First testing version of code

README.md

@@ -328,6 +328,13 @@ This command will delete all overlapping atoms within a specific cutoff radius `
 
 This option is primarily used when reading data from non .mb formats. This code simply sets the orientation variable for the specified sub box `sbox`.
 
+### Option redef_box 
+```
+-redef_box redef_dim {xlo xhi} {ylo yhi} {zlo zhi}
+```
+This option allows for the user to redefine box boundaries deleting atoms/elements outside of the new box boundaries. Elements are refined to atmoistics if they intersect the newly defined box boundaries.
+The arguments are described below:
+`redef_dim` - The dimensions to be redefined. Can be any permutation of `x`, `y`, `z`, `xy`, `yz`, `xz`, `xyz`. The order of the dimensions dictates the order that the new dimensions must be defined
 ****
 ## Position Specification
 

src/Makefile

@@ -2,7 +2,7 @@ FC=ifort
 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 opt_deform.o
+OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o opt_deform.o opt_redef_box.o
 OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o  $(MODES) $(OPTIONS) call_option.o sorts.o
 
 .SUFFIXES:

src/opt_redef_box.f90

@@ -0,0 +1,126 @@
+module opt_redef_box
+
+    use box
+    use elements
+    use subroutines
+    implicit none
+    
+    character(len=3) :: redef_dim, new_bc
+    real(kind=dp) :: new_bd(6)
+    public 
+    contains
+
+    subroutine redef_box(arg_pos)
+        !This is the main calling function for opt_redef_box
+        integer, intent(inout) :: arg_pos
+        integer :: i, inod, ibasis, iatom, delete_list(atom_num), delete_num, type_interp(max_basisnum*max_esize**3)
+        real(kind=dp):: r_interp(3, max_basisnum*max_esize**3)
+        logical :: node_out(8)
+
+        !First parse the argument
+        call parse_redef_box(arg_pos)
+
+        !Now first filter atoms that don't fit in the new box bounds and delete them
+        delete_num = 0
+        do i = 1, atom_num 
+            if(.not.in_block_bd(r_atom(:,i),new_bd)) then 
+                delete_num = delete_num + 1
+                delete_list(delete_num) = i
+            end if
+        end do
+        call delete_atoms(delete_num, delete_list(1:delete_num))
+
+        !Now loop over all elements
+        delete_num = 0
+        delete_list(:) = 0
+        do i = 1, ele_num
+            !Determine if all nodes are within the new boundaries
+            do inod = 1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                    node_out(:) = .false.
+                    if(.not.in_block_bd(r_node(:,ibasis,inod,i), new_bd)) then 
+                        node_out(inod) = .true.
+                    end if
+                end do
+            end do
+
+            !If all nodes are out just add the element to the delete list
+            if(all(node_out)) then 
+                delete_num = delete_num +1
+                delete_list(delete_num) = i
+
+            !If any nodes are out we add the element to the delete list, but then loop over the interpoalted atoms to figure out
+            !which ones fit inside the boundary to keep the box rectangular 
+            else if (any(node_out)) then 
+                delete_num = delete_num +1
+                delete_list(delete_num) = i
+
+                call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
+
+                !loop over all interpolated atoms and add them to the system
+                do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
+                    if(in_block_bd(r_interp(:,iatom), new_bd)) then 
+                        call add_atom(0,type_interp(iatom), sbox_ele(i), r_interp(:,iatom))
+                    end if
+                end do 
+            end if
+        end do
+
+        call delete_elements(delete_num, delete_list)
+
+        box_bd=new_bd
+        box_bc = new_bc
+
+    end subroutine redef_box
+
+    subroutine parse_redef_box(arg_pos)
+        !Parse the command
+        integer, intent(inout) :: arg_pos
+
+        integer :: i, j, arglen
+        character(len=100) textholder
+        
+
+        !First read in the dimensions that we are redefining
+        redef_dim = ''
+        arg_pos=arg_pos+1
+        call get_command_argument(arg_pos, redef_dim, arglen)
+        select case(trim(adjustl(redef_dim))) 
+        case('x','y','z','xy','yx','xz','zx','yz','zy','xyz','yxz','xzy','zyx','zxy','yzx')
+            continue
+        case default
+            print *, "Incorrect redef_dim ", redef_dim, "please select any permuation of x, y, z, xy, yz, xz, xyz"
+            stop 3
+        end select
+
+        !Now read in the new dimensions
+        new_bd = box_bd
+        new_bc = box_bc
+        do i = 1, 3
+            select case(trim(adjustl(redef_dim(i:i))))
+            case('x')
+                j = 1
+            case('y')
+                j = 2
+            case('z')
+                j = 3
+            case default
+                exit
+            end select 
+
+            arg_pos=arg_pos +1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if(arglen == 0) stop "Missing a box dimension in opt_redef_box"
+            call parse_pos(j, textholder,new_bd(2*j-1))
+
+            arg_pos=arg_pos +1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if(arglen == 0) stop "Missing a box dimension in opt_redef_box"
+            call parse_pos(j, textholder,new_bd(2*j))
+            new_bc(j:j) = 's'
+        end do 
+
+        arg_pos = arg_pos + 1
+    end subroutine parse_redef_box
+
+end module opt_redef_box