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Added sphere as a possible group shape

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This commit is contained in:
Alex Selimov 2020-06-04 12:13:42 -04:00
parent d01d0b0c57
commit 338587b7b7
2 changed files with 37 additions and 8 deletions
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5
README.md
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@ -218,6 +218,11 @@ This shape is similar to a wedge shape except instead of becoming atomically sha
`bw` - Base width `bw` - Base width
`tr` - Tip radius `tr` - Tip radius
*Sphere*
`-group atoms sphere x y z r`
This shape selects all atoms within a sphere centered at `(x,y,z)` with radius `r`.
**Displace:** **Displace:**
``` ```

38
src/opt_group.f90
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@ -10,7 +10,7 @@ module opt_group
integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2, random_num
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), centroid(3), vertices(3,3),disp_vec(3), tip_radius, bwidth real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), radius, bwidth
logical :: displace, delete, max_remesh, refine, group_nodes, flip logical :: displace, delete, max_remesh, refine, group_nodes, flip
integer, allocatable :: element_index(:), atom_index(:) integer, allocatable :: element_index(:), atom_index(:)
@ -171,7 +171,7 @@ module opt_group
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 tip radius in group notch command" if (arglen==0) STOP "Missing tip radius in group notch command"
read(textholder,*) tip_radius read(textholder,*) radius
!Calculate the vertex positions !Calculate the vertex positions
vertices(:,1) = centroid vertices(:,1) = centroid
@ -201,7 +201,7 @@ module opt_group
!Now update the centroid so that the desire tip diameter matches the wedge with !Now update the centroid so that the desire tip diameter matches the wedge with
if (bwidth > 0) then if (bwidth > 0) then
centroid(dim1) = centroid(dim1) + 2*tip_radius*(H)/bwidth centroid(dim1) = centroid(dim1) + 2*radius*(H)/bwidth
end if end if
!Read the ID type shape for group !Read the ID type shape for group
case('id') case('id')
@ -313,6 +313,21 @@ module opt_group
if(i ==1) arg_pos = arg_pos + 1 if(i ==1) arg_pos = arg_pos + 1
end do end do
end select end select
case('sphere')
!First extract the sphere centroid
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing sphere centroid in group command"
call parse_pos(i, textholder, centroid(i))
end do
!Now get the tip radius
arg_pos=arg_pos+1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing sphere radius in group command"
read(textholder, *) radius
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."
@ -376,11 +391,13 @@ module opt_group
case ('wedge') case ('wedge')
print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
case ('notch') case ('notch')
print *, "Group has notch shape with dim1", dim1, "and dim2", dim2, " tip radius ", tip_radius, "and vertices ", & print *, "Group has notch shape with dim1", dim1, "and dim2", dim2, " tip radius ", radius, "and vertices ", &
vertices vertices
case('id') case('id')
print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms." print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
return return
case('sphere')
print *, "Group has sphere shape with centroid ", centroid(:), " and radius ", radius
end select end select
!Reset group if needed !Reset group if needed
@ -837,7 +854,7 @@ module opt_group
function in_group(r) function in_group(r)
!This subroutine determines if a point is within the group boundaries !This subroutine determines if a point is within the group boundaries
real(kind=dp), intent(in) :: r(3) real(kind=dp), intent(in) :: r(3)
real(kind=dp) :: r_notch real(kind=dp) :: rnorm
integer :: dim3, i integer :: dim3, i
logical :: in_group logical :: in_group
@ -857,9 +874,16 @@ module opt_group
if (r(dim1) < centroid(dim1)) in_group = .false. if (r(dim1) < centroid(dim1)) in_group = .false.
end if end if
r_notch = sqrt((r(dim1) - centroid(dim1))**2 + (r(dim3)-centroid(dim3))**2) rnorm = sqrt((r(dim1) - centroid(dim1))**2 + (r(dim3)-centroid(dim3))**2)
in_group = in_group.or.(r_notch < tip_radius) in_group = in_group.or.(rnorm < radius)
case('sphere')
rnorm = norm2(r(:) - centroid(:))
if (rnorm <= radius) then
in_group = .true.
else
in_group = .false.
end if
end select end select
end function in_group end function in_group
end module opt_group end module opt_group