From 2ea388b82ad3c49ab5cb0c7c7e5699e68369fb4c Mon Sep 17 00:00:00 2001
From: Alex Selimov <alex@alexselimov.xyz>
Date: Fri, 23 Oct 2020 11:37:28 -0400
Subject: [PATCH] Current working changes with some updates to comments for
 accuracy

---
 src/elements.f90    |  5 ++---
 src/mode_metric.f90 | 18 ++++++++++--------
 src/opt_disl.f90    |  1 -
 src/opt_group.f90   |  2 +-
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/elements.f90 b/src/elements.f90
index 1254a43..226eb60 100644
--- a/src/elements.f90
+++ b/src/elements.f90
@@ -501,6 +501,7 @@ module elements
         !We go from largest index to smallest index just to make sure that we don't miss 
         !accidentally overwrite values which need to be deleted
         do i = num, 1, -1
+            node_num = node_num - ng_node(lat_ele(sorted_index(i)))
             if(sorted_index(i) == ele_num) then 
                 r_node(:,:,:,sorted_index(i)) = 0.0_dp
                 type_ele(sorted_index(i)) =''
@@ -509,7 +510,6 @@ module elements
                 sbox_ele(sorted_index(i)) = 0
                 tag_ele(sorted_index(i)) = 0
             else
-                node_num = node_num - ng_node(lat_ele(sorted_index(i)))
                 r_node(:,:,:,sorted_index(i)) = r_node(:,:,:,ele_num)
                 type_ele(sorted_index(i)) = type_ele(ele_num)
                 size_ele(sorted_index(i)) = size_ele(ele_num)
@@ -538,8 +538,7 @@ module elements
 
         max_bd(:) = -huge(1.0_dp)
         min_bd(:) = huge(1.0_dp)
-
-        do i = 1, atom_num
+do i = 1, atom_num
             do j = 1, 3
                 if (r_atom(j,i) > max_bd(j)) max_bd(j) = r_atom(j,i) + tol 
                 if (r_atom(j,i) < min_bd(j)) min_bd(j) = r_atom(j,i) - tol 
diff --git a/src/mode_metric.f90 b/src/mode_metric.f90
index 279e710..10838c6 100644
--- a/src/mode_metric.f90
+++ b/src/mode_metric.f90
@@ -10,11 +10,11 @@ module mode_metric
     
     integer :: nfiles
     character(len=100) :: metric_type
-    real(kind=dp), allocatable :: met(:,:)
+    real(kind=dp) :: rc_off
 
     !Save reference positions
     integer :: np, npreal, nmet
-    real(kind=dp), allocatable :: r_zero(:,:), r_curr(:,:)
+    real(kind=dp), allocatable :: r_zero(:,:), r_curr(:,:), met(:,:)
 
     public 
     contains
@@ -37,7 +37,6 @@ module mode_metric
         !Now read the first file 
         call read_in(1, (/ 0.0_dp, 0.0_dp, 0.0_dp /), temp_box_bd)
         np = atom_num + max_basisnum*max_ng_node*ele_num
-        print *,np 
         allocate(r_zero(3,atom_num+max_basisnum*max_ng_node*ele_num), &
                  r_curr(3,atom_num+max_basisnum*max_ng_node*ele_num)) 
         r_zero(:,:) = -huge(1.0_dp)
@@ -101,18 +100,23 @@ module mode_metric
             stop 3
         end select
 
+        !Now read the cutoff radius
+        call get_command_argument(3,textholder,arglen)
+        if (arglen == 0) stop "Incomplete mode metric command, check documentation"
+        read(textholder, *) rc_off
+
         !Now read the number of files to read and allocate the variables
-        call get_command_argument(3, textholder, arglen)
+        call get_command_argument(4, textholder, arglen)
         if (arglen == 0) stop "Incomplete mode metric command, check documentation"
         read(textholder, *) nfiles
 
         !Now read the files to be read 
         do i = 1, nfiles
-            call get_command_argument(3+i, textholder, arglen)
+            call get_command_argument(4+i, textholder, arglen)
             call get_in_file(textholder)
         end do 
 
-        arg_pos = 4+nfiles
+        arg_pos = 5+nfiles
         return
     end subroutine parse_command
 
@@ -184,8 +188,6 @@ module mode_metric
         integer :: i, inod, ibasis
 
         npoints=0
-        print *, atom_num + max_ng_node*max_basisnum*ele_num 
-        print *, rout(:,1) 
 
         if(atom_num > 0) then 
             do i = 1, atom_num
diff --git a/src/opt_disl.f90 b/src/opt_disl.f90
index 19f8ed8..dc0e72c 100644
--- a/src/opt_disl.f90
+++ b/src/opt_disl.f90
@@ -561,7 +561,6 @@ module opt_disl
         !Now reset the list for the scanning algorithm
 
         delete_num = 0
-        !Now scan over all atoms again and find the closest vloop_size number of atoms to the initial atom 
         !that reside on the same plane. If loop_radius is > 0 then we build a circular vacancy cluster
         if(loop_radius > 0) then 
             do i = 1, atom_num
diff --git a/src/opt_group.f90 b/src/opt_group.f90
index 855e04e..33cf685 100644
--- a/src/opt_group.f90
+++ b/src/opt_group.f90
@@ -87,7 +87,7 @@ module opt_group
             continue
         case default
             print *, "Select_type ", trim(adjustl(type)), " is not an accept group selection criteria. ", &
-                     "Please select from atoms, nodes, or both."
+                     "Please select from atoms, elements, or both."
         end select
 
         arg_pos = arg_pos + 1