Merge pull request #2 from aselimov/ft--mode-merge

Ft  mode merge

README.md

@@ -92,3 +92,23 @@ origin x y z
 Default origin is `0 0 0`. This command just sets the origin for where the simulation cell starts building.
 
 *Example:* `origin 10 0 1`
+
+### Mode Convert
+
+```
+cacmb --convert infile outfile
+```
+
+This mode converts a file `infile` to a file of  `outfile`. The extensions determine the conversion process.
+
+### Mode Merge
+
+```
+cacmb --merge dim N infiles outfile
+```
+
+This mode merges multiple data files and creates one big simulation cell. The parameters are:
+
+`N` - The number of files which are being read
+
+`dim` - the dimension they are to be stacked along, can be either `x`, `y`, or `z`. If the argument `none` is passed then the cells are just overlaid. Future options will include a 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
+FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
 #FFLAGS=-c -mcmodel=large -Ofast
-MODES=mode_create.o
+MODES=mode_create.o mode_merge.o mode_convert.o
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o  $(MODES)
+OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)
 
 .SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
@@ -28,6 +28,6 @@ $(OBJECTS) : parameters.o
 atoms.o subroutines.o testfuncs.o : functions.o
 main.o io.o build_subroutines.o: elements.o 
 call_mode.o : $(MODES)
-$(MODES) io.o: atoms.o 
+$(MODES) io.o: atoms.o box.o
 $(MODES) main.o : io.o
 testfuncs.o elements.o mode_create.o: subroutines.o

src/box.f90

@@ -0,0 +1,75 @@
+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
+    integer, allocatable :: sub_box_array_bd(:,:,:)!Boundaries in the atom and element arrays for each sub_box
+    real(kind=dp), allocatable :: sub_box_ori(:,:,:)!Orientations for each of the subboxes
+    real(kind=dp), allocatable :: sub_box_bd(:,:)!Boundaries for each of the sub_boxes
+
+    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
+
+        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
+
+    end subroutine alloc_sub_box
+
+    subroutine grow_sub_box(n)
+        !Grows sub box arrays, this is only called when a new file is read in
+        integer, intent(in) :: n
+
+        integer, allocatable :: temp_array_bd(:,:,:), temp_file(:)
+        real(kind=dp), allocatable :: temp_ori(:,:,:), temp_bd(:,:)
+        !Allocate temporary arrays
+        allocate(temp_ori(3,3,sub_box_num+n),temp_bd(6,sub_box_num+n), &
+                 temp_array_bd(2,2,sub_box_num+n), temp_file(sub_box_num+n))
+
+        !Move allocation for all sub_box_arrays
+        temp_ori(:,:,1:sub_box_num) = sub_box_ori
+        temp_ori(:,:,sub_box_num+1:) = 0.0_dp
+        call move_alloc(temp_ori, sub_box_ori)
+
+        temp_bd(:, 1:sub_box_num) = sub_box_bd
+        temp_bd(:, sub_box_num+1:) = 0.0_dp
+        call move_alloc(temp_bd, sub_box_bd)
+
+        temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
+        temp_array_bd(:,:,sub_box_num+1:) = 0.0_dp
+        call move_alloc(temp_array_bd, sub_box_array_bd)
+
+        return
+    end subroutine grow_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/call_mode.f90

@@ -3,6 +3,8 @@ subroutine call_mode(arg_num,mode)
     !mode module.
 
     use mode_create
+    use mode_convert
+    use mode_merge
     use parameters
 
     implicit none    
@@ -12,10 +14,13 @@ subroutine call_mode(arg_num,mode)
 
     select case(mode)
     case('--create')
-        call create()
+        call create
-
+    case('--convert')
+        call convert   
+    case('--merge')
+        call merge 
     case default
-        print *, "Mode ", mode, " currently not accepted. Please check documentation for ", &
+        print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
                  "accepted modes and rerun."
 
         stop 3

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
 
@@ -30,19 +29,15 @@ module elements
 
     !Below are lattice type arrays which provide information on the general form of the elements.
     !We currently have a limit of 10 lattice types for simplicities sake but this can be easily increased.
-    
+    integer :: lattice_types = 0
     integer :: max_ng_node, ng_node(10) !Max number of nodes per element and number of nodes per element for each lattice type
     integer :: max_esize=0 !Maximum number of atoms per side of element
 
