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Fixed the efill option to preserve interelement discontinuities

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development
Alex Selimov 4 years ago
parent c42db27f57
commit dadc1f7a4a
1 changed files with 127 additions and 146 deletions
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273
src/mode_create.f90
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@ -15,7 +15,7 @@ module mode_create
orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), duplicate(3)
integer :: esize, ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
basis_pos(3,10), esize_nums, esize_index(10)
logical :: dup_flag, dim_flag, efill(3)
logical :: dup_flag, dim_flag, efill
real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
integer, allocatable :: elat(:)
@ -46,7 +46,7 @@ module mode_create
basisnum = 0
lat_ele_num = 0
lat_atom_num = 0
efill(:) = .false.
efill = .false.
!First we parse the command
call parse_command(arg_pos)
@ -119,8 +119,8 @@ module mode_create
end do
end do
do i = 1,3
box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**-6.0_dp
box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**-6.0_dp
box_bd(2*i) = maxval(r_node_temp(i,:,:))+10.0_dp**(-6.0_dp)
box_bd(2*i-1) = minval(r_node_temp(i,:,:)) - 10.0_dp**(-6.0_dp)
end do
call add_element(0,element_type, esize, 1, 1, r_node_temp)
end if
@ -265,30 +265,7 @@ module mode_create
end do
case('efill')
call get_command_argument(arg_pos, textholder)
select case(trim(adjustl(textholder)))
case('x')
efill(1) = .true.
case('y')
efill(2) = .true.
case('z')
efill(3) = .true.
case('xy','yx')
efill(1) = .true.
efill(2) = .true.
case('yz','zy')
efill(2) = .true.
efill(3) = .true.
case('xz','zx')
efill(1) = .true.
efill(3) = .true.
case('xyz','xzy','yxz','yzx','zxy','zyx')
efill(:) = .true.
case default
print *, "Error: ", trim(adjustl(textholder)), " is not an acceptable argument for the efill argument"
stop 3
end select
arg_pos = arg_pos + 1
efill=.true.
case default
!If it isn't an option then you have to exit
arg_pos = arg_pos -1
@ -361,11 +338,12 @@ module mode_create
integer, dimension(3,8), intent(in) :: box_in_lat !The box vertices transformed to lattice space
real(kind=dp), dimension(3,3), intent(in) :: transform_matrix !The transformation matrix from lattice_space to real space
!Internal variables
integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), &
vlat(3), temp_lat(3,8), m, n, o, curr_esize, ei
integer :: i, inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz, numlatpoints, ele(3,8), rzero(3), efill_size, &
vlat(3), temp_lat(3,8), m, n, o, j, k, nump_ele, efill_temp_lat(3,8), filzero(3), bd_ele_lat(6),&
efill_ele(3,8), ebd(6)
real(kind=dp) :: v(3), temp_nodes(3,1,8), r(3), centroid_bd(6)
logical, allocatable :: lat_points(:,:,:)
logical :: node_in_bd(8), add
logical :: node_in_bd(8), add, lat_points_ele(esize,esize,esize), intersect_bd(3)
!Do some value initialization
max_esize = esize
@ -374,19 +352,6 @@ module mode_create
centroid_bd(2*i-1) = huge(1.0_dp)
end do
!Now initialize the code if we are doing efill. This means calculate the number of times we can divide the esize in 2 with
!the value still being > 7
if(any(efill)) then
curr_esize=esize
esize_nums=0
do while (curr_esize >= 7)
esize_nums=esize_nums+1
curr_esize = curr_esize -2
end do
else
esize_nums=1
end if
!First find the bounding lattice points (min and max points for the box in each dimension)
numlatpoints = 1
do i = 1, 3
@ -480,117 +445,134 @@ module mode_create
!Now build the finite element region
lat_ele_num = 0
lat_atom_num = 0
curr_esize=esize - 2*(esize_nums-1)
allocate(r_lat(3,8,numlatpoints/curr_esize), elat(numlatpoints/curr_esize))
allocate(r_lat(3,8,numlatpoints/esize), elat(numlatpoints/esize))
curr_esize=esize
do ei = 1, esize_nums
ele(:,:) = (curr_esize-1) * cubic_cell(:,:)
!Redefined the second 3 indices as the number of elements that fit in the bounds
do i = 1, 3
bd_in_array(3+i) = bd_in_array(i)/curr_esize
end do
ele(:,:) = (esize-1) * cubic_cell(:,:)
!Redefined the second 3 indices as the number of elements that fit in the bounds
do i = 1, 3
bd_in_array(3+i) = bd_in_array(i)/esize
end do
!Now start the element at rzero
do inod=1, 8
ele(:,inod) = ele(:,inod) + rzero
end do
do iz = -bd_in_array(6), bd_in_array(6)
do iy = -bd_in_array(5), bd_in_array(5)
do ix = -bd_in_array(4), bd_in_array(4)
node_in_bd(:) = .false.
