diff --git a/include/cantera/kinetics/InterfaceKinetics.h b/include/cantera/kinetics/InterfaceKinetics.h
index 98b57cc23..3b3258c19 100644
--- a/include/cantera/kinetics/InterfaceKinetics.h
+++ b/include/cantera/kinetics/InterfaceKinetics.h
@@ -312,9 +312,7 @@ public:
      * For a reaction rate that was given in units of Amps/m2 (exchange current
      *  density formulation with iECDFormulation == true), convert the rate to
      *  kmoles/m2/s.
-     *  RENAMED THIS METHOD from "apply" to "convert"
      */
-
     void convertExchangeCurrentDensityFormulation(doublereal* const kfwd);
 
     //! Set the existence of a phase in the reaction object
diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index 9012a00cc..989094783 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -111,10 +111,24 @@ public:
     //!     @param right Reference to the class to be used in the copy
     Phase& operator=(const Phase& right);
 
-    //! Returns a reference to the XML_Node stored for the phase.
-    //! The XML_Node for the phase contains all of the input data used to set
-    //! up the model for the phase, during its initialization.
-    XML_Node& xml();
+    //! Returns a const reference to the XML_Node that describes the phase.
+    /*!
+     *       The XML_Node for the phase contains all of the input data used to set
+     *       up the model for the phase during its initialization.
+     *
+     */
+    XML_Node& xml() const;
+
+    //! Stores the XML tree information for the current phase
+    /*!
+     *  This function now stores the complete XML_Node tree as read into the code
+     *  via a file. This is needed to move around within the XML tree during
+     *  construction of transport and kinetics mechanisms after copy
+     *  construction operations.
+     *
+     *  @param xmlPhase Reference to the XML node corresponding to the phase
+     */
+    void setXMLdata(XML_Node& xmlPhase);   
 
     /*! @name Name and ID
      * Class Phase contains two strings that identify a phase. The ID is the
@@ -122,13 +136,13 @@ public:
      * initialize a phase when it is read. The name field is also initialized
      * to the value of the ID attribute of the XML phase node.
      *
-     * However, the name field  may be changed to another value during the
+     * However, the name field may be changed to another value during the
      * course of a calculation. For example, if a phase is located in two
-     * places, but has the same constitutive input, the ids of the two phases
+     * places, but has the same constitutive input, the IDs of the two phases
      * will be the same, but the names of the two phases may be different.
      *
      * It is an error to have two phases in a single problem with the same name
-     * or the same id (or the name from one phase being the same as the id of
+     * and ID (or the name from one phase being the same as the id of
      * another phase). Thus, it is expected that there is a 1-1 correspondence
      * between names and unique phases within a Cantera problem.
      */
@@ -138,10 +152,15 @@ public:
     std::string id() const;
 
     //! Set the string id for the phase.
-    //!     @param id String id of the phase
+    /*!
+     *    @param id String id of the phase
+     */
     void setID(const std::string& id);
 
     //! Return the name of the phase.
+    /*!
+     *   Names are unique within a Cantera problem.
+     */
     std::string name() const;
 
     //! Sets the string name for the phase.
diff --git a/src/base/xml.cpp b/src/base/xml.cpp
index 64fc27b47..d53a3f9ef 100644
--- a/src/base/xml.cpp
+++ b/src/base/xml.cpp
@@ -1101,9 +1101,7 @@ XML_Node* findXMLPhase(XML_Node* root,
         idattrib = root->id();
         if (idtarget == idattrib) {
             return root;
-        } else {
-            return               0;
-        }
+        } 
     }
 
     const vector<XML_Node*> &vsc = root->children();
@@ -1121,12 +1119,12 @@ XML_Node* findXMLPhase(XML_Node* root,
     }
     for (size_t n = 0; n < root->nChildren(); n++) {
         sc = vsc[n];
-        if (sc->name() != "phase") {
+        //if (sc->name() != "phase") {
             scResult = findXMLPhase(sc, idtarget);
             if (scResult) {
                 return scResult;
             }
-        }
+        //}
     }
     return scResult;
 }
diff --git a/src/kinetics/InterfaceKinetics.cpp b/src/kinetics/InterfaceKinetics.cpp
index cbd668d06..7d9d14566 100644
--- a/src/kinetics/InterfaceKinetics.cpp
+++ b/src/kinetics/InterfaceKinetics.cpp
@@ -453,7 +453,7 @@ void InterfaceKinetics::applyButlerVolmerCorrection(doublereal* const kf)
     }
 }
 
