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!! |
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!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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!! |
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!! The University of Notre Dame grants you ("Licensee") a |
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!! non-exclusive, royalty free, license to use, modify and |
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!! redistribute this software in source and binary code form, provided |
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!! that the following conditions are met: |
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!! |
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!! 1. Acknowledgement of the program authors must be made in any |
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!! publication of scientific results based in part on use of the |
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!! program. An acceptable form of acknowledgement is citation of |
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!! the article in which the program was described (Matthew |
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!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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!! Parallel Simulation Engine for Molecular Dynamics," |
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!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
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!! |
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!! 2. Redistributions of source code must retain the above copyright |
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!! notice, this list of conditions and the following disclaimer. |
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!! |
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!! 3. Redistributions in binary form must reproduce the above copyright |
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!! notice, this list of conditions and the following disclaimer in the |
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!! documentation and/or other materials provided with the |
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!! distribution. |
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!! |
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!! This software is provided "AS IS," without a warranty of any |
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!! kind. All express or implied conditions, representations and |
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!! warranties, including any implied warranty of merchantability, |
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!! fitness for a particular purpose or non-infringement, are hereby |
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!! excluded. The University of Notre Dame and its licensors shall not |
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!! be liable for any damages suffered by licensee as a result of |
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!! using, modifying or distributing the software or its |
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!! derivatives. In no event will the University of Notre Dame or its |
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!! licensors be liable for any lost revenue, profit or data, or for |
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!! direct, indirect, special, consequential, incidental or punitive |
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!! damages, however caused and regardless of the theory of liability, |
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!! arising out of the use of or inability to use software, even if the |
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!! University of Notre Dame has been advised of the possibility of |
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!! such damages. |
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!! |
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|
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!! Fortran interface to C entry plug. |
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|
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module simulation |
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use definitions |
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use neighborLists |
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use force_globals |
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use vector_class |
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use atype_module |
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use switcheroo |
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#ifdef IS_MPI |
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use mpiSimulation |
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#endif |
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|
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implicit none |
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PRIVATE |
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|
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#define __FORTRAN90 |
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#include "brains/fSimulation.h" |
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#include "UseTheForce/fSwitchingFunction.h" |
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|
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type (simtype), public, save :: thisSim |
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|
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logical, save :: simulation_setup_complete = .false. |
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|
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integer, public, save :: nLocal, nGlobal |
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integer, public, save :: nGroups, nGroupGlobal |
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integer, public, save :: nExcludes_Global = 0 |
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integer, public, save :: nExcludes_Local = 0 |
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integer, allocatable, dimension(:,:), public :: excludesLocal |
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integer, allocatable, dimension(:), public :: excludesGlobal |
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integer, allocatable, dimension(:), public :: molMembershipList |
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integer, allocatable, dimension(:), public :: groupListRow |
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integer, allocatable, dimension(:), public :: groupStartRow |
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integer, allocatable, dimension(:), public :: groupListCol |
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integer, allocatable, dimension(:), public :: groupStartCol |
