mdtools/md_code/lj_FF.F90

!! 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 1.17 2003-02-03 21:15:59 chuckv Exp $, $Date: 2003-02-03 21:15:59 $, $Name: not supported by cvs2svn $, $Revision: 1.17 $


module lj_ff
  use simulation
  use definitions
  use generic_atypes
#ifdef IS_MPI
  use mpiSimulation
#endif
  implicit none
  PRIVATE

!! Number of lj_atypes in lj_atype_list
  integer, save :: n_lj_atypes = 0

!! Global list of lj atypes in simulation
  type (lj_atype), pointer :: ljListHead => null()
  type (lj_atype), pointer :: ljListTail => null()


!! LJ mixing array  
  type (lj_atype), dimension(:,:), pointer :: ljMixed => 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

  logical, save :: firstTime = .True.

!! Atype identity pointer lists
#ifdef IS_MPI
!! Row lj_atype pointer list
  type (lj_identPtrList), dimension(:), pointer :: identPtrListRow => null()
!! Column lj_atype pointer list
  type (lj_identPtrList), dimension(:), pointer :: identPtrListColumn => null()
#else
  type( lj_identPtrList ), dimension(:), pointer :: identPtrList => 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

!! Adds a new lj_atype to the list. 
  subroutine new_lj_atype(ident,mass,epsilon,sigma,status)
    real( kind = dp ), intent(in) :: mass
    real( kind = dp ), intent(in) :: epsilon
    real( kind = dp ), intent(in) :: sigma
    integer, intent(in) :: ident
    integer, intent(out) :: status

    type (lj_atype), pointer :: newLJ_atype
    integer :: alloc_error
    integer :: atype_counter = 0
    integer :: alloc_size
    integer :: err_stat
    status = 0


! allocate a new atype    
    allocate(newLJ_atype,stat=alloc_error)
    if (alloc_error /= 0 ) then
       status = -1
       return
    end if

! assign our new lj_atype information
    newLJ_atype%mass        = mass
    newLJ_atype%epsilon     = epsilon
    newLJ_atype%sigma       = sigma
    newLJ_atype%sigma2      = sigma * sigma
    newLJ_atype%sigma6      = newLJ_atype%sigma2 * newLJ_atype%sigma2 &
         * newLJ_atype%sigma2
! assume that this atype will be successfully added
    newLJ_atype%atype_ident = ident
    newLJ_atype%atype_number = n_lj_atypes + 1

    call add_atype(newLJ_atype,ljListHead,ljListTail,err_stat)
    if (err_stat /= 0 ) then 
       status = -1
       return
    endif

    n_lj_atypes = n_lj_atypes + 1


  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

    integer :: myNode
#ifdef IS_MPI
    integer, allocatable, dimension(:) :: identRow
    integer, allocatable, dimension(:) :: identCol
    integer :: nrow
    integer :: ncol
#endif
    status = 0
   

!! if were're not in MPI, we just update ljatypePtrList
#ifndef IS_MPI
    call create_IdentPtrlst(ident,ljListHead,identPtrList,thisStat)
    if ( thisStat /= 0 ) then
       status = -1
       return
    endif

!! 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
       write(default_error,*) "MPI is not set"
       status = -1
       return
    endif
    nrow = getNrow(plan_row)
    ncol = getNcol(plan_col)
    mynode = getMyNode()
!! 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 create_IdentPtrlst(identRow,ljListHead,identPtrListRow,thisStat)
    if (thisStat /= 0 ) then
       status = -1
       return
    endif
  
    call create_IdentPtrlst(identCol,ljListHead,identPtrListColumn,thisStat)
    if (thisStat /= 0 ) then
       status = -1
       return
    endif

!! free temporary ident arrays
    if (allocated(identCol)) then
       deallocate(identCol)
    end if
    if (allocated(identCol)) then
       deallocate(identRow)
    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
    
    call createMixingList(thisStat)
    if (thisStat /= 0) then
       status = -1
       return
    endif
    isljFFinit = .true.


  end subroutine init_ljFF


  subroutine createMixingList(status)
    integer :: listSize
    integer :: status
    integer :: i
    integer :: j

    integer :: outerCounter = 0
    integer :: innerCounter = 0
    type (lj_atype), pointer :: tmpPtrOuter => null()
    type (lj_atype), pointer :: tmpPtrInner => null()
    status = 0

    listSize = getListLen(ljListHead)
    if (listSize == 0) then
       status = -1
       return
    end if
  

    if (.not. associated(ljMixed)) then
       allocate(ljMixed(listSize,listSize))
    else
       status = -1
       return
    end if

    
    tmpPtrOuter => ljListHead
    tmpPtrInner => tmpPtrOuter%next
    do while (associated(tmpPtrOuter))
       outerCounter = outerCounter + 1
! do self mixing rule
       ljMixed(outerCounter,outerCounter)%sigma  = tmpPtrOuter%sigma
                                                                                                  
