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chuckv |
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module lj_module |
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use definitions, ONLY : DP,ndim |
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use parameter |
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use simulation |
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use second_deriv |
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use status, ONLY: error,info,warning |
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use force_utilities |
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#ifdef MPI |
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use mpi_module |
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#endif |
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integer, parameter :: n_ljatypes = 12 |
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real( kind = DP ),allocatable, dimension(:) :: lj_eps |
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real( kind = DP ),allocatable, dimension(:) :: lj_sigma |
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integer, allocatable, dimension(:) :: ljatype ! to be fixed in a module |
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public :: lj_eps,lj_sigma |
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public :: calc_lj_forces,initialize_lj |
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private :: mass_weight |
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contains |
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subroutine allocate_lj_module(n_size_atype) |
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integer, intent(in) :: n_size_atype |
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allocate(ljatype(n_size_atype)) |
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allocate(lj_eps(n_size_atype)) |
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allocate(lj_sigma(n_size_atype)) |
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end subroutine allocate_lj_module |
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subroutine deallocate_lj_module() |
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deallocate(lj_eps) |
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deallocate(lj_sigma) |
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deallocate(ljatype) |
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end subroutine deallocate_lj_module |
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subroutine calc_lj_forces(update_nlist, nmflag,pe) |
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! include 'headers/sizes.h' |
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! include 'headers/fileio.h' |
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#ifdef MPI |
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real( kind = DP ), dimension(3,ncol) :: efr |
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real( kind = DP ) :: pot_local |
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#else |
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real( kind = DP ), dimension(3,natoms) :: efr |
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#endif |
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real( kind = DP ), intent(out), optional :: pe |
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logical, intent(in) :: nmflag |
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logical, intent(in) :: update_nlist |
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logical :: do_pot |
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integer :: i, j, jbeg, jend, jnab, idim, jdim, idim2, jdim2, dim, dim2 |
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integer :: nlist |
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integer :: j_start |
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integer :: tag_i,tag_j |
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real( kind = DP ) :: r, pot, ftmp, dudr, d2, drdx1, kt1, kt2, kt3, ktmp |
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real( kind = DP ) :: rxi, ryi, rzi, rxij, ryij, rzij, rijsq |
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#ifndef MPI |
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integer :: nrow |
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integer :: ncol |
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nrow = natoms - 1 |
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ncol = natoms |
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#else |
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j_start = 1 |
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#endif |
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do_pot = .false. |
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if (present(pe)) do_pot = .true. |
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#ifndef MPI |
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if (do_pot) pot = 0.0E0_DP |
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f = 0.0E0_DP |
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e = 0.0E0_DP |
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#else |
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f_row = 0.0E0_DP |
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f_col = 0.0E0_DP |
