[ViewVC] Diff of: group/trunk/mdtools/md_code/lj

Comparing trunk/mdtools/md_code/lj_FF.F90 (file contents):
Revision 215 by chuckv, Thu Dec 19 21:59:51 2002 UTC vs.
Revision 246 by chuckv, Fri Jan 24 21:36:52 2003 UTC

-+
+!! Calculates Long Range forces Lennard-Jones interactions.
-+
+!! Corresponds to the force field defined in lj_FF.cpp
-+
+!! @author Charles F. Vardeman II
-+
+!! @author Matthew Meineke
-+
+!! @version $Id: lj_FF.F90,v 1.10 2003-01-24 21:36:52 chuckv Exp $, $Date: 2003-01-24 21:36:52 $, $Name: not supported by cvs2svn $, $Revision: 1.10 $
-+
-+
-+
+module lj_ff
+  use simulation
-<
+  use definitions, ONLY : dp, ndim
->
+  use definitions
->
+#ifdef IS_MPI
->
+  use mpiSimulation
->
+#endif
+  implicit none
-+
+  PRIVATE
-+
+!! Number of lj_atypes in lj_atype_list
+  integer, save :: n_lj_atypes = 0
-+
+!! Starting Size for ljMixed Array
-+
+  integer, parameter :: ljMixed_blocksize = 10
-+
-+
+!! Basic atom type for a Lennard-Jones Atom.
+  type, public :: lj_atype
+     private
+     sequence
-+
+!! Unique number for place in linked list
-+
+     integer :: atype_number = 0
-+
+!! Unique indentifier number (ie atomic no, etc)
+     integer :: atype_ident = 0
-<
+     character(len = 15) :: name = "NULL"
->
+!! Mass of Particle
+     real ( kind = dp )  :: mass = 0.0_dp
-<
+     real ( kind = dp )  :: epslon = 0.0_dp
->
+!! Lennard-Jones epslon
->
+     real ( kind = dp )  :: epsilon = 0.0_dp
->
+!! Lennard-Jones Sigma
+     real ( kind = dp )  :: sigma = 0.0_dp
-+
+!! Lennard-Jones Sigma Squared
-+
+     real ( kind = dp )  :: sigma2 = 0.0_dp
-+
+!! Lennard-Jones Sigma to sixth
-+
+     real ( kind = dp )  :: sigma6 = 0.0_dp
-+
+!! Pointer for linked list creation
+     type (lj_atype), pointer :: next => null()
+  end type lj_atype
-+
+!! Pointer type for atype ident array
-+
+  type, public :: lj_atypePtr
-+
+     type (lj_atype), pointer :: this => null()
-+
+  end type lj_atypePtr
-+
-+
+!! Global list of lj atypes in simulation
+  type (lj_atype), pointer :: lj_atype_list => null()
-+
+!! LJ mixing array
-+
+  type (lj_atype), dimension(:,:), pointer :: ljMixed => null()
-+
+!! identity pointer list for force loop.
-+
+  type (lj_atypePtr), dimension(:), pointer :: identPtrList => null()
-+
-+
+!! Neighbor list and commom arrays
-+
+!! This should eventally get moved to a neighbor list type
-+
+  integer, allocatable, dimension(:) :: point
-+
+  integer, allocatable, dimension(:) :: list
-+
+  integer, parameter :: listMultiplier = 80
-+
+  integer :: nListAllocs = 0
-+
+  integer, parameter :: maxListAllocs = 5
-+
-+
+#ifdef IS_MPI
-+
+! Universal routines: All types of force calculations will need these arrays
-+
+! Arrays specific to a type of force calculation should be declared in that module.
-+
+!! Row position array.
-+
+  real( kind = dp ), allocatable, dimension(:,:) :: qRow
-+
+!! Column position array.
-+
+  real( kind = dp ), allocatable, dimension(:,:) :: qColumn
-+
-+
+!! Row Force array.
-+
+  real( kind = dp ), allocatable, dimension(:,:) :: fRow
-+
+!! Column Force Array.
-+
+  real( kind = dp ), allocatable, dimension(:,:) :: fColumn
-+
-+
+!! Row potential energy array
-+
+  real( kind = dp ), allocatable, dimension(:) :: eRow
-+
+!! Column potential energy array
-+
+  real( kind = dp ), allocatable, dimension(:) :: eColumn
-+
-+
-+
+!! Row lj_atype pointer list
-+
+  type (lj_atypePtr), dimension(:), pointer :: identPtrListRow => null()
-+
+!! Column lj_atype pointer list
-+
+  type (lj_atypePtr), dimension(:), pointer :: identPtrListColumn => null()
-+
+#endif
-+
-+
-+
+!! Logical has lj force field module been initialized?
