From e6d7741060527382721d9672b11d3342ac8d15fc Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Tue, 21 Apr 2020 13:25:55 -0400
Subject: [PATCH 1/4] Working changes to io.f90

---
 src/io.f90 | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 2 deletions(-)

diff --git a/src/io.f90 b/src/io.f90
index f929e29..1e1d956 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -161,7 +161,7 @@ module io
         !Calculate total atom number
         write_num = atom_num
         do i = 1,ele_num
-            if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
+        if((type_ele(i) == 'fcc').or.(type_ele(i) == 'bcc')) write_num = write_num + size_ele(i)**3
         end do
         !Write total number of atoms + elements
         write(11, '(i16, a)') write_num, ' atoms'
@@ -196,7 +196,7 @@ module io
         do i = 1, ele_num
             call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
             select case(trim(adjustl(type_ele(i))))
-            case('fcc')
+            case('fcc','bcc')
                 do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
                     interp_num = interp_num+1
                     call apply_periodic(r_interp(:,iatom))
@@ -949,4 +949,66 @@ module io
             call set_max_esize
         end if
     end subroutine read_pycac
+
+    subroutine read_cac(file, displace, temp_box_bd)
+        !This subroutine is used to read .cac files which are used with the lammpsCAC format
+        character(len=100), intent(in) :: file
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind = dp), dimension(6), intent(out) :: temp_box_bd
+        
+        character(len=100) :: textholder, element_type, esize
+        character(len=2) :: atom_species
+       integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
+                
+        real(kind=dp) :: mass, r_in(3,10,8)
+        
+
+        !First open the file
+        open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
+
+        !Read header information
+        read(11, *) textholder
+        read(11, *) textholder
+
+        !Read number of elements
+        read(11, *) ele_in, textholder 
+        read(11, *) type_in, textholder
+
+        !Read box_boundaries
+        read(11,*) textholder
+        read(11,*) box_bd(1:2), texholder
+        read(11,*) box_bd(3:4), texholder
+        read(11,*) box_bd(5:6), texholder
+
+        !Read useless information
+        read(11,*) textholder 
+        read(11,*) textholder 
+
+        !Read atomic masses
+        do i = 1, type_in
+            read(11,*) j, mass, textholder
+            call ATOMMASSSPECIES(mass, atom_species) 
+            call add_atom_type(atom_species, type_map(i))
+        end do
+
+        !Read useless info
+        do i = 1, 3
+            read(11,*) textholder
+        end do
+
+        !Start the reading loop
+        do i = 1, ele_in
+            read(11,*) j, ele, element_type, in_basis, esize
+            select case(trim(adjustl(element_type)))
+            case('Eight_Node')
+                    !Read in all the data
+                    do j = 1, 8*in_basis 
+                        read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
+                    end do
+
+                    !
+            end select
+        end do
+
+    end subroutine read_cac
 end module io

From b3e05da6a4e55e01df9de7dae899dea4b1cc8f7d Mon Sep 17 00:00:00 2001
From: Alex Selimov <aselimov3@gatech.edu>
Date: Wed, 22 Apr 2020 12:52:37 -0400
Subject: [PATCH 2/4] Working changes for reading .cac files

---
 README.md           |  5 ++---
 src/call_option.f90 |  4 +++-
 src/elements.f90    | 38 +++++++++++++++++++++++++++++++++--
 src/io.f90          | 49 +++++++++++++++++++++++++++++++++++----------
 src/main.f90        |  5 +++++
 5 files changed, 84 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index 3455000..8f20ec6 100644
--- a/README.md
+++ b/README.md
@@ -191,7 +191,7 @@ This option creates a circular planar vacancy cluster of radius `radius` normal
 
 This option selects a group of either elements, nodes, atoms and applies some transformation to them.
 
-`select_type` - Either `nodes`, `atoms`, `elements`, `nodes/atoms`, `all`. When using the option `nodes` only nodes which are within the group are selected, `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group.  `all` selects elements based on the element center and atoms based on their position.
+`select_type` - Either `atoms`, `elements`,`both`. `elements` selects elements based on whether the element center is within the group, `nodes/atoms` selects both nodes and atoms for the group.  `both` selects elements based on the element center and atoms based on their position.
 