-/**
+/*
  * For a reaction rate that was given in units of Amps/m2 (exchange current
  *  density formulation with iECDFormulation == true), convert the rate to
  *  kmoles/m2/s.
diff --git a/src/kinetics/importKinetics.cpp b/src/kinetics/importKinetics.cpp
index e748a3145..612879c88 100644
--- a/src/kinetics/importKinetics.cpp
+++ b/src/kinetics/importKinetics.cpp
@@ -953,10 +953,12 @@ bool importKinetics(const XML_Node& phase, std::vector<ThermoPhase*> th,
     string owning_phase = phase["id"];
 
     bool check_for_duplicates = false;
-    if (phase.parent()->hasChild("validate")) {
-        const XML_Node& d = phase.parent()->child("validate");
-        if (d["reactions"] == "yes") {
-            check_for_duplicates = true;
+    if (phase.parent()) {
+        if (phase.parent()->hasChild("validate")) {
+            const XML_Node& d = phase.parent()->child("validate");
+            if (d["reactions"] == "yes") {
+                check_for_duplicates = true;
+            }
         }
     }
 
diff --git a/src/thermo/HMWSoln_input.cpp b/src/thermo/HMWSoln_input.cpp
index 072f1f927..be9c446e9 100644
--- a/src/thermo/HMWSoln_input.cpp
+++ b/src/thermo/HMWSoln_input.cpp
@@ -990,16 +990,16 @@ void HMWSoln::constructPhaseFile(std::string inputFile, std::string id_)
      * The phase object automatically constructs an XML object.
      * Use this object to store information.
      */
-    XML_Node& phaseNode_XML = xml();
     XML_Node* fxml = new XML_Node();
     fxml->build(fin);
     XML_Node* fxml_phase = findXMLPhase(fxml, id_);
+     
     if (!fxml_phase) {
         throw CanteraError("HMWSoln:constructPhaseFile",
                            "ERROR: Can not find phase named " +
                            id_ + " in file named " + inputFile);
     }
-    fxml_phase->copy(&phaseNode_XML);
+    setXMLdata(*fxml_phase);
     constructPhaseXML(*fxml_phase, id_);
     delete fxml;
 }
diff --git a/src/thermo/IonsFromNeutralVPSSTP.cpp b/src/thermo/IonsFromNeutralVPSSTP.cpp
index 16b9393ab..5a7e4c052 100644
--- a/src/thermo/IonsFromNeutralVPSSTP.cpp
+++ b/src/thermo/IonsFromNeutralVPSSTP.cpp
@@ -213,7 +213,7 @@ void IonsFromNeutralVPSSTP::constructPhaseFile(std::string inputFile, std::strin
      * The phase object automatically constructs an XML object.
      * Use this object to store information.
      */
-    XML_Node& phaseNode_XML = xml();
+    //XML_Node& phaseNode_XML = xml();
     XML_Node* fxml = new XML_Node();
     fxml->build(fin);
     XML_Node* fxml_phase = findXMLPhase(fxml, id_);
@@ -222,7 +222,8 @@ void IonsFromNeutralVPSSTP::constructPhaseFile(std::string inputFile, std::strin
                            "ERROR: Can not find phase named " +
                            id_ + " in file named " + inputFile);
     }
-    fxml_phase->copy(&phaseNode_XML);
+    setXMLdata(*fxml_phase);
+    //fxml_phase->copy(&phaseNode_XML);
     constructPhaseXML(*fxml_phase, id_);
     delete fxml;
 }
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 099aff0bf..88f095c84 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -46,7 +46,7 @@ Phase::Phase(const Phase& right) :
     m_elem_type(0)
 {
     // Use the assignment operator to do the actual copying
-    *this = operator=(right);
+    operator=(right);
 }
 