-+
+  logical, save :: isljFFinit = .false.
-+
-+
-+
+!! Public methods and data
+  public :: new_lj_atype
-+
+  public :: do_lj_ff
-+
+  public :: getLjPot
-+
+  public :: init_ljFF
-+
-+
-+
+contains
-<
+  subroutine new_lj_atype(name,mass,epslon,sigma,status)
-<
+    character( len = 15 ) :: name
->
+  subroutine new_lj_atype(ident,mass,epsilon,sigma,status)
+    real( kind = dp ), intent(in) :: mass
-<
+    real( kind = dp ), intent(in) :: epslon
-<
+    real( kind = dp ), intent(in) :: sigam
->
+    real( kind = dp ), intent(in) :: epsilon
->
+    real( kind = dp ), intent(in) :: sigma
->
+    integer, intent(in) :: ident
+    integer, intent(out) :: status
-+
+    type (lj_atype), pointer :: this_lj_atype
-+
+    type (lj_atype), pointer :: lj_atype_ptr
-+
-+
+    type (lj_atype), dimension(:,:), pointer :: thisMix
-+
+    type (lj_atype), dimension(:,:), pointer :: oldMix
-+
+    integer :: alloc_error
-+
+    integer :: atype_counter = 0
-+
+    integer :: alloc_size
-+
+    status = 0
-+
-+
-+
+! allocate a new atype
-+
+    allocate(this_lj_atype,stat=alloc_error)
-+
+    if (alloc_error /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    end if
-+
-+
+! assign our new lj_atype information
-+
+    this_lj_atype%mass        = mass
-+
+    this_lj_atype%epsilon     = epsilon
-+
+    this_lj_atype%sigma       = sigma
-+
+    this_lj_atype%sigma2      = sigma * sigma
-+
+    this_lj_atype%sigma6      = this_lj_atype%sigma2 * this_lj_atype%sigma2 &
-+
+         * this_lj_atype%sigma2
-+
+! assume that this atype will be successfully added
-+
+    this_lj_atype%atype_ident = ident
-+
+    this_lj_atype%atype_number = n_lj_atypes + 1
-+
-+
-+
+! First time through allocate a array of size ljMixed_blocksize
-+
+    if(.not. associated(ljMixed)) then
-+
+       allocate(thisMix(ljMixed_blocksize,ljMixed_blocksize))
-+
+       if (alloc_error /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       end if
-+
+       ljMixed => thisMix
-+
+! If we have outgrown ljMixed_blocksize, allocate a new matrix twice the size and
-+
+! point ljMix at the new matrix.
-+
+    else if( (n_lj_atypes + 1) > size(ljMixed)) then
-+
+       alloc_size = 2*size(ljMixed)
-+
+       allocate(thisMix(alloc_size,alloc_size))
-+
+       if (alloc_error /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       end if
-+
+! point oldMix at old ljMixed array
-+
+       oldMix => ljMixed
-+
+! Copy oldMix into new Mixed array
-+
+       thisMix = oldMix
-+
+! Point ljMixed at new array
-+
+       ljMixed => thisMix
-+
+! Free old array so we don't have a memory leak
-+
+       deallocate(oldMix)
-+
+    endif
-+
-+
-+
-+
-+
-+
+! Find bottom of atype master list
-+
+! if lj_atype_list is null then we are at the top of the list.
