Computer Physics Communications

A novel Eulerian-Lagrangian MPI parallelized solver is developed to resolve the dynamics of ellipsoidal fibers in the OpenFOAM platform. Due to the nonspherical shape of the ellipsoidal fibers and the dependence of the drag force on the orientation of the fiber, the solver solves the full conservation of linear and angular momentum equations, in addition to the time evolution equation for Euler's parameters, quaternions. To this end, a new parcel type is introduced to represent ellipsoidal fibers with several new properties, including Euler's parameters, angular velocity, and torque class. Finally, new member functions are defined to solve angular momentum and Euler's parameters time evolution equations. The solver is the first publicly available, robust and reliable computational framework for the numerical analysis of ellipsoidal fibers motion. It promotes the capability of the standard Lagrangian OpenFOAM solvers and libraries to capture the orientation and rotational dynamics of nonspherical particles. As validation cases, the solver was applied to four benchmarks: three-dimensional rotation of an ellipsoid in linear shear flow, two-dimensional rotation of a magnetic ellipsoid in linear shear flow subjected to a uniform magnetic field, motion of an ellipsoid in pipe flow, and ellipsoids deposition in three-dimensional bifurcation flow. Comparison of the results with analytical solutions, experimental data and in-silico results indicates close agreements and high accuracy of the developed numerical model for single- and multi-physics test cases.

Structural mechanics is pivotal in comprehending how structures respond to external forces and imposed displacements. Typically, the analysis of structures is performed numerically using the direct stiffness method, which is an implementation of the finite element method. This method is commonly associated with the numerical solution of large systems of equations. However, the underlying theory can also be conveniently used to perform the analysis of structures either symbolically or in a hybrid symbolic-numerical fashion. This approach is useful to mitigate the computational burden as the obtained partial or full symbolic solution can be simplified and used to generate lean code for efficient simulations. Nonetheless, the symbolic direct stiffness method is also useful for model reduction purposes, as it allows the derivation of small-scale models that can be used for diminishing simulation time. Despite the mentioned advantages, symbolic computation carries intrinsically complex operations. In particular, the symbolic solution of large linear systems of equations is hard to compute, and it may not always be available due to software capabilities. This paper introduces a toolbox named TrussMe-Fem, whose implementation is based on the direct stiffness method. TrussMe-Fem leverages Maple®'s symbolic computation and Matlab®'s numerical capabilities for symbolic and hybrid symbolic-numerical analyses and solutions of structures. Efficient code generation is also possible by exploiting the simplification of the problem's expressions. The challenges posed by symbolic computation on the solution of large linear systems are addressed by introducing novel routines for the symbolic matrix factorization with the hierarchical representation of large expressions. For this purpose, the TrussMe-Fem toolbox optionally uses the Lem and Last Maple® packages, which are also available as open-source software.

The set of Maple routines that comprises the package Ndynamics has been improved. Apart one of the main motivations for its creation, namely, the routines to calculate the fractal dimension of boundaries (via box counting), the package deals with the numerical evolution of dynamical systems and provide flexible plotting of the results. The package also brings an initial conditions generator, a numerical solver manager, and a focusing set of routines that allow for better analysis of the graphical display of the results. Many new Maple-in-built numerical solvers are now programmed and available for the user of the package. The novelty that the package presented at the time of its release, an optional numerical interface, is maintained and updated.

Since viscoelastic two-phase flows arise in various industrial and natural processes, developing accurate and efficient software for their detailed numerical simulation is a highly relevant and challenging research task. We present a geometrical unstructured Volume-of-Fluid (VOF) method for handling two-phase flows with viscoelastic liquid phase, where the latter is modeled via generic rate-type constitutive equations and a one-field description is derived by conditional volume averaging of the local instantaneous bulk equations and interface jump conditions. The method builds on the plicRDF-isoAdvector geometrical VOF solver that is extended and combined with the modular framework DeboRheo for viscoelastic computational fluid dynamics (CFD). A piecewise-linear geometrical interface reconstruction technique on general unstructured meshes is employed for discretizing the viscoelastic stresses across the fluid interface. DeboRheo facilitates a flexible combination of different rheological models with appropriate stabilization methods to address the high Weissenberg number problem.

The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and visualizing a broad variety of observables that are relevant to active matter systems. Examples range from the mean-square displacement and the structure factor to cluster-size distributions, binder cumulants, and growth exponents. AMEP is written in pure Python and is based on powerful libraries such as NumPy, SciPy, Matplotlib, and scikit-image. Computationally expensive methods are parallelized and optimized to run efficiently on workstations, laptops, and high-performance computing architectures, and an HDF5-based data format is used in the backend to store and handle simulation data as well as analysis results. AMEP provides the first comprehensive framework for analyzing simulation results of both particle-based and continuum simulations (as well as experimental data) of active matter systems. In particular, AMEP also allows it to analyze simulations that combine particle-based and continuum techniques such as used to study the motion of bacteria in chemical fields or for modeling particle motion in a flow field for example.

