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Merge pull request #26 from aselimov/ft--group-remesh-to-elements

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Ft  group remesh to elements
master
aselimov 5 years ago committed by GitHub
parent d0b6c595f0 d670bb5083
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4 changed files with 235 additions and 38 deletions
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10
README.md
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@ -217,7 +217,15 @@ This command wraps atoms back into the simulation cell as though periodic bounda
remesh esize
```
This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics.
This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation.
**Max**
```
max
```
This command attempts to reduce the degrees of freedom in the model by replacing them with graded elements. This code works by starting at elements with size `esize` and then checks all degrees of freedom to see which ones can be replaced by inserting the element. It then iterates over elements of `esize-2` to `esize=2` which is full atomic resolution.
**Delete**

20
src/io.f90
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@ -87,6 +87,9 @@ module io
call set_max_esize
do i = 1, outfilenum
print *, "Writing data out to ", trim(adjustl(outfiles(i)))
!Pull out the extension of the file and call the correct write subroutine
select case(trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))))
case('xyz')
@ -307,6 +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')
@ -355,6 +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
@ -621,8 +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
@ -714,7 +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

2
src/mode_create.f90
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@ -393,7 +393,7 @@ module mode_create
outerloop: do iz = 1, bd_in_array(3)
do iy = 1, bd_in_array(2)
do ix = 1, bd_in_array(1)
node_in_bd(8) = .false.
node_in_bd(:) = .false.
do inod = 1, 8
vlat = ele(:,inod) + (/ ix, iy, iz /)

241
src/opt_group.f90
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@ -8,10 +8,10 @@ module opt_group
use box
implicit none
integer :: group_ele_num, group_atom_num, remesh_size
integer :: group_ele_num, group_atom_num, remesh_size, remesh_type
character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
real(kind=dp) :: block_bd(6), disp_vec(3)
logical :: displace, delete
real(kind=dp) :: block_bd(6), disp_vec(3), remesh_lat_pam
logical :: displace, delete, max_remesh, refine
integer, allocatable :: element_index(:), atom_index(:)
@ -29,6 +29,8 @@ module opt_group
remesh_size=0
displace=.false.
delete=.false.
max_remesh=.false.
refine = .false.
if(allocated(element_index)) deallocate(element_index)
if(allocated(atom_index)) deallocate(atom_index)
@ -43,6 +45,9 @@ module opt_group
if(remesh_size > 0) call remesh_group
if(delete) call delete_group
if(refine) call refine_group
end subroutine group
subroutine parse_group(arg_pos)
@ -101,13 +106,24 @@ module opt_group
if (arglen==0) stop "Missing vector component for shift command"
read(textholder, *) disp_vec(i)
end do
case('refine')
refine=.true.
case('remesh')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing remesh element size in group command"
read(textholder, *) remesh_size
case('delete')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing remesh lattice parameter in group command"
read(textholder, *) remesh_lat_pam
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing remesh type in group command"
read(textholder, *) remesh_type
case('max')
max_remesh =.true.
case('delete')
delete=.true.
case default
!If it isn't an available option to opt_disl then we just exit
@ -211,48 +227,205 @@ module opt_group
end subroutine displace_group
subroutine remesh_group
subroutine refine_group
!This command is used to remesh the group to a desired element size
integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num
real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
!Refining to atoms and remeshing to elements are different processes so check which code we need to run
select case(remesh_size)
!Refining to atoms
case(2)
if(group_ele_num > 0) then
orig_atom_num = atom_num
!Estimate number of atoms we are adding, this doesn't have to be exact
add_atom_num = group_ele_num*basisnum(lat_ele(element_index(1)))*size_ele(element_index(1))**3
call grow_ele_arrays(0,add_atom_num)
do i = 1, group_ele_num
ie = element_index(i)
!Get the interpolated atom positions
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries
!here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j))
end do
if(group_ele_num > 0) then
orig_atom_num = atom_num
!Estimate number of atoms we are adding, this doesn't have to be exact