-+
+    if (.not. associated(lj_atype_list)) then
-+
-+
+       write(*,*) "Associating lists for first time"
-+
-+
-+
+       this_lj_atype%atype_number = 1
-+
-+
+       ljMixed(n_lj_atypes,n_lj_atypes)%sigma  = this_lj_atype%sigma
-+
-+
+       ljMixed(n_lj_atypes,n_lj_atypes)%sigma2  = ljMixed(n_lj_atypes,n_lj_atypes)%sigma &
-+
+            * ljMixed(n_lj_atypes,n_lj_atypes)%sigma
-+
-+
+       ljMixed(n_lj_atypes,n_lj_atypes)%sigma6 = ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 &
-+
+            * ljMixed(n_lj_atypes,n_lj_atypes)%sigma2 &
-+
+            * ljMixed(n_lj_atypes,n_lj_atypes)%sigma2
-+
-+
+       ljMixed(n_lj_atypes,n_lj_atypes)%epsilon = this_lj_atype%epsilon
-+
-+
+       lj_atype_list => this_lj_atype
-+
-+
+       write(*,*) "lj_atype_list first time through -- ident", lj_atype_list%atype_ident
-+
+    else ! we need to find the bottom of the list to insert new atype
-+
+       write(*,*) "Second time through"
-+
+       lj_atype_ptr => lj_atype_list
-+
+       write(*,*) "lj_atype_ptr to next"
-+
+       atype_counter = 1
-+
+       find_end: do
-+
+          if (.not. associated(lj_atype_ptr)) exit find_end
-+
-+
+          write(*,*) "Inside find_end-this ident", lj_atype_ptr%atype_ident
-+
+! Set up mixing for new atype and current atype in list
-+
+       ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma  =  &
-+
+            calcLJMix("sigma",this_lj_atype%sigma, &
-+
+            lj_atype_ptr%sigma)
-+
-+
+       ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2  = &
-+
+            ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma &
-+
+            * ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma
-+
-+
+       ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma6 = &
-+
+            ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 &
-+
+            * ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2 &
-+
+            * ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%sigma2
-+
-+
+       ljMixed(this_lj_atype%atype_number,lj_atype_ptr%atype_number)%epsilon = &
-+
+            calcLJMix("epsilon",this_lj_atype%epsilon, &
-+
+            lj_atype_ptr%epsilon)
-+
-+
+! Advance to next pointer
-+
+       lj_atype_ptr => lj_atype_ptr%next
-+
+       atype_counter = atype_counter + 1
-+
+       end do find_end
-+
-+
+       lj_atype_ptr => this_lj_atype
-+
+       write(*,*) "just added: ", lj_atype_ptr%atype_ident
-+
+    end if
-+
-+
+    write(*,*) "lj_atype_list now contains.."
-+
-+
+    lj_atype_ptr => lj_atype_list
-+
+    do while (associated(lj_atype_ptr))
-+
+       write(*,*) "lj_atype_list contains ident", lj_atype_ptr%atype_ident
-+
+       lj_atype_ptr => lj_atype_ptr%next
-+
+    end do
-+
-+
+! Insert new atype at end of list
-+
-+
+! Increment number of atypes
-+
-+
+    n_lj_atypes = n_lj_atypes + 1
-+
-+
+! Set up self mixing
-+
+  end subroutine new_lj_atype
-+
-+
-+
+  subroutine init_ljFF(nComponents,ident, status)
-+
+ !! Number of components in ident array
-+
+    integer, intent(inout) :: nComponents
-+
+!! Array of identities nComponents long corresponding to
-+
+!! ljatype ident.
-+
+    integer, dimension(nComponents),intent(inout) :: ident
-+
+!!  Result status, success = 0, error = -1
-+
+    integer, intent(out) :: Status
-+
-+
+    integer :: alloc_stat
-+
+    integer :: thisStat
-+
+    integer :: i
-+
+#ifdef IS_MPI
-+
+    integer, allocatable, dimension(:) :: identRow
-+
+    integer, allocatable, dimension(:) :: identCol
-+
+    integer :: nrow
-+
+    integer :: ncol
-+
+    integer :: alloc_stat
-+
+#endif
-+
+    status = 0
-+
+    write(*,*) "Initializing ljFF"
-+
+!! if were're not in MPI, we just update ljatypePtrList
-+
+#ifndef IS_MPI
-+
+    call new_ljatypePtrList(nComponents,ident,identPtrList,thisStat)
-+
+    if ( thisStat /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+    write(*,*) "component pointer list initialized"
-+
+!! Allocate pointer lists
-+
+    allocate(point(nComponents),stat=alloc_stat)
-+
+    if (alloc_stat /=0) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+    allocate(list(nComponents*listMultiplier),stat=alloc_stat)
-+
+    if (alloc_stat /=0) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
-+
+! if were're in MPI, we also have to worry about row and col lists
-+
+#else
-+
+! We can only set up forces if mpiSimulation has been setup.
