Removed extra variables from mode_create.f90, added a new module to contain simulation box information and changed code accordingly, new grow subroutine in elements.

src/box.f90

@@ -0,0 +1,48 @@
+module box
+    !This module contains information on the properties of the current box.
+    use parameters
+
+    implicit none 
+
+    real(kind=dp) :: box_bd(6) !Global box boundaries
+
+    !The subbox variables contain values for each subbox, being the boxes read in through some
+    !command. Currently only mode_merge will require sub_boxes, for mode_create it will always 
+    !allocate to only 1 sub_box
+    integer :: sub_box_num = 0
+    real(kind=dp), allocatable :: sub_box_ori(:,:,:)
+    real(kind=dp), allocatable :: sub_box_bd(:,:)
+
+    public 
+    contains 
+
+    subroutine box_init
+        !Initialize some box functions
+        box_bd(:) = 0.0_dp
+    end subroutine box_init
+
+    subroutine alloc_sub_box(n)
+        !Allocate the sub_box variables
+
+        integer, intent(in) :: n
+
+        sub_box_num = n
+        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n))
+    end subroutine alloc_sub_box
+
+    subroutine grow_box(temp_box_bd)
+        !This function takes in a temporary box boundary and adjusts the overall box boundaries
+        !to include  it
+
+        real(kind=dp), dimension(6), intent(in) :: temp_box_bd
+
+        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
+        return
+    end subroutine grow_box
+
+end module box

src/elements.f90

@@ -7,7 +7,6 @@ module elements
     implicit none
 
     !Data structures used to represent the CAC elements. Each index represents an element
-    integer,allocatable :: tag_ele(:) !Element tag (used to keep track of id's
     character(len=100), allocatable :: type_ele(:) !Element type 
     integer, allocatable :: size_ele(:), lat_ele(:) !Element siz
     real(kind=dp), allocatable :: r_node(:,:,:,:) !Nodal position array
@@ -16,7 +15,7 @@ module elements
     integer :: node_num=0 !Total number of nodes
 
     !Data structure used to represent atoms 
-    integer, allocatable :: tag_atom(:), type_atom(:)!atom id 
+    integer, allocatable ::  type_atom(:)!atom type 
     real(kind =dp),allocatable :: r_atom(:,:) !atom position
     integer :: atom_num=0 !Number of atoms
 
@@ -119,7 +118,7 @@ module elements
         
         !Allocate element arrays
         if(n > 0) then 
-            allocate(tag_ele(n), type_ele(n), size_ele(n), lat_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
+            allocate(type_ele(n), size_ele(n), lat_ele(n), r_node(3,max_basisnum, max_ng_node,n), &
                        stat=allostat)
             if(allostat > 0) then 
                 print *, "Error allocating element arrays in elements.f90 because of: ", allostat
@@ -129,7 +128,7 @@ module elements
 
         if(m > 0) then 
             !Allocate atom arrays
-            allocate(tag_atom(m), type_atom(m), r_atom(3,m), stat=allostat)
+            allocate(type_atom(m), r_atom(3,m), stat=allostat)
             if(allostat > 0) then 
                 print *, "Error allocating atom arrays in elements.f90 because of: ", allostat
                 stop
@@ -137,6 +136,58 @@ module elements
         end if    
     end subroutine
 