       ljMixed(outerCounter,outerCounter)%sigma2  = ljMixed(outerCounter,outerCounter)%sigma &
            * ljMixed(outerCounter,outerCounter)%sigma
                                                                                                  
       ljMixed(outerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,outerCounter)%sigma2 &
            * ljMixed(outerCounter,outerCounter)%sigma2 &
            * ljMixed(outerCounter,outerCounter)%sigma2
                                                                                                  
       ljMixed(outerCounter,outerCounter)%epsilon = tmpPtrOuter%epsilon

       innerCounter = outerCounter + 1
       do while (associated(tmpPtrInner))
          
          ljMixed(outerCounter,innerCounter)%sigma  =  &
               calcLJMix("sigma",tmpPtrOuter%sigma, &
               tmpPtrInner%sigma)
          
          ljMixed(outerCounter,innerCounter)%sigma2  = &
               ljMixed(outerCounter,innerCounter)%sigma &
               * ljMixed(outerCounter,innerCounter)%sigma
          
          ljMixed(outerCounter,innerCounter)%sigma6 = &
               ljMixed(outerCounter,innerCounter)%sigma2 &
               * ljMixed(outerCounter,innerCounter)%sigma2 &
               * ljMixed(outerCounter,innerCounter)%sigma2
          
          ljMixed(outerCounter,innerCounter)%epsilon = &
               calcLJMix("epsilon",tmpPtrOuter%epsilon, &
               tmpPtrInner%epsilon)
          ljMixed(innerCounter,outerCounter)%sigma = ljMixed(outerCounter,innerCounter)%sigma
          ljMixed(innerCounter,outerCounter)%sigma2 = ljMixed(outerCounter,innerCounter)%sigma2
          ljMixed(innerCounter,outerCounter)%sigma6 = ljMixed(outerCounter,innerCounter)%sigma6
          ljMixed(innerCounter,outerCounter)%epsilon = ljMixed(outerCounter,innerCounter)%epsilon


          tmpPtrInner => tmpPtrInner%next
          innerCounter = innerCounter + 1
       end do
! advance pointers 
       tmpPtrOuter => tmpPtrOuter%next
       if (associated(tmpPtrOuter)) then
          tmpPtrInner => tmpPtrOuter%next
       endif
       
    end do

  end subroutine createMixingList


!! 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 IS_MPI
  real( kind = DP ), dimension(3,getNcol(plan_col)) :: efr
  real( kind = DP ) :: pot_local
#else
  real( kind = DP ), dimension(3,getNlocal()) :: efr
#endif
  
!! Local arrays needed for MPI
#ifdef IS_MPI
  real(kind = dp), dimension(3,getNrow(plan_row)) :: qRow
  real(kind = dp), dimension(3,getNcol(plan_col)) :: qCol

  real(kind = dp), dimension(3,getNrow(plan_row)) :: fRow
  real(kind = dp), dimension(3,getNcol(plan_col)) :: fCol
  real(kind = dp), dimension(3,getNlocal()) :: fMPITemp

  real(kind = dp), dimension(getNrow(plan_row)) :: eRow
  real(kind = dp), dimension(getNcol(plan_col)) :: eCol

  real(kind = dp), dimension(getNlocal()) :: eTemp
#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)
  if (firstTime) then
     update_nlist = .true.
     firstTime = .false.
  endif

!--------------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
    fRow = 0.0E0_DP
    fCol = 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 IS_MPI    
    call gather(q,qRow,plan_row3d)
    call gather(q,qCol,plan_col3d)
#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 IS_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 IS_MPI
! Assign identity pointers and tags
           ljAtype_j => identPtrListColumn(j)%this
           tag_j = tagColumn(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 IS_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 IS_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 IS_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 IS_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 IS_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 IS_MPI
              ljAtype_j = identPtrListColumn(j)%this
              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
              
              if (rijsq <  rcutsq) then

                 r = dsqrt(rijsq)
                 
                 call getLJPot(r,pot,dudr,ljAtype_i,ljAtype_j)
#ifdef IS_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 IS_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 IS_MPI
    !!distribute forces

    call scatter(fRow,f,plan_row3d)

    call scatter(fCol,fMPITemp,plan_col3d)

    do i = 1,nlocal
       f(1:3,i) = f(1:3,i) + fMPITemp(1:3,i)
    end do


    if (do_pot) then
! scatter/gather pot_row into the members of my column
       call scatter(eRow,eTemp,plan_row)
       
       ! scatter/gather pot_local into all other procs
       ! add resultant to get total pot
       do i = 1, nlocal
          pe_local = pe_local + eTemp(i)
       enddo
       if (newtons_thrd) then
          eTemp = 0.0E0_DP
          call scatter(eCol,eTemp,plan_col)
          do i = 1, nlocal
             pe_local = pe_local + eTemp(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
Revision:	261
Committed:	Mon Feb 3 21:15:59 2003 UTC (21 years, 5 months ago) by chuckv
File size:	21225 byte(s)
Log Message:	We have working code today... MPI bug fixes to DumpWriter.