     !These variables contain information on the basis, for simplicities sake we limit 
     !the user to the definition of 10 lattice types with 10 basis atoms at each lattice point.
     !This can be easily increased with no change to efficiency
-    integer :: max_basisnum, basisnum(10), basis_type(10,10)!Max basis atom number, number of basis atoms in each lattice type 
+    integer :: max_basisnum, basisnum(10) !Max basis atom number, number of basis atoms in each lattice type 
-    real(kind=dp) :: basis_pos(3,10,10) !Basis atom positions
+    integer :: basis_type(10,10)
-
-    !Simulation cell parameters
-    real(kind=dp) :: box_bd(6)
-
 
     public 
     contains
@@ -89,7 +84,6 @@ module elements
 
         max_basisnum = 0
         basisnum(:) = 0
-        basis_pos(:,:,:) = 0.0_dp
         ng_node(:) = 0
     end subroutine lattice_init
 
@@ -124,7 +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
@@ -134,7 +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
@@ -142,6 +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+ele_num > size(size_ele)) then 
+            
+            allocate(temp_int(n+ele_num+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+ele_num+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+ele_num+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+ele_num+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_num > atom_size) then 
+            allocate(temp_int(m+atom_num+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+atom_num+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
@@ -149,7 +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
@@ -165,7 +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(:)
 
@@ -304,4 +348,5 @@ module elements
 
         return
     end subroutine rhombshape
+
 end module elements

src/io.f90

@@ -3,15 +3,17 @@ module io
     use elements
     use parameters
     use atoms
+    use box
 
     implicit none
 
-    integer :: outfilenum = 0
+    integer :: outfilenum = 0, infilenum = 0
-    character(len=100) :: outfiles(10)
+    character(len=100) :: outfiles(10), infiles(10)
 
    public 
    contains
 
+    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Subroutines for writing out data files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     subroutine get_out_file(filename)
 
