IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers
We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are...
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| Published in | International journal of modern physics. C, Computational physics, physical computation Vol. 8; no. 5; pp. 1131 - 1140 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
World Scientific Publishing Company
01.10.1997
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0129-1831 1793-6586 |
| DOI | 10.1142/S0129183197000990 |
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| Abstract | We report on implementation and performance of the program
IMD, designed for short range molecular dynamics simulations on
massively parallel computers. After a short explanation of the
cell-based algorithm, its extension to parallel computers as well as
two variants of the communication scheme are discussed. We provide
performance numbers for simulations of different sizes and compare
them with values found in the literature. Finally we describe two
applications, namely a very large scale simulation with more than
1.23×109 atoms, to our knowledge the largest published MD
simulation up to this day and a simulation of a crack propagating in a
two-dimensional quasicrystal. |
|---|---|
| AbstractList | We report on implementation and performance of the program
IMD, designed for short range molecular dynamics simulations on
massively parallel computers. After a short explanation of the
cell-based algorithm, its extension to parallel computers as well as
two variants of the communication scheme are discussed. We provide
performance numbers for simulations of different sizes and compare
them with values found in the literature. Finally we describe two
applications, namely a very large scale simulation with more than
1.23×109 atoms, to our knowledge the largest published MD
simulation up to this day and a simulation of a crack propagating in a
two-dimensional quasicrystal. We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are discussed. We provide performance numbers for simulations of different sizes and compare them with values found in the literature. Finally we describe two applications, namely a very large scale simulation with more than 1.23×10 9 atoms, to our knowledge the largest published MD simulation up to this day and a simulation of a crack propagating in a two-dimensional quasicrystal. |
| Author | Trebin, H.-R. Stadler, J. Mikulla, R. |
| Author_xml | – sequence: 1 givenname: J. surname: Stadler fullname: Stadler, J. email: joerg.stadler@itap.physik.uni-stuttgart.de organization: Institut für Theoretische und Angewandte Physik (ITAP), Universitäat Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany – sequence: 2 givenname: R. surname: Mikulla fullname: Mikulla, R. organization: Institut für Theoretische und Angewandte Physik (ITAP), Universitäat Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany – sequence: 3 givenname: H.-R. surname: Trebin fullname: Trebin, H.-R. organization: Institut für Theoretische und Angewandte Physik (ITAP), Universitäat Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany |
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| Cites_doi | 10.1006/jcph.1993.1094 10.1016/0167-8191(94)90080-9 10.1103/PhysRevLett.76.2318 10.1006/jcph.1995.1039 |
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IMD, designed for short range molecular dynamics simulations on
massively parallel computers. After... We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After... |
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