--- trunk/OOPSE/libmdtools/simulation_module.F90	2003/04/11 15:16:59	490
+++ trunk/OOPSE/libmdtools/simulation_module.F90	2004/05/07 21:35:05	1150
@@ -6,6 +6,7 @@ module simulation
   use force_globals
   use vector_class
   use atype_module
+  use switcheroo
 #ifdef IS_MPI
   use mpiSimulation
 #endif
@@ -15,37 +16,33 @@ module simulation
 
 #define __FORTRAN90
 #include "fSimulation.h"
+#include "fSwitchingFunction.h"
 
-  type (simtype), public :: thisSim
+  type (simtype), public, save :: thisSim
 
   logical, save :: simulation_setup_complete = .false.
 
-  integer, public, save :: natoms
+  integer, public, save :: nLocal, nGlobal
+  integer, public, save :: nGroup, nGroupGlobal
   integer, public, save :: nExcludes_Global = 0
   integer, public, save :: nExcludes_Local = 0
   integer, allocatable, dimension(:,:), public :: excludesLocal
   integer, allocatable, dimension(:), public :: excludesGlobal
   integer, allocatable, dimension(:), public :: molMembershipList
+  integer, allocatable, dimension(:), public :: groupList
+  integer, allocatable, dimension(:), public :: groupStart
+  real(kind=dp), allocatable, dimension(:), public :: mfact
 
-  real(kind=dp), save :: rcut2 = 0.0_DP
-  real(kind=dp), save :: rcut6 = 0.0_DP
-  real(kind=dp), save :: rlist2 = 0.0_DP
-  real(kind=dp), public, dimension(3), save :: box
-
+  real(kind=dp), public, dimension(3,3), save :: Hmat, HmatInv
+  logical, public, save :: boxIsOrthorhombic
   
   public :: SimulationSetup
   public :: getNlocal
   public :: setBox
-  public :: setBox_3d
-  public :: getBox
-  public :: setRcut
-  public :: getRcut
-  public :: getRlist
-  public :: getRrf
-  public :: getRt
   public :: getDielect
   public :: SimUsesPBC
   public :: SimUsesLJ
+  public :: SimUsesCharges
   public :: SimUsesDipoles
   public :: SimUsesSticky
   public :: SimUsesRF
@@ -54,36 +51,34 @@ module simulation
   public :: SimRequiresPrepairCalc
   public :: SimRequiresPostpairCalc
   public :: SimUsesDirectionalAtoms
-
-  interface getBox
-     module procedure getBox_3d
-     module procedure getBox_1d
-  end interface
   
-  interface setBox
-     module procedure setBox_3d
-     module procedure setBox_1d
-  end interface
-  
 contains
   
-  subroutine SimulationSetup(setThisSim, nGlobal, nLocal, c_idents, &
+  subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, &
        CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, &
-       CmolMembership, &
+       CmolMembership, Cmfact, CnGroup, CgroupList, CgroupStart, &
        status)    
 
     type (simtype) :: setThisSim
-    integer, intent(inout) :: nGlobal, nLocal
-    integer, dimension(nLocal),intent(inout) :: c_idents
+    integer, intent(inout) :: CnGlobal, CnLocal
+    integer, dimension(CnLocal),intent(inout) :: c_idents
 
     integer :: CnLocalExcludes
     integer, dimension(2,CnLocalExcludes), intent(in) :: CexcludesLocal
     integer :: CnGlobalExcludes
     integer, dimension(CnGlobalExcludes), intent(in) :: CexcludesGlobal
-    integer, dimension(nGlobal),intent(in) :: CmolMembership 
+    integer, dimension(CnGlobal),intent(in) :: CmolMembership 
     !!  Result status, success = 0, status = -1
     integer, intent(out) :: status
     integer :: i, me, thisStat, alloc_stat, myNode
+    integer :: gStart, gEnd, groupSize, biggestGroupSize, ia
+
+    !! mass factors used for molecular cutoffs
+    real ( kind = dp ), dimension(CnLocal) :: Cmfact
+    integer, intent(in):: CnGroup
+    integer, dimension(CnLocal),intent(in) :: CgroupList 
+    integer, dimension(CnGroup),intent(in) :: CgroupStart
+
 #ifdef IS_MPI
     integer, allocatable, dimension(:) :: c_idents_Row
     integer, allocatable, dimension(:) :: c_idents_Col
@@ -95,17 +90,17 @@ contains
     status = 0
 
