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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. 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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!! 2. 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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!! SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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!! research, please cite the appropriate papers when you publish your |
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!! work. Good starting points are: |
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!! |
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!! [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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!! [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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!! [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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!! [4] Vardeman & Gezelter, in progress (2009). |
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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 status |
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use linearAlgebra |
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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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#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.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 = 0 |
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integer, public, save :: nOneTwo = 0 |
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integer, public, save :: nOneThree = 0 |
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integer, public, save :: nOneFour = 0 |
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|
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integer, allocatable, dimension(:,:), public :: excludes |
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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 :: nSkipsForLocalAtom |
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integer, allocatable, dimension(:,:), public :: skipsForLocalAtom |
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integer, allocatable, dimension(:), public :: nSkipsForRowAtom |
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integer, allocatable, dimension(:,:), public :: skipsForRowAtom |
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integer, allocatable, dimension(:), public :: nTopoPairsForAtom |
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integer, allocatable, dimension(:,:), public :: toposForAtom |
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integer, allocatable, dimension(:,:), public :: topoDistance |
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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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logical, allocatable, dimension(:) :: simHasAtypeMap |
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#ifdef IS_MPI |
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logical, allocatable, dimension(:) :: simHasAtypeMapTemp |
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#endif |
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|
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real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv |
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real(kind=dp), save :: DangerRcut |
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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 :: checkBox |
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public :: SimUsesPBC |