OpenFOAM (Open-source Field Operation and Manipulation) has become an important scientific tool for solving computational fluid dynamics due to its free and open-source nature, but its application in reacting flows may be restricted due to either the use of a simplified transport model or the requirement for pre-specified species (binary) mass diffusion coefficients as well as the use of Sutherland's formula. To fill this gap, a detailed transport model using a mixture-averaged formulation based on the standard kinetic theory of gases is newly incorporated into combustion solvers for dealing with reacting flow simulations in OpenFOAM. This is achieved by developing a new utility to input molecular transport parameters and a new library to calculate transport properties. All the codes are completely written under the code framework of OpenFOAM, making them very easy to read, use, maintain, enhance and extend. The developed utility and library are then coupled with a new reacting flow solver developed for the governing equations in terms of mass, momentum, species and energy by configurating an interface. In the present study, the function of the new utility is firstly examined and then a new solver (i.e., standardReactingFoam) is developed for solving reacting flows. A systematical validation and assessment in different flame configurations with detailed chemical kinetics is studied to evaluate the computational performance of these new solvers. A zero-dimensional auto ignition, one-dimensional premixed flame and two-dimensional non-premixed counterflow flame are selected to validate the solvers against Cantera and CHEMKIN, while a realistic combustion simulation of a two-dimensional partially premixed coflow flame is also verified. Numerical simulation results show that very good agreements with the benchmark data are obtained for all studied flames, which demonstrates the high computational accuracy of the developed combustion solvers incorporating a detailed transport model.

We introduce the pCI software package for high-precision atomic structure calculations. The standard method of calculation is based on the configuration interaction (CI) method to describe valence correlations, but can be extended to attain better accuracy by including core correlations via many-body perturbation theory (CI+MBPT) or the all-order (CI+all-order) method. The software package enables calculations of atomic properties, including energy levels, g-factors, hyperfine structure constants, multipole transition matrix elements, polarizabilities, and isotope shifts. It also features modern high-performance computing paradigms, including dynamic memory allocations and large-scale parallelization via the message-passing interface, to optimize and accelerate computations. To improve accuracy of the calculations, we include a supplementary program package to calculate QED corrections via a variant of QEDMOD, as well as a package to include core correlations.

We present a Python-based implementation of a practical procedure of construction of simulation program, which facilitates the calculation of changes to the intensity of RHEED oscillations in the function of the glancing angle of incidence of the electron beam, employing various models of crystal potential for heteroepitaxial structures including the possible existence of various diffuse scattering models through the layer parallel to the surface. The calculations are based on the use of a one-dimensional dynamical diffraction theory. Although this theory has some limitations, in practice it is useful under so-called one-beam condition. Computation performance has been improved by using Numba as an open source, NumPy-aware optimising compiler for Python. The previous version of this program (AETW_v1_0) may be found at https://doi.org/10.1016/j.cpc.2014.07.003.

Quantum technologies like single photon emitters and qubits can be enabled by point defects in semiconductors, with the NV-center in diamond being the most prominent example. There are many different semiconductors, each potentially hosting interesting defects. The symmetry properties of the point defect orbitals can yield useful information about the behavior of the system, such as the interaction with polarized light. We have developed a tool to perform symmetry analysis of point defect orbitals obtained by plane-wave density functional theory simulations. The software tool, named ADAQ-SYM, calculates the characters for each orbital, finds the irreducible representations, and uses selection rules to find which optical transitions are allowed. The capabilities of ADAQ-SYM are demonstrated on several defects in diamond and 4H-SiC. The symmetry analysis explains the different zero phonon line (ZPL) polarization of the hk and kh divacancies in 4H-SiC.

We present MADWAVE3, a FORTRAN90 code designed for quantum time-dependent wave packet propagation in triatomic systems. This program allows the calculation of state-to-state probabilities for inelastic and reactive collisions, as well as photodissociation processes, over one or multiple coupled diabatic electronic states. The code is highly parallelized using MPI and OpenMP. The execution requires the potential energy surfaces of the different electronic states involved, as well as the transition dipole moments for photodissociation processes. The formalism underlying the code is presented in section 2, together with the modular structure of the code. This is followed by the installation procedures and a comprehensive list and explanation of the parameters that control the code, organized within their respective namelists. Finally, a case study is presented, focusing on the prototypical reactive collision H+DH(v, j)→ H2(v', j') + D. Both the potential energy surface and the input files required to reproduce the calculation are provided and are available on the repository's main page. This example is used to study the parallelization speedup of the code.