 `group_shape` - Specifies what shape the group takes and dictates which options must be passed. Each shape requires different arguments and these arguments are represented by the placeholder `shape_arguments`. The accepted group shapes and arguments are below:
 
@@ -230,7 +230,7 @@ This command wraps atoms back into the simulation cell as though periodic bounda
 **Remesh**
 
 ```
-remesh esize lattice_parameter lattice_type
+remesh esize 
 ```
 
 This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics. When remeshing to atomistics the group can contain any orientations of elements but when remeshing to different finite elements, the group must contain all atoms/elements with the same orientation. `lattice_parameter` is the lattice parameter for the elements within the group and `lattice_type` is the lattice type (integer) that these new elements will be assigned to. 
@@ -294,7 +294,6 @@ 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`.
 
 ****
-
 ## Position Specification
 
 Specifying positions in cacmb can be done through a variety of ways. Examples of each format is shown below.
diff --git a/src/call_option.f90 b/src/call_option.f90
index ead7af0..b8cc3b8 100644
--- a/src/call_option.f90
+++ b/src/call_option.f90
@@ -33,8 +33,10 @@ subroutine call_option(option, arg_pos)
         call sbox_ori(arg_pos)
     case('-delete')
         call run_delete(arg_pos)
+    case('-set_cac')
+        arg_pos = arg_pos+3
     case default
         print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
         stop 3 
     end select
-end subroutine call_option
\ No newline at end of file
+end subroutine call_option
diff --git a/src/elements.f90 b/src/elements.f90
index e9fc928..6265b3c 100644
--- a/src/elements.f90
+++ b/src/elements.f90
@@ -35,13 +35,13 @@ module elements
     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
+    real(kind=dp) :: lapa(10)
 
     !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) !Max basis atom number, number of basis atoms in each lattice type 
     integer :: basis_type(10,10)
-    real(kind=dp) :: lapa(10)
 
     !Additional module level variables we need 
     logical :: wrap_flag
@@ -632,4 +632,38 @@ module elements
     end select
     end subroutine
 
-end module elements
\ No newline at end of file
+    subroutine lattice_map(in_bnum, in_btypes, in_ngnodes, in_lapa, lat_type)
+        !This subroutine maps an input lattice type to either a new lattice type or an existing one depending on basis_type and 
+        !number of nodes at the atoms
+
+        integer, intent(in) :: in_ngnodes, in_bnum, in_btypes(10) !Input variables
+        real(kind=dp), intent(in) :: in_lapa
+        integer, intent(out) :: lat_type
+
+        integer j, ibasis
+
+        lat_type = 0
+        lat_loop:do j = 1, lattice_types
+            !Check all the lattice level variables
+            if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then 
+                !Now check lattice level variables 
+                do ibasis = 1, basisnum(j)
+                    if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle old_loop
+                end do
+                lat_type = j
+                exit lat_loop
+            end if
+        end do lat_loop
+
+        !If it doesn't match an existing lattice type we add it 
+        if( lat_type == 0) then 
+            lattice_types = lattice_types + 1
+            basisnum(lattice_types) = in_bnum
+            basis_types(:,lattice_types) = in_btypes
+            ng_node(lattice_types) = in_ngnodes
+            lapa(lattice_types) = in_lapa
+        end if
+
+    end subroutine lattice_map
+
+end module elements
diff --git a/src/io.f90 b/src/io.f90
index 1e1d956..22692e8 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -8,9 +8,9 @@ module io
     implicit none
 
     integer :: outfilenum = 0, infilenum = 0
-    character(len=100) :: outfiles(100), infiles(100)
+    character(len=100) :: outfiles(100), infiles(100), in_lattice_type=''
     logical :: force_overwrite
-
+    real(kind=dp) :: in_lapa=0.0
    public 
    contains
 
@@ -958,12 +958,15 @@ module io
         
         character(len=100) :: textholder, element_type, esize
         character(len=2) :: atom_species
-       integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
-                
-        real(kind=dp) :: mass, r_in(3,10,8)
+        integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
+        real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3), in_ori(3,3)
         
