--- trunk/OOPSE/libmdtools/do_Forces.F90	2003/03/21 22:11:50	388
+++ trunk/OOPSE/libmdtools/do_Forces.F90	2003/07/16 21:30:56	626
@@ -4,7 +4,7 @@
 
 !! @author Charles F. Vardeman II
 !! @author Matthew Meineke
-!! @version $Id: do_Forces.F90,v 1.2 2003-03-21 22:11:50 chuckv Exp $, $Date: 2003-03-21 22:11:50 $, $Name: not supported by cvs2svn $, $Revision: 1.2 $
+!! @version $Id: do_Forces.F90,v 1.21 2003-07-16 21:30:55 mmeineke Exp $, $Date: 2003-07-16 21:30:55 $, $Name: not supported by cvs2svn $, $Revision: 1.21 $
 
 module do_Forces
   use force_globals
@@ -17,6 +17,7 @@ module do_Forces
   use dipole_dipole
   use reaction_field
   use gb_pair
+  use vector_class
 #ifdef IS_MPI
   use mpiSimulation
 #endif
@@ -27,7 +28,8 @@ module do_Forces
 #define __FORTRAN90
 #include "fForceField.h"
 
-  logical, save :: do_forces_initialized = .false.
+  logical, save :: do_forces_initialized = .false., haveRlist = .false.
+  logical, save :: havePolicies = .false.
   logical, save :: FF_uses_LJ
   logical, save :: FF_uses_sticky
   logical, save :: FF_uses_dipoles
@@ -35,11 +37,26 @@ module do_Forces
   logical, save :: FF_uses_GB
   logical, save :: FF_uses_EAM
 
+  real(kind=dp), save :: rlist, rlistsq
+
   public :: init_FF
   public :: do_force_loop
+  public :: setRlistDF
 
 contains
 
+  subroutine setRlistDF( this_rlist )
+    
+    real(kind=dp) :: this_rlist
+
+    rlist = this_rlist
+    rlistsq = rlist * rlist
+    
+    haveRlist = .true.
+    if( havePolicies ) do_forces_initialized = .true.
+
+  end subroutine setRlistDF    
+
   subroutine init_FF(LJMIXPOLICY, use_RF_c, thisStat)
 
     integer, intent(in) :: LJMIXPOLICY
@@ -87,12 +104,9 @@ contains
     !! check to make sure the FF_uses_RF setting makes sense
     
     if (FF_uses_dipoles) then
-       rrf = getRrf()
-       rt = getRt()       
-       call initialize_dipole(rrf, rt)
        if (FF_uses_RF) then
           dielect = getDielect()
-          call initialize_rf(rrf, rt, dielect)
+          call initialize_rf(dielect)
        endif
     else
        if (FF_uses_RF) then          
@@ -100,17 +114,15 @@ contains
           thisStat = -1
           return
        endif
-    endif
+    endif 
 
     if (FF_uses_LJ) then
        
-       call getRcut(rcut)
-
        select case (LJMIXPOLICY)
        case (LB_MIXING_RULE)
-          call init_lj_FF(LB_MIXING_RULE, rcut, my_status)             
+          call init_lj_FF(LB_MIXING_RULE, my_status)             
        case (EXPLICIT_MIXING_RULE)
-          call init_lj_FF(EXPLICIT_MIXING_RULE, rcut, my_status)
+          call init_lj_FF(EXPLICIT_MIXING_RULE, my_status)
        case default
           write(default_error,*) 'unknown LJ Mixing Policy!'
           thisStat = -1
@@ -140,10 +152,19 @@ contains
 
     if (FF_uses_GB .and. FF_uses_LJ) then
     endif
+    if (.not. do_forces_initialized) then
+       !! Create neighbor lists
+       call expandNeighborList(getNlocal(), my_status)
+       if (my_Status /= 0) then
+          write(default_error,*) "SimSetup: ExpandNeighborList returned error."
+          thisStat = -1
+          return
+       endif
+    endif
 
-
-    do_forces_initialized = .true.    
- 
+    havePolicies = .true.
+    if( haveRlist ) do_forces_initialized = .true.
+     
   end subroutine init_FF
   
