Fast parallel algorithms for short-range molecular dynamics
01 May 1993-
TL;DR: 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.
Abstract: 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.
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TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
12,985 citations
TL;DR: The Open Visualization Tool (OVITO) as discussed by the authors is a 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations, which is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface.
Abstract: The Open Visualization Tool (OVITO) is a new 3D visualization software designed for post-processing atomistic data obtained from molecular dynamics or Monte Carlo simulations. Unique analysis, editing and animations functions are integrated into its easy-to-use graphical user interface. The software is written in object-oriented C++, controllable via Python scripts and easily extendable through a plug-in interface. It is distributed as open-source software and can be downloaded from the website http://ovito.sourceforge.net/.
8,956 citations
TL;DR: A review of the literature on thermal transport in nanoscale devices can be found in this article, where the authors highlight the recent developments in experiment, theory and computation that have occurred in the past ten years and summarizes the present status of the field.
Abstract: Rapid progress in the synthesis and processing of materials with structure on nanometer length scales has created a demand for greater scientific understanding of thermal transport in nanoscale devices, individual nanostructures, and nanostructured materials. This review emphasizes developments in experiment, theory, and computation that have occurred in the past ten years and summarizes the present status of the field. Interfaces between materials become increasingly important on small length scales. The thermal conductance of many solid–solid interfaces have been studied experimentally but the range of observed interface properties is much smaller than predicted by simple theory. Classical molecular dynamics simulations are emerging as a powerful tool for calculations of thermal conductance and phonon scattering, and may provide for a lively interplay of experiment and theory in the near term. Fundamental issues remain concerning the correct definitions of temperature in nonequilibrium nanoscale systems. Modern Si microelectronics are now firmly in the nanoscale regime—experiments have demonstrated that the close proximity of interfaces and the extremely small volume of heat dissipation strongly modifies thermal transport, thereby aggravating problems of thermal management. Microelectronic devices are too large to yield to atomic-level simulation in the foreseeable future and, therefore, calculations of thermal transport must rely on solutions of the Boltzmann transport equation; microscopic phonon scattering rates needed for predictive models are, even for Si, poorly known. Low-dimensional nanostructures, such as carbon nanotubes, are predicted to have novel transport properties; the first quantitative experiments of the thermal conductivity of nanotubes have recently been achieved using microfabricated measurement systems. Nanoscale porosity decreases the permittivity of amorphous dielectrics but porosity also strongly decreases the thermal conductivity. The promise of improved thermoelectric materials and problems of thermal management of optoelectronic devices have stimulated extensive studies of semiconductor superlattices; agreement between experiment and theory is generally poor. Advances in measurement methods, e.g., the 3ω method, time-domain thermoreflectance, sources of coherent phonons, microfabricated test structures, and the scanning thermal microscope, are enabling new capabilities for nanoscale thermal metrology.
2,933 citations
University of Udine1, École Polytechnique Fédérale de Lausanne2, University of Lugano3, Leipzig University4, University of Paris5, University of North Texas6, Princeton University7, National Research Council8, International School for Advanced Studies9, Cornell University10, University of Lincoln11, University of Milan12, École Polytechnique13, International Centre for Theoretical Physics14, University of Paderborn15, University of Oxford16, Jožef Stefan Institute17, University of Padua18, Sapienza University of Rome19, Vietnam Academy of Science and Technology20, University of British Columbia21, Centre national de la recherche scientifique22, University of Lorraine23, École Normale Supérieure24, University of Zurich25, Université Paris-Saclay26, Wake Forest University27, Temple University28
TL;DR: Quantum ESPRESSO as discussed by the authors is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density functional theory, density functional perturbation theory, and many-body perturbations theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches.
Abstract: Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.
2,818 citations
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TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
12,985 citations
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
Abstract: The equation of motion of a system of 864 particles interacting through a Lennard-Jones potential has been integrated for various values of the temperature and density, relative, generally, to a fluid state. The equilibrium properties have been calculated and are shown to agree very well with the corresponding properties of argon. It is concluded that, to a good approximation, the equilibrium state of argon can be described through a two-body potential.
7,564 citations
"Fast parallel algorithms for short-..." refers background in this paper
...For short–range MD the computational effort per timestep scales as N , the number of atoms....
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01 Jan 1966TL;DR: In this paper, a simulation program for particle-mesh force calculation is presented, based on a one-dimensional plasma model and a collisionless particle model, which is used to simulate collisionless particle models.
Abstract: Computer experiments using particle models A one-dimensional plasma model The simulation program Time integration schemes The particle-mesh force calculation The solution of field equations Collisionless particle models Particle-particle/particle-mesh algorithms Plasma simulation Semiconductor device simulation Astrophysics Solids, liquids and phase changes Fourier transforms Fourier series and finite Fourier transforms Bibliography Index
6,376 citations
TL;DR: In this paper, the authors derived an expression for the total energy of a metal using the embedding energy from which they obtained several ground-state properties, such as the lattice constant, elastic constants, sublimation energy, and vacancy-formation energy.
Abstract: We develop the embedded-atom method [Phys. Rev. Lett. 50, 1285 (1983)], based on density-functional theory, as a new means of calculating ground-state properties of realistic metal systems. We derive an expression for the total energy of a metal using the embedding energy from which we obtain several ground-state properties, such as the lattice constant, elastic constants, sublimation energy, and vacancy-formation energy. We obtain the embedding energy and accompanying pair potentials semiempirically for Ni and Pd, and use these to treat several problems: surface energy and relaxation of the (100), (110), and (111) faces; properties of H in bulk metal (H migration, binding of H to vacancies, and lattice expansion in the hydride phase); binding site and adsorption energy of hydrogen on (100), (110), and (111) surfaces; and lastly, fracture of Ni and the effects of hydrogen on the fracture. We emphasize problems with hydrogen and with surfaces because none of these can be treated with pair potentials. The agreement with experiment, the applicability to practical problems, and the simplicity of the technique make it an effective tool for atomistic studies of defects in metals.
5,912 citations
"Fast parallel algorithms for short-..." refers methods in this paper
...An implementation for the embedded atom method (EAM) potentials [18] used in modeling metals and metal alloys is discussed in [43] and a FD implementation of the many–body forces (angular, torsional) encountered in molecular simulations is presented in [42]....
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TL;DR: An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles whose interactions are Coulombic or gravitational in nature, making it considerably more practical for large-scale problems encountered in plasma physics, fluid dynamics, molecular dynamics, and celestial mechanics.
5,003 citations
"Fast parallel algorithms for short-..." refers background in this paper
...The fact that MD computations are inherently parallel has been extensively discussed in the literature [11, 22]....
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