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Volumn 126, Issue 3, 2000, Pages 310-329

Moldy: A portable molecular dynamics simulation program for serial and parallel computers

Author keywords

[No Author keywords available]

Indexed keywords

BOUNDARY CONDITIONS; C (PROGRAMMING LANGUAGE); COMPUTER SIMULATION; COMPUTER SOFTWARE; MATHEMATICAL MODELS; OPTIMIZATION; PARALLEL PROCESSING SYSTEMS;

EID: 0034635944     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4655(99)00496-8     Document Type: Article
Times cited : (262)

References (41)
  • 1
    • 34548717559 scopus 로고
    • Phase transitions for a hard sphere system
    • B.J. Alder, T.E. Wainwright, Phase transitions for a hard sphere system, J. Chemical Phys. 27 (1957) 1208-1209.
    • (1957) J. Chemical Phys. , vol.27 , pp. 1208-1209
    • Alder, B.J.1    Wainwright, T.E.2
  • 3
    • 0025236121 scopus 로고
    • Evaluation of temperature in molecular dynamics simulation
    • M. Amini, D. Fincham, Evaluation of temperature in molecular dynamics simulation, Comput. Phys. Commun. 56 (1990) 313-324.
    • (1990) Comput. Phys. Commun. , vol.56 , pp. 313-324
    • Amini, M.1    Fincham, D.2
  • 4
    • 0000394426 scopus 로고
    • Some multistep methods for use in molecular dynamics calculations
    • D. Beeman, Some multistep methods for use in molecular dynamics calculations, J. Comput. Phys. 20 (1976) 130-139.
    • (1976) J. Comput. Phys. , vol.20 , pp. 130-139
    • Beeman, D.1
  • 5
    • 0001568331 scopus 로고
    • L'énergie éectrostatique de rèseaux ioniques
    • F. Berthaut, L'énergie éectrostatique de rèseaux ioniques, J. Phys. Radium 13 (1952) 499-505.
    • (1952) J. Phys. Radium , vol.13 , pp. 499-505
    • Berthaut, F.1
  • 7
    • 0022099580 scopus 로고
    • Parallelism in computations in quantum and statistical mechanics
    • E. Clementi, G. Corongiu, J.H. Detrich, Parallelism in computations in quantum and statistical mechanics, Comput. Phys. Commun. 37 (1985) 287-294.
    • (1985) Comput. Phys. Commun. , vol.37 , pp. 287-294
    • Clementi, E.1    Corongiu, G.2    Detrich, J.H.3
  • 8
    • 0000623669 scopus 로고
    • On the representation of orientation space
    • D.J. Evans, On the representation of orientation space, Molecular Phys. 34 (2) (1977) 317-325.
    • (1977) Molecular Phys. , vol.34 , Issue.2 , pp. 317-325
    • Evans, D.J.1
  • 9
    • 84947409756 scopus 로고
    • Singularity free algorithm for molecular dynamics simulation of rigid polyatomics
    • D.J. Evans, S. Murad, Singularity free algorithm for molecular dynamics simulation of rigid polyatomics, Molecular Phys. 34 (2) (1977) 327-331.
    • (1977) Molecular Phys. , vol.34 , Issue.2 , pp. 327-331
    • Evans, D.J.1    Murad, S.2
  • 10
    • 53549097388 scopus 로고
    • Leapfrog rotational algorithms
    • D. Fincham, Leapfrog rotational algorithms, Molecular Simulations 8 (1992) 165-178.
    • (1992) Molecular Simulations , vol.8 , pp. 165-178
    • Fincham, D.1
  • 11
    • 0028043019 scopus 로고
    • Optimization of the ewald sum for large systems
    • D. Fincham, Optimization of the ewald sum for large systems, Molecular Simulations 13 (1) (1994) 1-
    • (1994) Molecular Simulations , vol.13 , Issue.1 , pp. 1
    • Fincham, D.1
  • 12
    • 0001439335 scopus 로고
    • MPI: A message-passing interface standard
    • M.P.I. Forum, MPI: A message-passing interface standard, Internat. J. Supercomput. Appl. 8 (3-4) (1994) 165.
    • (1994) Internat. J. Supercomput. Appl. , vol.8 , Issue.3-4 , pp. 165
  • 14
    • 0003437218 scopus 로고
    • Addison-Wesley, Reading, MA, 2nd edn.
    • H. Goldstein, Classical Mechanics (Addison-Wesley, Reading, MA, 2nd edn., 1980).
    • (1980) Classical Mechanics
    • Goldstein, H.1
  • 16
    • 85031576980 scopus 로고
    • Battelle Pacific Northwest Laboratory, Available by Internet ftp from URL
    • R.J. Harrison, TCGMSG Send/receive Subroutines, Battelle Pacific Northwest Laboratory, 1994. Available by Internet ftp from URL ftp://ftp.tcg.anl.gov/pub/tcgmst/tcgmsg-4.04.tar.Z .
    • (1994) TCGMSG Send/Receive Subroutines
    • Harrison, R.J.1
  • 17
    • 0007153809 scopus 로고
    • Large numbers of particles on the cray-1
    • D.M. Heyes, Large numbers of particles on the cray-1, Inform. Quarterly - CCP5 25 (1987) 57-61.
    • (1987) Inform. Quarterly - CCP5 , vol.25 , pp. 57-61
    • Heyes, D.M.1
  • 18
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover, Canonical dynamics: Equilibrium phase-space distributions, Phys. Rev. A 31 (1985) 1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 22
    • 0007286276 scopus 로고
    • Computer simulation package for liquids and solids with polar interactions. I. McMoldyn/H2O: Aqueous systems
    • IBM Corporation, Kingston