-+
+    if (.not. isMPISimSet()) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+    nrow = getNrow()
-+
+    ncol = getNcol()
-+
+!! Allocate temperary arrays to hold gather information
-+
+    allocate(identRow(nrow),stat=alloc_stat)
-+
+    if (alloc_stat /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+    allocate(identCol(ncol),stat=alloc_stat)
-+
+    if (alloc_stat /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+!! Gather idents into row and column idents
-+
+    call gather(ident,identRow,plan_row)
-+
+    call gather(ident,identCol,plan_col)
-+
+!! Create row and col pointer lists
-+
+    call new_ljatypePtrList(nrow,identRow,identPtrListRow,thisStat)
-+
+    if (thisStat /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
+    call new_ljatypePtrList(ncol,identCol,identPtrListCol,thisStat)
-+
+    if (thisStat /= 0 ) then
-+
+       status = -1
-+
+       return
-+
+    endif
-+
-+
+!! free temporary ident arrays
-+
+    deallocate(identCol)
-+
+    deallocate(identRow)
-+
-+
+!! Allocate Simulation arrays
-+
+!! NOTE: This bit of code should be fixed, it can cause large
-+
+!! memory fragmentation if call repeatedly
-+
-+
+    if (.not.allocated(qRow)) then
-+
+       allocate(qRow(3,nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(qrow)
-+
+       allocate(qRow(3,nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(3,qCol)) then
-+
+       allocate(qCol(ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(qCol)
-+
+       allocate(qCol(3,ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(fRow)) then
-+
+       allocate(fRow(3,nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(fRow)
-+
+       allocate(fRow(3,nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(fCol)) then
-+
+       allocate(fCol(3,ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(fCol)
-+
+       allocate(fCol(3,ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(eRow)) then
-+
+       allocate(eRow(nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(eRow)
-+
+       allocate(eRow(nrow),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(eCol)) then
-+
+       allocate(eCol(ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(eCol)
-+
+       allocate(eCol(ncol),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+    if (.not.allocated(eTemp)) then
-+
+       allocate(eTemp(nComponents),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(eTemp)
-+
+       allocate(eTemp(nComponets),stat=alloc_stat)
-+
+       if (alloc_stat /= 0 ) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
-+
+!! Allocate neighbor lists for mpi simulations.
-+
+    if (.not. allocated(point)) then
-+
+       allocate(point(nrow),stat=alloc_stat)
-+
+       if (alloc_stat /=0) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
-+
+       allocate(list(ncol*listMultiplier),stat=alloc_stat)
-+
+       if (alloc_stat /=0) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    else
-+
+       deallocate(list)
-+
+       deallocate(point)
-+
+       allocate(point(nrow),stat=alloc_stat)
-+
+       if (alloc_stat /=0) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
-+
+       allocate(list(ncol*listMultiplier),stat=alloc_stat)
-+
+       if (alloc_stat /=0) then
-+
+          status = -1
-+
+          return
-+
+       endif
-+
+    endif
-+
-+
+#endif
-+
-+
-+
+    do i = 1, nComponents
-+
+       write(*,*) "Ident pointer list ident: ", identPtrList(i)%this%atype_ident
-+
+    end do
-+
-+
+    isljFFinit = .true.
-+
-+
+  end subroutine init_ljFF
-+
-+
-+
-+
-+
-+
+!! Takes an ident array and creates an atype pointer list
-+
+!! based on those identities
-+
+  subroutine new_ljatypePtrList(mysize,ident,PtrList,status)
-+
+    integer, intent(in) :: mysize
-+
+    integer,dimension(:), intent(in) :: ident
-+
+    integer, optional :: status
-+
+    type(lj_atypePtr), dimension(:), pointer :: PtrList
-+
-+
+    integer :: thisIdent
-+
+    integer :: i
-+
+    integer :: alloc_error
-+
+    type (lj_atype), pointer :: tmpPtr
-+
-+
+    if (present(status)) status = 0
-+
-+
+    write(*,*) "Creating new ljatypePtrList...."
-+
+! First time through, allocate list
-+
+    if (.not.associated(PtrList)) then
-+
+       write(*,*) "allocating pointer list...."
-+
+       allocate(PtrList(mysize))
-+
+    else
-+
+! We want to creat a new ident list so free old list
-+
+       deallocate(PtrList)
-+
+       allocate(PtrList(mysize))
-+
+    endif
-+
-+
+! Match pointer list
-+
+    write(*,*) "Doing ident search"
-+
+    do i = 1, mysize
-+
+       thisIdent = ident(i)
-+
+       write(*,*) "Calling getLJatype for ident ", thisIdent
-+
+       call getLJatype(thisIdent,tmpPtr)
-+
-+
+      if (.not. associated(tmpPtr)) then
-+
+         write(*,*) "tmpptr was not associated"
-+
+          status = -1
-+
+          return
-+
+       endif
-+
-+
+       PtrList(i)%this => tmpPtr
-+
+    end do
-+
-+
+  end subroutine new_ljatypePtrList
-+
-+
+!! Finds a lj_atype based upon numerical ident
-+
+!! returns a null pointer if error
-+
+  subroutine getLJatype(ident,ljAtypePtr)
-+
+    integer, intent(in) :: ident
-+
+    type (lj_atype), pointer :: ljAtypePtr
-+
+    type (lj_atype), pointer :: tmplj_atype_ptr => null()
-+
-+
+    write(*,*) "Finding ljAtype for ident ", ident
-+
+    ljAtypePtr => null()
-+
-+
+    if(.not. associated(lj_atype_list)) return
-+
-+
+! Point at head of list.
