From 54aa50b605f5e8735f944cbf71e9108505417bee Mon Sep 17 00:00:00 2001
From: Alex Selimov <aselimov3@gatech.edu>
Date: Fri, 29 Nov 2019 13:36:19 -0500
Subject: [PATCH 1/5] Working writing to lammpsCAC format

---
 src/io.f90          | 161 +++++++++++++++++++++++++++++++++++++++-----
 src/mode_create.f90 |   2 -
 2 files changed, 146 insertions(+), 17 deletions(-)

diff --git a/src/io.f90 b/src/io.f90
index 7850ee2..948fd52 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -6,8 +6,8 @@ module io
 
     implicit none
 
-    integer :: outfilenum = 0
-    character(len=100) :: outfiles(10)
+    integer :: outfilenum = 0, infilenum = 0
+    character(len=100) :: outfiles(10), infiles(10)
 
    public 
    contains
@@ -41,6 +41,7 @@ module io
                 if((scan(overwrite, "n") > 0).or.(scan(overwrite, "N") > 0)) then 
                     print *, "Please specify a new filename with extension:"
                     read(*,*) temp_outfile
+                    cycle
                 else if((scan(overwrite, "y") > 0).or.(scan(overwrite, "Y") > 0)) then 
                     continue
                 else
@@ -56,21 +57,13 @@ module io
                 cycle
             end if
             select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
-            case('xyz')
+            case('xyz','lmp','vtk','cac')
                 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."
+                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, cac."
                 read(*,*) temp_outfile
 
             end select
@@ -78,6 +71,52 @@ module io
 
     end subroutine get_out_file 
 
+    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 with extension to read in:"
+            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 doesn't then ask the user for another input
+            inquire(file=trim(temp_infile), exist=file_exists)
+            if (.not.file_exists) then 
+                print *, "The file ", temp_infile, "does not exist, please input an existing file to read in."
+                read(*,*) temp_infile
+                cycle
+            end if
+
+            if (scan(temp_outfile,'.',.true.) == 0) then 
+                print *, "No extension included on filename, please type a full filename that includes an extension."
+                read(*,*) temp_infile
+                cycle
+            end if
+            select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
+            case('cac')
+                infilenum=infilenum+1
+                infiles(infilenum) =  temp_infile
+                exit
+            case default    
+                print *, "File type: ", trim(temp_infile(scan(temp_outfile,'.',.true.):)), " not currently accepted. ", &
+                         "please input a filename with extension from following list: cac."
+                read(*,*) temp_infile
+
+            end select
+        end do
+
+    end subroutine get_in_file 
 
     subroutine write_out
         !This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
@@ -96,6 +135,8 @@ module io
                 call write_lmp(outfiles(i))
             case('vtk')
                 call write_vtk(outfiles(i))
+            case('cac')
+                call write_lmpcac(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"
@@ -201,6 +242,71 @@ module io
         end do
     end subroutine write_lmp
 
