Current working changes to control-box code

README.md

@@ -58,7 +58,7 @@ Default duplicate is `1 1 1`. This is used to replicate the element along each d
 **Dimensions**
 
 ```
-dimensions dimx dimy dimz
+dim dimx dimy dimz
 ```
 
 There is no default dimensions as duplicate is the default option. This command assigns a box with user-assigned dimensions and fills it with the desired element. By default atoms fill in the jagged edges at the boundaries if the dimensions command is included.
@@ -129,6 +129,11 @@ wrap
 
 This will wrap atomic positions back inside the box. Effectively as if periodic boundary conditions are applied so that atoms which exit from one side of the simulation cell enter back in through the other.
 
+###Mode Metric
+```
+--metric cmetric nfiles {filepaths} 
+```
+
 ## Options
 
 Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files.

src/box.f90

@@ -97,4 +97,10 @@ module box
         end do 
     return 
     end subroutine in_sub_box
+
+    subroutine reset_box
+        !This subroutine just resets the box boundary and position
+        box_bc = "ppp"
+        box_bd(:) = 0
+    end subroutine reset_box
 end module box

src/elements.f90

@@ -793,4 +793,11 @@ module elements
         virial_node(:,:,:,ie) = virial
         return
     end subroutine add_element_data
+
+    subroutine reset_data
+        !This function resets all of the data arrays for the elements and atoms
+        atom_num = 0
+        ele_num = 0
+        node_num = 0
+    end subroutine reset_data
 end module elements

src/io.f90

@@ -583,22 +583,17 @@ module io
             temp_infile = filename
         end if
 
-        !Infinite loop which only exists if user provides valid filetype
-        do while(.true.)
-
         !Check to see if file exists, if it does then ask user if they would like to overwrite the file
         inquire(file=trim(temp_infile), exist=file_exists)
         if (.not.file_exists) then 
-                print *, "The file ", trim(adjustl(filename)), " does not exist. Please input a filename that exists"
+            print *, "The file ", trim(adjustl(filename)), " does not exist. Please input an existing file to read."
-                read(*,*) temp_infile
+            stop 3
-                cycle
         end if
 
         select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
         case('restart', 'mb', 'cac')
             infilenum=infilenum+1
             infiles(infilenum) =  temp_infile
-                exit
         case('out')
             if(atom_types == 0) then 
                 print *, "Please run -set_types command prior to running code requiring reading in pycac_*.out files"
@@ -608,7 +603,6 @@ module io
             case('--convert','--metric')
                 infilenum = infilenum+1
                 infiles(infilenum) = temp_infile
-                    exit
             case default
                 print *, "Files of type .out cannot be used with mode ", trim(adjustl(mode))
                 stop 3
@@ -617,15 +611,13 @@ module io
         case default    
             print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
                      "please input a filename with extension from following list: mb, restart, cac, or out."
-                read(*,*) temp_infile
+            stop 3
-
         end select
-        end do
 
     end subroutine get_in_file 
 
     subroutine read_in(i, displace, temp_box_bd)
-        !This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
+        !This subroutine reads in file i
 
         integer, intent(in) :: i 
         real(kind=dp), dimension(3), intent(in) :: displace
@@ -1067,6 +1059,7 @@ module io
                 end do
                 call add_element(tag, fcc, esize+1, lat_type, sub_box_num, re)
                 call add_element_data(ele_num, ee, fe, ve)
+                node_num = node_num + 8
             end do
         end if
         call set_max_esize

src/opt_delete.f90

@@ -3,6 +3,7 @@ module opt_delete
     use parameters
     use subroutines
     use elements
+    use neighbors
 
     implicit none 
 

src/subroutines.f90

@@ -198,66 +198,6 @@ module subroutines
         end do
     end subroutine
 
-    subroutine build_cell_list(numinlist, r_list, rc_off, cell_num, num_in_cell, cell_list, which_cell)
-        !This subroutine builds a cell list based on rc_off
-        
-        !----------------------------------------Input/output variables-------------------------------------------
-
-        integer, intent(in) :: numinlist !The number of points within r_list
-
-        real(kind=dp), dimension(3,numinlist), intent(in) :: r_list !List of points to be used for the construction of 
-                                                                    !the cell list.
-
-        real(kind=dp), intent(in) :: rc_off ! Cutoff radius which dictates the size of the cells
-
-        integer, dimension(3), intent(inout) :: cell_num !Number of cells in each dimension.
-
-        integer, allocatable, intent(inout) :: num_in_cell(:,:,:) !Number of points within each cell
-
-        integer, allocatable, intent(inout) :: cell_list(:,:,:,:) !Index of points from r_list within each cell.
-
-        integer, dimension(3,numinlist), intent(out) :: which_cell !The cell index for each point in r_list
-
-        !----------------------------------------Begin Subroutine -------------------------------------------
-
-        integer :: i, j, cell_lim, c(3)
-        real(kind=dp) :: box_len(3)
-        integer, allocatable :: resize_cell_list(:,:,:,:)
-
-        !First calculate the number of cells that we need in each dimension
-        do i = 1,3
-            box_len(i) = box_bd(2*i) - box_bd(2*i-1)
-            cell_num(i) = int(box_len(i)/(rc_off/2))+1
-        end do 
-
-        !Initialize/allocate variables 
-        cell_lim = 10
-        allocate(num_in_cell(cell_num(1),cell_num(2),cell_num(3)), cell_list(cell_lim, cell_num(1), cell_num(2), cell_num(3)))
-
-        !Now place points within cell
-        do i = 1, numinlist
-            !c is the position of the cell that the point belongs to 
-            do j = 1, 3
-                c(j) = int((r_list(j,i)-box_bd(2*j-1))/(rc_off/2)) + 1
-            end do
-
-            !Place the index in the correct position, growing if necessary
-            num_in_cell(c(1),c(2),c(3)) = num_in_cell(c(1),c(2),c(3)) + 1
-            if (num_in_cell(c(1),c(2),c(3)) > cell_lim) then 
-                allocate(resize_cell_list(cell_lim+10,cell_num(1),cell_num(2),cell_num(3)))
-                resize_cell_list(1:cell_lim, :, :, :) = cell_list
-                resize_cell_list(cell_lim+1:, :, :, :) = 0
-                call move_alloc(resize_cell_list, cell_list)
-            end if
-
-            cell_list(num_in_cell(c(1),c(2),c(3)),c(1),c(2),c(3)) = i
-            which_cell(:,i) = c
-        end do 
-
-        return
-    end subroutine build_cell_list
-
-
     subroutine check_right_ortho(ori, isortho, isrighthanded)
         !This subroutine checks whether provided orientations in the form:
         ! | x1  x2  x3 |
@@ -301,4 +241,5 @@ module subroutines
         return
     end subroutine check_right_ortho
 
+
 end module subroutines