Add periodic boundaries to metric calculation and energy to vtk out
This commit is contained in:
Alex Selimov
parent
8fd2a7f65b
commit
cffb460e09
24
src/io.f90
24
src/io.f90
@ -436,6 +436,7 @@ module io
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16 format(/'POINT_DATA', i16)
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16 format(/'POINT_DATA', i16)
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17 format('SCALARS weight float', / &
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17 format('SCALARS weight float', / &
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'LOOKUP_TABLE default')
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'LOOKUP_TABLE default')
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18 format('SCALARS atom_type float', / &
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18 format('SCALARS atom_type float', / &
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'LOOKUP_TABLE default')
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'LOOKUP_TABLE default')
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@ -445,6 +446,9 @@ module io
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21 format('SCALARS esize float', /&
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21 format('SCALARS esize float', /&
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'LOOKUP_TABLE default')
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'LOOKUP_TABLE default')
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22 format('SCALARS energy float', /&
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'LOOKUP_TABLE default')
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!First we write the vtk file containing the atoms
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!First we write the vtk file containing the atoms
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open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
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open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
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@ -467,6 +471,14 @@ module io
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do i = 1, atom_num
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do i = 1, atom_num
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write(11, '(i16)') type_atom(i)
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write(11, '(i16)') type_atom(i)
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end do
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end do
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!Write the atom data
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if(allocated(force_atom)) then
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write(11,22)
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do i =1, atom_num
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write(11, "(f23.15)") energy_atom(i)
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end do
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end if
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close(11)
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close(11)
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!Now we write the vtk file for the elements
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!Now we write the vtk file for the elements
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@ -499,6 +511,18 @@ module io
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do i = 1, ele_num
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do i = 1, ele_num
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write(11, '(i16)') size_ele(i)
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write(11, '(i16)') size_ele(i)
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end do
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end do
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if(allocated(force_node)) then
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write(11,16) node_num
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write(11,22)
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do i = 1, ele_num
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do inod=1, ng_node(lat_ele(i))
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do ibasis=1, basisnum(lat_ele(i))
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write(11,'(f23.15)') energy_node(ibasis, inod, i)
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end do
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end do
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end do
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end if
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close(11)
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close(11)
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end subroutine
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end subroutine
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@ -10,7 +10,7 @@ module mode_metric
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integer :: nfiles
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integer :: nfiles
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character(len=100) :: metric_type
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character(len=100) :: metric_type
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real(kind=dp) :: rc_off
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real(kind=dp) :: rc_off, old_box_len(3)
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!Save reference positions
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!Save reference positions
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integer :: np, npreal, nmet
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integer :: np, npreal, nmet
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@ -57,6 +57,10 @@ module mode_metric
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print *, "Getting initial neighbor list"
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print *, "Getting initial neighbor list"
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call calc_neighbor(rc_off, r_zero, np)
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call calc_neighbor(rc_off, r_zero, np)
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!Save box lengths for applying periodic boundaries
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do i=1,3
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old_box_len(i) = box_bd(2*i) - box_bd(2*i-1)
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end do
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!Reset element and box
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!Reset element and box
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call reset_data
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call reset_data
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call reset_box
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call reset_box
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@ -128,8 +132,11 @@ module mode_metric
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!This subroutine calculates the continuum metric that we require
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!This subroutine calculates the continuum metric that we require
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integer :: i, j, k, nei, ip, jp
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integer :: i, j, k, nei, ip, jp
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real(kind=dp) :: def_grad(3,3), omega(3,3), eta(3,3), rij(3), eta_inv(3,3), ftf(3,3), &
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real(kind=dp) :: def_grad(3,3), omega(3,3), eta(3,3), rij(3), eta_inv(3,3), ftf(3,3), &
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U(3,3), R(3,3), Rskew(3,3), oldrij(3)
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U(3,3), R(3,3), Rskew(3,3), oldrij(3), box_len(3)
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do i = 1, 3
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box_len(i) = box_bd(2*i) - box_bd(2*i-1)
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end do
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!Loop over all points
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!Loop over all points
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do ip = 1, np
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do ip = 1, np
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eta(:,:) = 0.0_dp
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eta(:,:) = 0.0_dp
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@ -138,8 +145,17 @@ module mode_metric
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do jp = 1, nei_num(ip)
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do jp = 1, nei_num(ip)
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!Calculate the neighbor vec in current configuration
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!Calculate the neighbor vec in current configuration
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nei = nei_list(jp, ip)
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nei = nei_list(jp, ip)
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rij = r_curr(:,nei) - r_curr(:,ip)
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rij = r_curr(:,nei) - r_curr(:,ip) +periodvec(:,jp,ip)*box_len
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oldrij = r_zero(:,nei) - r_zero(:,ip)
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if (norm2(rij) > 5*rc_off) then
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do j = 1, 3
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if (r_curr(j,nei) > r_curr(j,ip)) then
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rij(j) = rij(j) - box_len(j)
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else if(r_curr(j,nei) < r_curr(j,ip)) then
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rij(j) = rij(j) + box_len(j)
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end if
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end do
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end if
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oldrij = r_zero(:,nei) - r_zero(:,ip) + periodvec(:,jp,ip)*old_box_len
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!Calculate eta and omega
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!Calculate eta and omega
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do i = 1,3
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do i = 1,3
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@ -4,10 +4,12 @@ module neighbors
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use elements
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use elements