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pot_local = 0.0E0_DP |
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e_row = 0.0E0_DP |
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e_col = 0.0E0_DP |
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e_tmp = 0.0E0_DP |
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#endif |
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efr = 0.0E0_DP |
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! communicate MPI positions |
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#ifdef MPI |
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call gather(q,q_row,plan_row3) |
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call gather(q,q_col,plan_col3) |
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#endif |
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if (update_nlist) then |
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! save current configuration, contruct neighbor list, |
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! and calculate forces |
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call save_nlist() |
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nlist = 0 |
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do i = 1, nrow |
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point(i) = nlist + 1 |
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#ifdef MPI |
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tag_i = tag_row(i) |
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rxi = q_row(1,i) |
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ryi = q_row(2,i) |
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rzi = q_row(3,i) |
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#else |
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j_start = i + 1 |
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rxi = q(1,i) |
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ryi = q(2,i) |
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rzi = q(3,i) |
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#endif |
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inner: do j = j_start, ncol |
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#ifdef MPI |
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tag_j = tag_col(j) |
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if (newtons_thrd) then |
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if (tag_i <= tag_j) then |
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if (mod(tag_i + tag_j,2) == 0) cycle inner |
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else |
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if (mod(tag_i + tag_j,2) == 1) cycle inner |
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endif |
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endif |
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rxij = wrap(rxi - q_col(1,j), 1) |
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ryij = wrap(ryi - q_col(2,j), 2) |
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rzij = wrap(rzi - q_col(3,j), 3) |
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#else |
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rxij = wrap(rxi - q(1,j), 1) |
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ryij = wrap(ryi - q(2,j), 2) |
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rzij = wrap(rzi - q(3,j), 3) |
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#endif |
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rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
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#ifdef MPI |
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if (rijsq <= rlstsq .AND. & |
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tag_j /= tag_i) then |
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#else |
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if (rijsq < rlstsq) then |
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#endif |
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nlist = nlist + 1 |
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list(nlist) = j |
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if (rijsq < rcutsq) then |
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r = dsqrt(rijsq) |
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call LJ_mix(r,pot,dudr,d2,i,j) |
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#ifdef MPI |
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e_row(i) = e_row(i) + pot*0.5 |
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e_col(i) = e_col(i) + pot*0.5 |
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#else |
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if (do_pot) pe = pe + pot |
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#endif |
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efr(1,j) = -rxij |
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efr(2,j) = -ryij |
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efr(3,j) = -rzij |
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do dim = 1, 3 |
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drdx1 = efr(j,dim) / r |
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ftmp = dudr * drdx1 |
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#ifdef MPI |
