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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 |
153 |
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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 |
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if (jbeg .le. jend) then |
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#ifdef MPI |
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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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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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do jnab = jbeg, jend |
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j = list(jnab) |
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#ifdef MPI |
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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 |
256 |
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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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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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274 |
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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 |
280 |
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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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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 |
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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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enddo |
326 |
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endif |
327 |
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enddo |
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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 |
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! 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 |
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id1 = ident_row(atom1) |
393 |
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id2 = ident_col(atom2) |
394 |
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#else |
395 |
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id1 = ident(atom1) |
396 |
|
|
id2 = ident(atom2) |
397 |
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|
#endif |
398 |
|
|
if (id1.eq.id2) then |
399 |
|
|
this_sigma = lj_sigma(id1) |
400 |
|
|
this_eps = lj_eps(id1) |
401 |
|
|
else |
402 |
|
|
! use Lorentz-Berthelot mixing rules: |
403 |
|
|
this_sigma = 0.5E0_DP * (lj_sigma(id1) + lj_sigma(id2)) |
404 |
|
|
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 |
|
|
|
413 |
|
|
return |
414 |
|
|
end subroutine LJ_mix |
415 |
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|
416 |
|
|
subroutine LJ_pot(r, sigma, epsilon, u, dudr, d2) |
417 |
|
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|
418 |
|
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|
419 |
|
|
real( kind = DP ) :: r,sigma, epsilon, u, dudr, d2 |
420 |
|
|
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 |