         implicit none
@@ -56,18 +58,10 @@ module io
                 cycle
             end if
             select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
-            case('xyz')
+            case('xyz', 'lmp', 'vtk', 'mb')
                 outfilenum=outfilenum+1
                 outfiles(outfilenum) =  temp_outfile
                 exit
-            case('lmp')
-                outfilenum=outfilenum+1
-                outfiles(outfilenum) = temp_outfile
-                exit
-            case('vtk')
-                outfilenum=outfilenum+1
-                outfiles(outfilenum)=temp_outfile
-                exit
             case default    
                 print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), "not currently accepted. ", &
                          "please input a filename with extension from following list: xyz, lmp, vtk."
@@ -96,6 +90,8 @@ module io
                 call write_lmp(outfiles(i))
             case('vtk')
                 call write_vtk(outfiles(i))
+            case('mb')
+                call write_mb(outfiles(i))
             case default
                 print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
                          " is not accepted for writing. Please select from: xyz and try again"
@@ -276,4 +272,201 @@ module io
         end do
         close(11)
     end subroutine
+
+    subroutine write_mb(file)
+
+        !This subroutine writes the cacmb formatted file which provides necessary information for building models
+        character(len=100), intent(in) :: file
+
+        integer :: i, j, k, inod, ibasis
+
+        !Open the .mb file for writing
+        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
+
+        !First write the box boundary information
+        !Write the global box boundaries
+        write(11,*) box_bd(:)
+        !Write the number of sub_boxes in the system
+        write(11,*) sub_box_num
+        !For every subbox write the orientation, sub box boundary, and sub_box_array_bds
+        do i = 1, sub_box_num
+            write(11,*) sub_box_ori(:,:,i)
+            write(11,*) sub_box_bd(:,i)
+            write(11,*) ((sub_box_array_bd(j,k,i), j = 1, 2), k = 1, 2)
+        end do
+
+        !Write the number of atom types in the current model and all of their names
+        write(11,*) atom_types, (type_to_name(i), i=1, atom_types)
+        !Write the number of lattice_types, basisnum and number of nodes for each lattice type
+        write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
+        !Now for every lattice type write the basis atom types
+        write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
+
+        !Now write the numbers of elements and atoms
+        write(11,*) atom_num, ele_num
+
+        !Write out atoms first
+        do i = 1, atom_num
+            write(11,*) i, type_atom(i), r_atom(:,i)
+        end do
+
+        !Write out the elements, this is written in two stages, one line for the element and then 1 line for 
+        !every basis at every node
+        do i = 1, ele_num
+            write(11, *) i, lat_ele(i), size_ele(i), type_ele(i)
+            do inod = 1, ng_node(lat_ele(i))
+                do ibasis =1, basisnum(lat_ele(i))
+                    write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
+                end do
+            end do
+        end do
+
+    end subroutine write_mb
+
+    !!!!!!!!!!!!! Below are subroutines for reading files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+    subroutine get_in_file(filename)
+
+        implicit none
+
+        character(len=100), intent(in) :: filename
+        character(len=100) :: temp_infile
+        logical :: file_exists
+
+        !If no filename is provided then this function is called with none and prompts user input
+        if (filename=='none') then 
+            print *, "Please specify a filename or extension to output to:"
+            read(*,*) temp_infile
+        else
+            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"
+                read(*,*) temp_infile
+                cycle
+            end if
+
+            select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
+            case('xyz', 'lmp', 'vtk', 'mb')
+                infilenum=infilenum+1
+                infiles(infilenum) =  temp_infile
+                exit
+            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."
+                read(*,*) temp_infile
+
+            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
+
+        integer, intent(in) :: i 
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind=dp), dimension(6), intent(out) :: temp_box_bd
+
+        !Pull out the extension of the file and call the correct write subroutine
+        select case(trim(adjustl(infiles(i)(scan(infiles(i),'.',.true.)+1:))))
+        case('mb')
+            call read_mb(infiles(i), displace, temp_box_bd)
+        case default
+            print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
+                     " is not accepted for writing. Please select from: mb and try again"
+            stop 
+
+        end select
+
+    end subroutine read_in
+
+    subroutine read_mb(file, displace, temp_box_bd)
+        !This subroutine reads in an mb file for operation
+
+        character(len=100), intent(in) :: file
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind = dp), dimension(6), intent(out) :: temp_box_bd
+
+        integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles
+        character(len=100) :: etype
+        real(kind=dp) ::  r(3), newdisplace(3)
+        real(kind=dp), allocatable :: r_innode(:,:,:)
+        !First open the file
+        open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
+
+        !Read in the box boundary and grow the current active box bd 
+        read(11, *) temp_box_bd(:)
+
+        do i = 1, 3
+            newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
+            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 
+        
+        !Read in the number of sub_boxes and allocate the variables
+        read(11, *) n
+
+        if (sub_box_num == 0) then 
+            call alloc_sub_box(n)
+        else
+            call grow_sub_box(n)
+        end if
+
+        !Read in subbox orientations and boundaries
+        do i = 1,  n
+            !Read in orientation with column major ordering
+            read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 3), k = 1, 3)
+            !Read in subbox boundaries
+            read(11,*) sub_box_bd(:,sub_box_num+i)
+            sub_box_bd(:,sub_box_num+i) = sub_box_bd(:, sub_box_num+i) + displace(:)
+            !Read in sub_box_array_bd
+            read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
+
+        end do
+            sub_box_num = sub_box_num + n
+
+        !Read in the number of atom types and all their names
+        read(11, *) atom_types, (type_to_name(i), i = 1, atom_types)
+        !Read the number of lattice types, basisnum, and number of nodes for each lattice type
+        read(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
+        !Define max_ng_node and max_basis_num
+        max_basisnum = maxval(basisnum)
+        max_ng_node = maxval(ng_node)
+        !Read the basis atom types for every lattice
+        read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
+
+        !Read number of elements and atoms and allocate arrays
+        read(11, *) in_atoms, in_eles
+        call grow_ele_arrays(in_eles, in_atoms)
+        allocate(r_innode(3,max_basisnum, max_ng_node))
+
+        !Read the atoms 
+        do i = 1, in_atoms
+            read(11,*) j, type, r(:)
+            call add_atom(type, r+newdisplace)
+        end do
+
+        !Read the elements
+        do i = 1, in_eles
+            read(11, *) n, type, size, etype
+            do inod = 1, ng_node(type)
+                do ibasis =1, basisnum(type)
+                    read(11,*) j, k, r_innode(:, ibasis, inod)
+                    r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
+                end do
+            end do
+
+            call add_element(etype, size, type, r_innode)
+        end do
+
+        !Close the file being read
+        close(11)
+    end subroutine read_mb
 end module io

src/main.f90

@@ -20,7 +20,9 @@ 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_convert.f90

