Computer Physics Communications

An algorithm for evaluating Wigner coefficients of U(4) ⊃ SUS(2) ⊗ SUT(2) for the coupling [n14, n24, n34, n44] ⊗ [1, 0, 0, 0] ↓ [m14, m24, m34, m44] with arbitrary irreducible representation [n14, n24, n34, n44] is provided based on the algebraic expressions with the expansion coefficients of the U(4)⊃SUS(2)⊗SUT(2) states in terms of those in the U(4) canonical basis and the Clebsch-Gordan coefficients of U(4) in the canonical basis. The state expansion coefficients are evaluated as the components of the null space vectors of the spin-isospin projection matrices.

A new open source tool for fluid simulation of multi-component plasmas is presented, based on a flexible software design that is applicable to scientific simulations in a wide range of fields. Hermes-3 is built on plasma simulation framework BOUT++, consolidating earlier SD1D and Hermes models into a single code that can be configured at run-time to solve plasma models in 1D, 2D or 3D, either for transport (steady-state) or turbulent (time-evolving) problems, with an arbitrary number of ion and neutral species. We describe the improved numerical algorithms and software design that have been implemented in Hermes-3. To demonstrate the capabilities of this tool, applications relevant to the boundary of tokamak plasmas are presented: 1D simulations of diveror plasmas evolving equations for all charge states of neon and deuterium; 2D transport simulations of tokamak equilibria in single-null X-point geometry with plasma ion and neutral atom species; and simulations of the time-dependent propagation of plasma filaments (blobs). Hermes-3 is publicly available on Github under the GPL-3 open source license. The repository includes documentation and a suite of unit, integrated and convergence tests.

The cosmic ray modulation in the heliosphere models comes to a new phase of their evolution, where the still higher number of models will be public with published source code. At the dawn of this period, we want to address two topics, the statistical error of their results and the uniqueness of their solutions. We present a method for the evaluation of statistical error for the numerical stochastic differential equation method, which is probably the most used method to numerically solve Parker's equation. We defined a limit of statistical error, for which we present a method to estimate the number of particles needed to be simulated to reach this limit. The estimation of statistical error from a scan of parametric space of two currently available models with public code, for the SOLARPROP model and Geliosphere 2D model, is presented. We present a test of the uniqueness of the solution of Parker's equation for 1D and 2D models of heliospheric modulation. Namely for the 1D B-p model and Geliosphere 2D model. The dependence of solution uniqueness on the selected model's input parameters is presented and discussed.

The stability of colloid is closely related to the aggregation of colloidal particles and the dispersion of clusters in the system. Because aggregation changes the original state of the sol, previous studies have paid more attention to the aggregation process of the colloid. In fact, aggregation process and dispersion process coexist. The Cluster-Cluster Aggregation model has been widely used to simulate the process of colloidal agglomeration. In the aspect of cluster dispersion, people pay more attention to the simulation of cluster dispersion caused by external forces (such as shear force). In the actual system, the sudden decrease of electrolyte concentration leads to the increase of electrostatic repulsion between colloidal particles, resulting in the disintegration of the clusters. Inspired by the dimerization process of the traditional Cluster-Cluster Aggregation model, we previously proposed a dichotomy model to simulate the dispersion process of colloidal clusters. Here, we provide Java code for the dichotomy model, which can simulate dispersion caused by external forces and internal forces. This paper further elaborates the key points of the dichotomy model, mainly including: the definitions of the relevant probabilities involved in the dichotomy model, the data structures of particle, cluster and cube, and the functions of the relevant parameters related to the dichotomy model. Furthermore, the cluster's characteristics of erosion dispersion and collapse dispersion are studied respectively.

We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and usability. EasyScan_HEP allows us to connect different programs that calculate physical observables, and apply constraints by one human-readable configuration file. All programs executed through command lines can be connected to EasyScan_HEP by setting input and output parameters of the programs. The current version offers the sampling algorithms of Random, Grid, Markov chain Monte Carlo and MultiNest. We also implement features such as resume function, parallelization, post-processing, and quick analysis.

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 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. QMMM 2023 supports GAMESS-US, Gaussian, 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 scheme, balanced-RCD scheme, 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 QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. 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.

We present an open-source software package, TRAVOLTA (Terrific Refinements to Accelerate, Validate, and Optimize Large Time-dependent Algorithms), for carrying out massively parallelized quantum optimal control calculations on GPUs. The TRAVOLTA software package is a significant overhaul of our previous NIC-CAGE algorithm and also includes algorithmic improvements to the gradient ascent procedure to enable faster convergence. We examine three different variants of GPU parallelization to assess their performance in constructing optimal control fields in a variety of quantum systems. In addition, we provide several examples with extensive benchmarks of our GPU-enhanced TRAVOLTA code to show that it generates the same results as previous CPU-based algorithms but with a speedup that is more than ten times faster. Our GPU enhancements and algorithmic improvements enable large quantum optimal control calculations that can be efficiently and routinely executed on modern multi-core computational hardware.

Here we describe an efficient numerical implementation of the Bethe-Salpeter equation to obtain the excitonic spectrum of semiconductors. This is done on the electronic structure calculated either at the simplest tight-binding level or through density functional theory calculations based on local orbitals. We use a simplified model for the electron-electron interactions which considers atomic orbitals as point-like orbitals and a phenomenological screening. The optical conductivity can then be optionally computed within the Kubo formalism. Our results for paradigmatic two-dimensional materials such as hBN and MoS2, when compared with those of more sophisticated first-principles methods, are excellent and envision a practical use of our implementation beyond the computational limitations of such methods.

This paper contributes an open source software - SMIwiz, which integrates seismic modelling, reverse time migration (RTM), and full waveform inversion (FWI) into a unified computer implementation. SMIwiz has the machinery to do both 2D and 3D simulation in a consistent manner. The package features a number of computational recipes for efficient calculation of imaging condition and inversion gradient: a dynamic evolving computing box to limit the simulation cube and a well-designed wavefield reconstruction strategy to reduce the memory consumption when dealing with 3D problems. The modelling in SMIwiz runs independently: each shot corresponds to one processor in a bijective manner to maximize the scalability. A batchwise job scheduling strategy is designed to handle large 3D imaging tasks on computer with limited number of cores. The viability of SMIwiz is demonstrated by a number of applications on benchmark models.

We present the MsSpec Atomic Scattering Amplitude Package (MASAP), composed of a computation program and a graphical interface to generate atomic scattering amplitude (ASA) of an atom, either isolated or embedded in an environment, at any chosen energy of the impinging electron up to ≈15 KeV. The ASA is calculated using an effective, complex optical potential which provides damping effects in the scattering process in a fully relativistic framework. Optionally, scalar relativistic and non-relativistic approximations are also available to assess their applicability to a given problem. In order to describe electron propagation in solids we suggest to replace ASA's based on Plane Waves (PW) scattering with effective ASA's based on curved Spherical Waves (SW) using truncated-overlapped potentials of the Muffin-Tin (MT) type constructed according to the Mattheiss prescription. The graphical user interface generates not only ASA data files providing atomic Differential Cross Sections (DCS) but also files of related quantities such as total Cross Section (CS), both elastic and inelastic, atomic t_l-matrices and phase shifts. We found in general that the imaginary part of the optical potential enhances the calculated elastic DCSs in the forward direction compared to the same potential without the imaginary part, a feature related to the optical theorem, but gives rise to a lower intensity at all other directions as expected due to the damping effect of the complex part of the potential. We show calculated differential and transport Cross Sections for aluminum and gold atoms both in isolation and in crystals with the Face-Centered-Cubic (FCC) structure.