add_atom_num = group_ele_num*basisnum(lat_ele(element_index(1)))*size_ele(element_index(1))**3
call grow_ele_arrays(0,add_atom_num)
do i = 1, group_ele_num
ie = element_index(i)
!Get the interpolated atom positions
call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
!Loop over all interpolated atoms and add them to the system, we apply periodic boundaries
!here as well to make sure they are in the box
do j = 1, basisnum(lat_ele(ie))*size_ele(ie)**3
call apply_periodic(r_interp(:,j))
call add_atom(type_interp(j), sbox_ele(ie), r_interp(:,j))
end do
end do
!Once all atoms are added we delete all of the elements
call delete_elements(group_ele_num, element_index)
print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
end if
end subroutine
subroutine remesh_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
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(:,:,:)
character(len=100) :: remesh_ele_type
!Right now we just hardcode only remeshing to elements
remesh_ele_type = 'fcc'
!Get the orientations, this assumes that the orientation of the subbox for the first atom is the
!same as the rest of the atoms
!If this assumption is false then the code will break and exit
orient = sub_box_ori(:, :, sbox_atom(atom_index(1)))
call matrix_inverse(orient,3,ori_inv)
!First calculate max position in lattice space to be able to allocate lat_points array, also sum the total numbers of
!degrees of freedom which are added
dof = 0
select case(trim(adjustl(shape)))
case('block')
group_in_lat = reshape((/ block_bd(1),block_bd(3),block_bd(5), &
block_bd(2),block_bd(3),block_bd(5), &
block_bd(2),block_bd(4),block_bd(5), &
block_bd(1),block_bd(4),block_bd(5), &
block_bd(1),block_bd(3),block_bd(6), &
block_bd(2),block_bd(3),block_bd(6), &
block_bd(2),block_bd(4),block_bd(6), &
block_bd(1),block_bd(4),block_bd(6) /), [3,8])
group_in_lat = matmul(fcc_inv, matmul(ori_inv, group_in_lat/remesh_lat_pam))
do i = 1, 3
bd_in_lat(2*i-1) = nint(minval(group_in_lat(i,:)))
bd_in_lat(2*i) = nint(maxval(group_in_lat(i,:)))
end do
!Once all atoms are added we delete all of the elements
call delete_elements(group_ele_num, element_index)
end select
print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
allocate(lat_points(bd_in_lat(2)-bd_in_lat(1)+10, bd_in_lat(4)-bd_in_lat(3)+10, bd_in_lat(6)-bd_in_lat(5)+10))
lat_points(:,:,:) = .false.
dof = 0
end if
!Remeshing to elements, currently not available
case default
print *, "Remeshing to elements is currently not available. Please refine to atoms by passing a remsh size of 2"
end select
!Now place all group atoms and group interpolated atoms into lat_points
do i = 1, group_atom_num
r = r_atom(:,atom_index(i))/remesh_lat_pam
r = matmul(fcc_inv,matmul(ori_inv,r))
do j = 1, 3
r_lat(j) = nint(r(j))
end do
!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
!This is primarily a debugging statement
if(lat_points(r_lat(1)-bd_in_lat(1)+5,r_lat(2)-bd_in_lat(3)+5,r_lat(3)-bd_in_lat(5)+5)) then
stop "Multiple atoms share same position in lat point array, this shouldn't happen"
else
lat_points(r_lat(1)-bd_in_lat(1)+5, r_lat(2)-bd_in_lat(3)+5, r_lat(3)-bd_in_lat(5)+5) = .true.
dof = dof + 1
end if
end do
!Now place interpolated atoms within lat_points array
do i =1, group_ele_num
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))
r = r_interp(:,j)/remesh_lat_pam
r = matmul(fcc_inv,matmul(ori_inv,r))
do k = 1, 3
r_lat(k) = nint(r(k))
end do
!Do a check to make sure the code is working and that lattice points aren't being written on top of each other.
!This is primarily a debugging statement
if(lat_points(r_lat(1)-bd_in_lat(1)+5,r_lat(2)-bd_in_lat(3)+5,r_lat(3)-bd_in_lat(5)+5)) then
stop "Multiple atoms/interpolated atoms share same position in lat point array, this shouldn't happen"
else
lat_points(r_lat(1)-bd_in_lat(1)+5, r_lat(2)-bd_in_lat(3)+5, r_lat(3)-bd_in_lat(5)+5) = .true.
dof = dof + 1
end if
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
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
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
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 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)
do iy=1, bd_in_array(2)
do ix = 1, bd_in_array(1)
if(lat_points(ix,iy,iz)) then
vlat = (/ ix, iy, iz /)
do i = 1, 3
vlat(i) = vlat(i) + bd_in_lat(2*i-1)-5
end do
lat_points(ix,iy,iz) = .false.
r = matmul(orient, matmul(fcc_mat, vlat))*remesh_lat_pam
call add_atom(remesh_type, sbox_atom(atom_index(1)), r)
end if
end do
end do
end do
print *, "Remeshing has created ", ele_num-old_ele, " elements and ", atom_num-old_atom, " atoms."
end subroutine remesh_group
subroutine delete_group

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