fix issues with multiple uses of create_bonds command

doc/src/create_bonds.rst

@@ -125,6 +125,16 @@ cannot appear in the neighbor list, to avoid creation of duplicate
 bonds.  The neighbor list for all atom type pairs must also extend to
 a distance that encompasses the *rmax* for new bonds to create.
 
+.. note::
+
+   If you want to create bonds between pairs of 1-3 or 1-4 atoms in
+   the current bond topology, then you need to use :doc:`special_bonds
+   lj 0 1 1 <special_bonds>` to insure those pairs appear in the
+   neighbor list.  They will not appear with the default special_bonds
+   settings which are zero for 1-2, 1-3, and 1-4 atoms.  1-3 or 1-4
+   atoms are those which are 2 hops or 3 hops apart in the bond
+   topology.
+
 An additional requirement for this style is that your system must be
 ready to perform a simulation.  This means, for example, that all
 :doc:`pair_style <pair_style>` coefficients be set via the

src/create_bonds.cpp

@@ -233,7 +233,7 @@ void CreateBonds::many()
   // build neighbor list this command needs based on earlier request
 
   NeighList *list = neighbor->lists[irequest];
-  neighbor->build_one(list);
+  neighbor->build_one(list,1);
 
   // loop over all neighs of each atom
   // compute distance between two atoms consistently on both procs

src/neigh_request.cpp

@@ -225,6 +225,8 @@ void NeighRequest::copy_request(NeighRequest *other, int skipflag)
   int i,j;
   int ntypes = atom->ntypes;
 
+  skip = other->skip;
+  
   if (other->iskip) {
     iskip = new int[ntypes+1];
     for (i = 1; i <= ntypes; i++)