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f_col(dim,j) = f_col(dim,j) - ftmp |
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f_row(dim,i) = f_row(dim,i) + ftmp |
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#else |
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f(dim,j) = f(dim,j) - ftmp |
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f(dim,i) = f(dim,i) + ftmp |
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#endif |
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if (nmflag) then |
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idim = 3 * (i-1) + dim |
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jdim = 3 * (j-1) + dim |
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do dim2 = 1, 3 |
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kt1 = d2 * efr(dim,j) * efr(dim2,j)/r/r |
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kt2 = - dudr * efr(dim,j) * efr(dim2,j)/r/r/r |
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if (dim.eq.dim2) then |
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kt3 = dudr / r |
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else |
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kt3 = 0.0E0_DP |
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endif |
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! The factor of 2 below is to compensate for |
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! overcounting. |
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! Mass weighting is done separately... |
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ktmp = (kt1+kt2+kt3)/2.0E0_DP |
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idim2 = 3 * (i-1) + dim2 |
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jdim2 = 3 * (j-1) + dim2 |
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d(idim, idim2) = d(idim,idim2) + ktmp |
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d(idim2, idim) = d(idim2,idim) + ktmp |
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d(idim, jdim2) = d(idim,jdim2) - ktmp |
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d(idim2, jdim) = d(idim2,jdim) - ktmp |
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d(jdim, idim2) = d(jdim,idim2) - ktmp |
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d(jdim2, idim) = d(jdim2,idim) - ktmp |
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d(jdim, jdim2) = d(jdim,jdim2) + ktmp |
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d(jdim2, jdim) = d(jdim2,jdim) + ktmp |
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enddo |
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endif |
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enddo |
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endif |
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endif |
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enddo inner |
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enddo |
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#ifdef MPI |
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point(nrow + 1) = nlist + 1 |
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#else |
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point(natoms) = nlist + 1 |
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#endif |
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else |
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! use the list to find the neighbors |
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do i = 1, nrow |
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JBEG = POINT(i) |
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JEND = POINT(i+1) - 1 |
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! check thiat molecule i has neighbors |
| 239 |
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if (jbeg .le. jend) then |
| 240 |
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#ifdef MPI |
| 241 |
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rxi = q_row(1,i) |
| 242 |
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ryi = q_row(2,i) |
| 243 |
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rzi = q_row(3,i) |
| 244 |
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#else |
| 245 |
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rxi = q(1,i) |
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ryi = q(2,i) |
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rzi = q(3,i) |
| 248 |
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#endif |
| 249 |
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do jnab = jbeg, jend |
| 250 |
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j = list(jnab) |
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#ifdef MPI |
| 252 |
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rxij = wrap(rxi - q_col(1,j), 1) |
| 253 |
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ryij = wrap(ryi - q_col(2,j), 2) |
| 254 |
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rzij = wrap(rzi - q_col(3,j), 3) |
| 255 |
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#else |
| 256 |
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rxij = wrap(rxi - q(1,j), 1) |
| 257 |
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ryij = wrap(ryi - q(2,j), 2) |
| 258 |
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rzij = wrap(rzi - q(3,j), 3) |