     ! copy C struct into fortran type
+
+    nLocal = CnLocal
+    nGlobal = CnGlobal
+    nGroup = CnGroup
+
     thisSim = setThisSim
-    natoms = nLocal
-    rcut2 = thisSim%rcut * thisSim%rcut
-    rcut6 = rcut2 * rcut2 * rcut2
-    rlist2 = thisSim%rlist * thisSim%rlist
-    box = thisSim%box
 
     nExcludes_Global = CnGlobalExcludes
     nExcludes_Local = CnLocalExcludes
 
-    call InitializeForceGlobals(natoms, thisStat)
+    call InitializeForceGlobals(nLocal, thisStat)
     if (thisStat /= 0) then
        write(default_error,*) "SimSetup: InitializeForceGlobals error"
        status = -1
@@ -163,17 +158,16 @@ contains
        deallocate(c_idents_Row)
     endif
     
-#else
+#endif
+
+! We build the local atid's for both mpi and nonmpi
     do i = 1, nLocal
        
        me = getFirstMatchingElement(atypes, "c_ident", c_idents(i))
        atid(i) = me
   
     enddo
-#endif
 
-
-
     do i = 1, nExcludes_Local
        excludesLocal(1,i) = CexcludesLocal(1,i)
        excludesLocal(2,i) = CexcludesLocal(2,i)
@@ -185,98 +179,50 @@ contains
 
     do i = 1, nGlobal
        molMemberShipList(i) = CmolMembership(i)
-       ! write(0,*) 'molMembershipList(',i,') = ', molMemberShipList(i)
     enddo
+    
+    biggestGroupSize = 0
+    do i = 1, nGroup
+       groupStart(i) = CgroupStart(i)
+       groupSize = 0
+       gStart = groupStart(i)       
+       if (i .eq. nGroup) then
+          gEnd = nLocal
+       else
+          gEnd = CgroupStart(i+1) - 1
+       endif
+       do ia = gStart, gEnd
+          groupList(ia) = CgroupList(ia)
+          groupSize = groupSize + 1
+       enddo
+       if (groupSize .gt. biggestGroupSize) biggestGroupSize = groupSize       
+    enddo
+    groupStart(nGroup+1) = nLocal+1
 
+    do i = 1, nLocal
+       mfact(i) = Cmfact(i)
+    enddo    
+    
     if (status == 0) simulation_setup_complete = .true.
     
   end subroutine SimulationSetup
   
-  subroutine setBox_3d(new_box_size)
-    real(kind=dp), dimension(3) :: new_box_size
+  subroutine setBox(cHmat, cHmatInv, cBoxIsOrthorhombic)
+    real(kind=dp), dimension(3,3) :: cHmat, cHmatInv
+    integer :: cBoxIsOrthorhombic
     integer :: smallest, status, i
-
-    thisSim%box = new_box_size
-    box = thisSim%box
-
+    
+    Hmat = cHmat
+    HmatInv = cHmatInv
+    if (cBoxIsOrthorhombic .eq. 0 ) then
+       boxIsOrthorhombic = .false.
+    else 
+       boxIsOrthorhombic = .true.
+    endif
+    
     return     
-  end subroutine setBox_3d
-
-  subroutine setBox_1d(dim, new_box_size)
-    integer :: dim, status
-    real(kind=dp) :: new_box_size
-    thisSim%box(dim) = new_box_size
-    box(dim) = thisSim%box(dim)
-  end subroutine setBox_1d
+  end subroutine setBox
 
