Fixed group-group min bond distance in RGBI

foofiles/atom.foo

@@ -6040,22 +6040,16 @@ contains
 
 !  Bond distances and bonding
 
-   bond_distance_to(b,angstrom) result (res) ::: PURE
-   ! Return the bond distance between atoms "a" and "b"
+   bond_distance_to(that) result (res) ::: PURE
+   ! Return the distance between "self" and "that" other atom.
       self :: IN
-      b :: ATOM, IN
-      angstrom :: BIN, optional, IN
-      res :: REAL
+      that :: ATOM, IN
+      res  :: REAL
 
       r :: VEC{REAL}(3)
-      change :: BIN
-
-      r = b.position - .position
-      res = sqrt(r(1)*r(1) + r(2)*r(2) + r(3)*r(3))
 
-      change = FALSE
-      if (present (angstrom)) change = angstrom
-      if (change) res = res * STR:conversion_factor("angstrom")
+      r   = that.position - .position
+      res = sqrt(dot_product(r,r))
 
    end
 

foofiles/roby.foo

@@ -3889,6 +3889,7 @@ contains
    ENSURE(.atom.allocated,"no atom data")
 
       table   :: VEC{TABLE_COLUMN}@
+      group   :: VEC{INT}@
       symbols :: VEC{STR}@
       vals    :: VEC{REAL}@
       n_e, i  :: INT
@@ -3915,7 +3916,10 @@ contains
       if (.is_homoleptic) then
          ! Group atom indices
          do i = 1,.n_group
-            symbols(i) = .atom(.atom_group(i).element).chemical_formula
+            group = .atom_group(i).element
+            if (group.dim==1) then; symbols(i) = .atom(group(1)).tag
+            else;                   symbols(i) = .atom(group).chemical_formula
+            end
          end
          table.create(3)
          table(1).set_heading("Group")
@@ -3995,6 +3999,7 @@ contains
       table   :: VEC{TABLE_COLUMN}@
       symbol  :: VEC{STR}@
       g_A,g_B :: VEC{INT}@
+      grA,grB :: VEC{INT}@
       n_A,n_B :: VEC{REAL}@
       rAB,nAB,sAB,cAB,iAB :: VEC{REAL}@
       tAB,pAB,aAB :: VEC{REAL}@
@@ -4034,7 +4039,7 @@ contains
       table( 1).set_subhead("  A")
       table( 2).set_heading("Grp")
       table( 2).set_subhead("  B")
-      table( 3).set_heading("min R(AB)")
+      table( 3).set_heading("min r(AB)")
       table( 3).set_subheading("/Angs.")
       table( 3).set_width_from(ONE)
       table( 4).set_heading("n_A")
@@ -4069,9 +4074,9 @@ contains
       n_pair = n_pair.triangle_number
       g_A.create(n_pair)
       g_B.create(n_pair)
+      rAB.create(n_pair)
       n_A.create(n_pair)
       n_B.create(n_pair)
-      rAB.create(n_pair)
       nAB.create(n_pair)
       sAB.create(n_pair)
       cAB.create(n_pair)
@@ -4086,10 +4091,12 @@ contains
          i = i + 1
          g_A(i) = a
          g_B(i) = b
+         grA    = .atom_group(a)[:]
+         grB    = .atom_group(b)[:]
+         distAB = .atom.min_distance_between(grA,grB)
+         rAB(i) = distAB*ANGSTROM_PER_BOHR
          n_A(i) = .n1(a)
          n_B(i) = .n1(b)
-         distAB = .atom.min_bond_distance(.atom_group(a).element,.atom_group(b).element)
-         rAB(i) = distAB*ANGSTROM_PER_BOHR
          nAB(i) = .n2(a,b)
          sAB(i) = .n1(a) + .n1(b) - .n2(a,b)
          cAB(i) = .cov_index(a,b)
@@ -4103,9 +4110,9 @@ contains
       ! Set table data
       table( 1).set_values(g_A)
       table( 2).set_values(g_B)
-      table( 3).set_values(n_A)
-      table( 4).set_values(n_B)
-      table( 5).set_values(rAB)
+      table( 3).set_values(rAB)
+      table( 4).set_values(n_A)
+      table( 5).set_values(n_B)
       table( 6).set_values(nAB)
       table( 7).set_values(sAB)
       table( 8).set_values(cAB)

foofiles/vec{atom}.foo

@@ -8859,8 +8859,8 @@ contains
    end
 
 
-   min_bond_distance(group_a,group_b) result (res) ::: PURE
-   ! Return the minimum bond distance between the atoms whose 
+   min_distance_between(group_a,group_b) result (res) ::: PURE
+   ! Return the minimum distance between the atoms whose 
    ! indices are listed in "group_a" and "group_b".
       self    :: IN
       group_a :: VEC{INT}, IN