-
-        !First open the file
+        !First check to make sure that we have set the needed variables
+        if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then 
+            print *, "Please use set_cac to set needed parameters to read in .cac file"
+            stop 3
+        end if
+        !Open the file
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
 
         !Read header information
@@ -978,8 +981,7 @@ module io
         read(11,*) textholder
         read(11,*) box_bd(1:2), texholder
         read(11,*) box_bd(3:4), texholder
-        read(11,*) box_bd(5:6), texholder
-
+        read(11,*) box_bd(5:6), texholder 
         !Read useless information
         read(11,*) textholder 
         read(11,*) textholder 
@@ -1005,10 +1007,35 @@ module io
                     do j = 1, 8*in_basis 
                         read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
                     end do
-
-                    !
+                     
+                    !Now calculate the orientation matrix based on the lattice type.
+                    lat_vec = r_in(:,1,2) - r_in(:,1,1) 
+                    lat_vec = lat_vec / norm2(lat_vec)
+                    
+                    !Now figure out if is an existing lattice_type
+                    call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
+
+                    
             end select
         end do
 
     end subroutine read_cac
+
+    subroutine set_cac(apos)
+        !This code parses input values
+        integer, intent(in) :: apos
+        integer :: arglen, arg_pos
+        
+        arg_pos = apos + 1 
+        call get_command_argument(arg_pos, in_lapa, arglen)
+        if (arglen==0) then 
+            print *, "Missing lattice parameter for set_input_lat"
+        end if
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, in_lattice_type, arglen)
+        if (arglen==0) then 
+            print *, "Missing lattice type for set_input_lat"
+        end if
+    end subroutine set_input_lat(arg_pos)
 end module io
diff --git a/src/main.f90 b/src/main.f90
index 958a3c0..8d153ce 100644
--- a/src/main.f90
+++ b/src/main.f90
@@ -60,6 +60,11 @@ program main
         !This lets us know if we need to wrap atomic positions back into the cell
         case('-wrap')
             wrap_flag=.true.
+        
+        !This gives necessary information in order to correctly read .cac files
+        case('-set_cac')
+            call set_cac(i)
+
         end select 
     end do 
     !Determine if a mode is being used and what it is. The first argument has to be the mode

From 4038cab76fe4630e39710819423ce6ec11365302 Mon Sep 17 00:00:00 2001
From: Alex Selimov <aselimov3@gatech.edu>
Date: Thu, 23 Apr 2020 12:17:04 -0400
Subject: [PATCH 3/4] Latest working changes to read-CAC

---
 src/elements.f90 |  2 -
 src/io.f90       | 97 ++++++++++++++++++++++++++++++++++++++----------
 2 files changed, 77 insertions(+), 22 deletions(-)

diff --git a/src/elements.f90 b/src/elements.f90
index 6265b3c..484057f 100644
--- a/src/elements.f90
+++ b/src/elements.f90
@@ -294,8 +294,6 @@ module elements
 
         integer :: i
 
-        max_ng_node = 0
-
         do i=1, n
             select case(trim(adjustl(element_types(i))))
             case('fcc')
diff --git a/src/io.f90 b/src/io.f90
index 22692e8..964a816 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -776,7 +776,7 @@ module io
         integer :: i, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
                    atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), &
                    atom_type
-        real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
+        real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3)
         character(len=100) :: textholder, in_lattype_map(10) 
         character(len=2) :: atomic_element
         !First open the file
@@ -950,7 +950,7 @@ module io
         end if
     end subroutine read_pycac
 
-    subroutine read_cac(file, displace, temp_box_bd)
+    subroutine read_lmpcac(file, displace, temp_box_bd)
         !This subroutine is used to read .cac files which are used with the lammpsCAC format
         character(len=100), intent(in) :: file
         real(kind=dp), dimension(3), intent(in) :: displace
@@ -958,8 +958,8 @@ module io
         
         character(len=100) :: textholder, element_type, esize
         character(len=2) :: atom_species
-        integer :: i, j, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
-        real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3), in_ori(3,3)
+        integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
+        real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), temp_box_bd(6), newdisplace(3)
         
