Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel

G.B. Macpherson, M.K. Borg, J.M. Reese

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.
LanguageEnglish
Pages1199-1212
Number of pages13
JournalMolecular Simulation
Volume33
Issue number15
DOIs
Publication statusPublished - Dec 2007

Fingerprint

Molecular Dynamics
Molecular dynamics
mesh
molecular dynamics
Configuration
Molecules
Geometry
Arbitrary
geometry
configurations
cells
Mesh
molecules
Cell
Atoms
Regular hexahedron
preprocessing
Processing
Linearly
polyhedrons

Keywords

  • biochemistry
  • chemical physics
  • materials chemistry
  • physical chemistry
  • simulation
  • modeling
  • statistical mechanics
  • mechanical engineering

Cite this

Macpherson, G.B. ; Borg, M.K. ; Reese, J.M. / Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel. In: Molecular Simulation. 2007 ; Vol. 33, No. 15. pp. 1199-1212.
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Generation of initial molecular dynamics configurations in arbitrary geometries and in parallel. / Macpherson, G.B.; Borg, M.K.; Reese, J.M.

In: Molecular Simulation, Vol. 33, No. 15, 12.2007, p. 1199-1212.

Research output: Contribution to journalArticle

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AU - Borg, M.K.

AU - Reese, J.M.

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N2 - A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.

AB - A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM.

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KW - chemical physics

KW - materials chemistry

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KW - simulation

KW - modeling

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KW - mechanical engineering

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