First attempts at figuring out the element format for lammpscac

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
 

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,:))