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integer, allocatable, dimension(:), public :: groupListLocal |
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integer, allocatable, dimension(:), public :: groupStartLocal |
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integer, allocatable, dimension(:), public :: nSkipsForAtom |
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integer, allocatable, dimension(:,:), public :: skipsForAtom |
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real(kind=dp), allocatable, dimension(:), public :: mfactRow |
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real(kind=dp), allocatable, dimension(:), public :: mfactCol |
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real(kind=dp), allocatable, dimension(:), public :: mfactLocal |
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|
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real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
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logical, public, save :: boxIsOrthorhombic |
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|
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public :: SimulationSetup |
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public :: getNlocal |
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public :: setBox |
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public :: getDielect |
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public :: SimUsesPBC |
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|
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public :: SimUsesDirectionalAtoms |
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public :: SimUsesLennardJones |
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public :: SimUsesElectrostatics |
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public :: SimUsesCharges |
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public :: SimUsesDipoles |
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public :: SimUsesSticky |
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public :: SimUsesGayBerne |
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public :: SimUsesEAM |
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public :: SimUsesShapes |
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public :: SimUsesFLARB |
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public :: SimUsesRF |
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public :: SimRequiresPrepairCalc |
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public :: SimRequiresPostpairCalc |
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|
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|
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contains |
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|
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subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, & |
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CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, & |
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CmolMembership, Cmfact, CnGroups, CglobalGroupMembership, & |
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status) |
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|
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type (simtype) :: setThisSim |
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integer, intent(inout) :: CnGlobal, CnLocal |
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integer, dimension(CnLocal),intent(inout) :: c_idents |
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|
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integer :: CnLocalExcludes |
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integer, dimension(2,CnLocalExcludes), intent(in) :: CexcludesLocal |
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integer :: CnGlobalExcludes |
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integer, dimension(CnGlobalExcludes), intent(in) :: CexcludesGlobal |
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integer, dimension(CnGlobal),intent(in) :: CmolMembership |
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!! Result status, success = 0, status = -1 |
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integer, intent(out) :: status |
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integer :: i, j, me, thisStat, alloc_stat, myNode, id1, id2 |
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integer :: ia |
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|
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!! mass factors used for molecular cutoffs |
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real ( kind = dp ), dimension(CnLocal) :: Cmfact |
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integer, intent(in):: CnGroups |
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integer, dimension(CnGlobal), intent(in):: CglobalGroupMembership |
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integer :: maxSkipsForAtom, glPointer |
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|
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#ifdef IS_MPI |
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integer, allocatable, dimension(:) :: c_idents_Row |
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integer, allocatable, dimension(:) :: c_idents_Col |
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integer :: nAtomsInRow, nGroupsInRow, aid |
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integer :: nAtomsInCol, nGroupsInCol, gid |
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#endif |
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|
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simulation_setup_complete = .false. |
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status = 0 |
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|
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! copy C struct into fortran type |
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|
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nLocal = CnLocal |
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nGlobal = CnGlobal |
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nGroups = CnGroups |
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|
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thisSim = setThisSim |
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|
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nExcludes_Global = CnGlobalExcludes |
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nExcludes_Local = CnLocalExcludes |
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|
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call InitializeForceGlobals(nLocal, thisStat) |
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if (thisStat /= 0) then |
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write(default_error,*) "SimSetup: InitializeForceGlobals error" |