-+
+    write(*,*) "Searching at head of list"
-+
+    tmplj_atype_ptr => lj_atype_list
-+
+    find_ident: do
-+
+       if (.not.associated(tmplj_atype_ptr)) then
-+
+          write(*,*) "Find_ident, pointer not associated"
-+
+          exit find_ident
-+
+       else if( tmplj_atype_ptr%atype_ident == ident) then
-+
+          ljAtypePtr => tmplj_atype_ptr
-+
+          exit find_ident
-+
+       endif
-+
+       tmplj_atype_ptr => tmplj_atype_ptr%next
-+
+    end do find_ident
-+
-+
-+
-+
-+
+  end subroutine getLJatype
-+
-+
-+
+!! FORCE routine Calculates Lennard Jones forces.
-+
+!------------------------------------------------------------->
-+
+  subroutine do_lj_ff(q,f,potE,do_pot)
-+
+!! Position array provided by C, dimensioned by getNlocal
-+
+    real ( kind = dp ), dimension(3,getNlocal()) :: q
-+
+!! Force array provided by C, dimensioned by getNlocal
-+
+    real ( kind = dp ), dimension(3,getNlocal()) :: f
-+
+    real ( kind = dp ) :: potE
-+
+    logical ( kind = 2) :: do_pot
-+
-+
+    type(lj_atype), pointer :: ljAtype_i
-+
+    type(lj_atype), pointer :: ljAtype_j
-+
-+
+#ifdef MPI
-+
+  real( kind = DP ), dimension(3,getNcol()) :: efr
-+
+  real( kind = DP ) :: pot_local
-+
+#else
-+
+  real( kind = DP ), dimension(3,getNlocal()) :: efr
-+
+#endif
-+
-+
+  real( kind = DP )   :: pe
-+
+  logical             :: update_nlist
-+
-+
-+
+  integer ::  i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2
-+
+  integer :: nlist
-+
+  integer :: j_start
-+
+  integer :: tag_i,tag_j
-+
+  real( kind = DP ) ::  r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp
-+
+  real( kind = DP ) ::  rxi, ryi, rzi, rxij, ryij, rzij, rijsq
-+
+  real( kind = DP ) ::  rlistsq, rcutsq,rlist,rcut
-+
-+
+! a rig that need to be fixed.
-+
+#ifdef IS_MPI
-+
+  logical :: newtons_thrd = .true.
-+
+  real( kind = dp ) :: pe_local
-+
+  integer :: nlocal
-+
+#endif
-+
+  integer :: nrow
-+
+  integer :: ncol
-+
+  integer :: natoms
-+
-+
+! Make sure we are properly initialized.
-+
+  if (.not. isljFFInit) then
-+
+     write(default_error,*) "ERROR: lj_FF has not been properly initialized"
-+
+     return
-+
+  endif
-+
+#ifdef IS_MPI
-+
+    if (.not. isMPISimSet()) then
-+
+     write(default_error,*) "ERROR: mpiSimulation has not been properly initialized"
-+
+     return
-+
+  endif
-+
+#endif
-+
-+
+!! initialize local variables
-+
+  natoms = getNlocal()
-+
+  call getRcut(rcut,rcut2=rcutsq)
-+
+  call getRlist(rlist,rlistsq)
-+
+#ifndef IS_MPI
-+
+  nrow = natoms - 1
-+
+  ncol = natoms
-+
+#else
-+
+  nrow = getNrow(plan_row)
-+
+  ncol = getNcol(plan_col)
-+
+  nlocal = natoms
-+
+  j_start = 1
-+
+#endif
-+
-+
-+
+!! See if we need to update neighbor lists
-+
+  call check(q,update_nlist)
-+
-+
+!--------------WARNING...........................
-+
+! Zero variables, NOTE:::: Forces are zeroed in C
-+
+! Zeroing them here could delete previously computed
-+
+! Forces.
