#include "f_cart_components.h" module mod_neighbor_list use mod_memory, only: ip, rp, lp, mallocate, mfree use mod_adjacency_mat, only: yale_sparse use mod_io, only: ommp_message, fatal_error implicit none private type ommp_neigh_list integer(ip) :: n !! Number of particles in the system real(rp) :: cutoff !! Cutoff distance for the neighbor list integer(ip) :: cellf = 1 !! Number of subdivision of 'standard' cell. If you create smaller !! cells ([[cutoff]]/[[cellf]]) you can sensibly increase the performanc !! of the algorithm. See 10.1016/S0010-4655(98)00203-3 real(rp) :: celld !! Dimension of each cell integer(ip) :: ncell(3) !! Number of cell along each dimension integer(ip) :: ncells !! Total number of cells real(rp) :: offset(3) !! Coordinates offset along each dimension (that is the minimum value of !! each coordinate. integer(ip) :: nneigh !! Number of neighbor cells integer(ip), allocatable :: neigh_offset(:) !! Offsets of neighbor cells integer(ip), allocatable :: p2c(:) !! Cell of each particle type(yale_sparse) :: c2p !! Particles contained in each cell, sparse matrix format end type ommp_neigh_list public :: ommp_neigh_list, nl_init, nl_terminate, nl_update, get_ith_nl contains subroutine nl_init(nl, c, cutoff, f) implicit none real(rp), intent(in) :: c(:,:) !! Coordinates in input real(rp), intent(in) :: cutoff !! Cut off distance integer(ip), intent(in) :: f !! Subdivision required for each cell type(ommp_neigh_list), intent(inout) :: nl !! Neigh list object to initialize if(size(c,1) /= 3) then call fatal_error("In nl_init, coordinates should be shaped 3xn") end if nl%n = size(c,2) nl%cutoff = cutoff nl%cellf = f if(nl%cellf > 2 .or. nl%cellf < 0) then call fatal_error("Subdivision required is not implemented") end if nl%nneigh = (nl%cellf*2+1)**3 call mallocate('nl_init [neigh_offset]', nl%nneigh, nl%neigh_offset) nl%celld = nl%cutoff / nl%cellf call mallocate('nl_init [p2c]', nl%n, nl%p2c) call nl_update(nl, c) end subroutine subroutine nl_terminate(nl) use mod_adjacency_mat, only : free_yale_sparse implicit none type(ommp_neigh_list), intent(inout) :: nl call free_yale_sparse(nl%c2p) call mfree('nl_terminate [p2c]', nl%p2c) call mfree('nl_terminate [neigh_offset]', nl%neigh_offset) end subroutine subroutine nl_update(nl, c) use mod_io, only: ommp_message use mod_profiling, only: time_push, time_pull use mod_adjacency_mat, only: reverse_grp_tab use mod_constants, only: OMMP_VERBOSE_LOW implicit none type(ommp_neigh_list), intent(inout) :: nl !! Neigh list object to initialize real(rp), intent(in) :: c(3,nl%n) !! Coordinates in input integer(ip) :: i, j, k, l, cc(3), ccmap(3) call time_push() call ommp_message('Updating neighbor lists', OMMP_VERBOSE_LOW) do i=1, 3 !! TODO this should be improved nl%offset(i) = minval(c(i,:)) nl%ncell(i) = ceiling((maxval(c(i,:)) - nl%offset(i)) / nl%celld) end do nl%ncells = product(nl%ncell) ccmap(_x_) = nl%ncell(_y_) * nl%ncell(_z_) ccmap(_y_) = nl%ncell(_z_) ccmap(_z_) = 1 l = 1 do i=-nl%cellf, nl%cellf do j=-nl%cellf, nl%cellf do k=-nl%cellf, nl%cellf nl%neigh_offset(l) = i * ccmap(1) + j * ccmap(2) + k * ccmap(3) l = l + 1 end do end do end do ! Each particle is assigned to a cell do i=1, nl%n do j=1, 3 cc(j) = floor((c(j,i)-nl%offset(j)) / nl%celld) end do nl%p2c(i) = dot_product(cc, ccmap) + 1 end do ! Revert assignation to get neighbor list! ! The number of cell could be different... if(allocated(nl%c2p%ri)) then if(size(nl%c2p%ri) /= nl%ncells+1) then ! This automatically calls for the reallocation in ! reverse_grp_tab. call mfree('nl_update [ri]', nl%c2p%ri) end if end if call reverse_grp_tab(nl%p2c, nl%c2p, nl%ncells) call time_pull("Neighbor list update") end subroutine subroutine get_ith_nl(nl, i, c, neigh, dist, nn) !! Once that the neighbor list have been initialized and !! updated, this function provide a logical array for atom !! [[i]] with all interactions that should be computed and !! corresponding distances. implicit none type(ommp_neigh_list), intent(in) :: nl !! Neigh list object integer(ip), intent(in) :: i !! Index of atom for which the neigbor list is required real(rp), intent(in) :: c(3,nl%n) !! Coordinates in input integer(ip), intent(out) :: neigh(nl%n) !! Integer array with neighbors' indexes. !! Only the first nn elements are valid real(rp), intent(out) :: dist(nl%n) !! Array for returning distances. !! Only the first nn elements are valid integer(ip), intent(out) :: nn !! Number of neighbors integer(ip) :: icell, j, jid, jp, jjp real(rp) :: vdist(3), d2, thr2 icell = nl%p2c(i) thr2 = nl%cutoff * nl%cutoff nn = 0 do j=1, nl%nneigh jid = icell + nl%neigh_offset(j) if(jid > 0 .and. jid <= nl%ncells) then do jp=nl%c2p%ri(jid), nl%c2p%ri(jid+1)-1 jjp = nl%c2p%ci(jp) vdist = c(:,i)-c(:,jjp) d2 = dot_product(vdist, vdist) if(d2 < thr2) then nn = nn + 1 dist(nn) = sqrt(d2) neigh(nn) = jjp end if end do end if end do end subroutine end module