Updates to metric and emrge and adding read_lmp

src/Makefile

@@ -3,6 +3,7 @@
 
 FC=mpif90
 FFLAGS=-Wall -mcmodel=large -O0 -g -fbacktrace -fcheck=all -ffpe-trap=invalid,zero,overflow,underflow,denormal 
+FFLAGS=-O2 -mcmodel=large
 
 OBJDIR=obj
 SRCS := $(wildcard *.f90)

src/io.f90

@@ -635,7 +635,7 @@ module io
         end if
 
         select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
-        case('restart', 'mb', 'cac')
+        case('lmp','restart', 'mb', 'cac')
             infilenum=infilenum+1
             infiles(infilenum) =  temp_infile
         case('out')
@@ -673,6 +673,8 @@ module io
             call read_mb(infiles(i), displace, temp_box_bd)
         case('restart')
             call read_pycac(infiles(i), displace, temp_box_bd)
+        case('lmp')
+            call read_lmp(infiles(i), displace, temp_box_bd)
         case('cac')
             call read_lmpcac(infiles(i), displace, temp_box_bd)
         case('out')
@@ -1053,7 +1055,88 @@ module io
         return
     end subroutine
 
+    subroutine read_lmp(file, displace, temp_box_bd)
+        !This subroutine is used to read .cac files which are used with the lammpsCAC format
+        character(len=100), intent(in) :: file
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind = dp), dimension(6), intent(out) :: temp_box_bd
         
+        character(len=100) :: textholder, element_type
+        character(len=2) :: atom_species
+        integer :: i, j, k, atom_in, type_in, type_map(10), in_basis, node_types(10,8), &
+                   lat_type, id 
+        real(kind=dp) :: mass, r_in(3), newdisplace(3)
+        
+        !Open the file
+        open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
+        
+        !Now initialize some important variables if they aren't defined
+        if (max_basisnum==0) max_basisnum = 10
+        if (max_ng_node==0) max_ng_node=8
+
+        !Read header information
+        read(11, *) textholder
+
+        !Read number of elements
+        read(11, *) atom_in, textholder 
+        read(11, *) type_in, textholder
+
+        !Read box_boundaries
+        read(11,*) temp_box_bd(1:2), textholder, textholder
+        read(11,*) temp_box_bd(3:4), textholder, textholder
+        read(11,*) temp_box_bd(5:6), textholder, textholder
+
+        print *, "Read in ", atom_in, " atoms from ", trim(adjustl(file))
+        !Shift the box boundaries if needed
+        do i = 1, 3
+            if (abs(displace(i)) > lim_zero) then 
+                newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
+            else
+                newdisplace(i)=displace(i)
+            end if 
+            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 
+
+        !Grow box boundaries
+        call grow_box(temp_box_bd)
+
+        !Allocate sub_box 
+        if (sub_box_num == 0) then 
+            call alloc_sub_box(1)
+        else
+            call grow_sub_box(1)
+        end if
+
+        !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)
+        sub_box_bd(:, sub_box_num+1) = temp_box_bd
+        sub_box_num = sub_box_num + 1
+
+
+        !Read useless information
+        read(11,*) textholder 
+
+        !Read atomic masses
+        do i = 1, type_in
+            read(11,*) j, mass, textholder
+            call ATOMMASSSPECIES(mass, atom_species) 
+            call add_atom_type(atom_species, type_map(i))
+        end do
+
+        !Read useless info
+        read(11,*) textholder
+
+        !Start the reading loop
+        do i = 1, atom_in
+            read(11,*) id, type_in, r_in(:)
+            call add_atom(id, type_in, sub_box_num, r_in) 
+        end do
+
+        close(11)
+        return
+    end subroutine read_lmp
     
     subroutine read_lmpcac(file, displace, temp_box_bd)
         !This subroutine is used to read .cac files which are used with the lammpsCAC format

src/mode_merge.f90

@@ -58,6 +58,15 @@ module mode_merge
             if(shift_flag) call shift(new_starts, i)
         end do
 
+        !Now reset tags
+        do i = 1, atom_num
+            tag_atom(i) = i
+        end do
+        
+        do i = 1, ele_num
+            tag_ele(i) = i
+        end do
+
         return
     end subroutine merge
 

src/mode_metric.f90

@@ -50,10 +50,12 @@ module mode_metric
         end select
 
         !Now set the reference positions
+        print *, "Combining positions"
         call convert_positions(r_zero, npreal)
 
         !Now calculate the neighbor list for the reference configuration
-        call calc_neighbor(5.0_dp, r_zero, np)
+        print *, "Getting initial neighbor list"
+        call calc_neighbor(rc_off, r_zero, np)
 
         !Reset element and box
         call reset_data
@@ -67,6 +69,7 @@ module mode_metric
                 print *, "Error in mode_metric where number of points in ", i, "th file is ", np_temp, " and number of points in" &
                 // "reference file is", npreal
             end if
+            print *, "Calculating metric for file number ", i
             call calc_metric
             !Now create the output file num and write out to xyz format
             ppos = scan(trim(infiles(i)),".", BACK= .true.)

src/opt_group.f90

@@ -55,11 +55,6 @@ module opt_group
             call refinefill_group
         end if
 
-        if(displace)then 
-            call get_group
-            call displace_group
-        end if
-
         if(delete)then 
             call get_group
             call delete_group
@@ -75,6 +70,10 @@ module opt_group
             call change_group_type
         end if
 
+        if(displace)then 
+            call get_group
+            call displace_group
+        end if
     end subroutine group
 
     subroutine parse_group(arg_pos)