Add group shape id

src/opt_group.f90

@@ -54,8 +54,8 @@ module opt_group
         !Parse the group command
         integer, intent(inout) :: arg_pos
 
-        integer :: i,arglen
+        integer :: i, j, arglen, in_num
-        character(len=100) :: textholder
+        character(len=100) :: textholder, type_spec
         real(kind=dp) bwidth, wheight
 
         !Parse type and shape command
@@ -130,6 +130,117 @@ module opt_group
                     vertices(i,3) = centroid(i) - bwidth
                 end if
             end do 
+
+        !Read the ID type shape for group 
+        case('id')
+            arg_pos = arg_pos + 1
+            !For this type we have to call different options if type is atoms, elements, or both. Both is the most complex.
+            select case(trim(adjustl(type)))
+            case('atoms')
+                !Read number of ids
+                call get_command_argument(arg_pos, textholder, arglen)
+                if(arglen == 0) then 
+                    print *, "Missing number of input atoms for group id"
+                end if
+                read(textholder,*) in_num
+                
+                !allocate arrays
+                allocate(atom_index(in_num))
+                !Read ids
+                do i = 1, in_num
+                    arg_pos = arg_pos + 1
+                    call get_command_argument(arg_pos, textholder, arglen)
+                    if(arglen == 0) then 
+                        print *, "Missing atom id in group atom id"
+                        stop 3
+                    end if 
+                    read(textholder,*) atom_index(i)
+                end do 
+                group_atom_num = in_num
+
+            case('elements')
+                !Read number of ids
+                 call get_command_argument(arg_pos, textholder, arglen)
+                if(arglen == 0) then 
+                    print *, "Missing number of input elements for group id"
+                end if
+                read(textholder, *) in_num
+
+                !allocate arrays
+                allocate(element_index(in_num))
+                !Read ids
+                do i = 1, in_num
+                    arg_pos = arg_pos + 1
+                    call get_command_argument(arg_pos, textholder, arglen)
+                    if(arglen == 0) then 
+                        print *, "Missing element id in group element id"
+                        stop 3
+                    end if 
+                    read(textholder,*) element_index(i)
+                end do 
+                group_ele_num = in_num
+
+            case('both')
+                !We repeat this code twice, once for the atoms and once for the elements
+                allocate(element_index(1024),atom_index(1024))
+                do i = 1, 2
+                    !Read the first id type (either atoms or elements)
+                    call get_command_argument(arg_pos, type_spec, arglen)
+                    if (arglen == 0) then
+                        print *, "Missing type specifier in group id command"
+                        stop 3
+                    end if
+                    
+                    !Now read the first in_num
+                    arg_pos = arg_pos + 1
+                    call get_command_argument(arg_pos, textholder, arglen)
+                    if(arglen == 0) then 
+                        print *, "Missing input number in group_id"
+                        stop 3 
+                    end if
+                    read(textholder, *) in_num
+
+                    select case(trim(adjustl(type_spec)))
+                    case('atoms','atom')
+                        if (group_atom_num > 0) then
+                            print *, "Atoms specifier used more than once in group id command with type both, either use type ", &
+                                     "atoms or include elements identifier"
+                            stop 3
+
+                            do j = 1, in_num
+                                arg_pos = arg_pos + 1
+                                call get_command_argument(arg_pos, textholder, arglen)
+                                if (arglen == 0) then 
+                                    print *, "Missing atom id in group atom id"
+                                    stop 3
+                                end if
+                                read(textholder, *) atom_index(j)
+                            end do
+                            group_atom_num = in_num
+                        end if
+
+                    case('elements','element')
+                        if (group_ele_num > 0) then
+                            print *, "Elements specifier used more than once in group id command with type both, either use type ", &
+                                     "elements or include atoms identifier"
+                            stop 3
+
+                            do j = 1, in_num
+                                arg_pos = arg_pos + 1
+                                call get_command_argument(arg_pos, textholder, arglen)
+                                if (arglen == 0) then 
+                                    print *, "Missing element id in group element id"
+                                    stop 3
+                                end if
+                                read(textholder, *) element_index(j)
+                            end do
+                            group_ele_num = in_num
+                        end if
+
+                    end select
+                    if(i ==1) arg_pos = arg_pos + 1
+                end do
+            end select
         case default
             print *, "Group shape ", trim(adjustl(shape)), " is not currently accepted. Please check documentation ", &
                      "for accepted group shapes."
@@ -183,6 +294,9 @@ module opt_group
             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
+        case('id')
+            print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
+            return
         end select
 
         !Allocate variables to arbitrary size
@@ -274,7 +388,6 @@ module opt_group
         real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
 
         !Refining to atoms
-
         if(group_ele_num > 0) then 
             orig_atom_num = atom_num
             !Estimate number of atoms we are adding, this doesn't have to be exact