    • A. Laakonsen, Computer simulation package for liquids and solids with polar interactions. I. McMoldyn/H2O: Aqueous systems, Internal Report KGN-41, IBM Corporation, Kingston, 1985.
    • (1985) Internal Report KGN-41
    • Laakonsen, A.1
  • 24
    • 84943502952 scopus 로고
    • A molecular dynamics method for simulations in the canonical ensemble
    • S. Nosé, A molecular dynamics method for simulations in the canonical ensemble, Molecular Phys. 52 (1984) 255-268.
    • (1984) Molecular Phys. , vol.52 , pp. 255-268
    • Nosé, S.1
  • 25
    • 84926811618 scopus 로고
    • Constant pressure molecular dynamics for molecular systems
    • S. Nosé, M.L. Klein, Constant pressure molecular dynamics for molecular systems, Molecular Phys. 50 (5) (1983) 1055-1076.
    • (1983) Molecular Phys. , vol.50 , Issue.5 , pp. 1055-1076
    • Nosé, S.1    Klein, M.L.2
  • 26
    • 0019707626 scopus 로고
    • Polymorphic transitions in single crystals: A new molecular dynamics method
    • M. Parrinello, A. Rahman, Polymorphic transitions in single crystals: A new molecular dynamics method, J. Appl. Phys. 52 (12) (1981) 7182-7190.
    • (1981) J. Appl. Phys. , vol.52 , Issue.12 , pp. 7182-7190
    • Parrinello, M.1    Rahman, A.2
  • 29
    • 0007222009 scopus 로고
    • Quaternion-based reorientation conditions for molecular dynamics analyses
    • G.S. Pawley, M.T. Dove, Quaternion-based reorientation conditions for molecular dynamics analyses, Molecular Phys. 55 (5) (1985) 1147-1157.
    • (1985) Molecular Phys. , vol.55 , Issue.5 , pp. 1147-1157
    • Pawley, G.S.1    Dove, M.T.2
  • 32
    • 49549172545 scopus 로고
    • New methods for searching for neighbours in molecular dynamics computations
    • B. Quentrec, C. Brot, New methods for searching for neighbours in molecular dynamics computations, J. Comput. Phys. 13 (1975) 430- 432.
    • (1975) J. Comput. Phys. , vol.13 , pp. 430-432
    • Quentrec, B.1    Brot, C.2
  • 33
    • 33847005283 scopus 로고
    • Correlations in the motions of atoms in liquid argon
    • A. Rahman, Correlations in the motions of atoms in liquid argon, Phys. Rev. 136 A (1964) 405-411.
    • (1964) Phys. Rev. , vol.136 A , pp. 405-411
    • Rahman, A.1
  • 34
    • 0021478523 scopus 로고
    • Molecular dynamics simulation of solid n-butane
    • K. Refson, Molecular dynamics simulation of solid n-butane, Physica 131 B (1985) 256-266.
    • (1985) Physica , vol.131 B , pp. 256-266
    • Refson, K.1
  • 35
    • 0000915173 scopus 로고
    • Molecular dynamics studies of the condensed phases of n-butane and their transitions, I, Techniques and model results
    • K. Refson, G.S. Pawley, Molecular dynamics studies of the condensed phases of n-butane and their transitions, I, Techniques and model results, Molecular Phys. 61 (3) (1987) 669-692.
    • (1987) Molecular Phys. , vol.61 , Issue.3 , pp. 669-692
    • Refson, K.1    Pawley, G.S.2
  • 36
    • 0001678304 scopus 로고
    • On the accuracy of some common molecular dynamics algorithms
    • P.M. Rodger, On the accuracy of some common molecular dynamics algorithms, Molecular Simulations 3 (1989) 263-269.
    • (1989) Molecular Simulations , vol.3 , pp. 263-269
    • Rodger, P.M.1
  • 37
    • 0026120011 scopus 로고
    • Molecular dynamics on hypercube parallel computers
    • W. Smith, Molecular dynamics on hypercube parallel computers, Comput. Phys. Commun. 62 (1991) 229-248.
    • (1991) Comput. Phys. Commun. , vol.62 , pp. 229-248
    • Smith, W.1
  • 38
    • 0026624356 scopus 로고
    • A replicated-data molecular dynamics strategy for the parallel Ewald sum
    • W. Smith, A replicated-data molecular dynamics strategy for the parallel Ewald sum, Comput. Phys. Commun. 67 (1992) 392-406.
    • (1992) Comput. Phys. Commun. , vol.67 , pp. 392-406
    • Smith, W.1
  • 39
    • 0004322263 scopus 로고
    • SERC, Daresbury Laboratory, CCP5 Program Library
    • W. Smith, D. Fincham, The Program MDMPOL (SERC, Daresbury Laboratory, 1982). CCP5 Program Library .
    • (1982) The Program MDMPOL
    • Smith, W.1    Fincham, D.2
  • 40
    • 0000926374 scopus 로고
    • An improved algorithm for molecular dynamics simulation of rigid molecules
    • R. Sonnenschein, An improved algorithm for molecular dynamics simulation of rigid molecules, J. Comput. Phys. 59 (2) (1985) 347-350.
    • (1985) J. Comput. Phys. , vol.59 , Issue.2 , pp. 347-350
    • Sonnenschein, R.1
  • 41
    • 36049060961 scopus 로고
    • Computer 'experiments' on classical fluids, I, Thermodynamical properties of lennard-jones molecules
    • L. Verlet, Computer 'experiments' on classical fluids, I, Thermodynamical properties of lennard-jones molecules, Phys. Rev. 165 (1967) 201-214 .
    • (1967) Phys. Rev. , vol.165 , pp. 201-214
    • Verlet, L.1


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