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Working remesh command and remesh max command

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master
Alex 5 years ago
parent 5b925122df
commit d670bb5083
2 changed files with 60 additions and 35 deletions
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17
src/io.f90
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@ -310,6 +310,9 @@ module io
20 format('SCALARS lattice_type float', /&
'LOOKUP_TABLE default')
21 format('SCALARS esize 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')
@ -358,6 +361,10 @@ module io
do i = 1, ele_num
write(11, '(i16)') lat_ele(i)
end do
write(11,21)
do i = 1, ele_num
write(11, '(i16)') size_ele(i)
end do
close(11)
end subroutine
@ -624,8 +631,13 @@ module io
!Read in the box boundary and grow the current active box bd
read(11, *) temp_box_bd(:)
print *, "displace", displace
do i = 1, 3
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
if (displace(i) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
else
newdisplace=displace(i)
end if
temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do
@ -717,7 +729,8 @@ module io
!Read the atoms
do i = 1, in_atoms
read(11,*) j, type, sbox, r(:)
call add_atom(new_type_to_type(type), sbox, r+newdisplace )
r = r+newdisplace
call add_atom(new_type_to_type(type), sbox, r)
end do
!Read the elements

78
src/opt_group.f90
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@ -29,7 +29,7 @@ module opt_group
remesh_size=0
displace=.false.
delete=.false.
! max_remesh=.false.
max_remesh=.false.
refine = .false.
if(allocated(element_index)) deallocate(element_index)
@ -262,7 +262,9 @@ module opt_group
!This command is used to remesh the group to a desired element size
integer :: i, j, k, ix, iy, iz, inod, ibasis, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num, &
current_esize, dof, max_lat(3), r_lat(3), ele(3,8), vlat(3), bd_in_lat(6), bd_in_array(3), old_ele, old_atom
current_esize, dof, max_lat(3), r_lat(3), ele(3,8), vlat(3), bd_in_lat(6), bd_in_array(3), old_ele, old_atom, &
max_loops, working_esize
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), ori_inv(3,3), r(3), &
r_new_node(3,max_basisnum, max_ng_node), orient(3,3), group_in_lat(3,8)
logical, allocatable :: lat_points(:,:,:)
@ -352,48 +354,58 @@ module opt_group
old_atom = atom_num
old_ele = ele_num
!Now run remeshing algorithm, not the most optimized or efficient but gets the job done
ele = (remesh_size-1)*cubic_cell
!Now run remeshing algorithm, not the most optimized or efficient but gets the job done
!Figure out new looping boundaries
bd_in_array(1) = bd_in_lat(2) - bd_in_lat(1) + 10
bd_in_array(2) = bd_in_lat(4) - bd_in_lat(3) + 10
bd_in_array(3) = bd_in_lat(6) - bd_in_lat(5) + 10
zloop: do iz = 1, bd_in_array(3)
yloop: do iy = 1, bd_in_array(2)
xloop: do ix = 1, bd_in_array(1)
if (lat_points(ix, iy,iz)) then
!Check to see if the element overshoots the bound
if (iz+remesh_size-1 > bd_in_array(3)) then
exit zloop
else if (iy+remesh_size-1 > bd_in_array(2)) then
cycle zloop
else if (ix+remesh_size-1 > bd_in_array(1)) then
cycle yloop
end if
if (all(lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1))) then
do inod = 1, 8
vlat = ele(:,inod) + (/ix, iy, iz /)
do i = 1, 3
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
if (max_remesh) then
max_loops = (remesh_size-2)/2
else
max_loops = 1
end if
do j = 1, max_loops
working_esize = remesh_size - 2*(j-1)
ele = (working_esize-1)*cubic_cell
zloop: do iz = 1, bd_in_array(3)
yloop: do iy = 1, bd_in_array(2)
xloop: do ix = 1, bd_in_array(1)
if (lat_points(ix, iy,iz)) then
r_new_node(:,:,:) = 0.0_dp
!Check to see if the element overshoots the bound
if (iz+working_esize-1 > bd_in_array(3)) then
exit zloop
else if (iy+working_esize-1 > bd_in_array(2)) then
cycle zloop
else if (ix+working_esize-1 > bd_in_array(1)) then
cycle yloop
end if
if (all(lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1))) then
do inod = 1, ng_node(remesh_type)
vlat = ele(:,inod) + (/ix, iy, iz /)
do i = 1, 3
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
end do
r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
end do
r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
end do
lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1) = .false.
!Add the element, for the sbox we just set it to the same sbox that we get the orientation from.
!In this case it is from the sbox of the first atom in the group.
call add_element(remesh_ele_type, remesh_size, remesh_type, sbox_atom(atom_index(1)),r_new_node)
lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1) = .false.
!Add the element, for the sbox we just set it to the same sbox that we get the orientation from.
!In this case it is from the sbox of the first atom in the group.
call add_element(remesh_ele_type, working_esize, remesh_type, sbox_atom(atom_index(1)),r_new_node)
end if
end if
end if
end do xloop
end do yloop
end do zloop
end do xloop
end do yloop
end do zloop
end do
!Now we have to add any leftover lattice points as atoms
do iz = 1, bd_in_array(3)

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