| 1 |
gezelter |
1334 |
!! Fortran interface to C entry plug. |
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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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implicit none |
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PRIVATE |
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#define __FORTRAN90 |
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#include "fSimulation.h" |
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#include "fSwitchingFunction.h" |
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type (simtype), public, save :: thisSim |
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logical, save :: simulation_setup_complete = .false. |
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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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real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
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logical, public, save :: boxIsOrthorhombic |
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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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public :: SimUsesLJ |
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public :: SimUsesCharges |
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public :: SimUsesDipoles |
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public :: SimUsesSticky |
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public :: SimUsesRF |
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public :: SimUsesGB |
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public :: SimUsesEAM |
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public :: SimRequiresPrepairCalc |
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public :: SimRequiresPostpairCalc |
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public :: SimUsesDirectionalAtoms |
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contains |
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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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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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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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!! 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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#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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simulation_setup_complete = .false. |
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status = 0 |
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! copy C struct into fortran type |
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nLocal = CnLocal |
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nGlobal = CnGlobal |
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nGroups = CnGroups |
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thisSim = setThisSim |
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nExcludes_Global = CnGlobalExcludes |
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nExcludes_Local = CnLocalExcludes |
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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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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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#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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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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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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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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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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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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!! 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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#endif |
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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 |
| 199 |
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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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glPointer = 1 |
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do i = 1, nGroupsInRow |
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gid = GroupRowToGlobal(i) |
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groupStartRow(i) = glPointer |
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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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glPointer = 1 |
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| 229 |
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do i = 1, nGroupsInCol |
| 230 |
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gid = GroupColToGlobal(i) |
| 232 |
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groupStartCol(i) = glPointer |
| 233 |
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| 234 |
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do j = 1, nAtomsInCol |
| 235 |
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aid = AtomColToGlobal(j) |
| 236 |
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if (CglobalGroupMembership(aid) .eq. gid) then |
| 237 |
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groupListCol(glPointer) = j |
| 238 |
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glPointer = glPointer + 1 |
| 239 |
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endif |
| 240 |
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enddo |
| 241 |
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enddo |
| 242 |
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groupStartCol(nGroupsInCol+1) = nAtomsInCol + 1 |
| 243 |
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| 244 |
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mfactLocal = Cmfact |
| 245 |
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| 246 |
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call gather(mfactLocal, mfactRow, plan_atom_row) |
| 247 |
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call gather(mfactLocal, mfactCol, plan_atom_col) |
| 248 |
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| 249 |