-  subroutine setRcut(new_rcut, status) 
-    real(kind = dp) :: new_rcut
-    integer :: myStatus, status
-    thisSim%rcut = new_rcut
-    rcut2 = thisSim%rcut * thisSim%rcut
-    rcut6 = rcut2 * rcut2 * rcut2
-    status = 0
-    return
-  end subroutine setRcut
-
-  function getBox_3d() result(thisBox)
-    real( kind = dp ), dimension(3) :: thisBox
-    thisBox = thisSim%box
-  end function getBox_3d
-  
-  function getBox_1d(dim) result(thisBox)
-    integer, intent(in) :: dim
-    real( kind = dp ) :: thisBox
-    
-    thisBox = thisSim%box(dim)
-  end function getBox_1d
-     
-  subroutine getRcut(thisrcut,rc2,rc6,status)
-    real( kind = dp ), intent(out) :: thisrcut
-    real( kind = dp ), intent(out), optional :: rc2
-    real( kind = dp ), intent(out), optional :: rc6
-    integer, optional :: status
-
-    if (present(status)) status = 0
-    
-    if (.not.simulation_setup_complete ) then
-       if (present(status)) status = -1
-       return
-    end if
-    
-    thisrcut = thisSim%rcut
-    if(present(rc2)) rc2 = rcut2
-    if(present(rc6)) rc6 = rcut6
-  end subroutine getRcut
-  
-  subroutine getRlist(thisrlist,rl2,status)
-    real( kind = dp ), intent(out) :: thisrlist
-    real( kind = dp ), intent(out), optional :: rl2
-
-    integer, optional :: status
-
-    if (present(status)) status = 0
-
-    if (.not.simulation_setup_complete ) then
-       if (present(status)) status = -1
-       return
-    end if
-    
-    thisrlist = thisSim%rlist
-    if(present(rl2)) rl2 = rlist2
-  end subroutine getRlist
-
-  function getRrf() result(rrf)
-    real( kind = dp ) :: rrf
-    rrf = thisSim%rrf
-    write(*,*) 'getRrf = ', rrf, thisSim%rrf
-  end function getRrf
-  
-  function getRt() result(rt)
-    real( kind = dp ) :: rt
-    rt = thisSim%rt
-  end function getRt
-
   function getDielect() result(dielect)
     real( kind = dp ) :: dielect
     dielect = thisSim%dielect
@@ -297,6 +243,11 @@ contains
     doesit = thisSim%SIM_uses_sticky
   end function SimUsesSticky
 
+  function SimUsesCharges() result(doesit)
+    logical :: doesit
+    doesit = thisSim%SIM_uses_charges
+  end function SimUsesCharges
+
   function SimUsesDipoles() result(doesit)
     logical :: doesit
     doesit = thisSim%SIM_uses_dipoles
@@ -353,11 +304,29 @@ contains
        return
     endif
 
-    allocate(molMembershipList(getNlocal()), stat=alloc_stat)
+    allocate(molMembershipList(nGlobal), stat=alloc_stat)
     if (alloc_stat /= 0 ) then
        thisStat = -1
        return
     endif
+
+    allocate(groupStart(nGroup+1), stat=alloc_stat)
+    if (alloc_stat /= 0 ) then
+       thisStat = -1
+       return
+    endif
+
+    allocate(groupList(nLocal), stat=alloc_stat)
+    if (alloc_stat /= 0 ) then
+       thisStat = -1
+       return
+    endif
+
+    allocate(mfact(nLocal), stat=alloc_stat)
+    if (alloc_stat /= 0 ) then
+       thisStat = -1
+       return
+    endif
     
   end subroutine InitializeSimGlobals
   
@@ -365,16 +334,19 @@ contains
     
     !We free in the opposite order in which we allocate in.
 
+    if (allocated(mfact)) deallocate(mfact)
+    if (allocated(groupList)) deallocate(groupList)     
+    if (allocated(groupStart)) deallocate(groupStart)     
     if (allocated(molMembershipList)) deallocate(molMembershipList)     
     if (allocated(excludesGlobal)) deallocate(excludesGlobal)
     if (allocated(excludesLocal)) deallocate(excludesLocal)
-
+    
   end subroutine FreeSimGlobals
-
-  pure function getNlocal() result(nlocal)
-    integer :: nlocal
-    nlocal = natoms
+  
+  pure function getNlocal() result(n)
+    integer :: n
+    n = nLocal
   end function getNlocal
-
   
+  
 end module simulation