to-source translation to enable parallel execution of the code on large-scale supercomputers, including multi-GPU clusters. To date, OpenSBLI has largely been applied to compressible turbulence and shock-wave/boundary-layer interactions on very simple geometries comprised of single mesh blocks with essentially orthogonal grid lines. OpenSBLI has been extended in this new release to target strongly curvilinear cases, including transonic aerofoils using multi-block grids. In addition to multi-block mesh support, more efficient numerical shock-capturing methods and filters have been added to the codebase. Improvements to post-processing, reduced-dimension data output, and coupling to a modal decomposition library are also included. A set of validation cases are presented to showcase the new code features. Furthermore, state-of-the-art wide-span transonic aerofoil simulations on up to N = 2.5 x 10^9 grid points demonstrate that wider aspect ratios can alter buffet predictions and increase the regularity of the low-frequency shock oscillations by accommodating fully-developed trailing edge flow separation. Spectral Proper Orthogonal Decomposition (SPOD) analysis showed that overly-narrow aerofoil simulations contain additional domain-dependent energy content at a Strouhal number of St ≈ 3 associated with wake modes.

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated VAN-DAMME code, we carried out QOC calculations of systems containing 10 - 15 qubits, which showed that our GPU implementation is 18.4× faster than the corresponding CPU implementation. Our GPU-accelerated enhancements allow efficient calculations of multi-qubit systems, which can be used for the efficient implementation of QOC applications across multiple domains.

Since the universe is not transparent to gamma rays with energies above around one hundred GeV, it is necessary to account for the interaction of high-energy photons with intergalactic radiation fields in order to model gamma-ray propagation. Here, we present a public numerical software for the modeling of gamma-ray observables. This code computes the effects on gamma-ray spectra from the development of electromagnetic cascades and cosmological redshifting. The code introduced here is based on the original γ-Cascade, and builds on it by improving its performance at high redshifts, introducing new propagation modules, and adding many more extragalactic radiation field models, which enables the ability to estimate the uncertainties inherent to EBL modeling. We compare the results of this new code to existing Monte Carlo electromagnetic transport models, finding good agreement within EBL uncertainties.

We used a new Python code to reproduce the brackets for the Moshinsky harmonic oscillator, which was based on the generating function. We made these brackets by transforming the wave functions of two groups of coupled particle harmonic oscillators, $\Phi_{n_1l_1,n_2l_2,\Lambda}^{m_1,m_2,\lambda}\left(\vec{r}_1,\vec{r}_2\right)$ and $\Phi_{n_al_a,n_bl_b,\Lambda}^{m_a,m_b,\lambda}\left(\vec{r}_a,\vec{r}_b\right)$. To convert between the supplied position and momentum coordinates in both frames, we performed orthogonal transformations on nuclei with both low and high angular momentum. In our derivation, we have used the expansion of the generating functions $e^{2\vec{p}.\vec{r}-p^2}$ and $e^{2cp_i.p_j}$ in spherical coordinates in terms of harmonic oscillator wave functions. When we modified the Moshinsky brackets for two-coupled oscillator states, we used generating functions with two variables. The number of indices has significantly decreased compared to the oscillator brackets in previous references; this reduction in the program code's iterative process has yielded influential results. Compared to the previous version of the Moshinsky brackets code, the new Python code is easier to use. Our approach utilizes this code to assess Moshinsky brackets across a broad spectrum of quantum numbers. According to the revelation, adding more variables to the generating function makes the number of Moshinsky brackets that work for the higher body interactions increase.