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Add wedge group shape option to opt_group.f90, update the documentation, and add the relevant functions to functions.f90

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master
Alex Selimov 4 years ago
parent 975e2b3fc1
commit 9a484c86f6
3 changed files with 137 additions and 48 deletions
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10
README.md
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@ -203,6 +203,14 @@ This selects a group residing in a block with edges perpendicular to the simulat
`additional keywords`- Represents the various transformations which can be performed on a group. These additional keywords are given below.
*Wedge*
`-group nodes wedge dim1 dim2 bx by bz bw`
This selects a group which are within a wedge shape. The options are given as follows:
`dim1` - The dimension containing the plane normal of the wedge base.
`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
`bx by bz` - Centroid of the center of the base
`bw` - Base width
**Displace**
```
@ -323,4 +331,4 @@ Face 6: [5,6,7,8]
Image for vertex numbers is:
![](/home/alexselimov/Documents/CACmb/Numbered_element.png)
![](/home/alexselimov/Documents/CACmb/Numbered_element.png)

25
src/functions.f90
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@ -155,8 +155,7 @@ END FUNCTION StrDnCase
end function in_bd_lat
function in_block_bd(v, box_bd)
!This function returns whether a point is within a block in 3d
!This function determines whether a point is within a block in 3d
!Input/output
real(kind=dp), dimension(3), intent(in) :: v
real(kind=dp), dimension(6), intent(in) :: box_bd
@ -180,6 +179,28 @@ END FUNCTION StrDnCase
end do
end function in_block_bd
function in_wedge_bd(r,vertex)
!This code determines whether the 2dimensional projection of a point lies within the 2 dimensional projection of a wedge.
real(kind=dp), intent(in) :: r(3) !This is the point position
real(kind=dp), intent(in) :: vertex(3,3) !These are the relevant vertex positions for the wedge
real(kind=dp) :: v1(3), v2(3), v3(3), c1(3), c2(3) !Vertex vector to point and cross products
integer :: i
logical :: in_wedge_bd
in_wedge_bd = .true.
do i = 1, 3
v1 = vertex(:,mod(i,3)+1) - vertex(:,i)
v2 = r - vertex(:,i)
v3 = vertex(:,mod(i+1,3)+1) - vertex(:,i)
c1 = cross_product(v1,v2)
c2 = cross_product(v1,v3)
if(dot_product(c1,c2) < 0) then
in_wedge_bd=.false.
exit
end if
end do
end function in_wedge_bd
function lcm(a,b)
!This function returns the smallest least common multiple of two numbers

150
src/opt_group.f90
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@ -8,9 +8,9 @@ module opt_group
use box
implicit none
integer :: group_ele_num, group_atom_num, remesh_size, remesh_type
integer :: group_ele_num, group_atom_num, remesh_size,normal, remesh_type, dim1, dim2
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), remesh_lat_pam
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), remesh_lat_pam
logical :: displace, delete, max_remesh, refine
integer, allocatable :: element_index(:), atom_index(:)
@ -56,6 +56,7 @@ module opt_group
integer :: i,arglen
character(len=100) :: textholder
real(kind=dp) bwidth, wheight
!Parse type and shape command
arg_pos = arg_pos + 1
@ -79,10 +80,56 @@ module opt_group
do i= 1, 6
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing block boundary in dislgen command"
if (arglen==0) STOP "Missing block boundary in group command"
call parse_pos(int((i+1)/2), textholder, block_bd(i))
end do
case('wedge')
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing normal dim in group wedge command"
read(textholder,*) dim1
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing normal dim in group wedge command"
read(textholder,*) dim2
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing centroid in group wedge command"
call parse_pos(i, textholder, centroid(i))
end do
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing base width in group wedge command"
read(textholder,*) bwidth
!Calculate the vertex positions
vertices(:,1) = centroid
vertices(dim2,1) = 0.0_dp
do i = 1, 3
if (i == dim1) then
if (bwidth > 0) then
vertices(i,2) = box_bd(2*i)
vertices(i,3) = box_bd(2*i)
else if (bwidth < 0) then
vertices(i,2) = box_bd(2*i-1)
vertices(i,3) = box_bd(2*i-1)
else
print *, "bwidth cannot be 0 in wedge shaped group"
stop 3
end if
else if (i == dim2) then
vertices(i,2) = 0.0_dp
vertices(i,3) = 0.0_dp
else
vertices(i,2) = centroid(i) + bwidth
vertices(i,3) = centroid(i) - bwidth
end if
end do
case default
print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
"for accepted group shapes."
@ -141,54 +188,55 @@ module opt_group
select case(trim(adjustl(shape)))
case('block')
print *, "Group has block shape with boundaries: ", block_bd
case ('crack')
print *, "Group has crack shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
end select
!Allocate variables to arbitrary size
allocate(element_index(1024), atom_index(1024))
!Check the type to see whether we need to find the elements within the group
select case(trim(adjustl(type)))
case('elements', 'both')
do i = 1, ele_num
r_center(:) = 0.0_dp
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
end do
!Allocate variables to arbitrary size
allocate(element_index(1024), atom_index(1024))
!Check the type to see whether we need to find the elements within the group
select case(trim(adjustl(type)))
case('elements', 'both')
do i = 1, ele_num
r_center(:) = 0.0_dp
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
end do
end do
if (in_block_bd(r_center, block_bd)) then
group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024))
resize_array(1:group_ele_num-1) = element_index
resize_array(group_ele_num:) = 0
call move_alloc(resize_array, element_index)
end if
element_index(group_ele_num) = i
end if
end do
end select
if (in_group(r_center)) then
group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024))
resize_array(1:group_ele_num-1) = element_index
resize_array(group_ele_num:) = 0
call move_alloc(resize_array, element_index)
end if
!Check the type to see if we need to find the atoms within the group
select case(trim(adjustl(type)))
case('atoms','both')
do i = 1, atom_num
if(in_block_bd(r_atom(:,i),block_bd)) then
group_atom_num = group_atom_num + 1
if (group_atom_num > size(atom_index)) then
allocate(resize_array(size(atom_index) + 1024))
resize_array(1:group_atom_num -1) = atom_index
resize_array(group_atom_num:) = 0
call move_alloc(resize_array, atom_index)
end if
element_index(group_ele_num) = i
end if
end do
end select
atom_index(group_atom_num) = i
!Check the type to see if we need to find the atoms within the group
select case(trim(adjustl(type)))
case('atoms','both')
do i = 1, atom_num
if(in_group(r_atom(:,i))) then
group_atom_num = group_atom_num + 1
if (group_atom_num > size(atom_index)) then
allocate(resize_array(size(atom_index) + 1024))
resize_array(1:group_atom_num -1) = atom_index
resize_array(group_atom_num:) = 0
call move_alloc(resize_array, atom_index)
end if
end do
end select
end select
atom_index(group_atom_num) = i
end if
end do
end select
print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
end subroutine get_group
@ -440,4 +488,16 @@ module opt_group
call delete_elements(group_ele_num, element_index)
end subroutine delete_group
end module opt_group
function in_group(r)
!This subroutine determines if a point is within the group boundaries
real(kind=dp), intent(in) :: r(3)
logical :: in_group
select case(trim(adjustl(shape)))
case('block')
in_group=in_block_bd(r,block_bd)
case('wedge')
in_group = in_wedge_bd(r,vertices)
end select
end function in_group
end module opt_group

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