Computer Physics Communications

The two main thrusts of computational science are increasingly accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g. neural network potentials, and novel hardware architectures, e.g. GPUs. Current implementations of neural network potentials are orders of magnitude slower than traditional interatomic models and while looming exascale computing offers the ability to run large, accurate simulations with these models, achieving portable performance for MD with new and varied exascale hardware requires rethinking traditional algorithms, using novel data structures, and library solutions. We re-implement a neural network interatomic model in CabanaMD, an MD proxy application, built on libraries developed for performance portability. Our implementation shows significantly improved thread scaling in this complex kernel as compared to a current LAMMPS implementation, across both strong and weak scaling. Our single-source solution enables simulations up to 20 million atoms on a single CPU node and 4 million atoms with improved performance on a single GPU. We also explore parallelism and data layout choices (using flexible data structures called AoSoAs) and their effect on performance, seeing up to ∼50% and ∼5% improvements in performance on a GPU by choosing the right level of parallelism and data layout respectively.

In this paper, we present “QDD” (Quantum Dissipative Dynamics), a code package for simulating the dynamics of electrons and ions in finite electron systems (atoms, molecules, clusters) under the influence of external electromagnetic fields. Electron emission is properly accounted for. The novel feature of the present code is that it also covers the description of dissipative dynamics induced by dynamical correlations generated by electron-electron collisions. The paper reviews the underlying theoretical as well as numerical methods and demonstrates the code's capabilities on a selection of typical examples.

In this article we present REvolver, a C++ library for renormalization group evolution and automatic flavor matching of the QCD coupling and quark masses, as well as precise conversion between various quark mass renormalization schemes. The library systematically accounts for the renormalization group evolution of low-scale short-distance masses which depend linearly on the renormalization scale and sums logarithmic terms of high and low scales that are missed by the common logarithmic renormalization scale evolution. The library can also be accessed through Mathematica and Python interfaces and provides renormalization group evolution for complex renormalization scales as well.

In this release note we describe the 1.2 update to NLOX, a computer program for calculations in high-energy particle physics. New features since the 1.0 release and other changes are described, along with usage documentation.

We present a Mathematica program package MagneticTB, which can generate the tight-binding model for arbitrary magnetic space group. The only input parameters in MagneticTB are the (magnetic) space group number and the orbital information in each Wyckoff position. Some useful functions including getting the matrix expression for symmetry operators, manipulating the energy band structure by parameters, and interfacing with other software are also developed. MagneticTB can help to investigate the physical properties in both magnetic and non-magnetic system, especially for topological properties.

TUMME is a program for assembling and solving master equations for gas-phase chemical kinetics based on chemically significant eigenmodes. TUMME has interfaces to the Gaussian, Polyrate, and/or MSTor output files that allow the master equation code to obtain the microcanonical flux coefficients needed for the coefficient matrix of the master equation. The flux coefficients for reactions with barriers can be calculated by multi-structural variational transition state theory with small-curvature tunneling (MS-VTST/SCT) or by simpler approximations to this such as conventional transition state theory without tunneling (also called RRKM theory). The flux coefficients for barrierless reactions are provided by a hard-sphere model. TUMME is written in double precision with Python 3; quadruple and octuple precision are also available for some subtasks in C++. The Python code can run in serial or parallel (MP or MPI), and the C++ code can run on a single processor or on multiple processors with OpenMP.

In recent years three-, four- and five-loop beta functions have been computed for various phenomenologically interesting models. However, most of these results have not been implemented in easy to use software packages. RGE++ bridges this gap by providing a flexible, template-based, C++ library to solve renormalisation group equations. Furthermore, we implement the available beta functions for the Standard Model, the minimal supersymmetric extension of the Standard Model and two-Higgs-doublet models, as well as right-handed neutrino extensions of the former two.

Quantum transport has far-reaching applications in modern electronics as it enables the control of currents in nanoscale systems such as quantum dots. In this paper we introduce TINIE: a state-of-the-art quantum transport simulation framework, which can efficiently perform first-principle calculations based on the Landauer-Büttiker formalism. The computational repertoire of TINIE includes calculations of transmission, conductivity, and currents running through arbitrary multi-terminal two-dimensional transport devices, with additional tools that enable the computation of the local density of states. The generality of TINIE ranges from wide-band approximation calculations to investigating systems subject to an external magnetic field. The future prospects of TINIE include the simulation of, e.g., two-dimensional cavities, quantum dots, or molecular junctions. The package is written in Python 3.6, and its well-documented modular structure is designed with an intent to create a platform suited for continuous expansion and development. With TINIE it is possible to obtain specific information about the effects of impurities and imperfections in quantum devices, particularly between ballistic and diffusive transport regimes.

CMInject simulates nanoparticle injection experiments of particles with diameters in the micrometer to nanometer-regime, e.g., for single-particle-imaging experiments. Particle-particle interactions and particle-induced changes in the surrounding fields are disregarded, due to low nanoparticle concentration in these experiments. CMInject's focus lies on the correct modeling of different forces on such particles, such as fluid-dynamics or light-induced interactions, to allow for simulations that further the scientific development of nanoparticle injection pipelines. To provide a usable basis for this framework and allow for a variety of experiments to be simulated, we implemented first specific force models: fluid drag forces, Brownian motion, and photophoretic forces. For verification, we benchmarked a drag-force-based simulation against a nanoparticle focusing experiment. We envision its use and further development by experimentalists, theorists, and software developers.

The rise of virtual and augmented reality systems has prompted an increase in interest in the fields of 2D and 3D computer-generated holography (CGH). The numerical processing required to generate a hologram is high and requires significant domain expertise. This has historically slowed the adoption of CGH in emerging fields. In this paper we introduce HoloGen, an open-source Cuda C and C++ framework for computer-generated holography. HoloGen unites, for the first time, a wide array of existing hologram generation algorithms with state of the art performance while attempting to remain intuitive and easy to use. This is enabled by a IC# and Windows Presentation Framework (WPF) graphical user interface (GUI). A novel reflection based parameter hierarchy is used to ensure ease of modification. Extensive use of C++ templates based on the Standard Template Library (STL), compile time flexibility is preserved while maintaining runtime performance. The current release of HoloGen unites implementations of well known generation algorithms including Gerchberg-Saxton (GS), Liu-Taghizadeh (LT), direct search (DS), simulated annealing (SA) and one-step phase-retrieval (OSPR) with less known specialist variants including weighted GS and Adaptive OSPR. Benchmarking results are presented for several key algorithms. The software is freely available under an MIT license.