Added flip option to group to invert group selection

README.md

@@ -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 
 
 ```

src/opt_group.f90

@@ -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))