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Add periodic boundaries to metric calculation and energy to vtk out

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development
Alex Selimov 3 years ago
parent 8fd2a7f65b
commit cffb460e09
3 changed files with 84 additions and 15 deletions
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24
src/io.f90
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@ -436,6 +436,7 @@ module io
16 format(/'POINT_DATA', i16)
17 format('SCALARS weight float', / &
'LOOKUP_TABLE default')
18 format('SCALARS atom_type float', / &
'LOOKUP_TABLE default')
@ -445,6 +446,9 @@ module io
21 format('SCALARS esize float', /&
'LOOKUP_TABLE default')
22 format('SCALARS energy float', /&
'LOOKUP_TABLE default')
!First we write the vtk file containing the atoms
open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
@ -467,6 +471,14 @@ module io
do i = 1, atom_num
write(11, '(i16)') type_atom(i)
end do
!Write the atom data
if(allocated(force_atom)) then
write(11,22)
do i =1, atom_num
write(11, "(f23.15)") energy_atom(i)
end do
end if
close(11)
!Now we write the vtk file for the elements
@ -499,6 +511,18 @@ module io
do i = 1, ele_num
write(11, '(i16)') size_ele(i)
end do
if(allocated(force_node)) then
write(11,16) node_num
write(11,22)
do i = 1, ele_num
do inod=1, ng_node(lat_ele(i))
do ibasis=1, basisnum(lat_ele(i))
write(11,'(f23.15)') energy_node(ibasis, inod, i)
end do
end do
end do
end if
close(11)
end subroutine

24
src/mode_metric.f90
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@ -10,7 +10,7 @@ module mode_metric
integer :: nfiles
character(len=100) :: metric_type
real(kind=dp) :: rc_off
real(kind=dp) :: rc_off, old_box_len(3)
!Save reference positions
integer :: np, npreal, nmet
@ -57,6 +57,10 @@ module mode_metric
print *, "Getting initial neighbor list"
call calc_neighbor(rc_off, r_zero, np)
!Save box lengths for applying periodic boundaries
do i=1,3
old_box_len(i) = box_bd(2*i) - box_bd(2*i-1)
end do
!Reset element and box
call reset_data
call reset_box
@ -128,8 +132,11 @@ module mode_metric
!This subroutine calculates the continuum metric that we require
integer :: i, j, k, nei, ip, jp
real(kind=dp) :: def_grad(3,3), omega(3,3), eta(3,3), rij(3), eta_inv(3,3), ftf(3,3), &
U(3,3), R(3,3), Rskew(3,3), oldrij(3)
U(3,3), R(3,3), Rskew(3,3), oldrij(3), box_len(3)
do i = 1, 3
box_len(i) = box_bd(2*i) - box_bd(2*i-1)
end do
!Loop over all points
do ip = 1, np
eta(:,:) = 0.0_dp
@ -138,8 +145,17 @@ module mode_metric
do jp = 1, nei_num(ip)
!Calculate the neighbor vec in current configuration
nei = nei_list(jp, ip)
rij = r_curr(:,nei) - r_curr(:,ip)
oldrij = r_zero(:,nei) - r_zero(:,ip)
rij = r_curr(:,nei) - r_curr(:,ip) +periodvec(:,jp,ip)*box_len
if (norm2(rij) > 5*rc_off) then
do j = 1, 3
if (r_curr(j,nei) > r_curr(j,ip)) then
rij(j) = rij(j) - box_len(j)
else if(r_curr(j,nei) < r_curr(j,ip)) then
rij(j) = rij(j) + box_len(j)
end if
end do
end if
oldrij = r_zero(:,nei) - r_zero(:,ip) + periodvec(:,jp,ip)*old_box_len
!Calculate eta and omega
do i = 1,3

51
src/neighbors.f90
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@ -4,10 +4,12 @@ module neighbors
use elements
use subroutines
use functions
use box
integer, allocatable :: nei_list(:,:), nei_num(:), nn(:)
integer, allocatable :: nei_list(:,:), nei_num(:), nn(:), periodvec(:,:,:)
real(kind=dp), allocatable :: init_vec(:,:,:), output(:), microrotation(:,:)
public
contains
subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
@ -82,44 +84,68 @@ module neighbors
integer, intent(in) :: n
real(kind=dp), dimension(3,n) :: r_list
integer :: i, c(3), ci, cj, ck, num_nei, nei
integer :: i, j, c(3),cn(3), ci, cj, ck, num_nei, nei, v(3), period_dir(3)
!Variables for cell list code
integer, dimension(3) ::cell_num
integer, allocatable :: num_in_cell(:,:,:), cell_list(:,:,:,:)
integer :: which_cell(3,n)
real(kind=dp) :: r(3), box_len(3)
logical :: period_bd(3)
!First reallocate the neighbor list codes
if (allocated(nei_list)) then
deallocate(nei_list,nei_num)
deallocate(nei_list,nei_num, periodvec)
end if
allocate(nei_list(100,n),nei_num(n))
allocate(nei_list(100,n),nei_num(n), periodvec(3,100,n))
nei_list=0
periodvec=0
nei_num=0
!Now first pass the position list and and point num to the cell algorithm
call build_cell_list(n, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
do i=1, 3
if (box_bc(i:i) == 'p') then
period_bd(i) = .true.
else
period_bd(i)=.false.
end if
box_len(i) = box_bd(2*i) - box_bd(2*i-1)
end do
!Now loop over every point and find it's neighbors
pointloop: do i = 1, n
!First check to see if the point is a filler point, if so then skip it
if(r_list(1,i) < box_bd(1)) cycle
!c is the position of the cell that the point
!c is the position of the cell that the point belongs to
c = which_cell(:,i)
!Loop over all neighboring cells
do ci = -1, 1, 1
do cj = -1, 1, 1
do ck = -1, 1, 1
!First check to make sure that the neighboring cell exists
!First try to apply periodic boundaries
v=(/ ck, cj, ci /)
cn=0
period_dir=0
do j=1, 3
if ((c(j) + v(j) == 0).and.period_bd(j)) then
cn(j) = cell_num(j)
period_dir(j) = 1
else if ((c(j) + v(j) > cell_num(j)).and.period_bd(j)) then
cn(j) = 1
period_dir(j) = -1
else if ((c(j)+v(j) >= 1) .and. (c(j)+v(j) <= cell_num(j))) then
cn(j) = c(j) + v(j)
end if
end do
if(any((c + (/ ck, cj, ci /)) == 0)) cycle
if( (c(1) + ck > cell_num(1)).or.(c(2) + cj > cell_num(2)).or. &
(c(3) + ci > cell_num(3))) cycle
do num_nei = 1, num_in_cell(c(1) + ck, c(2) + cj, c(3) + ci)
nei = cell_list(num_nei,c(1) + ck, c(2) + cj, c(3) + ci)
do num_nei = 1, num_in_cell(cn(1),cn(2),cn(3))
nei = cell_list(num_nei,cn(1),cn(2),cn(3))
!Check to make sure the atom isn't the same index as the atom we are checking
!and that the neighbor hasn't already been deleted
@ -127,10 +153,13 @@ module neighbors
!Now check to see if it is in the cutoff radius, if it is add it to the neighbor list for that
!atom and calculate the initial neighbor vector
if (norm2(r_list(:,nei)-r_list(:,i)) < rc_off) then
r = r_list(:,nei) + period_dir*box_len
if (norm2(r-r_list(:,i)) < rc_off) then
nei_num(i) = nei_num(i) + 1
nei_list(nei_num(i), i) = nei
periodvec(:,nei_num(i),i) = period_dir
end if
end if

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