-+
+!------------------------------------------------
-+
+#ifndef IS_MPI
-+
+!  nloops = nloops + 1
-+
+  pe = 0.0E0_DP
-+
-+
+#else
-+
+    f_row = 0.0E0_DP
-+
+    f_col = 0.0E0_DP
-+
-+
+    pe_local = 0.0E0_DP
-+
-+
+    eRow = 0.0E0_DP
-+
+    eCol = 0.0E0_DP
-+
+    eTemp = 0.0E0_DP
-+
+#endif
-+
+    efr = 0.0E0_DP
-+
-+
+! communicate MPI positions
-+
+#ifdef MPI
-+
+    call gather(q,qRow,plan_row3)
-+
+    call gather(q,qCol,plan_col3)
-+
+#endif
-+
-+
-+
+  if (update_nlist) then
-+
-+
+     ! save current configuration, contruct neighbor list,
-+
+     ! and calculate forces
-+
+     call save_nlist(q)
-+
-+
+     nlist = 0
-+
-+
-+
-+
+     do i = 1, nrow
-+
+        point(i) = nlist + 1
-+
+#ifdef MPI
-+
+        ljAtype_i => identPtrListRow(i)%this
-+
+        tag_i = tagRow(i)
-+
+        rxi = qRow(1,i)
-+
+        ryi = qRow(2,i)
-+
+        rzi = qRow(3,i)
-+
+#else
-+
+        ljAtype_i   => identPtrList(i)%this
-+
+        j_start = i + 1
-+
+        rxi = q(1,i)
-+
+        ryi = q(2,i)
-+
+        rzi = q(3,i)
-+
+#endif
-+
-+
+        inner: do j = j_start, ncol
-+
+#ifdef MPI
-+
+! Assign identity pointers and tags
-+
+           ljAtype_j => identPtrListColumn(j)%this
-+
+           tag_j = tagCol(j)
-+
+           if (newtons_thrd) then
-+
+              if (tag_i <= tag_j) then
-+
+                 if (mod(tag_i + tag_j,2) == 0) cycle inner
-+
+              else
-+
+                 if (mod(tag_i + tag_j,2) == 1) cycle inner
-+
+              endif
-+
+           endif
-+
-+
+           rxij = wrap(rxi - qCol(1,j), 1)
-+
+           ryij = wrap(ryi - qCol(2,j), 2)
-+
+           rzij = wrap(rzi - qCol(3,j), 3)
-+
+#else
-+
+           ljAtype_j   => identPtrList(j)%this
-+
+           rxij = wrap(rxi - q(1,j), 1)
-+
+           ryij = wrap(ryi - q(2,j), 2)
-+
+           rzij = wrap(rzi - q(3,j), 3)
-+
-+
+#endif
-+
+           rijsq = rxij*rxij + ryij*ryij + rzij*rzij
-+
-+
+#ifdef MPI
-+
+             if (rijsq <=  rlistsq .AND. &
-+
+                  tag_j /= tag_i) then
-+
+#else
-+
+             if (rijsq <  rlistsq) then
-+
+#endif
-+
-+
+              nlist = nlist + 1
-+
+              if (nlist > size(list)) then
-+
+!!  "Change how nlist size is done"
-+
+                 write(DEFAULT_ERROR,*) "ERROR: nlist > list size"
-+
+              endif
-+
+              list(nlist) = j
-+
-+
-+
+              if (rijsq <  rcutsq) then
-+
-+
+                 r = dsqrt(rijsq)
-+
-+
+                 call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j)
-+
-+
+#ifdef MPI
-+
+                eRow(i) = eRow(i) + pot*0.5
-+
+                eCol(i) = eCol(i) + pot*0.5
-+
+#else
-+
+                pe = pe + pot
-+
+#endif
-+
-+
+                 efr(1,j) = -rxij
-+
+                 efr(2,j) = -ryij
-+
+                 efr(3,j) = -rzij
-+
-+
+                 do dim = 1, 3
-+
-+
-+
+                    drdx1 = efr(dim,j) / r
-+
+                    ftmp = dudr * drdx1
-+
-+
-+
+#ifdef MPI
-+
+                    fCol(dim,j) = fCol(dim,j) - ftmp
-+
+                    fRow(dim,i) = fRow(dim,i) + ftmp
-+
+#else
-+
-+
+                    f(dim,j) = f(dim,j) - ftmp
-+
+                    f(dim,i) = f(dim,i) + ftmp
-+
-+
+#endif
-+
+                 enddo
-+
+              endif
-+
