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

This text is a modern treatment of the theory of solids. The core of the book deals with the physics of electron and phonon states in crystals and how they determine the structure and properties of the solid. The discussion uses density functional theory as a starting point and covers electronic and optical phenomena, magnetism and superconductivity. There is also an extensive treatment of defects in solids, including point defects, dislocations, surfaces and interfaces. A number of modern topics where the theory of solids applies are also explored, including quasicrystals, amorphous solids, polymers, metal and semiconductor clusters, carbon nanotubes and biological macromolecules. Numerous examples are presented in detail and each chapter is accompanied by problems and suggested further readings. An extensive set of appendices provides all the necessary background for deriving all the results discussed in the main body of the text.

Atomic and Electronic Structure of Solids

http://library.um.ac.id/free-contents/downloadpdf.php/buku/molecular-dynamics-simulation-elementary-methods-j-m-haile-12315.pdf

Molecular dynamics simulation : elementary methods / J.M. Haile

Introduction to the theory of difference schemes

Supercomputing of the exascale era is going to be inevitably limited by power efficiency. Nowadays different possible variants of CPU architectures are considered. Recently the development of ARM processors has come to the point when their floating point performance can be seriously considered for a range of scientific applications. In this work we present the analysis of the floating point performance of the latest ARM cores and their efficiency for the algorithms of classical molecular dynamics.

https://iopscience.iop.org/article/10.1088/1742-6596/681/1/012049/pdf

Floating-point performance of ARM cores and their efficiency in classical molecular dynamics

This work is devoted to the molecular dynamic simulation of heat action on a metal sample consisting of nickel atoms. For the decision of this problem a continuous mathematical model based on equations of the Newton classical mechanics and a numerical method with the Verlet scheme; are used a parallel algorithm is proposed that is implemented within the MPI and OpenMP technologies. The developed program was used for the investigation the process of establishing thermodynamic equilibrium for nickel atoms at heating the sample up to the specified temperature. In the numerical experiment, both the optimal parameters of the calculation procedure and the physical parameters of the simulated process have been determined. The obtained numerical results are in good agreement with the known theoretical and experimental data.

Molecular dynamic simulation of thermodynamic equilibrium establishment in nickel

Two-scale computation of N 2 –H 2 jet flow based on QGD and MMD on heterogeneous multi-core hardware

The work is devoted to modeling the phase transformations of gas hydrate inclusions in porous media. Studying these problems makes it possible to elaborate various technologies for the development of gas hydrate deposits. A two-block mathematical model of the dissociation of gas hydrates in a porous medium based on splitting with respect to physical processes is proposed and studied. An absolutely stable difference scheme is constructed and implemented in the spatially onedimensional case to numerically analyze the model. The water saturation, thawing, and the thermodynamic parameters (pressure and temperature) are calculated based on this difference scheme. An analysis of the data obtained by the calculations has confirmed the possibility of solving a number of typical problems of gas hydrate fluid dynamics using the above approach, including the problem of the complex dynamics of water and hydrate saturation of a formation.

The Use of Splitting with Respect to Physical Processes for Modeling the Dissociation of Gas Hydrates

Simulation of a system of particles consisting of argon atoms using the molecular dynamics method is considered. An original molecular dynamics program was developed to calculate the parameters of gases on the basis of the Lennard-Jones potential. the conservativeness of the system in the process of calculation is provided by optimization of the time-step value. The process of establishing a uniform distribution of atoms in velocity is investigated.

Molecular dynamics method for simulation of thermodynamic equilibrium

A multiscale approach to computing real gas flows in engineering microchannels on high-performance computer systems in a wide range of Knudsen numbers is described. The numerical implementation of the approach combines the solution of quasigasdynamic equations and the molecular dynamics method. Following the approach, the parameters of the real gas equation of state are found at the molecular level, the kinetic gas properties are calculated, and the form of boundary conditions on the microchannel walls are determined. The technique is verified by computing several test problems. The results agree well with available theoretical and experimental data.

Viktoriia O. Podryga

Papers

Molecular dynamic simulation of thermodynamic equilibrium establishment in nickel

Two-scale computation of N 2 –H 2 jet flow based on QGD and MMD on heterogeneous multi-core hardware

The Use of Splitting with Respect to Physical Processes for Modeling the Dissociation of Gas Hydrates

Molecular dynamics method for simulation of thermodynamic equilibrium

Multiscale approach to computation of three-dimensional gas mixture flows in engineering microchannels