Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

VASPKIT: A user-friendly interface facilitating high-throughput computing and analysis using VASP code

International roadmap for devices and systems. Cryogenic electronics and quantum information processing. 2018 Update

Providing fresh and drinkable water is a grand challenge the world is facing today. Development in nanomaterials can create possibilities of using energy-efficient nanoporous materials for water desalination. In this work, we demonstrated that ultrathin conductive metal-organic framework (MOF) is capable of efficiently rejecting ions while giving access to high water flux. Through molecular dynamic simulation, we discovered perfect ion rejection rate by two-dimensional (2D) multilayer MOF. The naturally porous structure of 2D MOF enables significantly 3-6 orders of magnitude higher water permeation compared to that of traditional membranes. Few layers MOF membranes show 1 order of magnitude higher water flux compared to that of single-layer nanoporous graphene or molybdenum disulfide (MoS2) without the requirement of drilling pores. The excellent performance of 2D MOF membranes is supported by water permeation calculations, water density/velocity profiles at the pore, and the water interfacial diffusion near the pore. Water desalination performance of MOF offers a potential solution for energy-efficient water desalination.

Water Desalination with Two-Dimensional Metal-Organic Framework Membranes.

Ubiquitous oxygen vacancies (Vo) existing in metallic compounds can activate peroxymonosulfate (PMS) for water treatment. However, under environmental conditions, especially oxygenated surroundings...

Oxygen Vacancy-Induced Nonradical Degradation of Organics: Critical Trigger of Oxygen (O2) in the Fe-Co LDH/Peroxymonosulfate System.

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented,a#13; the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings,a#13; simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more.a#13; Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation detailsa#13; not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.a#13;

https://iopscience.iop.org/article/10.1088/1361-648X/ab4007/pdf

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

Filip Rasmussen

Papers

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

QuantumATK: An integrated platform of electronic and atomic-scale modelling tools