| 259 |
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#endif |
| 260 |
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rijsq = rxij*rxij + ryij*ryij + rzij*rzij |
| 261 |
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| 262 |
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if (rijsq < rcutsq) then |
| 263 |
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| 264 |
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r = dsqrt(rijsq) |
| 265 |
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| 266 |
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call LJ_mix(r,pot,dudr,d2,i,j) |
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#ifdef MPI |
| 268 |
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e_row(i) = e_row(i) + pot*0.5 |
| 269 |
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e_col(i) = e_col(i) + pot*0.5 |
| 270 |
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#else |
| 271 |
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if (do_pot) pe = pe + pot |
| 272 |
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#endif |
| 273 |
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| 274 |
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| 275 |
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efr(1,j) = -rxij |
| 276 |
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efr(2,j) = -ryij |
| 277 |
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efr(3,j) = -rzij |
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| 279 |
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do dim = 1, 3 |
| 280 |
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| 281 |
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drdx1 = efr(j,dim) / r |
| 282 |
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ftmp = dudr * drdx1 |
| 283 |
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#ifdef MPI |
| 284 |
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f_col(dim,j) = f_col(dim,j) - ftmp |
| 285 |
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f_row(dim,i) = f_row(dim,i) + ftmp |
| 286 |
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#else |
| 287 |
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f(dim,j) = f(dim,j) - ftmp |
| 288 |
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f(dim,i) = f(dim,i) + ftmp |
| 289 |
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#endif |
| 290 |
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if (nmflag) then |
| 291 |
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idim = 3 * (i-1) + dim |
| 292 |
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jdim = 3 * (j-1) + dim |
| 293 |
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| 294 |
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do dim2 = 1, 3 |
| 295 |
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| 296 |
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kt1 = d2 * efr(dim,j) * efr(dim2,j)/r/r |
| 297 |
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kt2 = - dudr * efr(dim,j) * efr(dim2,j)/r/r/r |
| 298 |
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| 299 |
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if (dim.eq.dim2) then |
| 300 |
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kt3 = dudr / r |
| 301 |
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else |
| 302 |
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kt3 = 0.0E0_DP |
| 303 |
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endif |
| 304 |
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| 305 |
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! The factor of 2 below is to compensate for |
| 306 |
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! overcounting. |
| 307 |
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! Mass weighting is done separately... |
| 308 |
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| 309 |
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ktmp = (kt1+kt2+kt3)/2.0E0_DP |
| 310 |
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idim2 = 3 * (i-1) + dim2 |
| 311 |
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jdim2 = 3 * (j-1) + dim2 |
| 312 |
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| 313 |
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d(idim, idim2) = d(idim,idim2) + ktmp |
| 314 |
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d(idim2, idim) = d(idim2,idim) + ktmp |
| 315 |
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| 316 |
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d(idim, jdim2) = d(idim,jdim2) - ktmp |
| 317 |
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d(idim2, jdim) = d(idim2,jdim) - ktmp |
| 318 |
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| 319 |
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d(jdim, idim2) = d(jdim,idim2) - ktmp |
| 320 |
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d(jdim2, idim) = d(jdim2,idim) - ktmp |
| 321 |
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| 322 |
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d(jdim, jdim2) = d(jdim,jdim2) + ktmp |
| 323 |
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d(jdim2, jdim) = d(jdim2,jdim) + ktmp |
| 324 |
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| 325 |