+    subroutine write_lmpcac(file)
+        !This subroutine writes out a .lmp style dump file
+        character(len=100), intent(in) :: file
+        integer :: write_num, i, inod, ibasis
+        real(kind=dp) :: mass
+
+1       format(i16, '   Eight_Node', 4i16)
+2       format(i16, '   Atom', 4i16)
+3       format(3i16,3f23.15)
+
+        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
+
+        !Comment line
+        write(11, '(a)') '# CAC input file made with cacmb'
+        write(11, '(a)')
+        !Calculate total atom number
+        write_num = atom_num + ele_num
+
+        !Write total number of atoms + elements
+        write(11, '(i16, a)') write_num, ' cac elements'
+        !Write number of atom types 
+        write(11, '(i16, a)') atom_types, ' atom types'
+
+        write(11,'(a)') ' '
+        !Write box bd
+        write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
+        write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
+        write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
+
+        !Masses
+        write(11, '(a)') 'Masses'
+
+        write(11, '(a)') ' '
+        do i =1, atom_types
+            call atommass(type_to_name(i),mass)
+            write(11, '(i16, f23.15, 2a)') i, mass, ' # ', type_to_name(i)
+        end do
+        write(11, '(a)') ' '
+
+        write(11, '(a)') 'CAC Elements'
+        write(11, '(a)') ' '
+
+        !Write element nodal positions
+        do i = 1, ele_num
+            select case(trim(adjustl(type_ele(i))))
+            case('fcc')
+                !The first entry is the element specifier 
+                write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
+                do ibasis = 1, basisnum(lat_ele(i))
+                    do inod = 1, 8
+                        !Nodal information for every node
+                        write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
+                    end do
+                end do
+            end select
+        end do
+
+        do i = 1, atom_num
+            !Element specifier dictating that it is an atom
+            write(11,2) ele_num+i, 1, 1, 1, 1
+            !Write the atomic information
+            write(11,3) 1, 1, type_atom(i), r_atom(:,i)
+        end do
+    end subroutine write_lmpcac
+
     subroutine write_vtk(file)
         !This subroutine writes out a vtk style dump file
         integer :: i, j, inod, ibasis
@@ -257,7 +363,7 @@ module io
         do i = 1, ele_num
             do inod=1, ng_node(lat_ele(i))  
                 do ibasis = 1, basisnum(lat_ele(i))
-                    write(11, '(3f23.1)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
+                    write(11, '(3f23.15)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
                 end do 
             end do 
         end do
@@ -276,4 +382,29 @@ module io
         end do
         close(11)
     end subroutine
-end module io
\ No newline at end of file
+
+
+! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! READ SUBROUTINES !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!     subroutine read_lmpcac(file, box_bd)
+!         !This subroutine reads in a lmpcac file which can be used with different options and modes
+
+!         !Arguments
+!         character(len=100), intent(in) :: file
+!         real(kind=wp), dimension(6), intent(out) :: box_bd
+
+!         !Internal variables
+!         character(len=1000) :: line
+!         integer :: read_num, atom_lim, ele_lim
+
+!         !Open the lmpcac file
+!         open(unit=11, file=file, action='read', position='rewind')
+
+!         !Skip header lines
+!         read(11,*) line
+!         read(11,*) line
+
+!         !Read total number of elements
+        
+
+!     end subroutine read_lmpcac
+end module io
diff --git a/src/mode_create.f90 b/src/mode_create.f90
index 52342e2..e822798 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -432,7 +432,6 @@ 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)
@@ -453,7 +452,6 @@ module mode_create
                 end do
             end do
 
-            print *, lat_atom_num
         end if 
 
     end subroutine build_with_rhomb

From c1150ae4b13b1418d9419452b455d41d028310fb Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Fri, 29 Nov 2019 22:23:22 -0500
Subject: [PATCH 2/5] First attempts at figuring out the element format for
 lammpscac

---
 src/io.f90          | 14 ++++++++++----
 src/mode_create.f90 | 46 ++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 49 insertions(+), 11 deletions(-)

diff --git a/src/io.f90 b/src/io.f90
index 948fd52..af66da3 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -8,6 +8,7 @@ module io
 
     integer :: outfilenum = 0, infilenum = 0
     character(len=100) :: outfiles(10), infiles(10)
+    logical lmpcac
 
    public 
    contains
@@ -57,7 +58,12 @@ module io
                 cycle
             end if
             select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
-            case('xyz','lmp','vtk','cac')
+            case('xyz','lmp','vtk')
+                outfilenum=outfilenum+1
+                outfiles(outfilenum) =  temp_outfile
+                exit
+            case('cac')
+                lmpcac = .true. 
                 outfilenum=outfilenum+1
                 outfiles(outfilenum) =  temp_outfile
                 exit
@@ -98,18 +104,18 @@ module io
                 cycle
             end if
 
