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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 5 years ago
parent 975e2b3fc1
commit 9a484c86f6
3 changed files with 137 additions and 48 deletions
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8
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. `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** **Displace**
``` ```

25
src/functions.f90
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@ -155,8 +155,7 @@ END FUNCTION StrDnCase
end function in_bd_lat end function in_bd_lat
function in_block_bd(v, box_bd) 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 !Input/output
real(kind=dp), dimension(3), intent(in) :: v real(kind=dp), dimension(3), intent(in) :: v
real(kind=dp), dimension(6), intent(in) :: box_bd real(kind=dp), dimension(6), intent(in) :: box_bd
@ -180,6 +179,28 @@ END FUNCTION StrDnCase
end do end do
end function in_block_bd 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) function lcm(a,b)
!This function returns the smallest least common multiple of two numbers !This function returns the smallest least common multiple of two numbers

144
src/opt_group.f90
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@ -8,9 +8,9 @@ module opt_group
use box use box
implicit none 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 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 logical :: displace, delete, max_remesh, refine
integer, allocatable :: element_index(:), atom_index(:) integer, allocatable :: element_index(:), atom_index(:)
@ -56,6 +56,7 @@ module opt_group
integer :: i,arglen integer :: i,arglen
character(len=100) :: textholder character(len=100) :: textholder
real(kind=dp) bwidth, wheight
!Parse type and shape command !Parse type and shape command
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
@ -79,10 +80,56 @@ module opt_group
do i= 1, 6 do i= 1, 6
arg_pos = arg_pos + 1 arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen) 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)) call parse_pos(int((i+1)/2), textholder, block_bd(i))
end do 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 case default
print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", & print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
"for accepted group shapes." "for accepted group shapes."
@ -141,53 +188,54 @@ module opt_group
select case(trim(adjustl(shape))) select case(trim(adjustl(shape)))
case('block') case('block')
print *, "Group has block shape with boundaries: ", block_bd 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 variables to arbitrary size
allocate(element_index(1024), atom_index(1024)) allocate(element_index(1024), atom_index(1024))
!Check the type to see whether we need to find the elements within the group !Check the type to see whether we need to find the elements within the group
select case(trim(adjustl(type))) select case(trim(adjustl(type)))
case('elements', 'both') case('elements', 'both')
do i = 1, ele_num do i = 1, ele_num
r_center(:) = 0.0_dp r_center(:) = 0.0_dp
do inod = 1, ng_node(lat_ele(i)) do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(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))) r_center = r_center + r_node(:,ibasis,inod,i)/(basisnum(lat_ele(i))*ng_node(lat_ele(i)))
end do
end do end do
end do
if (in_block_bd(r_center, block_bd)) then if (in_group(r_center)) then
group_ele_num = group_ele_num + 1 group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024)) allocate(resize_array(size(element_index) + 1024))
resize_array(1:group_ele_num-1) = element_index resize_array(1:group_ele_num-1) = element_index
resize_array(group_ele_num:) = 0 resize_array(group_ele_num:) = 0
call move_alloc(resize_array, element_index) call move_alloc(resize_array, element_index)
end if
element_index(group_ele_num) = i
end if end if
end do
end select
!Check the type to see if we need to find the atoms within the group element_index(group_ele_num) = i
select case(trim(adjustl(type))) end if
case('atoms','both') end do
do i = 1, atom_num end select
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
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 if
end do
end select atom_index(group_atom_num) = i
end if
end do
end select end select
print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms." print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
@ -440,4 +488,16 @@ module opt_group
call delete_elements(group_ele_num, element_index) call delete_elements(group_ele_num, element_index)
end subroutine delete_group end subroutine delete_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 end module opt_group
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