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enddo |
| 326 |
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endif |
| 327 |
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enddo |
| 328 |
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| 329 |
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endif |
| 330 |
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enddo |
| 331 |
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endif |
| 332 |
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enddo |
| 333 |
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endif |
| 334 |
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| 335 |
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#ifdef MPI |
| 336 |
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!!distribute forces |
| 337 |
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call scatter(f_row,f,plan_row3) |
| 338 |
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if (newtons_thrd) then |
| 339 |
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call scatter(f_col,f_tmp,plan_col3) |
| 340 |
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do i = 1,nlocal |
| 341 |
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do dim = 1,3 |
| 342 |
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f(dim,i) = f(dim,i) + f_tmp(dim,i) |
| 343 |
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end do |
| 344 |
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end do |
| 345 |
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endif |
| 346 |
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| 347 |
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| 348 |
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if (do_pot) then |
| 349 |
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! scatter/gather pot_row into the members of my column |
| 350 |
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call scatter(e_row,e_tmp,plan_row) |
| 351 |
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| 352 |
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! scatter/gather pot_local into all other procs |
| 353 |
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! add resultant to get total pot |
| 354 |
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do i = 1, nlocal |
| 355 |
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pot_local = pot_local + e_tmp(i) |
| 356 |
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enddo |
| 357 |
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if (newtons_thrd) then |
| 358 |
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e_tmp = 0.0E0_DP |
| 359 |
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call scatter(e_col,e_tmp,plan_col) |
| 360 |
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do i = 1, nlocal |
| 361 |
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pot_local = pot_local + e_tmp(i) |
| 362 |
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enddo |
| 363 |
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endif |
| 364 |
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| 365 |
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| 366 |
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call mpi_reduce(pot_local,pe,1,mpi_double_precision, & |
| 367 |
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mpi_sum,0,mpi_comm_world,mpi_err) |
| 368 |
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endif |
| 369 |
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#endif |
| 370 |
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| 371 |
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| 372 |
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| 373 |
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if (nmflag) then |
| 374 |
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call mass_weight() |
| 375 |
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endif |
| 376 |
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| 377 |
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|
return |
| 378 |
|
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end subroutine calc_lj_forces |
| 379 |
|
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|
| 380 |
|
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subroutine LJ_mix(r,pot,dudr,d2,atom1,atom2) |
| 381 |
|
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|
| 382 |
|
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! include 'headers/sizes.h' |
| 383 |
|
|
! include 'headers/atom.h' |
| 384 |
|
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| 385 |
|
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|
| 386 |
|
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integer :: atom1, atom2, id1, id2 |
| 387 |
|
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real( kind = DP ) :: r, pot, dudr, d2 |
| 388 |
|
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real( kind = DP ) :: u1, dudr1, d21 |
| 389 |
|
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real( kind = DP ) :: this_sigma, this_eps |
| 390 |
|
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|
| 391 |
|
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#ifdef MPI |
| 392 |
|
|
id1 = ident_row(atom1) |
| 393 |
|
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id2 = ident_col(atom2) |
| 394 |
|