@@ -0,0 +1,28 @@
+module mode_convert
+
+    use parameters
+    use box
+    use elements
+    use io
+
+    public 
+    contains
+
+    subroutine convert
+        !This subroutine converts a single input file from one format to another
+        character(len=100) :: infile, outfile
+        real(kind = dp) :: temp_box_bd(6)
+        !We have to allocate the element and atom arrays with a size of 1 for the read in code to work
+        call alloc_ele_arrays(1,1)
+        !First read in the file
+        call get_command_argument(2, infile)
+        call get_in_file(infile)
+        call read_in(1, (/0.0_dp,0.0_dp,0.0_dp/), temp_box_bd)
+        call grow_box(temp_box_bd)
+
+        !Now get the outfile, writing is done after all the codes complete
+        call get_command_argument(3, outfile)
+        call get_out_file(outfile)
+
+    end subroutine convert
+end module mode_convert

src/mode_create.f90

@@ -6,13 +6,15 @@ module mode_create
     use io
     use subroutines
     use elements
+    use box
 
     implicit none
 
     character(len=100) :: name, element_type
     real(kind = dp) :: lattice_parameter, orient(3,3), cell_mat(3,8), box_len(3), basis(3,3), origin(3), maxlen(3), &
                        orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3)
-    integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6)
+    integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6), &
+               basis_pos(3,10)
     logical :: dup_flag, dim_flag
 
     real(kind=dp), allocatable :: r_lat(:,:,:), r_atom_lat(:,:)
@@ -98,7 +100,7 @@ module mode_create
             !Add the basis atoms to the unit cell
             do inod = 1, max_ng_node
                 do ibasis = 1, basisnum(1)
-                    r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis,1) + origin(:)
+                    r_node_temp(:,ibasis,inod) = cell_mat(:,inod) + basis_pos(:,ibasis) + origin(:)
                 end do
             end do
             do i = 1,3
@@ -115,7 +117,7 @@ module mode_create
             if(lat_atom_num > 0) then 
                 do i = 1, lat_atom_num
                     do ibasis = 1, basisnum(1)
-                        call add_atom(basis_type(ibasis,1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis,1))
+                        call add_atom(basis_type(ibasis, 1), (r_atom_lat(:,i)*lattice_parameter)+basis_pos(:,ibasis))
                     end do
                 end do
                 deallocate(r_atom_lat)
@@ -125,7 +127,7 @@ module mode_create
                 do i = 1, lat_ele_num
                     do inod= 1, ng_node(1)
                         do ibasis = 1, basisnum(1)
-                            r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis,1)
+                            r_node_temp(:,ibasis,inod) = (r_lat(:,inod,i)*lattice_parameter)+basis_pos(:,ibasis)
                         end do
                     end do 
                     call add_element(element_type, esize, 1, r_node_temp)
@@ -133,6 +135,14 @@ 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_num = 1
+        sub_box_ori(:,:,1) = orient
+        sub_box_bd(:,1) = box_bd
+        sub_box_array_bd(1,:,1) = 1
+        sub_box_array_bd(2,1,1) = atom_num
+        sub_box_array_bd(2,2,1) = ele_num
     end subroutine create
     !This subroutine parses the command and pulls out information needed for mode_create
     subroutine parse_command()
@@ -258,13 +268,17 @@ module mode_create
         !Now normalize the orientation matrix
         orient =  matrix_normal(orient,3)
 
+        !Set lattice_num to 1 
+        lattice_types = 1
+
         !If we haven't defined a basis then define the basis and add the default basis atom type and position
         if (basisnum(1) == 0) then
             max_basisnum = 1
             basisnum(1) = 1
             call add_atom_type(name, basis_type(1,1)) !If basis command not defined then we use name as the atom_name
-            basis_pos(:,1,1) = 0.0_dp
+            basis_pos(:,1) = 0.0_dp
         end if
+        !
     end subroutine
     
     subroutine build_with_rhomb(box_in_lat, transform_matrix)
@@ -274,9 +288,9 @@ 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, &
+        integer :: i,  inod, bd_in_lat(6), bd_in_array(6), ix, iy, iz,  numlatpoints, ele(3,8), rzero(3), &
-                   type_interp(basisnum(1)*esize**3), vlat(3), temp_lat(3,8), m, n, o
+                   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)
+        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)
@@ -432,12 +446,11 @@ module mode_create
             end do
 