-            if (scan(temp_outfile,'.',.true.) == 0) then 
+            if (scan(temp_infile,'.',.true.) == 0) then 
                 print *, "No extension included on filename, please type a full filename that includes an extension."
                 read(*,*) temp_infile
                 cycle
             end if
-            select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
+            select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
             case('cac')
                 infilenum=infilenum+1
                 infiles(infilenum) =  temp_infile
                 exit
             case default    
-                print *, "File type: ", trim(temp_infile(scan(temp_outfile,'.',.true.):)), " not currently accepted. ", &
+                print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), " not currently accepted. ", &
                          "please input a filename with extension from following list: cac."
                 read(*,*) temp_infile
 
diff --git a/src/mode_create.f90 b/src/mode_create.f90
index e822798..53880c9 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -11,7 +11,7 @@ module mode_create
 
     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)
+                       orient_inv(3,3), box_vert(3,8), maxbd(3), lattice_space(3), adjustVar(3,8)
     integer :: esize, duplicate(3), ix, iy, iz, box_lat_vert(3,8), lat_ele_num, lat_atom_num, bd_in_lat(6)
     logical :: dup_flag, dim_flag
 
@@ -91,14 +91,30 @@ module mode_create
             continue
         else
 
-            call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) 
+            if(lmpcac) then 
+                 do inod = 1, 8
+                    do i = 1,3
+                        if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
+                            adjustVar(i,inod) = -0.5_dp*esize
+                        else 
+                            adjustVar(i, inod) = 0.5_dp*esize
+                        end if
+                    end do
+                end do
+            else
+                adjustVar(:,:)=0.0_dp
+            end if
+
+            ! call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) 
             !If the user doesn't pass any build instructions than we just put the cell mat into the element_array 
             call alloc_ele_arrays(1,0)
 
             !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) = lattice_parameter*matmul(orient, &
+                                                 matmul(fcc_mat, esize*(cubic_cell(:,inod)+adjustVar(:,inod)))) &
+                                                        + basis_pos(:,ibasis,1)
                 end do
             end do
             do i = 1,3
@@ -276,7 +292,7 @@ module mode_create
         !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)
+        real(kind=dp) :: v(3), temp_nodes(3,1,8), ele_atoms(3,esize**3), r_interp(3,basisnum(1)*esize**3), adjustVar(3,8)
         real(kind=dp), allocatable :: resize_lat_array(:,:)
         logical, allocatable :: lat_points(:,:,:)
         logical :: node_in_bd(8)
@@ -284,6 +300,21 @@ module mode_create
         !Do some value initialization
         max_esize = esize
 
+        !If we are writing out to lammpscac format then we have to adjust the nodal positions
+
+        if(lmpcac) then 
+             do inod = 1, 8
+                do i = 1,3
+                    if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
+                        adjustVar(i,inod) = -0.25_dp
+                    else 
+                        adjustVar(i, inod) = 0.25_dp
+                    end if
+                end do
+            end do
+        else
+            adjustVar(:,:)=0.0_dp
+        end if
         !First find the bounding lattice points (min and max points for the box in each dimension)
         numlatpoints = 1
         do i = 1, 3
@@ -301,7 +332,6 @@ module mode_create
             continue
         end select
 
-
         !Loop over all of lattice points within the boundary, we choose between two loops. One for the atomistic case 
         !and one for the regular case
         if (esize==2) then  
@@ -415,8 +445,10 @@ module mode_create
 
                         if(all(node_in_bd)) then 
                             lat_ele_num = lat_ele_num+1
-                            r_lat(:,:,lat_ele_num) = temp_nodes(:,1,:)
-
+                            do inod = 1, 8
+                                r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
+                            end do
+                            
                             !Now set all the lattice points contained within an element to false
                             do o = minval(temp_lat(3,:)), maxval(temp_lat(3,:))
                                 do n = minval(temp_lat(2,:)), maxval(temp_lat(2,:))

From 591762d2591ee26b79313f1ea661685b0b7edf4c Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Wed, 4 Dec 2019 21:03:13 -0500
Subject: [PATCH 3/5] Latest attempts to get the lammpscac data format working