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#else |
| 395 |
|
|
id1 = ident(atom1) |
| 396 |
|
|
id2 = ident(atom2) |
| 397 |
|
|
#endif |
| 398 |
|
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if (id1.eq.id2) then |
| 399 |
|
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this_sigma = lj_sigma(id1) |
| 400 |
|
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this_eps = lj_eps(id1) |
| 401 |
|
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else |
| 402 |
|
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! use Lorentz-Berthelot mixing rules: |
| 403 |
|
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this_sigma = 0.5E0_DP * (lj_sigma(id1) + lj_sigma(id2)) |
| 404 |
|
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this_eps = dsqrt(lj_eps(id1)*lj_eps(id2)) |
| 405 |
|
|
endif |
| 406 |
|
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|
| 407 |
|
|
call LJ_pot(r, this_sigma, this_eps, u1, dudr1, d21) |
| 408 |
|
|
|
| 409 |
|
|
pot = u1 |
| 410 |
|
|
dudr = dudr1 |
| 411 |
|
|
d2 = d21 |
| 412 |
|
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|
| 413 |
|
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return |
| 414 |
|
|
end subroutine LJ_mix |
| 415 |
|
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|
| 416 |
|
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subroutine LJ_pot(r, sigma, epsilon, u, dudr, d2) |
| 417 |
|
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|
| 418 |
|
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|
| 419 |
|
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real( kind = DP ) :: r,sigma, epsilon, u, dudr, d2 |
| 420 |
|
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real( kind = DP ) :: sigma2, sigma6, r2, r6, rcut2, rcut6 |
| 421 |
|
|
real( kind = DP ) :: t6, t12, tp6, tp12, delta |
| 422 |
|
|
|
| 423 |
|
|
sigma2 = sigma*sigma |
| 424 |
|
|
sigma6 = sigma2*sigma2*sigma2 |
| 425 |
|
|
|
| 426 |
|
|
r2 = r*r |
| 427 |
|
|
r6 = r2*r2*r2 |
| 428 |
|
|
|
| 429 |
|
|
|
| 430 |
|
|
rcut2 = rcut*rcut |
| 431 |
|
|
rcut6 = rcut2*rcut2*rcut2 |
| 432 |
|
|
|
| 433 |
|
|
t6 = sigma6 / r6 |
| 434 |
|
|
t12 = t6*t6 |
| 435 |
|
|
|
| 436 |
|
|
tp6 = sigma6 / rcut6 |
| 437 |
|
|
tp12 = tp6*tp6 |
| 438 |
|
|
|
| 439 |
|
|
delta = -4.0E0_DP*epsilon * (tp12 - tp6) |
| 440 |
|
|
|
| 441 |
|
|
if (r.le.rcut) then |
| 442 |
|
|
u = 4.0E0_DP * epsilon * (t12 - t6) + delta |
| 443 |
|
|
dudr = 24.0E0_DP * epsilon * (t6 - 2.0E0_DP*t12) / r |
| 444 |
|
|
d2 = 24.0E0_DP * epsilon * (26.0E0_DP*t12 - 7.0E0_DP*t6)/r/r |
| 445 |
|
|
else |
| 446 |
|
|
u = 0.0E0_DP |
| 447 |
|
|
dudr = 0.0E0_DP |
| 448 |
|
|
d2 = 0.0E0_DP |
| 449 |
|
|
endif |
| 450 |
|
|
|
| 451 |
|
|
return |
| 452 |
|
|
end subroutine LJ_pot |
| 453 |
|
|
|
| 454 |
|
|
subroutine initialize_lj() |
| 455 |
|
|
use model_module |
| 456 |
|
|
include 'headers/atom.h' |
| 457 |
|
|
|
| 458 |
|
|
integer :: n_atypes |
| 459 |
|
|
|
| 460 |
|
|
n_atypes = get_max_atype() |
| 461 |
|
|
call allocate_lj_module(n_atypes) |
| 462 |
|
|
|
| 463 |
|
|
|
| 464 |
|
|
ljatype(1) = H_atom |
| 465 |
|
|
ljatype(2) = He_atom |
| 466 |
|
|
ljatype(3) = C_atom |
| 467 |
|
|
ljatype(4) = N_atom |
| 468 |
|
|
ljatype(5) = O_atom |
| 469 |
|
|
ljatype(6) = F_atom |
| 470 |
|
|
ljatype(7) = Ne_atom |
| 471 |
|
|
ljatype(8) = S_atom |
| 472 |
|
|
ljatype(9) = Cl_atom |
| 473 |
|
|
ljatype(10) = Ar_atom |
| 474 |
|
|
ljatype(11) = Br_atom |
| 475 |
|
|
ljatype(12) = Kr_atom |
| 476 |
|
|
|
| 477 |
|
|
lj_sigma(H_atom) = 2.81E0_DP |
| 478 |
|
|
lj_sigma(He_atom) = 2.28E0_DP |
| 479 |
|
|
lj_sigma(C_atom) = 3.35E0_DP |
| 480 |
|
|
lj_sigma(N_atom) = 3.31E0_DP |
| 481 |
|
|
lj_sigma(O_atom) = 2.95E0_DP |
| 482 |
|
|
lj_sigma(F_atom) = 2.83E0_DP |
| 483 |
|
|
lj_sigma(Ne_atom) = 2.72E0_DP |
| 484 |
|
|
lj_sigma(S_atom) = 3.52E0_DP |
| 485 |
|
|
lj_sigma(Cl_atom) = 3.35E0_DP |
| 486 |
|
|
lj_sigma(Ar_atom) = 3.41E0_DP |
| 487 |
|
|
lj_sigma(Br_atom) = 3.54E0_DP |
| 488 |
|
|
lj_sigma(Kr_atom) = 3.83E0_DP |
| 489 |
|
|
|
| 490 |
|
|
lj_eps(H_atom) = 0.01708992E0_DP |
| 491 |
|
|
lj_eps(He_atom) = 0.02026944E0_DP |
| 492 |
|
|
lj_eps(C_atom) = 0.10174464E0_DP |
| 493 |
|
|
lj_eps(N_atom) = 0.07412256E0_DP |
| 494 |
|
|
lj_eps(O_atom) = 0.12241152E0_DP |
| 495 |
|
|
lj_eps(F_atom) = 0.10492416E0_DP |
| 496 |
|
|
lj_eps(Ne_atom) = 0.0933984E0_DP |
| 497 |
|
|
lj_eps(S_atom) = 0.3636576E0_DP |
| 498 |
|
|
lj_eps(Cl_atom) = 0.3447792E0_DP |
| 499 |
|
|
lj_eps(Ar_atom) = 0.23806656E0_DP |
| 500 |
|
|
lj_eps(Br_atom) = 0.51110784E0_DP |
| 501 |
|
|
lj_eps(Kr_atom) = 0.3259008E0_DP |
| 502 |
|
|
|
| 503 |
|
|
end subroutine initialize_lj |
| 504 |
|
|
|
| 505 |
|
|
subroutine mass_weight() |
| 506 |
|
|
integer ia, ja, dim, dim2, idim, idim2 |
| 507 |
|
|
real( kind = DP ) :: mt, m1, m2, wt |
| 508 |
|
|
|
| 509 |
|
|
|
| 510 |
|
|
do ia = 1, natoms |
| 511 |
|
|
m1 = mass(ia) |
| 512 |
|
|
do ja = 1, natoms |
| 513 |
|
|
m2 = mass(ja) |
| 514 |
|
|
wt = 1.0E0_DP/dsqrt(m1*m2) |
| 515 |
|
|
do dim = 1, 3 |
| 516 |
|
|
idim = 3 * (ia-1) + dim |
| 517 |
|
|
do dim2 = 1, 3 |
| 518 |
|
|
idim2 = 3 * (ja-1) + dim2 |
| 519 |
|
|
d(idim,idim2) = d(idim,idim2)*wt |
| 520 |
|
|
enddo |
| 521 |
|
|
enddo |
| 522 |
|
|
enddo |
| 523 |
|
|
enddo |
| 524 |
|
|
|
| 525 |
|
|
end subroutine mass_weight |
| 526 |
|
|
|
| 527 |
|
|
|
| 528 |
|
|
|
| 529 |
|
|
|
| 530 |
|
|
end module lj_module |
