Fixes to mode_create, moved basis_pos from elements to mode_create, added the mb file output style

src/elements.f90

@@ -30,19 +30,15 @@ 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 +85,6 @@ module elements
 
         max_basisnum = 0
         basisnum(:) = 0
-        basis_pos(:,:,:) = 0.0_dp
         ng_node(:) = 0
     end subroutine lattice_init
 
@@ -304,4 +299,5 @@ module elements
 
         return
     end subroutine rhombshape
+
 end module elements

src/io.f90

@@ -3,6 +3,7 @@ module io
     use elements
     use parameters
     use atoms
+    use box
 
     implicit none
 
@@ -56,18 +57,10 @@ 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 +89,8 @@ 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 +271,53 @@ 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, 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 and sub box boundary
+        do i = 1, sub_box_num
+            write(11,*) sub_box_ori(:,:,i)
+            write(11,*) sub_box_bd(:,i)
+        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,*) 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
 end module io

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)
@@ -258,13 +260,17 @@ 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)
@@ -432,12 +438,11 @@ 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 +458,6 @@ module mode_create
                 end do
             end do
 
-            print *, lat_atom_num
         end if 
 
     end subroutine build_with_rhomb