+           endif
-+
+        enddo inner
-+
+     enddo
-+
-+
+#ifdef MPI
-+
+     point(nrow + 1) = nlist + 1
-+
+#else
-+
+     point(natoms) = nlist + 1
-+
+#endif
-+
-+
+  else
-+
-+
+     ! use the list to find the neighbors
-+
+     do i = 1, nrow
-+
+        JBEG = POINT(i)
-+
+        JEND = POINT(i+1) - 1
-+
+        ! check thiat molecule i has neighbors
-+
+        if (jbeg .le. jend) then
-+
+#ifdef MPI
-+
+           ljAtype_i => identPtrListRow(i)%this
-+
+           rxi = qRow(1,i)
-+
+           ryi = qRow(2,i)
-+
+           rzi = qRow(3,i)
-+
+#else
-+
+           ljAtype_i   => identPtrList(i)%this
-+
+           rxi = q(1,i)
-+
+           ryi = q(2,i)
-+
+           rzi = q(3,i)
-+
+#endif
-+
+           do jnab = jbeg, jend
-+
+              j = list(jnab)
-+
+#ifdef MPI
-+
+              ljAtype_j = identPtrListColumn(j)%this
-+
+              rxij = wrap(rxi - q_col(1,j), 1)
-+
+              ryij = wrap(ryi - q_col(2,j), 2)
-+
+              rzij = wrap(rzi - q_col(3,j), 3)
-+
+#else
-+
+              ljAtype_j = identPtrList(j)%this
-+
+              rxij = wrap(rxi - q(1,j), 1)
-+
+              ryij = wrap(ryi - q(2,j), 2)
-+
+              rzij = wrap(rzi - q(3,j), 3)
-+
+#endif
-+
+              rijsq = rxij*rxij + ryij*ryij + rzij*rzij
-+
-+
+              if (rijsq <  rcutsq) then
-+
-+
+                 r = dsqrt(rijsq)
-+
-+
+                 call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j)
-+
+#ifdef MPI
-+
+                eRow(i) = eRow(i) + pot*0.5
-+
+                eCol(i) = eCol(i) + pot*0.5
-+
+#else
-+
+                pe = pe + pot
-+
+#endif
-+
-+
-+
+                 efr(1,j) = -rxij
-+
+                 efr(2,j) = -ryij
-+
+                 efr(3,j) = -rzij
-+
-+
+                 do dim = 1, 3
-+
-+
+                    drdx1 = efr(dim,j) / r
-+
+                    ftmp = dudr * drdx1
-+
+#ifdef MPI
-+
+                    fCol(dim,j) = fCol(dim,j) - ftmp
-+
+                    fRow(dim,i) = fRow(dim,i) + ftmp
-+
+#else
-+
+                    f(dim,j) = f(dim,j) - ftmp
-+
+                    f(dim,i) = f(dim,i) + ftmp
-+
+#endif
-+
+                 enddo
-+
+              endif
-+
+           enddo
-+
+        endif
-+
+     enddo
-+
+  endif
-+
-+
-+
-+
+#ifdef MPI
-+
+    !!distribute forces
-+
+    call scatter(fRow,f,plan_row3)
-+
-+
+    call scatter(fCol,f_tmp,plan_col3)
-+
-+
+    do i = 1,nlocal
-+
+       f(1:3,i) = f(1:3,i) + f_tmp(1:3,i)
-+
+    end do
-+
-+
-+
-+
+    if (do_pot) then
-+
+! scatter/gather pot_row into the members of my column
-+
+       call scatter(e_row,e_tmp,plan_row)
-+
-+
+       ! scatter/gather pot_local into all other procs
-+
+       ! add resultant to get total pot
-+
+       do i = 1, nlocal
-+
+          pe_local = pe_local + e_tmp(i)
-+
+       enddo
-+
+       if (newtons_thrd) then
-+
+          e_tmp = 0.0E0_DP
-+
+          call scatter(e_col,e_tmp,plan_col)
-+
+          do i = 1, nlocal
-+
+             pe_local = pe_local + e_tmp(i)
-+
+          enddo
-+
+       endif
-+
+    endif
-+
+    potE = pe_local
-+
+#endif
-+
-+
+    potE = pe
-+
-+
-+
+  end subroutine do_lj_ff
-+
-+
+!! Calculates the potential between two lj particles based on two lj_atype pointers, optionally returns second
-+
+!! derivatives.
