Fix to disl_gen. Problems with sub_box_bd and element dislocation displacement field

src/io.f90

@@ -642,7 +642,11 @@ module io
             read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 3), k = 1, 3)
             !Read in subbox boundaries
             read(11,*) sub_box_bd(:,sub_box_num+i)
-            sub_box_bd(:,sub_box_num+i) = sub_box_bd(:, sub_box_num+i) + displace(:)
+
+            do j = 1, 3
+                sub_box_bd(2*j-1,sub_box_num+i) = sub_box_bd(2*j-1, sub_box_num+i) + displace(j)
+                sub_box_bd(2*j,sub_box_num+i) = sub_box_bd(2*j, sub_box_num+i) + displace(j)
+            end do
             !Read in sub_box_array_bd
             read(11,*) ((sub_box_array_bd(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
         end do

src/opt_disl.f90

@@ -70,7 +70,11 @@ module opt_disl
             call parse_pos(i, textholder, centroid(i))           
         end do
 
-        print *, centroid
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing parameter in dislgen command"
+        read(textholder, *) b 
+
 
         arg_pos = arg_pos + 1
         call get_command_argument(arg_pos, textholder, arglen)
@@ -84,26 +88,6 @@ module opt_disl
         read(textholder, *) poisson
 
         arg_pos = arg_pos + 1
-        call get_command_argument(arg_pos, lattice, arglen)
-        if (arglen==0) STOP "Missing lattice in dislgen command"
-
-        arg_pos = arg_pos + 1
-        call get_command_argument(arg_pos, textholder, arglen)
-        if (arglen==0) STOP "Missing lattice parameter in dislgen command"
-        read(textholder, *) lattice_parameter
-
-        arg_pos = arg_pos + 1
-        !Now set the vurgers vector based on the lattice paarameter and lattice type
-        select case(lattice)
-            case('fcc')
-                b = lattice_parameter / sqrt(2.0_dp)
-            ! case('bcc')
-            !     b = lattice_parameter * sqrt(3.0_dp) / 2.0_dp
-            case default
-                print *, 'Error: Lattice structure', lattice, ' is not accepted for dislgen option'
-                STOP
-       end select
-
     end subroutine parse_dislgen
 
     subroutine dislgen
@@ -168,7 +152,7 @@ module opt_disl
             do i = 1, ele_num
                 do inod=1, ng_node(lat_ele(i))
                     do ibasis = 1, basisnum(lat_ele(i))
-                        r = r_node(:,ibasis,inod,i)
+                        r = r_node(:,ibasis,inod,i)-centroid
                         r = matmul(inv_transform, r)
                         if (r(1) == 0) then 
                             actan = pi/2