Copy provenance info when cloning a Hierarchy.

If any part of the Hierarchy has any attached provenance
information, also clone that and attach it to the cloned
Hierarchy in the same place.

modules/atom/include/Hierarchy.h

@@ -451,7 +451,7 @@ IMPATOMEXPORT bool get_is_heterogen(Hierarchy h);
 
 //! Clone the Hierarchy
 /** This method copies the Bond, Bonded, Atom,
-    Residue, and Domain data and the particle name to the
+    Residue, Domain, and provenance data and the particle name to the
     new copies in addition to the Hierarchy relationships.
 
     \relates Hierarchy
@@ -460,7 +460,7 @@ IMPATOMEXPORT Hierarchy create_clone(Hierarchy d);
 
 //! Clone the node in the Hierarchy
 /** This method copies the Atom,
-    Residue, Chain and Domain data and the particle name.
+    Residue, Chain, Domain, and provenance data and the particle name.
 
     \relates Hierarchy
 */

modules/atom/src/Hierarchy.cpp

@@ -438,6 +438,11 @@ Hierarchy clone_internal(Hierarchy d,
   if (Representation::get_is_setup(d.get_particle())) {
     nd = Representation::setup_particle(p, Representation(d.get_particle()));
   }
+  if (core::Provenanced::get_is_setup(d.get_particle())) {
+    core::Provenanced pd(d.get_particle());
+    core::Provenance prov = core::create_clone(pd.get_provenance());
+    core::Provenanced::setup_particle(p, prov);
+  }
 
   if (nd == Hierarchy()) nd = Hierarchy::setup_particle(p);
   using core::XYZ;