---
 src/mode_create.f90 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/mode_create.f90 b/src/mode_create.f90
index 53880c9..6c465a3 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -95,9 +95,9 @@ module mode_create
                  do inod = 1, 8
                     do i = 1,3
                         if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
-                            adjustVar(i,inod) = -0.5_dp*esize
+                            adjustVar(i,inod) = -0.5_dp
                         else 
-                            adjustVar(i, inod) = 0.5_dp*esize
+                            adjustVar(i, inod) = 0.5_dp
                         end if
                     end do
                 end do
@@ -113,7 +113,7 @@ module mode_create
             do inod = 1, max_ng_node
                 do ibasis = 1, basisnum(1)
                     r_node_temp(:,ibasis,inod) = lattice_parameter*matmul(orient, &
-                                                 matmul(fcc_mat, esize*(cubic_cell(:,inod)+adjustVar(:,inod)))) &
+                                                 matmul(fcc_mat, (esize+1)*cubic_cell(:,inod)+adjustVar(:,inod))) &
                                                         + basis_pos(:,ibasis,1)
                 end do
             end do

From ba28734fd7ccf34b2a816910528c57d225cabcc4 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Mon, 13 Jan 2020 16:54:52 -0500
Subject: [PATCH 4/5] Working changes to write lammps cac

---
 src/mode_create.f90 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/mode_create.f90 b/src/mode_create.f90
index 6c465a3..b65d62e 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -306,9 +306,9 @@ module mode_create
              do inod = 1, 8
                 do i = 1,3
                     if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
-                        adjustVar(i,inod) = -0.25_dp
+                        adjustVar(i,inod) = -0.5_dp
                     else 
-                        adjustVar(i, inod) = 0.25_dp
+                        adjustVar(i, inod) = 0.5_dp
                     end if
                 end do
             end do

From fbae3a15946d52fa55513ee2759ba18389913bc4 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Mon, 13 Jan 2020 20:12:46 -0500
Subject: [PATCH 5/5] Working version of CACmb capable of building simple
 models for lammpsCAC

---
 src/Makefile        |  9 +++++----
 src/elements.f90    | 20 +++++++++++++++++-
 src/io.f90          | 49 +--------------------------------------------
 src/main.f90        | 11 ++++++++++
 src/mode_create.f90 | 18 +++--------------
 src/parameters.f90  |  2 ++
 6 files changed, 41 insertions(+), 68 deletions(-)

diff --git a/src/Makefile b/src/Makefile
index c84186e..e1a1145 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,6 +1,7 @@
+ 
 FC=ifort
-#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
-FFLAGS=-mcmodel=large -Ofast
+FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
+#FFLAGS=-mcmodel=large -Ofast
 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 box.o $(MODES)
 
@@ -8,7 +9,7 @@ OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box
 .SUFFIXES: .c .f .f90 .F90 .o
 
 cacmb: $(OBJECTS) 
-	$(FC) $(FFLAGS) $(OBJECTS) -o $@
+	$(FC) $(FFLAGS) $(OBJECTS) parameters.o -o $@
 
 .f90.o: 
 	$(FC) $(FFLAGS) -c $< 
@@ -30,4 +31,4 @@ main.o io.o build_subroutines.o: elements.o
 call_mode.o : $(MODES)
 $(MODES) io.o: atoms.o box.o
 $(MODES) main.o : io.o
-testfuncs.o elements.o mode_create.o: subroutines.o
+testfuncs.o elements.o mode_create.o: subroutines.o
\ No newline at end of file
diff --git a/src/elements.f90 b/src/elements.f90
index 22e6eff..d6545d6 100644
--- a/src/elements.f90
+++ b/src/elements.f90
@@ -101,10 +101,28 @@ module elements
 
         real(kind=dp), dimension(3,max_ng_node), intent(out) :: cell_mat
 
+        integer :: inod, i
+        real(kind=dp), dimension(3,max_ng_node) :: adjustVar
+
+        adjustVar(:,:) = 0.0_dp
+
         select case(trim(ele_type))
 