temp_nodes(:,:,:) = 0.0_dp
temp_lat(:,:) = 0
do inod = 1, 8
vlat= ele(:,inod) + (/ ix*(curr_esize), iy*(curr_esize), iz*(curr_esize) /)
!Transform point back to real space for easier checking
! v = matmul(orient, matmul(transform_matrix,v))
do i = 1,3
v(i) = real(vlat(i) + bd_in_lat(2*i-1) - 5)
end do
temp_nodes(:,1, inod) = matmul(orient, matmul(transform_matrix, v))
temp_lat(:,inod) = vlat
!Check to see if the lattice point values are greater then the array limits
if(any(vlat > shape(lat_points)).or.any(vlat < 1)) then
exit
!If within array boundaries check to see if it is a lattice point
else if(lat_points(vlat(1),vlat(2),vlat(3))) then
node_in_bd(inod) = .true.
else
exit
end if
!Now start the element at rzero
do inod=1, 8
ele(:,inod) = ele(:,inod) + rzero
end do
do iz = -bd_in_array(6), bd_in_array(6)
do iy = -bd_in_array(5), bd_in_array(5)
do ix = -bd_in_array(4), bd_in_array(4)
node_in_bd(:) = .false.
temp_nodes(:,:,:) = 0.0_dp
temp_lat(:,:) = 0
do inod = 1, 8
vlat= ele(:,inod) + (/ ix*(esize), iy*(esize), iz*(esize) /)
!Transform point back to real space for easier checking
! v = matmul(orient, matmul(transform_matrix,v))
do i = 1,3
v(i) = real(vlat(i) + bd_in_lat(2*i-1) - 5)
end do
temp_nodes(:,1, inod) = matmul(orient, matmul(transform_matrix, v))
temp_lat(:,inod) = vlat
!If we are on the first round of element building then we can just add the element if all(node_in_bd) is
!true
if(all(node_in_bd).and.(ei==1)) then
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = curr_esize
!Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
do m = minval(temp_lat(1,:)), maxval(temp_lat(1,:))
lat_points(m,n,o) = .false.
end do
end do
end do
!Check to see if the lattice point values are greater then the array limits
if(any(vlat > shape(lat_points)).or.any(vlat < 1)) then
continue
!If within array boundaries check to see if it is a lattice point
else if(lat_points(vlat(1),vlat(2),vlat(3))) then
node_in_bd(inod) = .true.
end if
end do
!Otherwise we have to also do a box boundary check
else if(all(node_in_bd)) then
r(:) = 0.0_dp
add = .false.
do inod = 1,8
r = r+ temp_nodes(:,1,inod)/8.0_dp
!If we are on the first round of element building then we can just add the element if all(node_in_bd) is
!true
if(all(node_in_bd)) then
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = esize
!Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
do m = minval(temp_lat(1,:)), maxval(temp_lat(1,:))
lat_points(m,n,o) = .false.
end do
end do
end do
!Here we check to make sure the centroid of the element we are adding is outside of the bounds set
!by the centroids of the elements of the initial iteration
!If any nodes are in the boundary and we want to efill then run the efill code
else if(any(node_in_bd).and.efill) then
do i = 1,3
if(efill(i)) then
if((r(i) > centroid_bd(2*i)).or.(r(i) < centroid_bd(2*i-1)))then
add = .true.