 Phase& Phase::operator=(const Phase& right)
@@ -86,11 +86,23 @@ Phase& Phase::operator=(const Phase& right)
      * to have our own individual copies of the XML data tree
      * in each object
      */
-    delete m_xml;
-    m_xml = 0;
+    if (m_xml) {
+        XML_Node* rroot = &(m_xml->root());
+        delete rroot;
+        m_xml = 0;
+    }
     if (right.m_xml) {
-        m_xml = new XML_Node();
-        (right.m_xml)->copy(m_xml);
+        XML_Node *rroot = &(right.m_xml->root());
+        XML_Node *root_xml = new XML_Node();
+        (rroot)->copy(root_xml);
+        string iidd = right.m_xml->id();
+        m_xml = findXMLPhase(root_xml, iidd); 
+        if (!m_xml) {
+          throw CanteraError("Phase::operator=()", "Confused: Couldn't find original phase " + iidd);
+        }
+        if (&(m_xml->root()) != root_xml) {
+          throw CanteraError("Phase::operator=()", "confused: root changed");
+        }
     }
     m_id    = right.m_id;
     m_name  = right.m_name;
@@ -100,15 +112,38 @@ Phase& Phase::operator=(const Phase& right)
 
 Phase::~Phase()
 {
-    delete m_xml;
+    if (m_xml) {
+        XML_Node* xroot = &(m_xml->root());
+        delete xroot;
+    }
     m_xml = 0;
 }
 
-XML_Node& Phase::xml()
+XML_Node& Phase::xml() const
 {
     return *m_xml;
 }
 
+void Phase::setXMLdata(XML_Node& xmlPhase)
+{
+    XML_Node* xroot = &(xmlPhase.root());
+    XML_Node *root_xml = new XML_Node();
+    (xroot)->copy(root_xml);
+    std::string iidd = xmlPhase.id();
+    if (m_xml) {
+       XML_Node *rOld = &(m_xml->root());
+       delete rOld;
+       m_xml = 0;
+    }
+    m_xml = findXMLPhase(root_xml, iidd);
+    if (!m_xml) {
+        throw CanteraError("Phase::setXMLdata()", "confused");
+    }
+    if (&(m_xml->root()) != root_xml) {
+        throw CanteraError("Phase::setXMLdata()", "confused");
+    }
+}
+
 std::string Phase::id() const
 {
     return m_id;
diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp
index 424933e92..37da68aa9 100644
--- a/src/thermo/ThermoFactory.cpp
+++ b/src/thermo/ThermoFactory.cpp
@@ -333,9 +333,7 @@ bool importPhase(XML_Node& phase, ThermoPhase* th,
      * we are about to use to construct the object. We will then
      * be able to resurrect the information later by calling xml().
      */
-    XML_Node& phaseNode_XML = th->xml();
-    phaseNode_XML.clear();
-    phase.copy(&phaseNode_XML);
+    th->setXMLdata(phase);
 
     // set the id attribute of the phase to the 'id' attribute in the XML tree.
     th->setID(phase.id());
diff --git a/test_problems/SConscript b/test_problems/SConscript
index 271ddefbc..e560bf784 100644
--- a/test_problems/SConscript
+++ b/test_problems/SConscript
@@ -41,6 +41,7 @@ class Test(object):
             self.artifacts = [self.artifacts]
         self.comparisons = kwargs.get('comparisons') or ()
         self.tolerance = kwargs.get('tolerance') or 1e-5 # error tolerance for CSV comparison
+        # self.tolerance = kwargs.get('tolerance') or 1e-7 # error tolerance for CSV comparison
         self.threshold = kwargs.get('threshold') or 1e-14 # error threshold for CSV comparison
 
         # ignore lines starting with specified strings when comparing output files