 
@@ -167,7 +188,7 @@ contains
     logical ( kind = 2) :: do_pot_c, do_stress_c
     logical :: do_pot
     logical :: do_stress
-#ifdef IS_MPI
+#ifdef IS_MPI 
     real( kind = DP ) :: pot_local
     integer :: nrow
     integer :: ncol
@@ -177,7 +198,7 @@ contains
     logical :: update_nlist   
     integer :: i, j, jbeg, jend, jnab
     integer :: nlist
-    real( kind = DP ) ::  rijsq, rlistsq, rcutsq, rlist, rcut
+    real( kind = DP ) ::  rijsq 
     real(kind=dp),dimension(3) :: d
     real(kind=dp) :: rfpot, mu_i, virial
     integer :: me_i
@@ -186,9 +207,13 @@ contains
     integer :: listerror, error
     integer :: localError
 
+    real(kind=dp) :: listSkin = 1.0
+    
+
     !! initialize local variables  
 
 #ifdef IS_MPI
+    pot_local = 0.0_dp
     nlocal = getNlocal()
     nrow   = getNrow(plan_row)
     ncol   = getNcol(plan_col)
@@ -196,10 +221,7 @@ contains
     nlocal = getNlocal()
     natoms = nlocal
 #endif
-
-    call getRcut(rcut,rc2=rcutsq)
-    call getRlist(rlist,rlistsq)
-    
+   
     call check_initialization(localError)
     if ( localError .ne. 0 ) then
        error = -1
@@ -229,14 +251,14 @@ contains
     
     if (FF_RequiresPrepairCalc() .and. SimRequiresPrepairCalc()) then
        !! See if we need to update neighbor lists
-       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)   
+       call checkNeighborList(nlocal, q, listSkin, update_nlist)   
        !! if_mpi_gather_stuff_for_prepair
        !! do_prepair_loop_if_needed
        !! if_mpi_scatter_stuff_from_prepair
        !! if_mpi_gather_stuff_from_prepair_to_main_loop
     else
        !! See if we need to update neighbor lists
-       call checkNeighborList(nlocal, q, rcut, rlist, update_nlist)   
+       call checkNeighborList(nlocal, q, listSkin, update_nlist)   
     endif
     
 #ifdef IS_MPI
@@ -245,7 +267,7 @@ contains
        
        !! save current configuration, construct neighbor list, 
        !! and calculate forces
-       call saveNeighborList(q)
+       call saveNeighborList(nlocal, q)
        
        neighborListSize = size(list)
        nlist = 0       
@@ -259,7 +281,7 @@ contains
              
              call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
              
-             if (rijsq <  rlistsq) then             
+             if (rijsq < rlistsq) then             
                 
                 nlist = nlist + 1
                 
@@ -275,10 +297,9 @@ contains
                 
                 list(nlist) = j
                                 
-                if (rijsq <  rcutsq) then
-                   call do_pair(i, j, rijsq, d, do_pot, do_stress, &
-                        u_l, A, f, t,pot)
-                endif
+                call do_pair(i, j, rijsq, d, do_pot, do_stress, &
+                     u_l, A, f, t, pot_local)
+                
              endif
           enddo inner
        enddo
@@ -299,7 +320,7 @@ contains
 
                 call get_interatomic_vector(q_Row(:,i), q_Col(:,j), d, rijsq)
                 call do_pair(i, j, rijsq, d, do_pot, do_stress, &
-                     u_l, A, f, t,pot)
+                     u_l, A, f, t, pot_local)
 
              enddo
           endif
@@ -312,7 +333,7 @@ contains
        
        ! save current configuration, contruct neighbor list, 
        ! and calculate forces
-       call saveNeighborList(q)
+       call saveNeighborList(natoms, q)
        
        neighborListSize = size(list)
    
@@ -328,7 +349,7 @@ contains
              call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
            
