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Added flip option to group to invert group selection

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This commit is contained in:
Alex Selimov 2020-05-27 14:53:44 -04:00
parent 43025d0b67
commit 65c2b380cd
2 changed files with 26 additions and 9 deletions
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24
README.md
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@ -185,15 +185,15 @@ This option creates a circular planar vacancy cluster of radius `radius` normal
`-group select_type group_shape shape_arguments additional keywords`
This option selects a group of either elements, nodes, atoms and applies some transformation to them.
This option selects a group of either elements or atoms and applies some transformation to them.
`select_type` - Either `nodes`, `atoms`, `elements`, `nodes/atoms`, `all`. When using the option `nodes` only nodes which are within the group are selected, `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group. `all` selects elements based on the element center and atoms based on their position.
`select_type` - Either `atoms`, `elements`, or 'both'. `elements` selects elements based on whether the element center is within the group. `both` selects elements based on the element center and atoms based on their position.
`group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
*Block:*
`-group nodes block xlo xhi ylo yhi zlo zhi`
`-group atoms block xlo xhi ylo yhi zlo zhi`
This selects a group residing in a block with edges perpendicular to the simulation cell. The block boundaries are given by `xlo xhi ylo yhi zlo zhi`.
@ -201,7 +201,7 @@ This selects a group residing in a block with edges perpendicular to the simulat
*Wedge:*
`-group nodes wedge dim1 dim2 bx by bz bw`
`-group atoms 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.
@ -210,7 +210,7 @@ This selects a group which are within a wedge shape. The options are given as fo
*Notch:*
`-group nodes notch dim1 dim2 bx by bz bw tr`
`-group atoms notch dim1 dim2 bx by bz bw tr`
This shape is similar to a wedge shape except instead of becoming atomically sharp, it finishes in a rounded tip with tip radius `tr`. Options are 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.
@ -266,7 +266,21 @@ random n
This command selects `n` random atoms and `n` random elements within your group bounds. If using group type `atoms` or `elements` then only `n` random atoms or elements are selected. This random atoms/elements then form the new group.
**Nodes**
```
nodes
```
This keyword changes the selection criteria when using `elements` or `both` to element nodes instead of element centroids.
**Flip**
```
flip
```
This keyword changes the group selection criteria from the atoms/elements inside a region to the atoms/elements outside the group.
### Option overwrite
```

11
src/opt_group.f90
View File

@ -11,7 +11,7 @@ module opt_group
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
real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), tip_radius, bwidth
logical :: displace, delete, max_remesh, refine, group_nodes
logical :: displace, delete, max_remesh, refine, group_nodes, flip
integer, allocatable :: element_index(:), atom_index(:)
@ -32,6 +32,7 @@ module opt_group
delete=.false.
max_remesh=.false.
refine = .false.
flip = .false.
if(allocated(element_index)) deallocate(element_index)
if(allocated(atom_index)) deallocate(atom_index)
@ -353,6 +354,8 @@ module opt_group
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) stop "Missing number of random atoms in group command"
read(textholder, *) random_num
case('flip')
flip=.true.
case default
!If it isn't an available option to opt_disl then we just exit
exit
@ -398,7 +401,7 @@ module opt_group
end do
end do
if (in_group(r_center)) then
if (in_group(r_center).neqv.flip) then
group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024))
@ -416,7 +419,7 @@ module opt_group
r_center(:) = 0.0_dp
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
if (in_group(r_node(:,ibasis,inod,i))) then
if (in_group(r_node(:,ibasis,inod,i)).neqv.flip) then
group_ele_num = group_ele_num + 1
if(group_ele_num > size(element_index)) then
allocate(resize_array(size(element_index) + 1024))
@ -451,7 +454,7 @@ module opt_group
select case(trim(adjustl(type)))
case('atoms','both')
do i = 1, atom_num
if(in_group(r_atom(:,i))) then
if(in_group(r_atom(:,i)).neqv.flip) then
group_atom_num = group_atom_num + 1
if (group_atom_num > size(atom_index)) then
allocate(resize_array(size(atom_index) + 1024))