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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

http://kth.diva-portal.org/smash/get/diva2:1303357/FULLTEXT01

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

In this work, two-dimensional particle-in-cell simulations are used to examine the electron physics in the rod-pinch diode, a device that can be used to produce a relatively low-energy (a few MeV) radiographic electron source. It is found that with diode parameters for which the electrons’ dominant dynamics are approximated well as a magnetized fluid, the diode produces an electron source with a desired small spot size as the electrons drift to and impinge on the anode tip. However, for a large cathode-to-anode radius ratio, a population of electrons that consists predominantly of electrons emitted from the downstream surface of the cathode is found to propagate in the upstream direction and the diode may perform anomalously as a consequence. A method is proposed for improving the quality of the electron source by suppressing electron emission from the downstream cathode surface to reduce the presence of unmagnetized electrons.

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Electron Dynamics of the Rod-Pinch Diode in the Cygnus Experiment at Los Alamos

Summary form only given, as follows Discharges driven at the series resonance frequency have many desirable properties The input resistance is small, and the voltage and current are in phase The voltage drive is small (/spl sim/Te) and the average plasma potential is low (/spl sim/10 Te) Such is observed experimentally and in our PIC-MCC simulations Scaling laws at fixed pressure show peak electron density proportional to the cube of the drive frequency (capacitive discharge is as the square), permitting the density to be controlled Simulation results show at low pressure, the ion energy distribution at the target has a sharp peak at the plasma potential with narrow angular spread about the normal The V-I phase angle versus I curve is measured in simulation and compared with experimental results and the theoretical scaling laws are compared with simulation results and the transition of a capacitively coupled plasma to a resonantly sustained plasma is discussed During this transition or "lock-on" (which occurs in a few RF cycles, a time scale much faster then ion related frequencies), the plasma changes dramatically: the electron kinetic energy and the plasma potential more than doubles; the circuit impedance of the discharge goes from capacitive to resistive; the motion of bulk plasma changes from nearly in phase to nearly out of phase with the voltage drive; and the characteristic heating pattern of these discharges takes shape In these discharges, the formation of high velocity electron bunches in the sheath regions is seen During an RF cycle, these bunches are alternately accelerated from each sheath into the bulk plasma We speculate these bunches provide the ionization in resonantly sustained discharges We also speculate that the lock-on process is similar to the mode-jumping seen in other resonantly and surface wave sustained discharges

Resonant discharges: initiation and steady state; comparisons with theory, simulation and experiment

Recent innovations in large-scale 3-D kinetic simulations along with advanced visualization techniques are facilitating new scientific discoveries into the basic physics of collisionless magnetic reconnection. Present supercomputers are now fully capable of exploring the dynamics of large-scale electron-positron plasmas, whereas the next generation will extend this capability to allow first-principle simulations of magnetic reconnection in electron-proton plasmas.

Kevin J. Bowers

Papers

Electron Dynamics of the Rod-Pinch Diode in the Cygnus Experiment at Los Alamos

Resonant discharges: initiation and steady state; comparisons with theory, simulation and experiment

New Insights Into Collisionless Magnetic Reconnection Enabled by Ultra-High Performance Three-Dimensional Kinetic Simulations

Is Guide Field Reconnection Inherently Turbulent

Fully Kinetic 3D Simulations of Collisionless Reconnection in Large-Scale Pair Plasmas