 
-             if (rijsq <  rlistsq) then
+             if (rijsq < rlistsq) then
                 
                 nlist = nlist + 1
               
@@ -344,10 +365,9 @@ contains
                 
                 list(nlist) = j
                 
-                if (rijsq <  rcutsq) then
-                   call do_pair(i, j, rijsq, d, do_pot, do_stress, &
-                        u_l, A, f, t,pot)
-                endif
+                call do_pair(i, j, rijsq, d, do_pot, do_stress, &
+                        u_l, A, f, t, pot)
+                
              endif
           enddo inner
        enddo
@@ -368,7 +388,7 @@ contains
 
                 call get_interatomic_vector(q(:,i), q(:,j), d, rijsq)
                 call do_pair(i, j, rijsq, d, do_pot, do_stress, &
-                     u_l, A, f, t,pot)
+                     u_l, A, f, t, pot)
 
              enddo
           endif
@@ -381,15 +401,26 @@ contains
     
 #ifdef IS_MPI
     !!distribute forces
-    
-    call scatter(f_Row,f,plan_row3d)
+   
+    f_temp = 0.0_dp
+    call scatter(f_Row,f_temp,plan_row3d)
+    do i = 1,nlocal
+       f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
+    end do
+
+    f_temp = 0.0_dp
     call scatter(f_Col,f_temp,plan_col3d)
     do i = 1,nlocal
        f(1:3,i) = f(1:3,i) + f_temp(1:3,i)
     end do
     
     if (FF_UsesDirectionalAtoms() .and. SimUsesDirectionalAtoms()) then
-       call scatter(t_Row,t,plan_row3d)
+       t_temp = 0.0_dp
+       call scatter(t_Row,t_temp,plan_row3d)
+       do i = 1,nlocal
+          t(1:3,i) = t(1:3,i) + t_temp(1:3,i)
+       end do
+       t_temp = 0.0_dp
        call scatter(t_Col,t_temp,plan_col3d)
        
        do i = 1,nlocal
@@ -400,20 +431,20 @@ contains
     if (do_pot) then
        ! scatter/gather pot_row into the members of my column
        call scatter(pot_Row, pot_Temp, plan_row)
-       
+
        ! scatter/gather pot_local into all other procs
        ! add resultant to get total pot
        do i = 1, nlocal
           pot_local = pot_local + pot_Temp(i)
        enddo
+       
+       pot_Temp = 0.0_DP 
 
-       pot_Temp = 0.0_DP
-
        call scatter(pot_Col, pot_Temp, plan_col)
        do i = 1, nlocal
           pot_local = pot_local + pot_Temp(i)
        enddo
-       
+
     endif    
 #endif
 
@@ -461,15 +492,15 @@ contains
 #ifdef IS_MPI
 
     if (do_pot) then
-       pot = pot_local
+       pot = pot + pot_local
        !! we assume the c code will do the allreduce to get the total potential
        !! we could do it right here if we needed to...
     endif
 
     if (do_stress) then
-       call mpi_allreduce(tau, tau_Temp,9,mpi_double_precision,mpi_sum, &
+      call mpi_allreduce(tau_Temp, tau, 9,mpi_double_precision,mpi_sum, &
             mpi_comm_world,mpi_err)
-       call mpi_allreduce(virial, virial_Temp,1,mpi_double_precision,mpi_sum, &
+       call mpi_allreduce(virial_Temp, virial,1,mpi_double_precision,mpi_sum, &
             mpi_comm_world,mpi_err)
     endif
 
@@ -484,13 +515,13 @@ contains
     
   end subroutine do_force_loop
 
-  subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t,pot)
+  subroutine do_pair(i, j, rijsq, d, do_pot, do_stress, u_l, A, f, t, pot)
 
     real( kind = dp ) :: pot
-    real( kind = dp ), dimension(:,:) :: u_l
-    real (kind=dp), dimension(:,:) :: A
-    real (kind=dp), dimension(:,:) :: f
-    real (kind=dp), dimension(:,:) :: t
+    real( kind = dp ), dimension(3,getNlocal()) :: u_l
+    real (kind=dp), dimension(9,getNlocal()) :: A
+    real (kind=dp), dimension(3,getNlocal()) :: f
+    real (kind=dp), dimension(3,getNlocal()) :: t
 
     logical, intent(inout) :: do_pot, do_stress
     integer, intent(in) :: i, j
@@ -506,6 +537,9 @@ contains
     r = sqrt(rijsq)
 