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if (allocated(mfactLocal)) then |
| 250 |
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deallocate(mfactLocal) |
| 251 |
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end if |
| 252 |
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#else |
| 253 |
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allocate(groupStartRow(nGroups+1),stat=alloc_stat) |
| 254 |
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if (alloc_stat /= 0 ) then |
| 255 |
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status = -1 |
| 256 |
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return |
| 257 |
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endif |
| 258 |
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allocate(groupStartCol(nGroups+1),stat=alloc_stat) |
| 259 |
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if (alloc_stat /= 0 ) then |
| 260 |
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status = -1 |
| 261 |
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return |
| 262 |
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endif |
| 263 |
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allocate(groupListRow(nLocal),stat=alloc_stat) |
| 264 |
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if (alloc_stat /= 0 ) then |
| 265 |
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status = -1 |
| 266 |
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return |
| 267 |
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endif |
| 268 |
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allocate(groupListCol(nLocal),stat=alloc_stat) |
| 269 |
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if (alloc_stat /= 0 ) then |
| 270 |
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status = -1 |
| 271 |
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return |
| 272 |
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endif |
| 273 |
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allocate(mfactRow(nLocal),stat=alloc_stat) |
| 274 |
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if (alloc_stat /= 0 ) then |
| 275 |
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status = -1 |
| 276 |
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return |
| 277 |
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endif |
| 278 |
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allocate(mfactCol(nLocal),stat=alloc_stat) |
| 279 |
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if (alloc_stat /= 0 ) then |
| 280 |
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status = -1 |
| 281 |
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return |
| 282 |
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endif |
| 283 |
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allocate(mfactLocal(nLocal),stat=alloc_stat) |
| 284 |
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if (alloc_stat /= 0 ) then |
| 285 |
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status = -1 |
| 286 |
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return |
| 287 |
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endif |
| 288 |
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| 289 |
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glPointer = 1 |
| 290 |
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do i = 1, nGroups |
| 291 |
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groupStartRow(i) = glPointer |
| 292 |
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groupStartCol(i) = glPointer |
| 293 |
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do j = 1, nLocal |
| 294 |
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if (CglobalGroupMembership(j) .eq. i) then |
| 295 |
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groupListRow(glPointer) = j |
| 296 |
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groupListCol(glPointer) = j |
| 297 |
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glPointer = glPointer + 1 |
| 298 |
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endif |
| 299 |
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enddo |
| 300 |
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enddo |
| 301 |
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groupStartRow(nGroups+1) = nLocal + 1 |
| 302 |
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groupStartCol(nGroups+1) = nLocal + 1 |
| 303 |
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| 304 |
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do i = 1, nLocal |
| 305 |
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mfactRow(i) = Cmfact(i) |
| 306 |
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mfactCol(i) = Cmfact(i) |
| 307 |
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end do |
| 308 |
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| 309 |
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#endif |
| 310 |
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| 311 |
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| 312 |
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! We build the local atid's for both mpi and nonmpi |
| 313 |
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do i = 1, nLocal |
| 314 |
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| 315 |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
| 316 |
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atid(i) = me |
| 317 |
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| 318 |
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enddo |
| 319 |
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| 320 |
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do i = 1, nExcludes_Local |
| 321 |
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excludesLocal(1,i) = CexcludesLocal(1,i) |
| 322 |
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excludesLocal(2,i) = CexcludesLocal(2,i) |
| 323 |
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enddo |
| 324 |
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| 325 |
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#ifdef IS_MPI |
| 326 |
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allocate(nSkipsForAtom(nAtomsInRow), stat=alloc_stat) |
| 327 |
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#else |
| 328 |
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allocate(nSkipsForAtom(nLocal), stat=alloc_stat) |
| 329 |
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#endif |
| 330 |
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if (alloc_stat /= 0 ) then |
| 331 |
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thisStat = -1 |
| 332 |
