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Final changes fixing remesh group

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This commit is contained in:
Alex Selimov 2020-04-15 11:55:26 -04:00
parent babf4e176d
commit f6c0cf93f2
1 changed files with 59 additions and 27 deletions
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86
src/opt_group.f90
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@ -302,12 +302,12 @@ 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, &
max_loops, working_esize, group_lat_num, lat_list(10), group_sbox_num, sbox_list(100), is, ilat
current_esize, dof, max_lat(3), r_lat(3), ele(3,8), vlat(3), bd_in_lat(6), bd_in_array(3), new_ele, new_atom, &
max_loops, working_esize, group_lat_num, lat_list(10), group_sbox_num, sbox_list(100), is, ilat, tot_dof
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), group_bd(6)
logical, allocatable :: lat_points(:,:,:)
logical, allocatable :: lat_points(:,:,:), new_sbox, new_lat
character(len=100) :: remesh_ele_type
@ -318,35 +318,67 @@ module opt_group
group_sbox_num = 0
group_lat_num = 0
do i = 1, group_atom_num
new_sbox=.true.
new_lat=.true.
do j = 1, group_sbox_num
if (sbox_list(j) == sbox_atom(atom_index(i))) exit
group_sbox_num = group_sbox_num + 1
sbox_list(group_sbox_num) = sbox_atom(atom_index(i))
if (sbox_list(j) == sbox_atom(atom_index(i))) then
new_sbox=.false.
exit
end if
end do
if(new_sbox) then
group_sbox_num = group_sbox_num + 1
sbox_list(group_sbox_num) = sbox_atom(atom_index(i))
end if
do j = 1, group_lat_num
if (basis_type(1,lat_list(j)) == type_atom(atom_index(i))) exit
if (basis_type(1,lat_list(j)) == type_atom(atom_index(i))) then
new_lat = .false.
exit
end if
end do
if (new_lat) then
group_lat_num = group_lat_num + 1
do k = 1, lattice_types
if (basis_type(1,k) == type_atom(atom_index(i))) lat_list(group_lat_num) = k
if (basis_type(1,k) == type_atom(atom_index(i))) lat_list(group_lat_num) = k
end do
end do
end if
end do
do i = 1, group_ele_num
new_sbox=.true.
new_lat = .true.
do j = 1, group_sbox_num
if (sbox_list(j) == sbox_ele(element_index(i))) exit
group_sbox_num = group_sbox_num + 1
sbox_list(group_sbox_num) = sbox_ele(element_index(i))
if (sbox_list(j) == sbox_ele(element_index(i))) then
new_sbox = .false.
exit
end if
end do
if (new_sbox) then
group_sbox_num = group_sbox_num + 1
sbox_list(group_sbox_num) = sbox_ele(element_index(i))
end if
do j = 1, group_lat_num
if (lat_list(group_lat_num) == lat_ele(element_index(i))) exit
if (lat_list(group_lat_num) == lat_ele(element_index(i))) then
new_lat=.false.
exit
end if
end do
if (new_lat) then
group_lat_num = group_lat_num + 1
lat_list(group_lat_num) = lat_ele(element_index(i))
end do
end if
end do
new_atom = 0
new_ele=0
tot_dof=0
do is = 1, group_sbox_num
orient = sub_box_ori(:, :, sbox_list(is))
@ -388,6 +420,7 @@ module opt_group
!If for some reason there are no dof in this loop then cycle out
if(dof == 0) cycle
tot_dof = tot_dof+dof
group_in_lat = reshape((/ group_bd(1),group_bd(3),group_bd(5), &
group_bd(2),group_bd(3),group_bd(5), &
@ -410,6 +443,7 @@ module opt_group
!Now place all group atoms and group interpolated atoms into lat_points
do i = 1, group_atom_num
if (.not.((sbox_atom(atom_index(i)) == is).and.(basis_type(1,ilat) == type_atom(atom_index(i))))) cycle
r = r_atom(:,atom_index(i))/lapa(ilat)
r = matmul(fcc_inv,matmul(ori_inv,r))
do j = 1, 3
@ -427,6 +461,7 @@ module opt_group
!Now place interpolated atoms within lat_points array
do i =1, group_ele_num
if (.not.((sbox_ele(element_index(i)) == is).and.( lat_ele(element_index(i)) == ilat))) cycle
ie = element_index(i)
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
do j = 1, size_ele(ie)**3 * basisnum(lat_ele(ie))
@ -446,17 +481,6 @@ module opt_group
end do
end do
print *, "Group has ", dof, " degrees of freedom to remesh"
!Delete all elements and atoms to make space for new elements and atoms
call delete_atoms(group_atom_num, atom_index)
call delete_elements(group_ele_num, element_index)
old_atom = atom_num
old_ele = ele_num
!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
@ -499,6 +523,7 @@ module opt_group
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.
new_ele = new_ele+1
call add_element(remesh_ele_type, working_esize, ilat, sbox_atom(atom_index(1)),r_new_node)
end if
@ -519,15 +544,22 @@ module opt_group
end do
lat_points(ix,iy,iz) = .false.
r = matmul(orient, matmul(fcc_mat, vlat))*lapa(ilat)
call add_atom(basis_type(1,ilat), sbox_atom(atom_index(1)), r)
new_atom=new_atom+1
call add_atom(basis_type(1,ilat), is, r)
end if
end do
end do
end do
deallocate(lat_points)
end do
end do
print *, "Remeshing has created ", ele_num-old_ele, " elements and ", atom_num-old_atom, " atoms."
!Delete all elements and atoms to make space for new elements and atoms
call delete_atoms(group_atom_num, atom_index)
call delete_elements(group_ele_num, element_index)
print *, tot_dof, " degrees of freedom in group"
print *, "remesh_group creates ", new_atom, " atoms and ", new_ele, " elements."
end subroutine remesh_group
subroutine delete_group