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public :: SimUsesAtomicVirial |
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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 :: SimUsesStickyPower |
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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 :: SimUsesSF |
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public :: SimUsesSP |
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public :: SimUsesBoxDipole |
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public :: SimRequiresPrepairCalc |
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public :: SimRequiresPostpairCalc |
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public :: SimHasAtype |
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public :: SimUsesSC |
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public :: SimUsesMNM |
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public :: setHmatDangerousRcutValue |
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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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CnExcludes, Cexcludes, CnOneTwo, ConeTwo, CnOneThree, ConeThree, & |
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CnOneFour, ConeFour, CmolMembership, Cmfact, CnGroups, & |
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CglobalGroupMembership, 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 :: CnExcludes |
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integer, dimension(2,CnExcludes), intent(in) :: Cexcludes |
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integer :: CnOneTwo |
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integer, dimension(2,CnOneTwo), intent(in) :: ConeTwo |
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integer :: CnOneThree |
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integer, dimension(2,CnOneThree), intent(in) :: ConeThree |
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integer :: CnOneFour |
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integer, dimension(2,CnOneFour), intent(in) :: ConeFour |
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|
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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, jend |
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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 :: maxSkipsForLocalAtom, maxToposForAtom, glPointer |
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integer :: maxSkipsForRowAtom |
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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 = CnExcludes |
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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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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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#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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! We build the local atid's for both mpi and nonmpi |
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do i = 1, nLocal |
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me = getFirstMatchingElement(atypes, "c_ident", c_idents(i)) |
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atid(i) = me |
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c_idents_local(i) = c_idents(i) |
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enddo |
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|
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do i = 1, nExcludes |
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excludes(1,i) = Cexcludes(1,i) |