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use subroutines
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use subroutines
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use functions
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use functions
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use box
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integer, allocatable :: nei_list(:,:), nei_num(:), nn(:)
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integer, allocatable :: nei_list(:,:), nei_num(:), nn(:), periodvec(:,:,:)
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real(kind=dp), allocatable :: init_vec(:,:,:), output(:), microrotation(:,:)
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real(kind=dp), allocatable :: init_vec(:,:,:), output(:), microrotation(:,:)
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public
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public
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contains
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contains
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subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
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subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
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@ -82,44 +84,68 @@ module neighbors
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integer, intent(in) :: n
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integer, intent(in) :: n
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real(kind=dp), dimension(3,n) :: r_list
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real(kind=dp), dimension(3,n) :: r_list
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integer :: i, c(3), ci, cj, ck, num_nei, nei
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integer :: i, j, c(3),cn(3), ci, cj, ck, num_nei, nei, v(3), period_dir(3)
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!Variables for cell list code
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!Variables for cell list code
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integer, dimension(3) ::cell_num
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integer, dimension(3) ::cell_num
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integer, allocatable :: num_in_cell(:,:,:), cell_list(:,:,:,:)
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integer, allocatable :: num_in_cell(:,:,:), cell_list(:,:,:,:)
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integer :: which_cell(3,n)
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integer :: which_cell(3,n)
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real(kind=dp) :: r(3), box_len(3)
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logical :: period_bd(3)
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!First reallocate the neighbor list codes
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!First reallocate the neighbor list codes
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if (allocated(nei_list)) then
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if (allocated(nei_list)) then
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deallocate(nei_list,nei_num)
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deallocate(nei_list,nei_num, periodvec)
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end if
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end if
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allocate(nei_list(100,n),nei_num(n))
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allocate(nei_list(100,n),nei_num(n), periodvec(3,100,n))
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nei_list=0
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nei_list=0
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periodvec=0
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nei_num=0
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nei_num=0
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!Now first pass the position list and and point num to the cell algorithm
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!Now first pass the position list and and point num to the cell algorithm
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call build_cell_list(n, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
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call build_cell_list(n, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
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do i=1, 3
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if (box_bc(i:i) == 'p') then
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period_bd(i) = .true.
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else
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period_bd(i)=.false.
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end if
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box_len(i) = box_bd(2*i) - box_bd(2*i-1)
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end do
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!Now loop over every point and find it's neighbors
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!Now loop over every point and find it's neighbors
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pointloop: do i = 1, n
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pointloop: do i = 1, n
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!First check to see if the point is a filler point, if so then skip it
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!First check to see if the point is a filler point, if so then skip it
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if(r_list(1,i) < box_bd(1)) cycle
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if(r_list(1,i) < box_bd(1)) cycle
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!c is the position of the cell that the point
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!c is the position of the cell that the point belongs to
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c = which_cell(:,i)
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c = which_cell(:,i)
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!Loop over all neighboring cells
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!Loop over all neighboring cells
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do ci = -1, 1, 1
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do ci = -1, 1, 1
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do cj = -1, 1, 1
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do cj = -1, 1, 1
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do ck = -1, 1, 1
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do ck = -1, 1, 1
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!First check to make sure that the neighboring cell exists
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!First try to apply periodic boundaries
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if(any((c + (/ ck, cj, ci /)) == 0)) cycle
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v=(/ ck, cj, ci /)
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if( (c(1) + ck > cell_num(1)).or.(c(2) + cj > cell_num(2)).or. &
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cn=0
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(c(3) + ci > cell_num(3))) cycle
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period_dir=0
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do j=1, 3
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if ((c(j) + v(j) == 0).and.period_bd(j)) then
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cn(j) = cell_num(j)
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period_dir(j) = 1
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else if ((c(j) + v(j) > cell_num(j)).and.period_bd(j)) then
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cn(j) = 1
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period_dir(j) = -1
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do num_nei = 1, num_in_cell(c(1) + ck, c(2) + cj, c(3) + ci)
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else if ((c(j)+v(j) >= 1) .and. (c(j)+v(j) <= cell_num(j))) then
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nei = cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci)
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cn(j) = c(j) + v(j)
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end if
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end do
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if(any((c + (/ ck, cj, ci /)) == 0)) cycle
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do num_nei = 1, num_in_cell(cn(1),cn(2),cn(3))
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nei = cell_list(num_nei,cn(1),cn(2),cn(3))
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!Check to make sure the atom isn't the same index as the atom we are checking
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!Check to make sure the atom isn't the same index as the atom we are checking
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!and that the neighbor hasn't already been deleted
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!and that the neighbor hasn't already been deleted
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@ -127,10 +153,13 @@ module neighbors
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!Now check to see if it is in the cutoff radius, if it is add it to the neighbor list for that
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!Now check to see if it is in the cutoff radius, if it is add it to the neighbor list for that
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!atom and calculate the initial neighbor vector
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!atom and calculate the initial neighbor vector
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if (norm2(r_list(:,nei)-r_list(:,i)) < rc_off) then
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r = r_list(:,nei) + period_dir*box_len
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if (norm2(r-r_list(:,i)) < rc_off) then
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nei_num(i) = nei_num(i) + 1
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nei_num(i) = nei_num(i) + 1
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nei_list(nei_num(i), i) = nei
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nei_list(nei_num(i), i) = nei
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periodvec(:,nei_num(i),i) = period_dir
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end if
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end if
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end if
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end if
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