Added delete option with delete overlap command

src/Makefile

@@ -1,8 +1,8 @@
 FC=ifort
-FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
-#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin
+FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
+#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
 MODES=mode_create.o mode_merge.o mode_convert.o
-OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o
+OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o 
 OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o  $(MODES) $(OPTIONS) call_option.o
 
 .SUFFIXES:

src/opt_delete.f90

@@ -21,6 +21,8 @@ module opt_delete
 
         call parse_delete(arg_pos)
 
+        print *, atom_num
+
         if (rc_off > 0.0_dp) call delete_overlap
     end subroutine run_delete
 
@@ -41,7 +43,6 @@ module opt_delete
                 arg_pos=arg_pos + 1
                 call get_command_argument(arg_pos, textholder, arg_len)
                 if(arg_len==0) stop "Missing argument to delete overlap command"
-                print *, textholder
                 read(textholder, *) rc_off
             case default
                 print *, "Command ", trim(adjustl(textholder)), " is not accepted for option delete"
@@ -57,12 +58,17 @@ module opt_delete
 
         integer :: i, c(3), ci, cj, ck, num_nei, nei, delete_num
         integer, dimension(atom_num) :: for_delete
-        integer, dimension(3,atom_num) :: which_cell
 
         !These are the variables containing the cell list information
         integer, dimension(3) :: cell_num
-        integer, allocatable :: num_in_cell(:,:,:)
+        integer, allocatable :: num_in_cell(:,:,:), which_cell(:,:)
         integer, allocatable :: cell_list(:,:,:,:)
+        
+        allocate(which_cell(3,atom_num))
+
+        print *, atom_num
+        print *, for_delete(atom_num)
+        print *, which_cell(1,1)
 
         !First pass the atom list and atom num to the algorithm which builds the cell list
         call build_cell_list(atom_num, r_atom, rc_off, cell_num, num_in_cell, cell_list, which_cell)
@@ -122,4 +128,4 @@ module opt_delete
         !Now delete all the atoms
         call delete_atoms(delete_num, for_delete(1:delete_num))
     end subroutine delete_overlap
-end module opt_delete
+end module opt_delete