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write(*,*) 'Could not allocate nSkipsForAtom array' |
| 333 |
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return |
| 334 |
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endif |
| 335 |
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| 336 |
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maxSkipsForAtom = 0 |
| 337 |
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#ifdef IS_MPI |
| 338 |
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do j = 1, nAtomsInRow |
| 339 |
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#else |
| 340 |
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do j = 1, nLocal |
| 341 |
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#endif |
| 342 |
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nSkipsForAtom(j) = 0 |
| 343 |
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#ifdef IS_MPI |
| 344 |
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id1 = AtomRowToGlobal(j) |
| 345 |
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#else |
| 346 |
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id1 = j |
| 347 |
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#endif |
| 348 |
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do i = 1, nExcludes_Local |
| 349 |
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if (excludesLocal(1,i) .eq. id1 ) then |
| 350 |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 351 |
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| 352 |
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if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
| 353 |
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maxSkipsForAtom = nSkipsForAtom(j) |
| 354 |
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endif |
| 355 |
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endif |
| 356 |
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if (excludesLocal(2,i) .eq. id1 ) then |
| 357 |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 358 |
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| 359 |
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if (nSkipsForAtom(j) .gt. maxSkipsForAtom) then |
| 360 |
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maxSkipsForAtom = nSkipsForAtom(j) |
| 361 |
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endif |
| 362 |
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endif |
| 363 |
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end do |
| 364 |
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enddo |
| 365 |
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| 366 |
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#ifdef IS_MPI |
| 367 |
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allocate(skipsForAtom(nAtomsInRow, maxSkipsForAtom), stat=alloc_stat) |
| 368 |
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#else |
| 369 |
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allocate(skipsForAtom(nLocal, maxSkipsForAtom), stat=alloc_stat) |
| 370 |
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#endif |
| 371 |
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if (alloc_stat /= 0 ) then |
| 372 |
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write(*,*) 'Could not allocate skipsForAtom array' |
| 373 |
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return |
| 374 |
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endif |
| 375 |
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| 376 |
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#ifdef IS_MPI |
| 377 |
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do j = 1, nAtomsInRow |
| 378 |
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#else |
| 379 |
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do j = 1, nLocal |
| 380 |
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#endif |
| 381 |
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nSkipsForAtom(j) = 0 |
| 382 |
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#ifdef IS_MPI |
| 383 |
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id1 = AtomRowToGlobal(j) |
| 384 |
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#else |
| 385 |
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id1 = j |
| 386 |
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#endif |
| 387 |
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do i = 1, nExcludes_Local |
| 388 |
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if (excludesLocal(1,i) .eq. id1 ) then |
| 389 |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 390 |
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! exclude lists have global ID's so this line is |
| 391 |
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! the same in MPI and non-MPI |
| 392 |
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id2 = excludesLocal(2,i) |
| 393 |
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skipsForAtom(j, nSkipsForAtom(j)) = id2 |
| 394 |
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endif |
| 395 |
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if (excludesLocal(2, i) .eq. id1 ) then |
| 396 |
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nSkipsForAtom(j) = nSkipsForAtom(j) + 1 |
| 397 |
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! exclude lists have global ID's so this line is |
| 398 |
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! the same in MPI and non-MPI |
| 399 |
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id2 = excludesLocal(1,i) |
| 400 |
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skipsForAtom(j, nSkipsForAtom(j)) = id2 |
| 401 |
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endif |
| 402 |
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end do |
| 403 |
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enddo |
| 404 |
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| 405 |
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do i = 1, nExcludes_Global |
| 406 |
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excludesGlobal(i) = CexcludesGlobal(i) |
| 407 |
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enddo |
| 408 |
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| 409 |
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do i = 1, nGlobal |
| 410 |
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molMemberShipList(i) = CmolMembership(i) |
| 411 |
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enddo |
| 412 |
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| 413 |
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if (status == 0) simulation_setup_complete = .true. |
| 414 |