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excludes(2,i) = Cexcludes(2,i) |
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enddo |
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|
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#ifdef IS_MPI |
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allocate(nSkipsForRowAtom(nAtomsInRow), stat=alloc_stat) |
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#endif |
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|
| 382 |
allocate(nSkipsForLocalAtom(nLocal), stat=alloc_stat) |
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|
| 384 |
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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#ifdef IS_MPI |
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maxSkipsForRowAtom = 0 |
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do j = 1, nAtomsInRow |
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nSkipsForRowAtom(j) = 0 |
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id1 = AtomRowToGlobal(j) |
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do i = 1, nExcludes |
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if (excludes(1,i) .eq. id1 ) then |
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nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 398 |
if (nSkipsForRowAtom(j) .gt. maxSkipsForRowAtom) then |
| 399 |
maxSkipsForRowAtom = nSkipsForRowAtom(j) |
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endif |
| 401 |
endif |
| 402 |
if (excludes(2,i) .eq. id1 ) then |
| 403 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 404 |
if (nSkipsForRowAtom(j) .gt. maxSkipsForRowAtom) then |
| 405 |
maxSkipsForRowAtom = nSkipsForRowAtom(j) |
| 406 |
endif |
| 407 |
endif |
| 408 |
end do |
| 409 |
enddo |
| 410 |
#endif |
| 411 |
maxSkipsForLocalAtom = 0 |
| 412 |
do j = 1, nLocal |
| 413 |
nSkipsForLocalAtom(j) = 0 |
| 414 |
#ifdef IS_MPI |
| 415 |
id1 = AtomLocalToGlobal(j) |
| 416 |
#else |
| 417 |
id1 = j |
| 418 |
#endif |
| 419 |
do i = 1, nExcludes |
| 420 |
if (excludes(1,i) .eq. id1 ) then |
| 421 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 422 |
if (nSkipsForLocalAtom(j) .gt. maxSkipsForLocalAtom) then |
| 423 |
maxSkipsForLocalAtom = nSkipsForLocalAtom(j) |
| 424 |
endif |
| 425 |
endif |
| 426 |
if (excludes(2,i) .eq. id1 ) then |
| 427 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 428 |
if (nSkipsForLocalAtom(j) .gt. maxSkipsForLocalAtom) then |
| 429 |
maxSkipsForLocalAtom = nSkipsForLocalAtom(j) |
| 430 |
endif |
| 431 |
endif |
| 432 |
end do |
| 433 |
enddo |
| 434 |
|
| 435 |
#ifdef IS_MPI |
| 436 |
allocate(skipsForRowAtom(nAtomsInRow, maxSkipsForRowAtom), stat=alloc_stat) |
| 437 |
#endif |
| 438 |
allocate(skipsForLocalAtom(nLocal, maxSkipsForLocalAtom), stat=alloc_stat) |
| 439 |
|
| 440 |
if (alloc_stat /= 0 ) then |
| 441 |
write(*,*) 'Could not allocate skipsForAtom arrays' |
| 442 |
return |
| 443 |
endif |
| 444 |
|
| 445 |
#ifdef IS_MPI |
| 446 |
do j = 1, nAtomsInRow |
| 447 |
nSkipsForRowAtom(j) = 0 |
| 448 |
id1 = AtomRowToGlobal(j) |
| 449 |
do i = 1, nExcludes |
| 450 |
if (excludes(1,i) .eq. id1 ) then |
| 451 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 452 |
! exclude lists have global ID's |
| 453 |
id2 = excludes(2,i) |
| 454 |
skipsForRowAtom(j, nSkipsForRowAtom(j)) = id2 |
| 455 |
endif |
| 456 |
if (excludes(2, i) .eq. id1 ) then |
| 457 |
nSkipsForRowAtom(j) = nSkipsForRowAtom(j) + 1 |
| 458 |
! exclude lists have global ID's |
| 459 |
id2 = excludes(1,i) |
| 460 |
skipsForRowAtom(j, nSkipsForRowAtom(j)) = id2 |
| 461 |
endif |
| 462 |
end do |
| 463 |
enddo |
| 464 |
#endif |
| 465 |
do j = 1, nLocal |
| 466 |
nSkipsForLocalAtom(j) = 0 |
| 467 |