         !First check to make sure that we have set the needed variables
         if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then 
@@ -968,6 +968,9 @@ module io
         end if
         !Open the file
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
+        
+        !Now initialiaze some important variables
+        max_basis_num = 10
 
         !Read header information
         read(11, *) textholder
@@ -979,9 +982,38 @@ module io
 
         !Read box_boundaries
         read(11,*) textholder
-        read(11,*) box_bd(1:2), texholder
-        read(11,*) box_bd(3:4), texholder
-        read(11,*) box_bd(5:6), texholder 
+        read(11,*) temp_box_bd(1:2), texholder
+        read(11,*) temp_box_bd(3:4), texholder
+        read(11,*) temp_box_bd(5:6), texholder 
+
+        !Shift the box boundaries if needed
+        do i = 1, 3
+            if (abs(displace(i)) > lim_zero) then 
+                newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
+            else
+                newdisplace(i)=displace(i)
+            end if 
+            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 
+
+        !Grow box boundaries
+        call grow_box(temp_box_bd)
+
+        !Allocate sub_box 
+        if (sub_box_num == 0) then 
+            call alloc_sub_box(1)
+        else
+            call grow_sub_box(1)
+        end if
+
+        !Because orientations and other needed sub_box information isn't really 
+        !present within the .cac file we just default a lot of it.
+        sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
+        sub_box_bd(:, sub_box_num+1) = temp_box_bd
+        sub_box_num = sub_box_num + 1
+
+
         !Read useless information
         read(11,*) textholder 
         read(11,*) textholder 
@@ -1001,25 +1033,50 @@ module io
         !Start the reading loop
         do i = 1, ele_in
             read(11,*) j, ele, element_type, in_basis, esize
+            !Check to see if we need to grow the max_basis_num
             select case(trim(adjustl(element_type)))
             case('Eight_Node')
-                    !Read in all the data
-                    do j = 1, 8*in_basis 
-                        read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
+                !Read in all the data
+                do j = 1, 8*in_basis 
+                    read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,ibasis,inod)
+                end do
+                
+                !Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
+                !Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
+                !calculation
+                lat_vec(:,1) = (r_node(:,1,2) - r_node(:,1,1))/esize
+                lat_vec(:,2) = (r_node(:,1,4) - r_node(:,1,1))/esize
+                lat_vec(:,3) = (r_node(:,1,5) - r_node(:,1,1))/esize
+               
+                !Now shift all the nodal positions 
+                select case(trim(adjustl(in_lattice_type)))
+                case('fcc','FCC')
+                    do ibasis = 1, in_basis 
+                        r_in(:,ibasis,1) = r_in(:,ibasis,1) + lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,2) = r_in(:,ibasis,2) - lat_vec(:,1) + lat_vec(:,2) + lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,3) = r_in(:,ibasis,3) - lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,4) = r_in(:,ibasis,4) + lat_vec(:,1) - lat_vec(:,2) + lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,5) = r_in(:,ibasis,5) + lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,6) = r_in(:,ibasis,6) - lat_vec(:,1) + lat_vec(:,2) - lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,7) = r_in(:,ibasis,7) - lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
+                        r_in(:,ibasis,8) = r_in(:,ibasis,8) + lat_vec(:,1) - lat_vec(:,2) - lat_vec(:,3) + newdisplace
                     end do
-                     
-                    !Now calculate the orientation matrix based on the lattice type.
-                    lat_vec = r_in(:,1,2) - r_in(:,1,1) 
-                    lat_vec = lat_vec / norm2(lat_vec)
-                    
-                    !Now figure out if is an existing lattice_type
-                    call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
-
-                    
+                case default
+                    print *, in_lattice_type, " is not an accepted lattice type. Please select from: fcc"
+                end select 
+                !Now map it to either an existing or new lattice type
+                call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
+
+                !Now add the element 
+                call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in)
+                
+            case('Atom')
+                read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
+                call add_atom(in_basis_types(ibasis), sub_box_num, r_in(:,1,1)) 
             end select
         end do
 
