--- trunk/OOPSE/libmdtools/simulation_module.F90	2004/05/01 18:52:38	1144
+++ 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
@@ -15,17 +16,22 @@ module simulation
 
 #define __FORTRAN90
 #include "fSimulation.h"
+#include "fSwitchingFunction.h"
 
   type (simtype), public, save :: thisSim
 
   logical, save :: simulation_setup_complete = .false.
 
   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), public, dimension(3,3), save :: Hmat, HmatInv
   logical, public, save :: boxIsOrthorhombic
@@ -50,7 +56,7 @@ contains
   
   subroutine SimulationSetup(setThisSim, CnGlobal, CnLocal, c_idents, &
        CnLocalExcludes, CexcludesLocal, CnGlobalExcludes, CexcludesGlobal, &
-       CmolMembership, mfact, ngroup, groupList, groupStart, &
+       CmolMembership, Cmfact, CnGroup, CgroupList, CgroupStart, &
        status)    
 
     type (simtype) :: setThisSim
@@ -65,12 +71,13 @@ contains
     !!  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(3,nLocal) :: mfact
-    integer, intent(in):: ngroup
-    integer, dimension(nLocal),intent(in) :: groupList 
-    integer, dimension(ngroup),intent(in) :: groupStart
+    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
@@ -86,6 +93,7 @@ contains
 
     nLocal = CnLocal
     nGlobal = CnGlobal
+    nGroup = CnGroup
 
     thisSim = setThisSim
 
@@ -160,9 +168,6 @@ contains
   
     enddo
 
-
-
-
     do i = 1, nExcludes_Local
        excludesLocal(1,i) = CexcludesLocal(1,i)
        excludesLocal(2,i) = CexcludesLocal(2,i)
@@ -174,8 +179,30 @@ contains
 
     do i = 1, nGlobal
        molMemberShipList(i) = CmolMembership(i)
-     enddo
+    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
@@ -282,6 +309,24 @@ contains
        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
   
@@ -289,16 +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(n)
     integer :: n
     n = nLocal
   end function getNlocal
-
   
+  
 end module simulation