Computer Physics Communications

Introduction of a twist between layers of two-dimensional materials which leads to the formation of a moiré pattern is an emerging pathway to tune the electronic, vibrational and optical properties. The fascinating properties of these systems are often linked to large-scale structural reconstruction of the moiré pattern. Hence, an essential first step in the theoretical study of these systems is the construction and structural relaxation of the atoms in the moiré superlattice. We present the Twister package, a collection of tools that constructs commensurate superlattices for any combination of 2D materials and also helps perform structural relaxations of the moiré superlattice. Twister constructs commensurate moiré superlattices using the coincidence lattice method and provides an interface to perform structural relaxations using classical forcefields.

We present a package to perform partial fraction decompositions of multivariate rational functions. The algorithm allows to systematically avoid spurious denominator factors and is capable of producing unique results also when being applied to terms of a sum separately. The package is designed to work in Mathematica, but also provides interfaces to the Form and Singular computer algebra systems.

RichardsFoam3 is an updated version of the OpenFOAM® solver RichardsFoam, previously presented in “An open source massively parallel solver for Richards equation: Mechanistic modelling of water fluxes at the watershed scale” by L. Orgogozo, N. Renon, C. Soulaine, F. Hénon, S.K. Tomer, D. Labat, O.S. Pokrovsky, M. Sekhar, R. Ababou, M. Quintard (Comput. Phys. Commun. 185 (2014) 3358-3371, https://doi.org/10.1016/j.cpc.2014.08.004), and in the new version announcement “RichardsFOAM2: a new version of RichardsFOAM devoted to the modelling of the vadose zone” by L. Orgogozo (Comput. Phys. Commun. 196 (2015) 619-620, https://doi.org/10.1016/j.cpc.2015.07.009). This new version includes improvements of memory handling and of on-the-fly control of computations, a better integration in the OpenFOAM® framework, simplifications of the coding of some expressions, as well as new advanced boundary conditions. All together these developments allow to enhance the ease of application of the code to continental surfaces hydrogeology modelling, its computational performances and its readability. The description of the elements contained in this release may be found in the readMe file. Please note that you may also find RichardsFoam3 on the hydrology page of the develop.openfoam.com interface: https://develop.openfoam.com/Community/hydrology/ The previous version of this program (AEUF_v2_0) may be found at https://doi.org/10.1016/j.cpc.2015.07.009.

FourPhonon is a computational package that can calculate four-phonon scattering rates in crystals. It is built within ShengBTE framework, which is a well-recognized lattice thermal conductivity solver based on Boltzmann transport equation. An adaptive energy broadening scheme is implemented for the calculation of four-phonon scattering rates. In analogy with thirdorder.py in ShengBTE, we also provide a separate python script, Fourthorder.py, to calculate fourth-order interatomic force constants. The extension module preserves all the nice features of the well-recognized lattice thermal conductivity solver ShengBTE, including good parallelism and straightforward workflow. In this paper, we discuss the general theory, program design, and example calculations on Si, BAs and LiCoO_2.

Fragmentation-based (FB) methods have been developed for enabling ab initio calculations on large molecules and clusters. However, a well-benchmarked FB-based utility, for calculating the vibrational spectra is not available. The present article reports a software package MTASpec, based on the FB-molecular tailoring approach (MTA), for computing the single point energy followed by vibrational IR and Raman spectra for spatially extended molecular systems. Accuracy and efficiency of MTASpec are assessed vis-à-vis their full calculation counterparts for some medium- to large-sized molecular systems using HF, DFT and MP2 theory employing large basis sets. The code is fully automated for use on linux platform, with the Gaussian suite of software at the back-end. It is envisaged that the MTASpec package would enable spectral studies of molecular systems containing ∼100 atoms and/or ∼10000 basis functions employing correlated theories with computational economy.

FSDS is Fluorescence Spectral Dynamics Simulator, designed to investigate photoinduced charge transfer and its manifestations in time-resolved fluorescence spectra of a dye in a solvent. The project is implemented in C, using the MPI library. The computer model simulates stationary absorption and fluorescence spectra, as well as the time evolution of population distributions along the solvent reaction coordinate, to calculate spectral dynamics. Excitation and relaxation of intramolecular high-frequency vibrations are described at the quantum level. FSDS can fit the physical parameters of the dyes to experimental data. The dye excitation is consistently described accounting for the finite duration of the pump pulse. The program code implements two evolutionary models: a spin-boson model within the harmonic potential and a stochastic model based on the Smoluchowski diffusion operator for an arbitrary free energy surface. Computer simulation shows the numerical coincidence of the calculations performed in the framework of these models for the harmonic free energy surface. The detail description of the code and numerical schemes are presented.

A set of basic components needed for the analysis of state-to-state transitions in molecular dynamics (MD) trajectories is provided in the form of a toolkit. The toolkit can be used to (a) determine long-lived states of the system, (b) identify mechanism for transition from one state to another by listing atoms that participate in the transition, and (c) calculate kinetic parameters associated with the rate process, e.g., rate constants and Arrhenius parameters. Additionally, the toolkit enables the study of rare kinetic events using the temperature programmed MD (TPMD) method. Results obtained with two prototype systems, namely, Ag trimer diffusion, and Li diffusion in LiFePO_4, are discussed to illustrate the application of the toolkit.

We present an approach for integrating the time evolution of quantum systems. We leverage the computation power of graphics processing units (GPUs) to perform the integration of all time steps in parallel. The performance boost is especially prominent for small to medium-sized quantum systems. The devised algorithm can largely be implemented using the recently-specified batched versions of the BLAS routines, and can therefore be easily ported to a variety of platforms. Our PARAllelized Matrix Exponentiation for Numerical Time evolution (PARAMENT) implementation runs on CUDA-enabled graphics processing units.

We present the ElasTool package, an automated toolkit for calculating the second-order elastic constants (SOECs) of any two- (2D) and three-dimensional (3D) crystal systems. ElasTool uses three kinds of strain-matrix sets, i.e., the high-efficiency strain-matrix sets (OHESS), the universal linear-independent coupling strains (ULICS), and the all-single-element strain-matrix sets (ASESS), to calculate the SOECs automatically. ElasTool can efficiently compute both zero- and high-temperature elastic constants. We describe in detail the theoretical background and computational method of elastic constants, the package structure, the installation, and run, the input/output files, the controlling parameters, and two representative examples of how to use the ElasTool package. ElasTool is useful for either the exploration of materials' elastic properties or high-throughput new materials screening and design. ElasTool is freely available on GitHub: https://github.com/elastool

We provide an efficient ready-to-run code gensaw that generates single or large ensembles of self-avoiding, flexible, semiflexible, rotationally isometric or helical chains in the bulk or subject to arbitrary confinement and tethering conditions, where we allow for arbitrary intramolecular bending and dihedral energy functions. The resulting configuration files are provided in various common formats and can be immediately used to do molecular simulations or statistical analysis. We work out analytic expressions for the mean squared end-to-end distance and gyration radius of the semiflexible, helical and rotational isomeric state models with a finite number of bonds and arbitrary interaction potentials for direct comparison and testing of the code in the limiting case of unconfined phantom chains. In addition to the graphics-free linux standalone batch version gensaw that creates configuration and other files for high throughput applications from the command line, we provide an interactive online version gensaw-visualization that serves as platform-independent graphical user interface, and animates the resulting conformations using a remote gensaw server.