From 612cea3891460e07460e4c35f184dac9801ecc47 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alex@alexselimov.xyz>
Date: Wed, 9 Mar 2022 14:11:03 -0500
Subject: [PATCH] Fix group implementation to abide by new atom type
 formulation

---
 src/opt_group.f90 | 23 +++++++++--------------
 1 file changed, 9 insertions(+), 14 deletions(-)

diff --git a/src/opt_group.f90 b/src/opt_group.f90
index 776d161..58b81bb 100644
--- a/src/opt_group.f90
+++ b/src/opt_group.f90
@@ -2,6 +2,7 @@ module opt_group
 
     !This module contains all code associated with dislocations
 
+    use atoms
     use parameters
     use elements
     use subroutines
@@ -106,7 +107,7 @@ module opt_group
 
         integer :: i, j, arglen, in_num
         character(len=100) :: textholder, type_spec
-        real(kind=dp)  H
+        real(kind=dp)  H, mass
 
         !Parse type and shape command
         arg_pos = arg_pos + 1
@@ -493,7 +494,8 @@ module opt_group
                 arg_pos = arg_pos + 1
                 call get_command_argument(arg_pos, textholder, arglen)
                 if (arglen==0) stop "Missing atom type for group"
-                call add_atom_type(textholder, group_type)
+                call atommass(textholder, mass)
+                call add_atom_type(mass, group_type)
             case('notsize')
                 arg_pos = arg_pos + 1
                 call get_command_argument(arg_pos, textholder, arglen)
@@ -521,7 +523,8 @@ module opt_group
                 arg_pos=arg_pos+1
                 call get_command_argument(arg_pos, textholder, arglen)
                 if (arglen==0) stop "Missing element type for insert command"
-                call add_atom_type(textholder, insert_type)
+                call atommass(textholder, mass)
+                call add_atom_type(mass, insert_type)
                 arg_pos=arg_pos + 1 
                 call get_command_argument(arg_pos, textholder, arglen)
                 select case(trim(adjustl(textholder)))
@@ -643,15 +646,6 @@ module opt_group
             end if
         end select
         
-        j = 0
-        do i = 1, group_atom_num
-            if (atom_index(i) == 23318348) then
-                j = j + 1
-            end if
-        end do  
-
-        if (j > 1) stop "Code broken"
-
         print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
     end subroutine get_group 
 
@@ -1193,7 +1187,7 @@ module opt_group
     subroutine alloy_group
         !This subroutine randomizes the atom types to reach desired concentrations, this only operates on atoms
         integer :: i, j, ia, type_map(10), added_types(num_species)
-        real(kind=dp) ::  rand
+        real(kind=dp) ::  rand, mass
 
 
         print *, "Alloying group with desired fractions", s_fractions(1:num_species)
@@ -1203,7 +1197,8 @@ module opt_group
 
         !Now get the atom type maps for all the atoms and make the fractions a running sum
         do i = 1, num_species
-            call add_atom_type(species_type(i), type_map(i))
+            call atommass(species_type(i), mass)
+            call add_atom_type(mass, type_map(i))
             if(i > 1) s_fractions(i) = s_fractions(i) + s_fractions(i-1)
         end do
         !Now randomize the atom types