-+
+  subroutine getLjPot(r,pot,dudr,atype1,atype2,d2,status)
-+
+! arguments
-+
+!! Length of vector between particles
-+
+    real( kind = dp ), intent(in)  :: r
-+
+!! Potential Energy
-+
+    real( kind = dp ), intent(out) :: pot
-+
+!! Derivatve wrt postion
-+
+    real( kind = dp ), intent(out) :: dudr
-+
+!! Second Derivative, optional, used mainly for normal mode calculations.
-+
+    real( kind = dp ), intent(out), optional :: d2
-+
-+
+    type (lj_atype), pointer :: atype1
-+
+    type (lj_atype), pointer :: atype2
-+
-+
+    integer, intent(out), optional :: status
-+
-+
+! local Variables
-+
+    real( kind = dp ) :: sigma
-+
+    real( kind = dp ) :: sigma2
-+
+    real( kind = dp ) :: sigma6
-+
+    real( kind = dp ) :: epsilon
-+
-+
+    real( kind = dp ) :: rcut
-+
+    real( kind = dp ) :: rcut2
-+
+    real( kind = dp ) :: rcut6
-+
+    real( kind = dp ) :: r2
-+
+    real( kind = dp ) :: r6
-+
-+
+    real( kind = dp ) :: t6
-+
+    real( kind = dp ) :: t12
-+
+    real( kind = dp ) :: tp6
-+
+    real( kind = dp ) :: tp12
-+
+    real( kind = dp ) :: delta
-+
-+
+    logical :: doSec = .false.
-+
-+
+    integer :: errorStat
-+
-+
+!! Optional Argument Checking
-+
+! Check to see if we need to do second derivatives
-+
-+
+    if (present(d2))     doSec = .true.
-+
+    if (present(status)) status = 0
-+
-+
+! Look up the correct parameters in the mixing matrix
-+
+    sigma    = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma
-+
+    sigma2   = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma2
-+
+    sigma6   = ljMixed(atype1%atype_ident,atype2%atype_ident)%sigma6
-+
+    epsilon  = ljMixed(atype1%atype_ident,atype2%atype_ident)%epsilon
-+
-+
-+
-+
+    call getRcut(rcut,rcut2=rcut2,rcut6=rcut6,status=errorStat)
-+
-+
+    r2 = r * r
-+
+    r6 = r2 * r2 * r2
-+
-+
+    t6  = sigma6/ r6
-+
+    t12 = t6 * t6
-+
-+
-+
-+
+    tp6 = sigma6 / rcut6
-+
+    tp12 = tp6*tp6
-+
-+
+    delta = -4.0E0_DP*epsilon * (tp12 - tp6)
-+
-+
+    if (r.le.rcut) then
-+
+       pot = 4.0E0_DP * epsilon * (t12 - t6) + delta
-+
+       dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r
-+
+       if(doSec)  d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r
-+
+    else
-+
+       pot = 0.0E0_DP
-+
+       dudr = 0.0E0_DP
-+
+       if(doSec) d2 = 0.0E0_DP
-+
+    endif
-+
-+
+  return
-+
-+
-+
-+
+  end subroutine getLjPot
-+
-+
-+
+!! Calculates the mixing for sigma or epslon based on character string for initialzition of mixing array.
-+
+  function calcLJMix(thisParam,param1,param2,status) result(myMixParam)
-+
+    character(len=*) :: thisParam
-+
+    real(kind = dp)  :: param1
-+
+    real(kind = dp)  :: param2
-+
+    real(kind = dp ) :: myMixParam
-+
+    integer, optional :: status
-+
-+
-+
+    myMixParam = 0.0_dp
-+
-+
+    if (present(status)) status = 0
-+
-+
+    select case (thisParam)
-+
-+
+    case ("sigma")
-+
+       myMixParam = 0.5_dp * (param1 + param2)
-+
+    case ("epsilon")
-+
+       myMixParam = sqrt(param1 * param2)
-+
+    case default
-+
+       status = -1
-+
+    end select
-+
-+
+  end function calcLJMix
-+
-+
-+
+end module lj_ff

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Comparing trunk/mdtools/md_code/lj_FF.F90 (file contents): Revision 215 by chuckv, Thu Dec 19 21:59:51 2002 UTC vs. Revision 246 by chuckv, Fri Jan 24 21:36:52 2003 UTC

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Comparing trunk/mdtools/md_code/lj_FF.F90 (file contents):
Revision 215 by chuckv, Thu Dec 19 21:59:51 2002 UTC vs.
Revision 246 by chuckv, Fri Jan 24 21:36:52 2003 UTC