#ifdef IS_MPI |
| 468 |
id1 = AtomLocalToGlobal(j) |
| 469 |
#else |
| 470 |
id1 = j |
| 471 |
#endif |
| 472 |
do i = 1, nExcludes |
| 473 |
if (excludes(1,i) .eq. id1 ) then |
| 474 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 475 |
! exclude lists have global ID's |
| 476 |
#ifdef IS_MPI |
| 477 |
id2 = AtomGlobalToLocal(excludes(2,i)) |
| 478 |
#else |
| 479 |
id2 = excludes(2,i) |
| 480 |
#endif |
| 481 |
skipsForLocalAtom(j, nSkipsForLocalAtom(j)) = id2 |
| 482 |
endif |
| 483 |
if (excludes(2, i) .eq. id1 ) then |
| 484 |
nSkipsForLocalAtom(j) = nSkipsForLocalAtom(j) + 1 |
| 485 |
! exclude lists have global ID's |
| 486 |
#ifdef IS_MPI |
| 487 |
id2 = AtomGlobalToLocal(excludes(1,i)) |
| 488 |
#else |
| 489 |
id2 = excludes(1,i) |
| 490 |
#endif |
| 491 |
skipsForLocalAtom(j, nSkipsForLocalAtom(j)) = id2 |
| 492 |
endif |
| 493 |
end do |
| 494 |
enddo |
| 495 |
|
| 496 |
do i = 1, nGlobal |
| 497 |
molMemberShipList(i) = CmolMembership(i) |
| 498 |
enddo |
| 499 |
|
| 500 |
#ifdef IS_MPI |
| 501 |
allocate(nTopoPairsForAtom(nAtomsInRow), stat=alloc_stat) |
| 502 |
#else |
| 503 |
allocate(nTopoPairsForAtom(nLocal), stat=alloc_stat) |
| 504 |
#endif |
| 505 |
if (alloc_stat /= 0 ) then |
| 506 |
thisStat = -1 |
| 507 |
write(*,*) 'Could not allocate nTopoPairsForAtom array' |
| 508 |
return |
| 509 |
endif |
| 510 |
|
| 511 |
#ifdef IS_MPI |
| 512 |
jend = nAtomsInRow |
| 513 |
#else |
| 514 |
jend = nLocal |
| 515 |
#endif |
| 516 |
|
| 517 |
do j = 1, jend |
| 518 |
nTopoPairsForAtom(j) = 0 |
| 519 |
#ifdef IS_MPI |
| 520 |
id1 = AtomRowToGlobal(j) |
| 521 |
#else |
| 522 |
id1 = j |
| 523 |
#endif |
| 524 |
do i = 1, CnOneTwo |
| 525 |
if (ConeTwo(1,i) .eq. id1 ) then |
| 526 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 527 |
endif |
| 528 |
if (ConeTwo(2,i) .eq. id1 ) then |
| 529 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 530 |
endif |
| 531 |
end do |
| 532 |
|
| 533 |
do i = 1, CnOneThree |
| 534 |
if (ConeThree(1,i) .eq. id1 ) then |
| 535 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 536 |
endif |
| 537 |
if (ConeThree(2,i) .eq. id1 ) then |
| 538 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 539 |
endif |
| 540 |
end do |
| 541 |
|
| 542 |
do i = 1, CnOneFour |
| 543 |
if (ConeFour(1,i) .eq. id1 ) then |
| 544 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 545 |
endif |
| 546 |
if (ConeFour(2,i) .eq. id1 ) then |
| 547 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 548 |
endif |
| 549 |
end do |
| 550 |
enddo |
| 551 |
|
| 552 |
maxToposForAtom = maxval(nTopoPairsForAtom) |
| 553 |
#ifdef IS_MPI |
| 554 |
allocate(toposForAtom(nAtomsInRow, maxToposForAtom), stat=alloc_stat) |
| 555 |
allocate(topoDistance(nAtomsInRow, maxToposForAtom), stat=alloc_stat) |
| 556 |
#else |
| 557 |
allocate(toposForAtom(nLocal, maxToposForAtom), stat=alloc_stat) |
| 558 |
allocate(topoDistance(nLocal, maxToposForAtom), stat=alloc_stat) |
| 559 |
#endif |
| 560 |
if (alloc_stat /= 0 ) then |
| 561 |
write(*,*) 'Could not allocate topoDistance array' |
| 562 |
return |
| 563 |
endif |
| 564 |
|
| 565 |
#ifdef IS_MPI |
| 566 |
jend = nAtomsInRow |
| 567 |
#else |
| 568 |
jend = nLocal |
| 569 |
#endif |
| 570 |
do j = 1, jend |
| 571 |
nTopoPairsForAtom(j) = 0 |
| 572 |
#ifdef IS_MPI |
| 573 |
id1 = AtomRowToGlobal(j) |
| 574 |
#else |
| 575 |
id1 = j |
| 576 |
#endif |
| 577 |
do i = 1, CnOneTwo |
| 578 |
if (ConeTwo(1,i) .eq. id1 ) then |
| 579 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 580 |
id2 = ConeTwo(2,i) |
| 581 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 582 |
topoDistance(j, nTopoPairsForAtom(j)) = 1 |
| 583 |
endif |
| 584 |
if (ConeTwo(2, i) .eq. id1 ) then |
| 585 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 586 |