 #ifdef IS_MPI
+    if (tagRow(i) .eq. tagColumn(j)) then
+       write(0,*) 'do_pair is doing', i , j, tagRow(i), tagColumn(j)
+    endif
 
     me_i = atid_row(i)
     me_j = atid_col(j)
@@ -564,6 +598,8 @@ contains
        endif
     endif
      
+
+
   end subroutine do_pair
 
 
@@ -572,21 +608,52 @@ contains
     real (kind = dp), dimension(3) :: q_i
     real (kind = dp), dimension(3) :: q_j
     real ( kind = dp ), intent(out) :: r_sq
-    real( kind = dp ) :: d(3)
-    real( kind = dp ) :: d_old(3)
-    d(1:3) = q_i(1:3) - q_j(1:3)
-    d_old = d
+    real( kind = dp ) :: d(3), scaled(3)
+    integer i
+
+    d(1:3) = q_j(1:3) - q_i(1:3)
+
     ! Wrap back into periodic box if necessary
     if ( SimUsesPBC() ) then
+       
+       if( .not.boxIsOrthorhombic ) then
+          ! calc the scaled coordinates.
+          
+          scaled = matmul(HmatInv, d)
+          
+          ! wrap the scaled coordinates
 
-       d(1:3) = d(1:3) - box(1:3) * sign(1.0_dp,d(1:3)) * &
-            int(abs(d(1:3)/box(1:3)) + 0.5_dp)
+          scaled = scaled  - anint(scaled)
+          
 
+          ! calc the wrapped real coordinates from the wrapped scaled 
+          ! coordinates
+
+          d = matmul(Hmat,scaled)
+
+       else
+          ! calc the scaled coordinates.
+          
+          do i = 1, 3
+             scaled(i) = d(i) * HmatInv(i,i)
+             
+             ! wrap the scaled coordinates
+             
+             scaled(i) = scaled(i) - anint(scaled(i))
+             
+             ! calc the wrapped real coordinates from the wrapped scaled 
+             ! coordinates
+
+             d(i) = scaled(i)*Hmat(i,i)
+          enddo
+       endif
+       
     endif
+    
     r_sq = dot_product(d,d)
-        
+    
   end subroutine get_interatomic_vector
-
+  
   subroutine check_initialization(error)
     integer, intent(out) :: error
     
@@ -643,7 +710,6 @@ contains
     rf = 0.0_dp
     tau_Temp = 0.0_dp
     virial_Temp = 0.0_dp
-    
   end subroutine zero_work_arrays
   
   function skipThisPair(atom1, atom2) result(skip_it)
@@ -687,7 +753,7 @@ contains
 #else
     unique_id_2 = atom2
 #endif
-    
+
 #ifdef IS_MPI
     !! this situation should only arise in MPI simulations
     if (unique_id_1 == unique_id_2) then
@@ -697,14 +763,18 @@ contains
     
     !! this prevents us from doing the pair on multiple processors
     if (unique_id_1 < unique_id_2) then
-       if (mod(unique_id_1 + unique_id_2,2) == 0) skip_it = .true.
-       return
+       if (mod(unique_id_1 + unique_id_2,2) == 0) then
+          skip_it = .true.
+          return
+       endif
     else                
-       if (mod(unique_id_1 + unique_id_2,2) == 1) skip_it = .true.
-       return
+       if (mod(unique_id_1 + unique_id_2,2) == 1) then 
+          skip_it = .true.
+          return
+       endif
     endif
 #endif
-
+ 
     !! the rest of these situations can happen in all simulations:
     do i = 1, nExcludes_global       
        if ((excludesGlobal(i) == unique_id_1) .or. &
@@ -713,7 +783,7 @@ contains
           return
        endif
     enddo
- 
+
     do i = 1, nExcludes_local
        if (excludesLocal(1,i) == unique_id_1) then
           if (excludesLocal(2,i) == unique_id_2) then