Changed the conventions on specifying the element E.

Now it is optional to specify E in the atomArray. The value is
calculated from the species Charge automatically. E is still in the
element list for the phase.

  Now, you don't have to put E explicitly in the element list for
the phase. It's automatically included if it's needed.

Cantera/src/thermo/Constituents.cpp

@@ -156,9 +156,10 @@ namespace Cantera {
      * -> Passthrough to the Element lvl.
      */
     void Constituents::
-    addUniqueElement(const std::string& symbol, doublereal weight)
+    addUniqueElement(const std::string& symbol, doublereal weight,
+		     int atomicNumber, doublereal entropy298)
     {
-      m_Elements->addUniqueElement(symbol, weight);
+      m_Elements->addUniqueElement(symbol, weight, atomicNumber, entropy298);
     }
 
     void Constituents::
@@ -290,12 +291,13 @@ namespace Cantera {
      *            and it need not be supplied on the command line.
      */
     void Constituents::
-    addSpecies(const std::string& name, const doublereal* comp,
+    addSpecies(const std::string& name, doublereal* comp,
 	       doublereal charge, doublereal size) {  
       m_Elements->freezeElements();
       m_speciesNames.push_back(name);
       m_speciesCharge.push_back(charge);
       m_speciesSize.push_back(size);
+      vector_fp compNew;;
       double wt = 0.0;
       int m_mm = m_Elements->nElements();
       const vector_fp &aw = m_Elements->atomicWeights();
@@ -304,12 +306,40 @@ namespace Cantera {
         if (eindex >= 0) {
           doublereal ecomp = comp[eindex];
           if (fabs (charge + ecomp) > 0.001) {
-            throw CanteraError("Constituents::addSpecies",
-                              "Input charge and element E compositions differ for species " + name);
+	    if (ecomp != 0.0) {
+	      throw CanteraError("Constituents::addSpecies",
+				 "Input charge and element E compositions differ for species " + name);
+	    } else {
+	      // Just fix up the element E composition based on the input species charge
+	      comp[eindex] = -charge;
+	    }
           }
         } else {
-          throw CanteraError("Constituents::addSpecies",
-                             "Input charge and element E compositions differ for species " + name);
+	  m_Elements->m_elementsFrozen = false;
+	  addUniqueElement("E", 0.000545, 0, 0.0);
+	  m_Elements->m_elementsFrozen = true;
+	  m_mm = m_Elements->nElements();
+	  if (m_kk > 0) {
+	    vector_fp old(m_speciesComp);
+	    m_speciesComp.resize(m_kk*m_mm, 0.0);
+	    for (int k = 0; k < m_kk; k++) {
+	      int m_old = m_mm - 1;
+	      for (int m = 0; m < m_old; m++) {
+		m_speciesComp[k * m_mm + m] =  old[k * (m_old) + m];
+	      }
+	      m_speciesComp[k * (m_mm) + (m_mm-1)] = 0.0; 
+	    }
+	  }
+	  eindex = m_Elements->elementIndex("E");
+	  compNew.resize(m_mm);
+	  for (int m = 0; m < m_mm-1; m++) {
+	    compNew[m] = comp[m];
+	  }
+	  compNew[m_mm-1] = - charge;
+	  comp = DATA_PTR(compNew);
+	  //comp[eindex] = -charge;
+	  // throw CanteraError("Constituents::addSpecies",
+	  //                 "Element List doesn't include E, yet this species has charge:" + name);
         }
       }
       for (int m = 0; m < m_mm; m++) {
@@ -330,7 +360,7 @@ namespace Cantera {
      *   existing species in the phase.
      */
     void Constituents::
-    addUniqueSpecies(const std::string& name, const doublereal* comp, 
+    addUniqueSpecies(const std::string& name, doublereal* comp, 
 		     doublereal charge, doublereal size) {
       vector<string>::const_iterator it = m_speciesNames.begin();
       for (int k = 0; k < m_kk; k++) {

Cantera/src/thermo/Constituents.h

@@ -18,12 +18,12 @@
 
 
 #include "ct_defs.h"
-//using namespace std;
 
 #include "SpeciesThermo.h"
 #include "ctexceptions.h"
 #include "stringUtils.h"
 #include "xml.h"
+#include "Elements.h"
 
 namespace Cantera {
 
@@ -187,7 +187,9 @@ namespace Cantera {
        * @param symbol  String symbol of the element
        * @param weight  Atomic weight of the element (kg kmol-1).
        */
-      void addUniqueElement(const std::string& symbol, doublereal weight);
+      void addUniqueElement(const std::string& symbol, doublereal weight,
+			    int atomicNumber = 0,
+			    doublereal entropy298 = ENTROPY298_UNKNOWN);
 
       //! Adde an element, checking for uniqueness
       /*!
@@ -256,7 +258,7 @@ namespace Cantera {
        * They are not usually called by user programs.
        */
       //@{
-      void addSpecies(const std::string& name, const doublereal* comp,
+      void addSpecies(const std::string& name, doublereal* comp,
 		      doublereal charge = 0.0, doublereal size = 1.0);
 
       //! Add a species to the phase, checking for uniqueness of the name
@@ -270,7 +272,7 @@ namespace Cantera {
        * @param charge  Charge of the species. Defaults to zero.
        * @param size    Size of the species (meters). Defaults to 1 meter.
        */
-      void addUniqueSpecies(const std::string& name, const doublereal* comp,
+      void addUniqueSpecies(const std::string& name, doublereal* comp,
 			    doublereal charge = 0.0, 
 			    doublereal size = 1.0);
       

Cantera/src/thermo/Elements.h

@@ -278,6 +278,7 @@ namespace Cantera {
 	 */
 	static std::vector<Elements *> Global_Elements_List;
 
+      friend class Constituents;
     };  
     
 }  // namespace