+    subroutine grow_ele_arrays(n, m)
+
+        integer, intent(in) :: n, m
+
+        integer :: ele_size, atom_size, buffer_size
+        integer, allocatable :: temp_int(:)
+        real(kind=dp), allocatable :: temp_ele_real(:,:,:,:), temp_real(:,:)
+        character(len=100), allocatable :: char_temp(:)
+
+        !The default size we grow the 
+        buffer_size = 1024
+        !Figure out the size of the atom and element arrays
+        ele_size = size(size_ele)
+        atom_size = size(type_atom)
+
+        !Check if we need to grow the ele_size, if so grow all the variables
+        if ( n > size(size_ele)) then 
+            
+            allocate(temp_int(n+buffer_size))
+            temp_int(1:ele_size) = lat_ele
+            temp_int(ele_size+1:) = 0
+            call move_alloc(temp_int(1:ele_size), lat_ele)
+
+            allocate(temp_int(n+buffer_size))
+            temp_int(1:ele_size) = size_ele
+            temp_int(ele_size+1:) = 0
+            call move_alloc(temp_int(1:ele_size), size_ele)
+
+            allocate(char_temp(n+buffer_size))
+            char_temp(1:ele_size) = type_ele
+            call move_alloc(char_temp, type_ele)
+
+            allocate(temp_ele_real(3, max_basisnum, max_ng_node, n+buffer_size))
+            temp_ele_real(:,:,:,1:ele_size) = r_node
+            temp_ele_real(:,:,:,ele_size+1:) = 0.0_dp
+            call move_alloc(temp_ele_real, r_node)
+        end if
+
+        !Now grow atom arrays if needed
+        if (m > atom_size) then 
+            allocate(temp_int(m+buffer_size))
+            temp_int(1:atom_size) = type_atom
+            temp_int(atom_size+1:) = 0
+            call move_alloc(temp_int, type_atom)
+
+            allocate(temp_real(3,m+buffer_size))
+            temp_real(:,1:atom_size) = r_atom
+            temp_real(:, atom_size+1:) = 0.0_dp
+            call move_alloc(temp_real, r_atom)
+        end if
+    end subroutine
+
     subroutine add_element(type, size, lat, r)
         !Subroutine which adds an element to the element arrays
         integer, intent(in) :: size, lat
@@ -144,7 +195,6 @@ module elements
         real(kind=dp), intent(in) :: r(3, max_basisnum, max_ng_node)
 
         ele_num = ele_num + 1
-        tag_ele(ele_num) = ele_num
         type_ele(ele_num) = type
         size_ele(ele_num) = size
         lat_ele(ele_num) = lat
@@ -160,7 +210,6 @@ module elements
         real(kind=dp), intent(in), dimension(3) :: r
 
         atom_num = atom_num+1
-        tag_atom(atom_num) = atom_num
         type_atom(atom_num) = type
         r_atom(:,atom_num) = r(:)
 

src/main.f90

@@ -20,8 +20,10 @@ program main
     integer ::  arg_num
     character(len=100) ::  mode
 
+    !Call initialization functions
     call lattice_init
-
+    call box_init
+    
     ! Command line parsing
     arg_num = command_argument_count()
 

src/mode_create.f90

@@ -135,6 +135,10 @@ module mode_create
             end if
         end if
 
+        !The last thing we do is setup the sub_box_boundaries
+        call alloc_sub_box(1)
+        sub_box_ori(:,:,1) = orient
+        sub_box_bd(:,1) = box_bd
     end subroutine create
     !This subroutine parses the command and pulls out information needed for mode_create
     subroutine parse_command()
@@ -280,9 +284,9 @@ module mode_create
         integer, dimension(3,8), intent(in) :: box_in_lat !The box vertices transformed to lattice space
         real(kind=dp), dimension(3,3), intent(in) :: transform_matrix !The transformation matrix from lattice_space to real space
         !Internal variables
-        integer :: i,  inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz,  numlatpoints, templatpoints, ele(3,8), rzero(3), ilat, &
-                   type_interp(basisnum(1)*esize**3), vlat(3), temp_lat(3,8), m, n, o
-        real(kind=dp) :: v(3), temp_nodes(3,1,8), ele_atoms(3,esize**3), r_interp(3,basisnum(1)*esize**3)
+        integer :: i,  inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz,  numlatpoints, ele(3,8), rzero(3), &
+                   vlat(3), temp_lat(3,8), m, n, o
+        real(kind=dp) :: v(3), temp_nodes(3,1,8)
         real(kind=dp), allocatable :: resize_lat_array(:,:)
         logical, allocatable :: lat_points(:,:,:)
         logical :: node_in_bd(8)