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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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15
src/io.f90
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@ -310,6 +310,9 @@ module io
20 format('SCALARS lattice_type float', /& 20 format('SCALARS lattice_type float', /&
'LOOKUP_TABLE default') 'LOOKUP_TABLE default')
21 format('SCALARS esize float', /&
'LOOKUP_TABLE default')
!First we write the vtk file containing the atoms !First we write the vtk file containing the atoms
open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind') 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 do i = 1, ele_num
write(11, '(i16)') lat_ele(i) write(11, '(i16)') lat_ele(i)
end do end do
write(11,21)
do i = 1, ele_num
write(11, '(i16)') size_ele(i)
end do
close(11) close(11)
end subroutine end subroutine
@ -624,8 +631,13 @@ module io
!Read in the box boundary and grow the current active box bd !Read in the box boundary and grow the current active box bd
read(11, *) temp_box_bd(:) read(11, *) temp_box_bd(:)
print *, "displace", displace
do i = 1, 3 do i = 1, 3
if (displace(i) > lim_zero) then
newdisplace(i) = displace(i) - temp_box_bd(2*i-1) 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-1) = temp_box_bd(2*i-1) + newdisplace(i)
temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i) temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
end do end do
@ -717,7 +729,8 @@ module io
!Read the atoms !Read the atoms
do i = 1, in_atoms do i = 1, in_atoms
read(11,*) j, type, sbox, r(:) 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 end do
!Read the elements !Read the elements

34
src/opt_group.f90
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@ -29,7 +29,7 @@ module opt_group
remesh_size=0 remesh_size=0
displace=.false. displace=.false.
delete=.false. delete=.false.
! max_remesh=.false. max_remesh=.false.
refine = .false. refine = .false.
if(allocated(element_index)) deallocate(element_index) 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 !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, & 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), & 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) r_new_node(3,max_basisnum, max_ng_node), orient(3,3), group_in_lat(3,8)
logical, allocatable :: lat_points(:,:,:) logical, allocatable :: lat_points(:,:,:)
@ -352,31 +354,40 @@ module opt_group
old_atom = atom_num old_atom = atom_num
old_ele = ele_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 !Figure out new looping boundaries
bd_in_array(1) = bd_in_lat(2) - bd_in_lat(1) + 10 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(2) = bd_in_lat(4) - bd_in_lat(3) + 10
bd_in_array(3) = bd_in_lat(6) - bd_in_lat(5) + 10 bd_in_array(3) = bd_in_lat(6) - bd_in_lat(5) + 10
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) zloop: do iz = 1, bd_in_array(3)
yloop: do iy = 1, bd_in_array(2) yloop: do iy = 1, bd_in_array(2)
xloop: do ix = 1, bd_in_array(1) xloop: do ix = 1, bd_in_array(1)
if (lat_points(ix, iy,iz)) then if (lat_points(ix, iy,iz)) then
r_new_node(:,:,:) = 0.0_dp
!Check to see if the element overshoots the bound !Check to see if the element overshoots the bound
if (iz+remesh_size-1 > bd_in_array(3)) then if (iz+working_esize-1 > bd_in_array(3)) then
exit zloop exit zloop
else if (iy+remesh_size-1 > bd_in_array(2)) then else if (iy+working_esize-1 > bd_in_array(2)) then
cycle zloop cycle zloop
else if (ix+remesh_size-1 > bd_in_array(1)) then else if (ix+working_esize-1 > bd_in_array(1)) then
cycle yloop cycle yloop
end if end if
if (all(lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1))) then if (all(lat_points(ix:ix+working_esize-1,iy:iy+working_esize-1,iz:iz+working_esize-1))) then
do inod = 1, 8 do inod = 1, ng_node(remesh_type)
vlat = ele(:,inod) + (/ix, iy, iz /) vlat = ele(:,inod) + (/ix, iy, iz /)
do i = 1, 3 do i = 1, 3
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5 vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
@ -384,16 +395,17 @@ module opt_group
r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam r_new_node(:,1,inod) = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
end do end do
lat_points(ix:ix+remesh_size-1,iy:iy+remesh_size-1,iz:iz+remesh_size-1) = .false. 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. !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. !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) 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 if
end do xloop end do xloop
end do yloop end do yloop
end do zloop end do zloop
end do
!Now we have to add any leftover lattice points as atoms !Now we have to add any leftover lattice points as atoms
do iz = 1, bd_in_array(3) do iz = 1, bd_in_array(3)

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