             !Now figure out how many lattice points could not be contained in elements
-            print *, count(lat_points)
             allocate(r_atom_lat(3,count(lat_points)))
             lat_atom_num = 0
-            do ix  = 1, bd_in_array(3)
+            do iz  = 1, bd_in_array(3)
                 do iy = 1, bd_in_array(2)
-                    do iz = 1, bd_in_array(1)
+                    do ix = 1, bd_in_array(1)
                         !If this point is a lattice point then save the lattice point as an atom
                         if (lat_points(ix,iy,iz)) then 
                             v= (/ real(ix,dp), real(iy, dp), real(iz,dp) /)
@@ -453,7 +466,6 @@ module mode_create
                 end do
             end do
 
-            print *, lat_atom_num
         end if 
 
     end subroutine build_with_rhomb

src/mode_merge.f90

@@ -0,0 +1,102 @@
+module mode_merge
+    !This module contains the code needed for merging several .mb files together
+
+    use parameters
+    use atoms   
+    use io
+    use subroutines
+    use elements
+
+    character(len=4) :: dim
+    integer :: in_num
+
+    public 
+    contains
+    subroutine merge
+        
+        integer :: i
+        real(kind=dp) :: displace(3), temp_box_bd(6)
+
+        !First we parse the merge command
+        call parse_command
+
+        !Now loop over all files and stack them 
+        do i = 1, in_num
+            displace(:) = 0.0_dp
+            if ((i==1).or.(trim(adjustl(dim)) == 'none')) then 
+                call read_in(i, displace, temp_box_bd)
+                call grow_box(temp_box_bd)
+            else
+                select case(trim(adjustl(dim)))
+                case('x')
+                    displace(1) = box_bd(2)
+                case('y')
+                    displace(2) = box_bd(4)
+                case('z')
+                    displace(3) = box_bd(6)
+                end select
+
+                call read_in(i, displace, temp_box_bd)
+                call grow_box(temp_box_bd)
+            end if 
+        end do
+
+        return
+    end subroutine merge
+
+    subroutine parse_command
+
+        character(len=100) :: textholder
+        integer :: i, stat, arglen, arg_pos
+
+        !Get dimension to concatenate along
+        call get_command_argument(2, dim, arglen)
+        if (arglen == 0) STOP "Missing dim in mode_merge command"
+        select case(trim(adjustl(dim)))
+        case('x','y','z','none')
+            continue
+        case default
+            print *, dim, " not accepted as a dimension in mode_merge"
+            stop 3
+        end select
+        !Get number of files to read in 
+        call get_command_argument(3, textholder, arglen)
+        if (arglen == 0) STOP "Number of files to read missing in mode_merge command"
+        read(textholder, *, iostat = stat) in_num
+        if (stat > 0) STOP "Error reading number of files in, must be integer"
+
+        !Now loop and pull out all files 
+        do i = 1, in_num
+            call get_command_argument(3+i, textholder, arglen)
+            if (arglen == 0) STOP "Fewer files to read in then specified"
+            !Make sure this file is readable
+            call get_in_file(textholder)
+        end do
+
+        !Set argpos accordingly
+        arg_pos = 3+in_num+1
+        !Now options loop
+        !Check for optional keywords
+        do while(.true.)
+            if(arg_pos > command_argument_count()) exit
+            !Pull out the next argument which should either be a keyword or an option
+            call get_command_argument(arg_pos, textholder)
+            textholder=adjustl(textholder)
+            arg_pos=arg_pos+1
+
+            !Choose what to based on what the option string is 
+            select case(trim(textholder))
+
+            case default
+                !Check to see if it is an option command, if so then mode_create must be finished
+                if(textholder(1:1) == '-') then 
+                    exit
+                !Check to see if a filename was passed
+                elseif(scan(textholder,'.',.true.) > 0) then 
+                    call get_out_file(textholder)
+                end if
+            end select
+        end do
+
+    end subroutine parse_command
+end module mode_merge