exit
end if
end if
end do
if(add) then
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = curr_esize
!Now set all the lattice points contained within an element to false
do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))
do m = minval(temp_lat(1,:)), maxval(temp_lat(1,:))
lat_points(m,n,o) = .false.
end do
end do
end do
!Pull out the section of the lat points array
lat_points_ele(:,:,:)=.false.
do i = 1,3
if (minval(temp_lat(i,:)) <lim_zero) then
bd_ele_lat(2*i-1) = 1
else
bd_ele_lat(2*i-1) = minval(temp_lat(i,:))
end if
end if
end do
if(maxval(temp_lat(i,:))>size(lat_points,i)) then
bd_ele_lat(2*i) = size(temp_lat(i,:))
else
bd_ele_lat(2*i) = maxval(temp_lat(i,:))
end if
end do
lat_points_ele(1:(bd_ele_lat(2)-bd_ele_lat(1)),1:(bd_ele_lat(4)-bd_ele_lat(3)),&
1:(bd_ele_lat(6)-bd_ele_lat(5)))= lat_points(bd_ele_lat(1):bd_ele_lat(2), &
bd_ele_lat(3):bd_ele_lat(4), &
bd_ele_lat(5):bd_ele_lat(6))
!Now start looping through elements and try to fit as many as you can
efill_size = esize-2
i=1
j=1
k=1
nump_ele = count(lat_points_ele)
do i = 1, 3
filzero(i) = bd_ele_lat(2*i-1) -1
end do
do while(efill_size>9)
!First check whether there are enough lattice points to house the current element size
efill_ele=cubic_cell*(efill_size-1)
if (nump_ele < efill_size**3) then
efill_size = efill_size - 2
else
ze: do k = 1, (esize-efill_size)
ye: do j = 1, (esize-efill_size)
xe: do i = 1, (esize-efill_size)
do inod = 1,8
vlat = efill_ele(:,inod) + (/ i, j, k /)
if (.not.lat_points_ele(vlat(1),vlat(2),vlat(3))) cycle xe
do o = 1,3
v(o) = real(vlat(o) + filzero(o) + bd_in_lat(2*o-1) -5)
end do
temp_nodes(:,1, inod) = matmul(orient, matmul(transform_matrix, v))
efill_temp_lat(:,inod) = vlat
end do
do o = 1,3
ebd(2*o-1) = minval(efill_temp_lat(o,:))
ebd(2*o) = maxval(efill_temp_lat(o,:))
end do
lat_ele_num = lat_ele_num+1
r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
elat(lat_ele_num) = efill_size
nump_ele = nump_ele - efill_size**3
!Now set all the lattice points contained within an element to false
do o = ebd(5), ebd(6)
do n = ebd(3), ebd(4)
do m = ebd(1), ebd(2)
lat_points(m+filzero(1),n+filzero(2),o+filzero(3)) = .false.
lat_points_ele(m,n,o) = .false.
end do
end do
end do
end do xe
end do ye
end do ze
efill_size = efill_size-2
end if
end do
end if
end do
end do
curr_esize=curr_esize-2
!If we are running efill code, after the first iteration we have to calculate the min and max element centroids in
!each dimension
if((ei == 1).and.(any(efill))) then
do i = 1, lat_ele_num
!Calculate the current element centroid
r(:) = 0.0_dp
do inod = 1,8
r = r + r_lat(:,inod,i)/8.0_dp
end do
!Check to see if it's a min or max
do o = 1,3
if(r(o) > centroid_bd(2*o)) centroid_bd(2*o) = r(o)
if(r(o) < centroid_bd(2*o-1)) centroid_bd(2*o-1) = r(o)
end do
end do
end if
end do
!Now figure out how many lattice points could not be contained in elements
allocate(r_atom_lat(3,count(lat_points)))
@ -641,6 +623,5 @@ module mode_create
STOP 3
end subroutine error_message
end module mode_create

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