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| 415 |
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end subroutine SimulationSetup |
| 416 |
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| 417 |
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subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
| 418 |
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real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
| 419 |
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integer :: cBoxIsOrthorhombic |
| 420 |
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integer :: smallest, status, i |
| 421 |
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| 422 |
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Hmat = cHmat |
| 423 |
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HmatInv = cHmatInv |
| 424 |
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if (cBoxIsOrthorhombic .eq. 0 ) then |
| 425 |
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boxIsOrthorhombic = .false. |
| 426 |
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else |
| 427 |
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boxIsOrthorhombic = .true. |
| 428 |
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endif |
| 429 |
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| 430 |
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return |
| 431 |
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end subroutine setBox |
| 432 |
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| 433 |
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function getDielect() result(dielect) |
| 434 |
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real( kind = dp ) :: dielect |
| 435 |
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dielect = thisSim%dielect |
| 436 |
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end function getDielect |
| 437 |
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| 438 |
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function SimUsesPBC() result(doesit) |
| 439 |
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logical :: doesit |
| 440 |
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doesit = thisSim%SIM_uses_PBC |
| 441 |
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end function SimUsesPBC |
| 442 |
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|
| 443 |
|
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function SimUsesLJ() result(doesit) |
| 444 |
|
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logical :: doesit |
| 445 |
|
|
doesit = thisSim%SIM_uses_LJ |
| 446 |
|
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end function SimUsesLJ |
| 447 |
|
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|
| 448 |
|
|
function SimUsesSticky() result(doesit) |
| 449 |
|
|
logical :: doesit |
| 450 |
|
|
doesit = thisSim%SIM_uses_sticky |
| 451 |
|
|
end function SimUsesSticky |
| 452 |
|
|
|
| 453 |
|
|
function SimUsesCharges() result(doesit) |
| 454 |
|
|
logical :: doesit |
| 455 |
|
|
doesit = thisSim%SIM_uses_charges |
| 456 |
|
|
end function SimUsesCharges |
| 457 |
|
|
|
| 458 |
|
|
function SimUsesDipoles() result(doesit) |
| 459 |
|
|
logical :: doesit |
| 460 |
|
|
doesit = thisSim%SIM_uses_dipoles |
| 461 |
|
|
end function SimUsesDipoles |
| 462 |
|
|
|
| 463 |
|
|
function SimUsesRF() result(doesit) |
| 464 |
|
|
logical :: doesit |
| 465 |
|
|
doesit = thisSim%SIM_uses_RF |
| 466 |
|
|
end function SimUsesRF |
| 467 |
|
|
|
| 468 |
|
|
function SimUsesGB() result(doesit) |
| 469 |
|
|
logical :: doesit |
| 470 |
|
|
doesit = thisSim%SIM_uses_GB |
| 471 |
|
|
end function SimUsesGB |
| 472 |
|
|
|
| 473 |
|
|
function SimUsesEAM() result(doesit) |
| 474 |
|
|
logical :: doesit |
| 475 |
|
|
doesit = thisSim%SIM_uses_EAM |
| 476 |
|
|
end function SimUsesEAM |
| 477 |
|
|
|
| 478 |
|
|
function SimUsesDirectionalAtoms() result(doesit) |
| 479 |
|
|
logical :: doesit |
| 480 |
|
|
doesit = thisSim%SIM_uses_dipoles .or. thisSim%SIM_uses_sticky .or. & |
| 481 |
|
|
thisSim%SIM_uses_GB .or. thisSim%SIM_uses_RF |
| 482 |
|
|
end function SimUsesDirectionalAtoms |
| 483 |
|
|
|
| 484 |
|
|
function SimRequiresPrepairCalc() result(doesit) |
| 485 |
|
|
logical :: doesit |
| 486 |
|
|
doesit = thisSim%SIM_uses_EAM |
| 487 |
|
|
end function SimRequiresPrepairCalc |
| 488 |
|
|
|
| 489 |
|
|
function SimRequiresPostpairCalc() result(doesit) |
| 490 |
|
|
logical :: doesit |
| 491 |
|
|
doesit = thisSim%SIM_uses_RF |
| 492 |
|
|
end function SimRequiresPostpairCalc |
| 493 |
|
|
|
| 494 |
|
|
subroutine InitializeSimGlobals(thisStat) |
| 495 |
|
|
integer, intent(out) :: thisStat |
| 496 |
|
|
integer :: alloc_stat |
| 497 |
|
|
|
| 498 |
|
|
thisStat = 0 |
| 499 |
|
|
|
| 500 |
|
|
call FreeSimGlobals() |
| 501 |
|
|
|
| 502 |
|
|
allocate(excludesLocal(2,nExcludes_Local), stat=alloc_stat) |
| 503 |
|
|
if (alloc_stat /= 0 ) then |
| 504 |
|
|
thisStat = -1 |
| 505 |
|
|
return |
| 506 |
|
|
endif |
| 507 |
|
|
|
| 508 |
|
|
allocate(excludesGlobal(nExcludes_Global), stat=alloc_stat) |
| 509 |
|
|
if (alloc_stat /= 0 ) then |
| 510 |
|
|
thisStat = -1 |
| 511 |
|
|
return |
| 512 |
|
|
endif |
| 513 |
|
|
|
| 514 |
|
|
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
| 515 |
|
|
if (alloc_stat /= 0 ) then |
| 516 |
|
|
thisStat = -1 |
| 517 |
|
|
return |
| 518 |
|
|
endif |
| 519 |
|
|
|
| 520 |
|
|
end subroutine InitializeSimGlobals |
| 521 |
|
|
|
| 522 |
|
|
subroutine FreeSimGlobals() |
| 523 |
|
|
|
| 524 |
|
|
!We free in the opposite order in which we allocate in. |
| 525 |
|
|
|
| 526 |
|
|
if (allocated(skipsForAtom)) deallocate(skipsForAtom) |
| 527 |
|
|
if (allocated(nSkipsForAtom)) deallocate(nSkipsForAtom) |
| 528 |
|
|
if (allocated(mfactLocal)) deallocate(mfactLocal) |
| 529 |
|
|
if (allocated(mfactCol)) deallocate(mfactCol) |
| 530 |
|
|
if (allocated(mfactRow)) deallocate(mfactRow) |
| 531 |
|
|
if (allocated(groupListCol)) deallocate(groupListCol) |
| 532 |
|
|
if (allocated(groupListRow)) deallocate(groupListRow) |
| 533 |
|
|
if (allocated(groupStartCol)) deallocate(groupStartCol) |
| 534 |
|
|
if (allocated(groupStartRow)) deallocate(groupStartRow) |
| 535 |
|
|
if (allocated(molMembershipList)) deallocate(molMembershipList) |
| 536 |
|
|
if (allocated(excludesGlobal)) deallocate(excludesGlobal) |
| 537 |
|
|
if (allocated(excludesLocal)) deallocate(excludesLocal) |
| 538 |
|
|
|
| 539 |
|
|
end subroutine FreeSimGlobals |
| 540 |
|
|
|
| 541 |
|
|
pure function getNlocal() result(n) |
| 542 |
|
|
integer :: n |
| 543 |
|
|
n = nLocal |
| 544 |
|
|
end function getNlocal |
| 545 |
|
|
|
| 546 |
|
|
|
| 547 |
|
|
end module simulation |