-    end subroutine read_cac
+    end subroutine read_lmpcac
 
     subroutine set_cac(apos)
         !This code parses input values

From b52d7761e09795fc9fd050615d1edcb68a26dc75 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Tue, 2 Jun 2020 16:42:12 -0400
Subject: [PATCH 4/4] First working version of reading in .cac format. Works
 for two separate orientations

---
 src/call_option.f90 |  2 +-
 src/elements.f90    |  5 +++--
 src/io.f90          | 54 +++++++++++++++++++++++++--------------------
 src/main.f90        |  2 --
 4 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/src/call_option.f90 b/src/call_option.f90
index b8cc3b8..368e542 100644
--- a/src/call_option.f90
+++ b/src/call_option.f90
@@ -34,7 +34,7 @@ subroutine call_option(option, arg_pos)
     case('-delete')
         call run_delete(arg_pos)
     case('-set_cac')
-        arg_pos = arg_pos+3
+        arg_pos=arg_pos +3
     case default
         print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
         stop 3 
diff --git a/src/elements.f90 b/src/elements.f90
index 484057f..6252427 100644
--- a/src/elements.f90
+++ b/src/elements.f90
@@ -646,7 +646,7 @@ module elements
             if ((basisnum(j) == in_bnum).and.(ng_node(j) == in_ngnodes).and.(is_equal(lapa(j),in_lapa))) then 
                 !Now check lattice level variables 
                 do ibasis = 1, basisnum(j)
-                    if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle old_loop
+                    if(basis_type(ibasis,j) /= in_btypes(ibasis)) cycle lat_loop
                 end do
                 lat_type = j
                 exit lat_loop
@@ -657,9 +657,10 @@ module elements
         if( lat_type == 0) then 
             lattice_types = lattice_types + 1
             basisnum(lattice_types) = in_bnum
-            basis_types(:,lattice_types) = in_btypes
+            basis_type(:,lattice_types) = in_btypes
             ng_node(lattice_types) = in_ngnodes
             lapa(lattice_types) = in_lapa
+            lat_type = lattice_types
         end if
 
     end subroutine lattice_map
diff --git a/src/io.f90 b/src/io.f90
index 964a816..ab90f85 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -591,7 +591,7 @@ module io
             end if
 
             select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
-            case('restart', 'mb')
+            case('restart', 'mb', 'cac')
                 infilenum=infilenum+1
                 infiles(infilenum) =  temp_infile
                 exit
@@ -618,6 +618,8 @@ module io
             call read_mb(infiles(i), displace, temp_box_bd)
         case('restart')
             call read_pycac(infiles(i), displace, temp_box_bd)
+        case('cac')
+            call read_lmpcac(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"
@@ -956,10 +958,11 @@ module io
         real(kind=dp), dimension(3), intent(in) :: displace
         real(kind = dp), dimension(6), intent(out) :: temp_box_bd
         
-        character(len=100) :: textholder, element_type, esize
+        character(len=100) :: textholder, element_type
         character(len=2) :: atom_species
-        integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10)
-        real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), temp_box_bd(6), newdisplace(3)
+        integer :: i, j, k, ele_in, type_in, type_map(10), in_basis, node_types(10,8), inod, ibasis, in_basis_types(10), esize, &
+                   lat_type  
+        real(kind=dp) :: mass, r_in(3,10,8), lat_vec(3,3), in_ori(3,3), newdisplace(3)
         
         !First check to make sure that we have set the needed variables
         if(is_equal(in_lapa,0.0_dp).or.(in_lattice_type=='')) then 
@@ -969,22 +972,21 @@ module io
         !Open the file
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
         
-        !Now initialiaze some important variables
-        max_basis_num = 10
+        !Now initialiaze some important variables if they aren't defined
+        if (max_basisnum==0) max_basisnum = 10
+        if (max_ng_node==0) max_ng_node=8
 
         !Read header information
         read(11, *) textholder
-        read(11, *) textholder
 
         !Read number of elements
         read(11, *) ele_in, textholder 
         read(11, *) type_in, textholder
 
