From db8428113d54b888da8f96d5fa32496637600ba7 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alex@alexselimov.xyz>
Date: Thu, 25 Mar 2021 11:40:47 -0400
Subject: [PATCH] Changes to restart file format

---
 src/io.f90 | 35 +++++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/io.f90 b/src/io.f90
index d2ffa21..5472c00 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -241,7 +241,6 @@ module io
 
         open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
         
-        print *, max_basisnum, max_esize
         !Write header information 
         write(11,1) timestep
 
@@ -639,10 +638,10 @@ module io
             infilenum=infilenum+1
             infiles(infilenum) =  temp_infile
         case('out')
-            if(atom_types == 0) then 
-                print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
-                stop 3
-            end if
+!            if(atom_types == 0) then 
+!                print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
+!                stop 3
+!            end if
             select case(trim(adjustl(mode)))
             case('--calc', '--convert','--metric')
                 infilenum = infilenum+1
@@ -968,12 +967,13 @@ module io
         real(kind=dp), dimension(6), intent(out) :: temp_box_bd
 
         !Internal Variables
-        integer :: i, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
-            id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip
+        integer :: i, j, in_eles, in_atoms, inbtypes(10), lat_type, ia, ie, inod, &
+            id, type_node, ilat, esize, tag, type, bnum, n, ibasis, ip, atom_type_map(100)
         real(kind=dp) :: newdisplace(3), ra(3), in_lapa, ea, fa(3), va(6), &
-                         ee(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8)
+                         ee(10,8), fe(3,10,8), ve(6,10,8), re(3,10,8), atomic_masses(10)
         character(len=100) :: textholder, fcc
         character(len=1000) :: line
+        character(len=2) :: atomic_element
 
 
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind') 
@@ -1016,6 +1016,19 @@ module io
             call grow_sub_box(1)
         end if
 
+        !Now read in masses for atoms
+        read(11, '(a)') line
+        j = tok_count(line)
+        read(line, *) textholder, (atomic_masses(i), i=1, j-1)
+
+        !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))
+        end do 
+
+
+
         !Because orientations and other needed sub_box information isn't really 
         !present within the .cac file we just default a lot of it.
         sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
@@ -1028,7 +1041,7 @@ module io
             do ia = 1, in_atoms
                 read(11,'(a)')  line(:)
                 read(line,*) tag, type, ra(:), ea, fa(:), va(:)         
-                call add_atom(tag, type, sub_box_num, ra)
+                call add_atom(tag, atom_type_map(type), sub_box_num, ra)
                 call add_atom_data(atom_num, ea, fa, va)
             end do
 
@@ -1046,6 +1059,9 @@ module io
                 do inod =1, n*bnum
                     read(11,*)  ip, ibasis, inbtypes(ibasis), re(:,ibasis,ip), ee(ibasis,ip), fe(:,ibasis,ip), ve(:,ibasis,ip)
                 end do
+                do i = 1, bnum
+                    inbtypes(ibasis) = atom_type_map(inbtypes(ibasis))
+                end do
                 call lattice_map(bnum, inbtypes, n, 1.0_dp, lat_type)
                 call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
                 call add_element_data(ele_num, ee, fe, ve)
@@ -1276,7 +1292,6 @@ module io
             print *, "Missing lattice parameter for set_input_lat"
         end if
         read(textholder,*) in_lapa
-        print *, in_lapa
 
         arg_pos = arg_pos + 1
         call get_command_argument(arg_pos, textholder, arglen)