id2 = ConeTwo(1,i) |
| 587 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 588 |
topoDistance(j, nTopoPairsForAtom(j)) = 1 |
| 589 |
endif |
| 590 |
end do |
| 591 |
|
| 592 |
do i = 1, CnOneThree |
| 593 |
if (ConeThree(1,i) .eq. id1 ) then |
| 594 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 595 |
id2 = ConeThree(2,i) |
| 596 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 597 |
topoDistance(j, nTopoPairsForAtom(j)) = 2 |
| 598 |
endif |
| 599 |
if (ConeThree(2, i) .eq. id1 ) then |
| 600 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 601 |
id2 = ConeThree(1,i) |
| 602 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 603 |
topoDistance(j, nTopoPairsForAtom(j)) = 2 |
| 604 |
endif |
| 605 |
end do |
| 606 |
|
| 607 |
do i = 1, CnOneFour |
| 608 |
if (ConeFour(1,i) .eq. id1 ) then |
| 609 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 610 |
id2 = ConeFour(2,i) |
| 611 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 612 |
topoDistance(j, nTopoPairsForAtom(j)) = 3 |
| 613 |
endif |
| 614 |
if (ConeFour(2, i) .eq. id1 ) then |
| 615 |
nTopoPairsForAtom(j) = nTopoPairsForAtom(j) + 1 |
| 616 |
id2 = ConeFour(1,i) |
| 617 |
toposForAtom(j, nTopoPairsForAtom(j)) = id2 |
| 618 |
topoDistance(j, nTopoPairsForAtom(j)) = 3 |
| 619 |
endif |
| 620 |
end do |
| 621 |
enddo |
| 622 |
|
| 623 |
call createSimHasAtype(alloc_stat) |
| 624 |
if (alloc_stat /= 0) then |
| 625 |
status = -1 |
| 626 |
end if |
| 627 |
|
| 628 |
if (status == 0) simulation_setup_complete = .true. |
| 629 |
|
| 630 |
end subroutine SimulationSetup |
| 631 |
|
| 632 |
subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic) |
| 633 |
real(kind=dp), dimension(3,3) :: cHmat, cHmatInv |
| 634 |
integer :: cBoxIsOrthorhombic |
| 635 |
integer :: smallest, status |
| 636 |
|
| 637 |
Hmat = cHmat |
| 638 |
HmatInv = cHmatInv |
| 639 |
if (cBoxIsOrthorhombic .eq. 0 ) then |
| 640 |
boxIsOrthorhombic = .false. |
| 641 |
else |
| 642 |
boxIsOrthorhombic = .true. |
| 643 |
endif |
| 644 |
|
| 645 |
call checkBox() |
| 646 |
return |
| 647 |
end subroutine setBox |
| 648 |
|
| 649 |
subroutine checkBox() |
| 650 |
|
| 651 |
integer :: i |
| 652 |
real(kind=dp), dimension(3) :: hx, hy, hz, ax, ay, az, piped |
| 653 |
character(len = statusMsgSize) :: errMsg |
| 654 |
|
| 655 |
hx = Hmat(1,:) |
| 656 |
hy = Hmat(2,:) |
| 657 |
hz = Hmat(3,:) |
| 658 |
|
| 659 |
ax = cross_product(hy, hz) |
| 660 |
ay = cross_product(hx, hz) |
| 661 |
az = cross_product(hx, hy) |
| 662 |
|
| 663 |
ax = ax / length(ax) |
| 664 |
ay = ay / length(ay) |
| 665 |
az = az / length(az) |
| 666 |
|
| 667 |
piped(1) = abs(dot_product(ax, hx)) |
| 668 |
piped(2) = abs(dot_product(ay, hy)) |
| 669 |
piped(3) = abs(dot_product(az, hz)) |
| 670 |
|
| 671 |
do i = 1, 3 |
| 672 |
if ((0.5_dp * piped(i)).lt.DangerRcut) then |
| 673 |
write(errMsg, '(a94,f9.4,a1)') 'One of the dimensions of the Periodic ' & |
| 674 |
// 'Box is smaller than ' // newline // tab // & |
| 675 |
'the largest cutoff radius' // & |
| 676 |
' (rCut = ', DangerRcut, ')' |
| 677 |
call handleError("checkBox", errMsg) |
| 678 |
|
| 679 |
end if |
| 680 |
enddo |
| 681 |
return |
| 682 |
end subroutine checkBox |
| 683 |
|
| 684 |
function SimUsesPBC() result(doesit) |
| 685 |
logical :: doesit |
| 686 |
doesit = thisSim%SIM_uses_PBC |
| 687 |
end function SimUsesPBC |
| 688 |
|
| 689 |
function SimUsesAtomicVirial() result(doesit) |
| 690 |
logical :: doesit |
| 691 |
doesit = thisSim%SIM_uses_AtomicVirial |
| 692 |
end function SimUsesAtomicVirial |
| 693 |
|
| 694 |
function SimUsesDirectionalAtoms() result(doesit) |
| 695 |
logical :: doesit |
| 696 |
doesit = thisSim%SIM_uses_dipoles .or. thisSim%SIM_uses_Sticky .or. & |