         !Read box_boundaries
-        read(11,*) textholder
-        read(11,*) temp_box_bd(1:2), texholder
-        read(11,*) temp_box_bd(3:4), texholder
-        read(11,*) temp_box_bd(5:6), texholder 
+        read(11,*) temp_box_bd(1:2), textholder
+        read(11,*) temp_box_bd(3:4), textholder
+        read(11,*) temp_box_bd(5:6), textholder 
 
         !Shift the box boundaries if needed
         do i = 1, 3
@@ -1016,7 +1018,6 @@ module io
 
         !Read useless information
         read(11,*) textholder 
-        read(11,*) textholder 
 
         !Read atomic masses
         do i = 1, type_in
@@ -1026,13 +1027,11 @@ module io
         end do
 
         !Read useless info
-        do i = 1, 3
-            read(11,*) textholder
-        end do
+        read(11,*) textholder
 
         !Start the reading loop
         do i = 1, ele_in
-            read(11,*) j, ele, element_type, in_basis, esize
+            read(11,*) j, element_type, in_basis, esize
             !Check to see if we need to grow the max_basis_num
             select case(trim(adjustl(element_type)))
             case('Eight_Node')
@@ -1044,10 +1043,10 @@ module io
                 !Now calculate the lattice vectors and shift the nodal points from the corners to the center of the unit cell
                 !Please check the nodal numbering figure in the readme in order to understand which nodes are used for the
                 !calculation
-                lat_vec(:,1) = (r_node(:,1,2) - r_node(:,1,1))/esize
-                lat_vec(:,2) = (r_node(:,1,4) - r_node(:,1,1))/esize
-                lat_vec(:,3) = (r_node(:,1,5) - r_node(:,1,1))/esize
-               
+                lat_vec(:,1) = (r_in(:,1,2) - r_in(:,1,1))/(2*esize)
+                lat_vec(:,2) = (r_in(:,1,4) - r_in(:,1,1))/(2*esize)
+                lat_vec(:,3) = (r_in(:,1,5) - r_in(:,1,1))/(2*esize)
+                
                 !Now shift all the nodal positions 
                 select case(trim(adjustl(in_lattice_type)))
                 case('fcc','FCC')
@@ -1068,7 +1067,7 @@ module io
                 call lattice_map(in_basis, in_basis_types, 8, in_lapa, lat_type)
 
                 !Now add the element 
-                call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in)
+                call add_element(in_lattice_type, esize, lat_type, sub_box_num, r_in(:,1:max_basisnum,1:max_ng_node))
                 
             case('Atom')
                 read(11, *) inod, ibasis, in_basis_types(ibasis), r_in(:,1,1)
@@ -1082,17 +1081,24 @@ module io
         !This code parses input values
         integer, intent(in) :: apos
         integer :: arglen, arg_pos
+
+        character(len=100) :: textholder
         
         arg_pos = apos + 1 
-        call get_command_argument(arg_pos, in_lapa, arglen)
+        call get_command_argument(arg_pos, textholder, arglen)
         if (arglen==0) then 
             print *, "Missing lattice parameter for set_input_lat"
         end if
+        read(textholder,*) in_lapa
+        print *, in_lapa
 
         arg_pos = arg_pos + 1
-        call get_command_argument(arg_pos, in_lattice_type, arglen)
+        call get_command_argument(arg_pos, textholder, arglen)
         if (arglen==0) then 
             print *, "Missing lattice type for set_input_lat"
         end if
-    end subroutine set_input_lat(arg_pos)
+        read(textholder,*) in_lattice_type
+        print *, in_lattice_type
+
+    end subroutine set_cac
 end module io
diff --git a/src/main.f90 b/src/main.f90
index 8d153ce..53fa4fa 100644
--- a/src/main.f90
+++ b/src/main.f90
@@ -61,10 +61,8 @@ program main
         case('-wrap')
             wrap_flag=.true.
         
-        !This gives necessary information in order to correctly read .cac files
         case('-set_cac')
             call set_cac(i)
-
         end select 
     end do 
     !Determine if a mode is being used and what it is. The first argument has to be the mode