Added right hand rule check to orientation in mode_create

src/mode_create.f90

@@ -169,6 +169,7 @@ module mode_create
         integer ::  ori_pos, i, j, arglen, stat
         character(len=100) :: textholder
         character(len=8) :: orient_string
+        logical :: isortho, isrighthanded
 
 
         !Pull out all required positional arguments
@@ -224,8 +225,6 @@ module mode_create
                     ! end do
                 end do
 
-
-
             !If the duplicate command is passed then we extract the information on the new bounds.
             case('duplicate')
                 if(dim_flag) STOP "Both duplicate and dim options cannot be used in mode_create"
@@ -286,6 +285,13 @@ module mode_create
         end select 
         !Now normalize the orientation matrix
         orient =  matrix_normal(orient,3)
+        !Now check these to make sure they are right handed and orthogonal
+        call check_right_ortho(orient, isortho, isrighthanded)
+        if (.not.isortho) then 
+            stop "Directions in orient are not orthogonal"
+        else if (.not.isrighthanded) then 
+            stop "Directions in orient are not righthanded"
+        end if
 
         !Set lattice_num to 1 and add the lattice_parameter to the elements module lattice paramter variable
         lattice_types = 1

src/opt_delete.f90

@@ -21,8 +21,6 @@ module opt_delete
 
         call parse_delete(arg_pos)
 
-        print *, atom_num
-
         if (rc_off > 0.0_dp) call delete_overlap
     end subroutine run_delete
 
@@ -66,10 +64,6 @@ module opt_delete
         
         allocate(which_cell(3,atom_num))
 
-        print *, atom_num
-        print *, for_delete(atom_num)
-        print *, which_cell(1,1)
-
         !First pass the atom list and atom num to the algorithm which builds the cell list
         call build_cell_list(atom_num, r_atom, rc_off, cell_num, num_in_cell, cell_list, which_cell)
 

src/subroutines.f90

@@ -358,4 +358,48 @@ module subroutines
         return
     end subroutine build_cell_list
 
+
+    subroutine check_right_ortho(ori, isortho, isrighthanded)
+        !This subroutine checks whether provided orientations in the form:
+        ! | x1  x2  x3 |
+        ! | y1  y2  y3 |
+        ! | z1  z2  z3 |
+        !are right handed
+        
+        real(kind=dp), dimension(3,3), intent(in) :: ori
+        logical, intent(out) :: isortho, isrighthanded
+
+        integer :: i, j 
+        real(kind=dp) :: v(3), v_k(3)
+        !Initialize variables
+        isortho = .true.
+        isrighthanded=.true.
+
+        do i = 1, 3
+            do j = i+1, 3
+
+                if(abs(dot_product(ori(i,:), ori(j,:))) > lim_zero) then 
+                    isortho = .false.
+                end if
+
+                !Check if they are righthanded
+                if (j == i+1) then 
+                    v(:) = cross_product(ori(i,:), ori(j,:))
+                    v_k(:) = v(:) - ori(mod(j, 3)+1,:)
+                else if ((i==1).and.(j==3)) then 
+                    v(:) = cross_product(ori(j,:),ori(i,:))
+                    v_k(:) = v(:) - ori(i+1, :)
+                end if
+
+                if(norm2(v_k) > 10.0_dp**(-8.0_dp)) then 
+                    isrighthanded=.false.
+                end if
+
+            end do 
+
+        end do
+
+        return
+    end subroutine check_right_ortho
+
 end module subroutines