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status = -1 |
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return |
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endif |
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|
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call InitializeSimGlobals(thisStat) |
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if (thisStat /= 0) then |
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write(default_error,*) "SimSetup: InitializeSimGlobals error" |
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status = -1 |
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return |
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endif |
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|
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#ifdef IS_MPI |
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! We can only set up forces if mpiSimulation has been setup. |
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if (.not. isMPISimSet()) then |
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write(default_error,*) "MPI is not set" |
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status = -1 |
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return |
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endif |
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nAtomsInRow = getNatomsInRow(plan_atom_row) |
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nAtomsInCol = getNatomsInCol(plan_atom_col) |
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nGroupsInRow = getNgroupsInRow(plan_group_row) |
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nGroupsInCol = getNgroupsInCol(plan_group_col) |
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mynode = getMyNode() |
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|
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allocate(c_idents_Row(nAtomsInRow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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allocate(c_idents_Col(nAtomsInCol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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call gather(c_idents, c_idents_Row, plan_atom_row) |
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call gather(c_idents, c_idents_Col, plan_atom_col) |
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|
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do i = 1, nAtomsInRow |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents_Row(i)) |
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atid_Row(i) = me |
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enddo |
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|
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do i = 1, nAtomsInCol |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents_Col(i)) |
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atid_Col(i) = me |
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enddo |
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|
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!! free temporary ident arrays |
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if (allocated(c_idents_Col)) then |
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deallocate(c_idents_Col) |
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end if |
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if (allocated(c_idents_Row)) then |
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deallocate(c_idents_Row) |
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endif |
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|
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#endif |
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|
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#ifdef IS_MPI |
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allocate(groupStartRow(nGroupsInRow+1),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupStartCol(nGroupsInCol+1),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupListRow(nAtomsInRow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupListCol(nAtomsInCol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactRow(nAtomsInRow),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactCol(nAtomsInCol),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactLocal(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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glPointer = 1 |
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|
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do i = 1, nGroupsInRow |
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|
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gid = GroupRowToGlobal(i) |
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groupStartRow(i) = glPointer |
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|
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do j = 1, nAtomsInRow |
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aid = AtomRowToGlobal(j) |
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if (CglobalGroupMembership(aid) .eq. gid) then |
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groupListRow(glPointer) = j |
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glPointer = glPointer + 1 |
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endif |
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enddo |
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enddo |
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groupStartRow(nGroupsInRow+1) = nAtomsInRow + 1 |
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|
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glPointer = 1 |
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|
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do i = 1, nGroupsInCol |
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|
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gid = GroupColToGlobal(i) |
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groupStartCol(i) = glPointer |
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|
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do j = 1, nAtomsInCol |
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aid = AtomColToGlobal(j) |
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if (CglobalGroupMembership(aid) .eq. gid) then |
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groupListCol(glPointer) = j |
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glPointer = glPointer + 1 |
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endif |
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enddo |
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enddo |
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groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1 |
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|
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mfactLocal = Cmfact |
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|
