From f92e80f9dbd6ee1fa18592d79822c3adfc103f2d Mon Sep 17 00:00:00 2001
From: Alex Selimov <alex@alexselimov.xyz>
Date: Thu, 19 Nov 2020 13:57:57 -0500
Subject: [PATCH] Added fixes to redef_box and to writing pycac restart files

---
 src/box.f90           | 13 +++++++++----
 src/io.f90            |  7 ++++---
 src/mode_convert.f90  |  3 ++-
 src/mode_merge.f90    |  5 ++---
 src/opt_redef_box.f90 |  5 +++++
 5 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/box.f90 b/src/box.f90
index c179136..9f2c7b2 100644
--- a/src/box.f90
+++ b/src/box.f90
@@ -73,10 +73,15 @@ module box
 
         integer :: i
 
-        do i = 1, 3
-            if(temp_box_bd(2*i-1) < box_bd(2*i-1)) box_bd(2*i-1) = temp_box_bd(2*i-1)
-            if(temp_box_bd(2*i) > box_bd(2*i)) box_bd(2*i) = temp_box_bd(2*i)
-        end do
+        if(all(abs(box_bd) < lim_zero)) then 
+            box_bd = temp_box_bd
+        else
+            do i = 1, 3
+                if(temp_box_bd(2*i-1) < box_bd(2*i-1)) box_bd(2*i-1) = temp_box_bd(2*i-1)
+                if(temp_box_bd(2*i) > box_bd(2*i)) box_bd(2*i) = temp_box_bd(2*i)
+            end do
+        end if
+
         return
     end subroutine grow_box
 
diff --git a/src/io.f90 b/src/io.f90
index b1bd053..95760c9 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -379,7 +379,7 @@ module io
         !NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the 
         !each element has only 1 atom type at the node.
         character(len=100), intent(in) :: file
-        integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_num, &
+        integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_type(50), unique_num, &
                    etype
         real(kind=dp) :: box_vec(3)
 
@@ -426,6 +426,7 @@ module io
                 unique_num = unique_num + 1
                 unique_index(unique_num) = i
                 unique_size(unique_num) = size_ele(i)
+                unique_type(unique_num) = lat_ele(i)
             end do eleloop
 
         !Calculate the max number of atoms per element
@@ -486,7 +487,7 @@ module io
             do i = 1, ele_num
                 !Figure out the ele type
                 do j = 1, unique_num
-                    if ( unique_size(j) == size_ele(i)) then
+                    if ( (unique_size(j) == size_ele(i)).and.(unique_type(j) == lat_ele(i))) then
                         etype = j
                         exit
                     endif
@@ -670,7 +671,7 @@ module io
             temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
             temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
         end do 
-       
+      
         call grow_box(temp_box_bd)
         !Read in the number of sub_boxes and allocate the variables
         read(11, *) n
diff --git a/src/mode_convert.f90 b/src/mode_convert.f90
index 3bb8a3b..eb89994 100644
--- a/src/mode_convert.f90
+++ b/src/mode_convert.f90
@@ -14,6 +14,7 @@ module mode_convert
         character(len=100) :: infile
         real(kind = dp) :: temp_box_bd(6)
         !First read in the file
+        temp_box_bd(:) = 0.0_dp
         call get_command_argument(2, infile)
         call get_in_file(infile)
         call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd)
@@ -21,4 +22,4 @@ module mode_convert
         arg_pos = 3
 
     end subroutine convert
-end module mode_convert
\ No newline at end of file
+end module mode_convert
diff --git a/src/mode_merge.f90 b/src/mode_merge.f90
index afc9bba..242ecd2 100644
--- a/src/mode_merge.f90
+++ b/src/mode_merge.f90
@@ -25,6 +25,7 @@ module mode_merge
         shift_flag = .false.
 
         shift_vec(:) = 0.0_dp
+        temp_box_bd(:) = 0.0_dp
         !First we parse the merge command
         call parse_command(arg_pos)
 
@@ -41,7 +42,6 @@ module mode_merge
 
             if ((i==1).or.(trim(adjustl(dim)) == 'none')) then 
                 call read_in(i, displace, temp_box_bd)
-                call grow_box(temp_box_bd)
             else
                 select case(trim(adjustl(dim)))
                 case('x')
@@ -53,7 +53,6 @@ module mode_merge
                 end select
 
                 call read_in(i, displace, temp_box_bd)
-                call grow_box(temp_box_bd)
             end if 
 
             if(shift_flag) call shift(new_starts, i)
@@ -168,4 +167,4 @@ module mode_merge
         end if
 
     end subroutine shift
-end module mode_merge
\ No newline at end of file
+end module mode_merge
diff --git a/src/opt_redef_box.f90 b/src/opt_redef_box.f90
index 8d0d30f..da86342 100644
--- a/src/opt_redef_box.f90
+++ b/src/opt_redef_box.f90
@@ -20,6 +20,10 @@ module opt_redef_box
         !First parse the argument
         call parse_redef_box(arg_pos)
 
+        print *, '------------------------------------------------------------'
+        print *, 'Option redef_box'
+        print *, '------------------------------------------------------------'
+
         !Now first filter atoms that don't fit in the new box bounds and delete them
         delete_num = 0
         do i = 1, atom_num 
@@ -68,6 +72,7 @@ module opt_redef_box
 
         call delete_elements(delete_num, delete_list(1:delete_num))
 
+        print *, "Old box_bd: ", box_bd, " is redefined to new box boundaries: ", new_bd
         box_bd=new_bd
         box_bc = new_bc