Added random option which can be used to create vacancy fields

README.md

@@ -258,6 +258,15 @@ delete
 
 This command deletes all selected atoms and elements within the group.
 
+
+**Random**
+```
+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.
+
+
 ### Option overwrite 
 
 ```

src/opt_group.f90

@@ -8,7 +8,7 @@ module opt_group
     use box 
     implicit none
 
-    integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2
+    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
@@ -27,6 +27,7 @@ module opt_group
         group_ele_num = 0
         group_atom_num = 0
         remesh_size=0
+        random_num=0
         displace=.false.
         delete=.false.
         max_remesh=.false.
@@ -347,6 +348,11 @@ module opt_group
                 delete=.true.
             case('nodes')
                 group_nodes=.true.
+            case('random')
+                arg_pos = arg_pos + 1
+                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 default
                 !If it isn't an available option to opt_disl then we just exit
                 exit 
@@ -357,15 +363,18 @@ module opt_group
     subroutine get_group
         !This subroutine finds all elements and/or atoms within the group boundaries
         !specified by the user.
-        integer :: i, j, inod, ibasis
+        integer :: i, j, inod, ibasis, temp
         integer, allocatable :: resize_array(:) 
-        real(kind=dp) :: r_center(3)
+        real(kind=dp) :: r_center(3), rand
 
         select case(trim(adjustl(shape)))
         case('block')
             print *, "Group has block shape with boundaries: ", block_bd
         case ('wedge')
             print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
+        case ('notch')
+            print *, "Group has notch shape with dim1", dim1, "and dim2", dim2, " tip radius ", tip_radius,  "and vertices ", &
+                      vertices
         case('id')
             print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
             return
@@ -401,6 +410,7 @@ module opt_group
                         element_index(group_ele_num) = i
                     end if 
                 end do 
+
             else if(group_nodes) then 
                 eleloop:do i = 1, ele_num
                     r_center(:) = 0.0_dp
@@ -421,6 +431,21 @@ module opt_group
                     end do
                 end do eleloop
             end if
+
+            if(random_num > 0) then 
+                !If we have the random option enabled then we select random_num number of elements from the group and overwrite 
+                !the group with those elements
+                do i = 1, random_num
+                    call random_number(rand)
+                    j = i + floor((group_ele_num+1-i)*rand)
+                    temp = element_index(j)
+                    element_index(j) = element_index(i)
+                    element_index(i) = temp
+                end do
+
+                group_ele_num = random_num
+            end if
+
         end select
                 !Check the type to see if we need to find the atoms within the group
         select case(trim(adjustl(type)))
@@ -438,6 +463,19 @@ module opt_group
                     atom_index(group_atom_num) = i
                 end if
             end do
+            if(random_num > 0) then 
+                !If we have the random option enabled then we select random_num number of atom from the group and overwrite 
+                !the group with those atom
+                do i = 1, random_num
+                    call random_number(rand)
+                    j = i + floor((group_atom_num+1-i)*rand)
+                    temp = atom_index(j)
+                    atom_index(j) = atom_index(i)
+                    atom_index(i) = temp
+                end do
+
+                group_atom_num = random_num
+            end if
         end select
         
         j = 0