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call gather(mfactLocal, mfactRow, plan_atom_row) |
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call gather(mfactLocal, mfactCol, plan_atom_col) |
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|
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if (allocated(mfactLocal)) then |
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deallocate(mfactLocal) |
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end if |
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#else |
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allocate(groupStartRow(nGroups+1),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupStartCol(nGroups+1),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupListRow(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(groupListCol(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactRow(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactCol(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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allocate(mfactLocal(nLocal),stat=alloc_stat) |
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if (alloc_stat /= 0 ) then |
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status = -1 |
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return |
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endif |
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|
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glPointer = 1 |
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do i = 1, nGroups |
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groupStartRow(i) = glPointer |
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groupStartCol(i) = glPointer |
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do j = 1, nLocal |
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if (CglobalGroupMembership(j) .eq. i) then |
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groupListRow(glPointer) = j |
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groupListCol(glPointer) = j |
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glPointer = glPointer + 1 |
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endif |
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enddo |
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enddo |
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groupStartRow(nGroups+1) = nLocal + 1 |
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groupStartCol(nGroups+1) = nLocal + 1 |
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|
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do i = 1, nLocal |
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mfactRow(i) = Cmfact(i) |
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mfactCol(i) = Cmfact(i) |
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end do |
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|
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#endif |
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|
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|
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! We build the local atid's for both mpi and nonmpi |
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do i = 1, nLocal |
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|
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me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
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atid(i) = me |
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|
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enddo |
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|
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do i = 1, nExcludes_Local |
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excludesLocal(1,i) = CexcludesLocal(1,i) |
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excludesLocal(2,i) = CexcludesLocal(2,i) |
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enddo |
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|
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#ifdef IS_MPI |
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allocate(nSkipsForAtom(nAtomsInRow), stat=alloc_stat) |
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#else |
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allocate(nSkipsForAtom(nLocal), stat=alloc_stat) |
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#endif |
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if (alloc_stat /= 0 ) then |
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thisStat = -1 |
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write(*,*) 'Could not allocate nSkipsForAtom array' |
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return |
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endif |
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|
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maxSkipsForAtom = 0 |
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#ifdef IS_MPI |
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do j = 1, nAtomsInRow |
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#else |
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do j = 1, nLocal |
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#endif |
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nSkipsForAtom(j) = 0 |
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#ifdef IS_MPI |
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id1 = AtomRowToGlobal(j) |
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#else |
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id1 = j |
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#endif |
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do i = 1, nExcludes_Local |
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if (excludesLocal(1,i) .eq. id1 ) then |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
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|
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if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
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maxSkipsForAtom = nSkipsForAtom(j) |
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endif |
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endif |
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if (excludesLocal(2,i) .eq. id1 ) then |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
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|
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if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
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maxSkipsForAtom = nSkipsForAtom(j) |
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endif |
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endif |
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end do |
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enddo |
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|
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#ifdef IS_MPI |
