Working changes for reading .cac files

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.

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
+end subroutine call_option

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
+    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

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

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