Add all new option

src/caller.f90

@@ -64,6 +64,8 @@ module caller
             arg_pos = arg_pos + 1
         case('-norefine')
             arg_pos = arg_pos + 1
+        case('all_new')
+            arg_pos = arg_pos + 1
         case('-orient')
             call orient_opt(arg_pos)
         case('-unorient')

src/elements.f90

@@ -332,22 +332,32 @@ module elements
 
     end subroutine add_atom
 
-    subroutine add_atom_type(type, inttype)
+    subroutine add_atom_type(type, inttype, force_new)
         !This subroutine adds a new atom type to the module list of atom types
         character(len=2), intent(in) :: type
         integer, intent(out) :: inttype
 
+        logical, optional, intent(in) :: force_new
+
         integer :: i
-        logical :: exists
+        logical :: exists, force
         
+        if(present(force_new)) then 
+            force = force_new
+        else 
+            force = .false.
+        end if
+
         exists = .false.
-        do i=1, 10
-            if(type == type_to_name(i)) then 
-                exists = .true.
-                inttype = i
-                exit
-            end if
-        end do 
+        if(.not.force) then 
+            do i=1, 10
+                if(type == type_to_name(i)) then 
+                    exists = .true.
+                    inttype = i
+                    exit
+                end if
+            end do 
+        end if
 
         if (exists.eqv..false.) then 
             atom_types = atom_types+1

src/io.f90

@@ -10,7 +10,7 @@ module io
 
     integer :: outfilenum = 0, infilenum = 0
     character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
-    logical :: force_overwrite, norefine
+    logical :: force_overwrite, norefine, all_new
     real(kind=dp) :: in_lapa=0.0
    public 
    contains
@@ -772,7 +772,7 @@ module io
         !Now fit these into the global list of atom types, after this new_type_to_type is the actual global 
         !type of the atoms within this file
         do i = 1, new_atom_types
-            call add_atom_type(new_type_to_name(i), new_type_to_type(i))
+            call add_atom_type(new_type_to_name(i), new_type_to_type(i), all_new)
         end do
         !Read the number of lattice types, basisnum, and number of nodes for each lattice type
         read(11,*) new_lattice_types, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
@@ -903,7 +903,7 @@ module io
         print *, j
         do i = 1, j
             call atommassspecies(atomic_masses(i), atomic_element)
-            call add_atom_type(atomic_element, atom_type_map(i))
+            call add_atom_type(atomic_element, atom_type_map(i), all_new)
             print *, i, atom_type_map(i)
         end do 
 
@@ -1057,7 +1057,7 @@ module io
         !Read define atom_types by mass
         do i = 1, j
             call atommassspecies(atomic_masses(i), atomic_element)
-            call add_atom_type(atomic_element, atom_type_map(i))
+            call add_atom_type(atomic_element, atom_type_map(i), all_new)
         end do 
 
 
@@ -1171,7 +1171,7 @@ module io
         do i = 1, type_in
             read(11,*) j, mass
             call ATOMMASSSPECIES(mass, atom_species) 
-            call add_atom_type(atom_species, type_map(i))
+            call add_atom_type(atom_species, type_map(i), all_new)
         end do
 
         !Read useless info
@@ -1259,7 +1259,7 @@ module io
         do i = 1, type_in
             read(11,*) j, mass, textholder
             call ATOMMASSSPECIES(mass, atom_species) 
-            call add_atom_type(atom_species, type_map(i))
+            call add_atom_type(atom_species, type_map(i), all_new)
         end do
 
         !Read useless info

src/main.f90

@@ -42,6 +42,7 @@ program main
     force_overwrite=.false.
     norefine=.false.
     wrap_flag = .false.
+    all_new = .false.
 
     end_mode_arg = 0
     
@@ -70,6 +71,8 @@ program main
             call set_cac(i)
         case('-set_types')
             call set_types(i)
+        case('-all_new')
+            all_new=.true.
         end select 
     end do 
     !Determine if a mode is being used and what it is. The first argument has to be the mode