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allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat) |
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#else |
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allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat) |
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#endif |
| 417 |
if (alloc_stat /= 0 ) then |
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write(*,*) 'Could not allocate skipsForAtom array' |
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return |
| 420 |
endif |
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|
| 422 |
#ifdef IS_MPI |
| 423 |
do j = 1, nAtomsInRow |
| 424 |
#else |
| 425 |
do j = 1, nLocal |
| 426 |
#endif |
| 427 |
nSkipsForAtom(j) = 0 |
| 428 |
#ifdef IS_MPI |
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id1 = AtomRowToGlobal(j) |
| 430 |
#else |
| 431 |
id1 = j |
| 432 |
#endif |
| 433 |
do i = 1, nExcludes_Local |
| 434 |
if (excludesLocal(1,i) .eq. id1 ) then |
| 435 |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 436 |
! exclude lists have global ID's so this line is |
| 437 |
! the same in MPI and non-MPI |
| 438 |
id2 = excludesLocal(2,i) |
| 439 |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
| 440 |
endif |
| 441 |
if (excludesLocal(2, i) .eq. id1 ) then |
| 442 |
nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 443 |
! exclude lists have global ID's so this line is |
| 444 |
! the same in MPI and non-MPI |
| 445 |
id2 = excludesLocal(1,i) |
| 446 |
skipsForAtom(j, nSkipsForAtom(j)) = id2 |
| 447 |
endif |
| 448 |
end do |
| 449 |
enddo |
| 450 |
|
| 451 |
do i = 1, nExcludes_Global |
| 452 |
excludesGlobal(i) = CexcludesGlobal(i) |
| 453 |
enddo |
| 454 |
|
| 455 |
do i = 1, nGlobal |
| 456 |
molMemberShipList(i) = CmolMembership(i) |
| 457 |
enddo |
| 458 |
|
| 459 |
if (status == 0) simulation_setup_complete = .true. |
| 460 |
|
| 461 |
end subroutine SimulationSetup |
| 462 |
|
| 463 |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
| 464 |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
| 465 |
integer :: cBoxIsOrthorhombic |
| 466 |
integer :: smallest, status, i |
| 467 |
|
| 468 |
Hmat = cHmat |
| 469 |
HmatInv = cHmatInv |
| 470 |
if (cBoxIsOrthorhombic .eq. 0 ) then |
| 471 |
boxIsOrthorhombic = .false. |
| 472 |
else |
| 473 |
boxIsOrthorhombic = .true. |
| 474 |
endif |
| 475 |
|
| 476 |
return |
| 477 |
end subroutine setBox |
| 478 |
|
| 479 |
function getDielect() result(dielect) |
| 480 |
real( kind = dp ) :: dielect |
| 481 |
dielect = thisSim%dielect |
| 482 |
end function getDielect |
| 483 |
|
| 484 |
function SimUsesPBC() result(doesit) |
| 485 |
logical :: doesit |
| 486 |
doesit = thisSim%SIM_uses_PBC |
| 487 |
end function SimUsesPBC |
| 488 |
|
| 489 |
function SimUsesDirectionalAtoms() result(doesit) |
| 490 |
logical :: doesit |
| 491 |
doesit = thisSim%SIM_uses_dipoles .or. thisSim%SIM_uses_sticky .or. & |
| 492 |
thisSim%SIM_uses_GayBerne .or. thisSim%SIM_uses_Shapes |
| 493 |
end function SimUsesDirectionalAtoms |
| 494 |
|
| 495 |
function SimUsesLennardJones() result(doesit) |
| 496 |
logical :: doesit |
| 497 |
doesit = thisSim%SIM_uses_LennardJones |
| 498 |
end function SimUsesLennardJones |
| 499 |
|
| 500 |
function SimUsesElectrostatics() result(doesit) |
| 501 |
logical :: doesit |
| 502 |
doesit = thisSim%SIM_uses_Electrostatics |
| 503 |
end function SimUsesElectrostatics |
| 504 |
|
| 505 |
function SimUsesCharges() result(doesit) |
| 506 |
logical :: doesit |
| 507 |
doesit = thisSim%SIM_uses_Charges |
| 508 |
end function SimUsesCharges |
| 509 |
|
| 510 |
function SimUsesDipoles() result(doesit) |
| 511 |
logical :: doesit |
| 512 |
doesit = thisSim%SIM_uses_Dipoles |
| 513 |
end function SimUsesDipoles |
| 514 |
|
| 515 |
function SimUsesSticky() result(doesit) |
| 516 |
logical :: doesit |
| 517 |
doesit = thisSim%SIM_uses_Sticky |
| 518 |
end function SimUsesSticky |
| 519 |
|
| 520 |
function SimUsesGayBerne() result(doesit) |
| 521 |
logical :: doesit |
| 522 |
doesit = thisSim%SIM_uses_GayBerne |
| 523 |
end function SimUsesGayBerne |
| 524 |
|
| 525 |
function SimUsesEAM() result(doesit) |
| 526 |
logical :: doesit |
| 527 |
doesit = thisSim%SIM_uses_EAM |
| 528 |
end function SimUsesEAM |
| 529 |
|
| 530 |
function SimUsesShapes() result(doesit) |
| 531 |
logical :: doesit |
| 532 |
doesit = thisSim%SIM_uses_Shapes |
| 533 |
end function SimUsesShapes |
| 534 |
|
| 535 |
function SimUsesFLARB() result(doesit) |
| 536 |
logical :: doesit |
| 537 |
doesit = thisSim%SIM_uses_FLARB |
| 538 |
end function SimUsesFLARB |
| 539 |
|
| 540 |
function SimUsesRF() result(doesit) |
| 541 |
logical :: doesit |
| 542 |
doesit = thisSim%SIM_uses_RF |
| 543 |
end function SimUsesRF |
| 544 |
|
| 545 |
function SimRequiresPrepairCalc() result(doesit) |
| 546 |
logical :: doesit |
| 547 |
doesit = thisSim%SIM_uses_EAM |
| 548 |
end function SimRequiresPrepairCalc |
| 549 |
|
| 550 |
function SimRequiresPostpairCalc() result(doesit) |
| 551 |
logical :: doesit |
| 552 |
doesit = thisSim%SIM_uses_RF |
| 553 |
end function SimRequiresPostpairCalc |
| 554 |
|
| 555 |
subroutine InitializeSimGlobals(thisStat) |
| 556 |
integer, intent(out) :: thisStat |
| 557 |
integer :: alloc_stat |
| 558 |
|
| 559 |
thisStat = 0 |
| 560 |
|
| 561 |
call FreeSimGlobals() |
| 562 |
|
| 563 |
allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat) |
| 564 |
if (alloc_stat /= 0 ) then |
| 565 |
thisStat = -1 |
| 566 |
return |
| 567 |
endif |
| 568 |
|
| 569 |
allocate(excludesGlobal(nExcludes_Global), stat=alloc_stat) |
| 570 |
if (alloc_stat /= 0 ) then |
| 571 |
thisStat = -1 |
| 572 |
return |
| 573 |
endif |
| 574 |
|
| 575 |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
| 576 |
if (alloc_stat /= 0 ) then |
| 577 |
thisStat = -1 |
| 578 |
return |
| 579 |
endif |
| 580 |
|
| 581 |
end subroutine InitializeSimGlobals |
| 582 |
|
| 583 |
subroutine FreeSimGlobals() |
| 584 |
|
| 585 |
!We free in the opposite order in which we allocate in. |
| 586 |
|
| 587 |
if (allocated(skipsForAtom)) deallocate(skipsForAtom) |
| 588 |
if (allocated(nSkipsForAtom)) deallocate(nSkipsForAtom) |
| 589 |
if (allocated(mfactLocal)) deallocate(mfactLocal) |
| 590 |
if (allocated(mfactCol)) deallocate(mfactCol) |
| 591 |
if (allocated(mfactRow)) deallocate(mfactRow) |
| 592 |
if (allocated(groupListCol)) deallocate(groupListCol) |
| 593 |
if (allocated(groupListRow)) deallocate(groupListRow) |
| 594 |
if (allocated(groupStartCol)) deallocate(groupStartCol) |
| 595 |
if (allocated(groupStartRow)) deallocate(groupStartRow) |
| 596 |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
| 597 |
if (allocated(excludesGlobal)) deallocate(excludesGlobal) |
| 598 |
if (allocated(excludesLocal)) deallocate(excludesLocal) |
| 599 |
|
| 600 |
end subroutine FreeSimGlobals |
| 601 |
|
| 602 |
pure function getNlocal() result(n) |
| 603 |
integer :: n |
| 604 |
n = nLocal |
| 605 |
end function getNlocal |
| 606 |
|
| 607 |
end module simulation |