| 697 |
thisSim%SIM_uses_StickyPower .or. & |
| 698 |
thisSim%SIM_uses_GayBerne .or. thisSim%SIM_uses_Shapes |
| 699 |
end function SimUsesDirectionalAtoms |
| 700 |
|
| 701 |
function SimUsesLennardJones() result(doesit) |
| 702 |
logical :: doesit |
| 703 |
doesit = thisSim%SIM_uses_LennardJones |
| 704 |
end function SimUsesLennardJones |
| 705 |
|
| 706 |
function SimUsesElectrostatics() result(doesit) |
| 707 |
logical :: doesit |
| 708 |
doesit = thisSim%SIM_uses_Electrostatics |
| 709 |
end function SimUsesElectrostatics |
| 710 |
|
| 711 |
function SimUsesCharges() result(doesit) |
| 712 |
logical :: doesit |
| 713 |
doesit = thisSim%SIM_uses_Charges |
| 714 |
end function SimUsesCharges |
| 715 |
|
| 716 |
function SimUsesDipoles() result(doesit) |
| 717 |
logical :: doesit |
| 718 |
doesit = thisSim%SIM_uses_Dipoles |
| 719 |
end function SimUsesDipoles |
| 720 |
|
| 721 |
function SimUsesSticky() result(doesit) |
| 722 |
logical :: doesit |
| 723 |
doesit = thisSim%SIM_uses_Sticky |
| 724 |
end function SimUsesSticky |
| 725 |
|
| 726 |
function SimUsesStickyPower() result(doesit) |
| 727 |
logical :: doesit |
| 728 |
doesit = thisSim%SIM_uses_StickyPower |
| 729 |
end function SimUsesStickyPower |
| 730 |
|
| 731 |
function SimUsesGayBerne() result(doesit) |
| 732 |
logical :: doesit |
| 733 |
doesit = thisSim%SIM_uses_GayBerne |
| 734 |
end function SimUsesGayBerne |
| 735 |
|
| 736 |
function SimUsesEAM() result(doesit) |
| 737 |
logical :: doesit |
| 738 |
doesit = thisSim%SIM_uses_EAM |
| 739 |
end function SimUsesEAM |
| 740 |
|
| 741 |
|
| 742 |
function SimUsesSC() result(doesit) |
| 743 |
logical :: doesit |
| 744 |
doesit = thisSim%SIM_uses_SC |
| 745 |
end function SimUsesSC |
| 746 |
|
| 747 |
function SimUsesMNM() result(doesit) |
| 748 |
logical :: doesit |
| 749 |
doesit = thisSim%SIM_uses_MNM |
| 750 |
end function SimUsesMNM |
| 751 |
|
| 752 |
|
| 753 |
function SimUsesShapes() result(doesit) |
| 754 |
logical :: doesit |
| 755 |
doesit = thisSim%SIM_uses_Shapes |
| 756 |
end function SimUsesShapes |
| 757 |
|
| 758 |
function SimUsesFLARB() result(doesit) |
| 759 |
logical :: doesit |
| 760 |
doesit = thisSim%SIM_uses_FLARB |
| 761 |
end function SimUsesFLARB |
| 762 |
|
| 763 |
function SimUsesRF() result(doesit) |
| 764 |
logical :: doesit |
| 765 |
doesit = thisSim%SIM_uses_RF |
| 766 |
end function SimUsesRF |
| 767 |
|
| 768 |
function SimUsesSF() result(doesit) |
| 769 |
logical :: doesit |
| 770 |
doesit = thisSim%SIM_uses_SF |
| 771 |
end function SimUsesSF |
| 772 |
|
| 773 |
function SimUsesSP() result(doesit) |
| 774 |
logical :: doesit |
| 775 |
doesit = thisSim%SIM_uses_SP |
| 776 |
end function SimUsesSP |
| 777 |
|
| 778 |
function SimUsesBoxDipole() result(doesit) |
| 779 |
logical :: doesit |
| 780 |
doesit = thisSim%SIM_uses_BoxDipole |
| 781 |
end function SimUsesBoxDipole |
| 782 |
|
| 783 |
function SimRequiresPrepairCalc() result(doesit) |
| 784 |
logical :: doesit |
| 785 |
doesit = thisSim%SIM_uses_EAM .or. thisSim%SIM_uses_SC |
| 786 |
end function SimRequiresPrepairCalc |
| 787 |
|
| 788 |
function SimRequiresPostpairCalc() result(doesit) |
| 789 |
logical :: doesit |
| 790 |
doesit = thisSim%SIM_uses_RF .or. thisSim%SIM_uses_SF & |
| 791 |
.or. thisSim%SIM_uses_SP .or. thisSim%SIM_uses_BoxDipole |
| 792 |
end function SimRequiresPostpairCalc |
| 793 |
|
| 794 |
! Function returns true if the simulation has this atype |
| 795 |
function SimHasAtype(thisAtype) result(doesit) |
| 796 |
logical :: doesit |
| 797 |
integer :: thisAtype |
| 798 |
doesit = .false. |
| 799 |
if(.not.allocated(SimHasAtypeMap)) return |
| 800 |
|
| 801 |
doesit = SimHasAtypeMap(thisAtype) |
| 802 |
|
| 803 |
end function SimHasAtype |
| 804 |