         case('fcc')
-            cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, fcc_cell))
+            if(lmpcac) then 
+                do inod = 1, 8
+                    do i = 1,3
+                        if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
+                            adjustVar(i,inod) = -0.5_dp
+                        else 
+                            adjustVar(i, inod) = 0.5_dp
+                        end if
+                    end do
+                end do
+                adjustVar(:,1:8) = matmul(fcc_mat, adjustVar(:,1:8))
+            end if
+            cell_mat(:, 1:8) = fcc_cell + adjustVar(:,1:8)
+            cell_mat(:,1:8) = lapa * ((esize-1)*matmul(orient_mat, cell_mat(:,1:8)))
         case default
             print *, "Element type ", trim(ele_type), " currently not accepted"
             stop
diff --git a/src/io.f90 b/src/io.f90
index dd49096..9d5537a 100644
--- a/src/io.f90
+++ b/src/io.f90
@@ -9,7 +9,7 @@ module io
 
     integer :: outfilenum = 0, infilenum = 0
     character(len=100) :: outfiles(10), infiles(10)
-    logical lmpcac
+    
 
    public 
    contains
@@ -78,53 +78,6 @@ module io
 
     end subroutine get_out_file 
 
-    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 with extension to read in:"
-            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 doesn't then ask the user for another input
-            inquire(file=trim(temp_infile), exist=file_exists)
-            if (.not.file_exists) then 
-                print *, "The file ", temp_infile, "does not exist, please input an existing file to read in."
-                read(*,*) temp_infile
-                cycle
-            end if
-
-            if (scan(temp_infile,'.',.true.) == 0) then 
-                print *, "No extension included on filename, please type a full filename that includes an extension."
-                read(*,*) temp_infile
-                cycle
-            end if
-            select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
-            case('cac')
-                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: cac."
-                read(*,*) temp_infile
-
-            end select
-        end do
-
-    end subroutine get_in_file 
-
     subroutine write_out
         !This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
 
diff --git a/src/main.f90 b/src/main.f90
index a681d33..f90b731 100644
--- a/src/main.f90
+++ b/src/main.f90
@@ -27,6 +27,17 @@ program main
     ! Command line parsing
     arg_num = command_argument_count()
 
+    !First check if we are writing out to lammpscac format by looping over all arguments
+    do i = 1, arg_num
+        call get_command_argument(i, argument)
+        select case(argument(scan(argument,'.',.true.)+1:))
+        case('cac')
+            lmpcac = .true.
+        case default
+            continue
+        end select
+    end do 
+
     !Determine if a mode is being used and what it is. The first argument has to be the mode
     !if a mode is being used
     call get_command_argument(1, argument)
diff --git a/src/mode_create.f90 b/src/mode_create.f90
index d5995e8..a669f93 100644
--- a/src/mode_create.f90
+++ b/src/mode_create.f90
@@ -91,20 +91,6 @@ module mode_create
             end do 
         else
 
-            if(lmpcac) then 
-                 do inod = 1, 8
-                    do i = 1,3
-                        if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
-                            adjustVar(i,inod) = -0.5_dp
-                        else 
-                            adjustVar(i, inod) = 0.5_dp
-                        end if
-                    end do
-                end do
-            else
-                adjustVar(:,:)=0.0_dp
-            end if
-
             call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) 
             !If the user doesn't pass any build instructions than we just put the cell mat into the element_array 
             call alloc_ele_arrays(1,0)
@@ -333,6 +319,8 @@ module mode_create
                     end if
                 end do
             end do
+
+            adjustVar(:,1:8) = matmul(orient,matmul(fcc_mat,adjustVar(:,1:8)))
         else
             adjustVar(:,:)=0.0_dp
         end if
@@ -465,7 +453,7 @@ module mode_create
                         end do
 
                         if(all(node_in_bd)) then 
-                            lat_ele_num = lat_ele_num+1
+                            lat_ele_num = lat_ele_num+1 
                             do inod = 1, 8
                                 r_lat(:,inod,lat_ele_num) = temp_nodes(:,1,inod) + adjustVar(:,inod)
                             end do
diff --git a/src/parameters.f90 b/src/parameters.f90
index 0443622..9e9d9d8 100644
--- a/src/parameters.f90
+++ b/src/parameters.f90
@@ -5,4 +5,6 @@ module parameters
     integer, parameter :: dp= selected_real_kind(15,307)
     real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
                                 lim_large = huge(1.0_dp)
+    logical, save :: lmpcac
+    
 end module parameters
\ No newline at end of file