|
| 805 |
subroutine createSimHasAtype(status) |
| 806 |
integer, intent(out) :: status |
| 807 |
integer :: alloc_stat |
| 808 |
integer :: me_i |
| 809 |
integer :: mpiErrors |
| 810 |
integer :: nAtypes |
| 811 |
status = 0 |
| 812 |
|
| 813 |
nAtypes = getSize(atypes) |
| 814 |
! Setup logical map for atypes in simulation |
| 815 |
if (.not.allocated(SimHasAtypeMap)) then |
| 816 |
allocate(SimHasAtypeMap(nAtypes),stat=alloc_stat) |
| 817 |
if (alloc_stat /= 0 ) then |
| 818 |
status = -1 |
| 819 |
return |
| 820 |
end if |
| 821 |
SimHasAtypeMap = .false. |
| 822 |
end if |
| 823 |
|
| 824 |
! Loop through the local atoms and grab the atypes present |
| 825 |
do me_i = 1,nLocal |
| 826 |
SimHasAtypeMap(atid(me_i)) = .true. |
| 827 |
end do |
| 828 |
! For MPI, we need to know all possible atypes present in |
| 829 |
! simulation on all processors. Use LOR operation to set map. |
| 830 |
#ifdef IS_MPI |
| 831 |
if (.not.allocated(SimHasAtypeMapTemp)) then |
| 832 |
allocate(SimHasAtypeMapTemp(nAtypes),stat=alloc_stat) |
| 833 |
if (alloc_stat /= 0 ) then |
| 834 |
status = -1 |
| 835 |
return |
| 836 |
end if |
| 837 |
end if |
| 838 |
call mpi_allreduce(SimHasAtypeMap, SimHasAtypeMaptemp, nAtypes, & |
| 839 |
mpi_logical, MPI_LOR, mpi_comm_world, mpiErrors) |
| 840 |
simHasAtypeMap = simHasAtypeMapTemp |
| 841 |
deallocate(simHasAtypeMapTemp) |
| 842 |
#endif |
| 843 |
end subroutine createSimHasAtype |
| 844 |
|
| 845 |
subroutine InitializeSimGlobals(thisStat) |
| 846 |
integer, intent(out) :: thisStat |
| 847 |
integer :: alloc_stat |
| 848 |
|
| 849 |
thisStat = 0 |
| 850 |
|
| 851 |
call FreeSimGlobals() |
| 852 |
|
| 853 |
allocate(excludes(2,nExcludes), stat=alloc_stat) |
| 854 |
if (alloc_stat /= 0 ) then |
| 855 |
thisStat = -1 |
| 856 |
return |
| 857 |
endif |
| 858 |
|
| 859 |
allocate(molMembershipList(nGlobal), stat=alloc_stat) |
| 860 |
if (alloc_stat /= 0 ) then |
| 861 |
thisStat = -1 |
| 862 |
return |
| 863 |
endif |
| 864 |
|
| 865 |
end subroutine InitializeSimGlobals |
| 866 |
|
| 867 |
subroutine FreeSimGlobals() |
| 868 |
|
| 869 |
!We free in the opposite order in which we allocate in. |
| 870 |
if (allocated(topoDistance)) deallocate(topoDistance) |
| 871 |
if (allocated(toposForAtom)) deallocate(toposForAtom) |
| 872 |
if (allocated(nTopoPairsForAtom)) deallocate(nTopoPairsForAtom) |
| 873 |
if (allocated(skipsForLocalAtom)) deallocate(skipsForLocalAtom) |
| 874 |
if (allocated(nSkipsForLocalAtom)) deallocate(nSkipsForLocalAtom) |
| 875 |
if (allocated(skipsForRowAtom)) deallocate(skipsForRowAtom) |
| 876 |
if (allocated(nSkipsForRowAtom)) deallocate(nSkipsForRowAtom) |
| 877 |
if (allocated(mfactLocal)) deallocate(mfactLocal) |
| 878 |
if (allocated(mfactCol)) deallocate(mfactCol) |
| 879 |
if (allocated(mfactRow)) deallocate(mfactRow) |
| 880 |
if (allocated(groupListCol)) deallocate(groupListCol) |
| 881 |
if (allocated(groupListRow)) deallocate(groupListRow) |
| 882 |
if (allocated(groupStartCol)) deallocate(groupStartCol) |
| 883 |
if (allocated(groupStartRow)) deallocate(groupStartRow) |
| 884 |
if (allocated(molMembershipList)) deallocate(molMembershipList) |
| 885 |
if (allocated(excludes)) deallocate(excludes) |
| 886 |
|
| 887 |
end subroutine FreeSimGlobals |
| 888 |
|
| 889 |
pure function getNlocal() result(n) |
| 890 |
integer :: n |
| 891 |
n = nLocal |
| 892 |
end function getNlocal |
| 893 |
|
| 894 |
subroutine setHmatDangerousRcutValue(dangerWillRobinson) |
| 895 |
real(kind=dp), intent(in) :: dangerWillRobinson |
| 896 |
DangerRcut = dangerWillRobinson |
| 897 |
|
| 898 |
call checkBox() |
| 899 |
|
| 900 |
return |
| 901 |
end subroutine setHmatDangerousRcutValue |
| 902 |
|
| 903 |
|
| 904 |
|
| 905 |
end module simulation |
