Added back constructPhaseFile() and constructPhaseXML().

All molten salt problems were broken and some brine problems were broken.

ext/SConscript

@@ -3,6 +3,10 @@ from buildutils import *
 Import('env', 'build', 'install', 'libraryTargets')
 localenv = env.Clone()
 
+#
+# prep function seem to return the environment
+#
+
 def prep_default(env):
     return env.Clone()
 
@@ -19,6 +23,15 @@ def prep_f2c(env):
         localenv.Append(CPPDEFINES=['USE_CLOCK'])
     if not localenv['HAS_UNISTD_H']:
         localenv.Append(CPPDEFINES=['MSDOS'])
+        if env['VERBOSE'] :
+           print "INFO 2:    prep_f2c: adding MSDOS to CPPDEFINES"
+
+    if env['VERBOSE'] :
+           localenv.Append(CPPDEFINES=['added'])
+           print "INFO 2:     CPPDEFINES     ", localenv['CPPDEFINES']
+           #print "localenv", localenv.Dump()
+           #exit(0)
+
  
     # The F2C code generates a lot of warnings designed to catch
     # programmer errors, but since this is autogenerated code, those
@@ -52,6 +65,10 @@ def prep_gtest(env):
                     CPPDEFINES={'GTEST_HAS_PTHREAD': 0})
     return localenv
 
+# libs is a list of length 3
+#     0 subdir for execution
+#     1 file extension
+#     2 function pointer
 # (subdir, (file extensions), prepfunction)
 libs = [('libexecstream', ['cpp'], prep_default)]
 
@@ -95,6 +112,10 @@ if env['use_sundials'] == 'n':
 
 
 for subdir, extensions, prepFunction in libs:
+
+    if env['VERBOSE']:
+      print "INFO 2: Prep the environment for ", subdir, ' with extensions ', extensions, ' by calling func ', prepFunction.__name__
+
     localenv = prepFunction(env)
 
     if localenv['single_library']:
@@ -120,6 +141,10 @@ for subdir, extensions, prepFunction in libs:
         else:
             sharedLibName = libName
 
+        if env['VERBOSE'] :
+            print "INFO 2:" , subdir , ' with ', extensions
+            print "        libName = ", libName, " sharedLibName = ", sharedLibName
+           
         objects = localenv.SharedObject(mglob(localenv, subdir, *extensions))
 
         # Build the static library

include/cantera/thermo/HMWSoln.h

@@ -1333,6 +1333,46 @@ public:
      */
     ThermoPhase* duplMyselfAsThermoPhase() const;
 
+
+     //!   Import, construct, and initialize a HMWSoln phase
+     /*!   specification from an XML tree into the current object.
+      *
+      * This routine is a precursor to constructPhaseXML(XML_Node*)
+      * routine, which does most of the work.
+      *
+      * @param inputfile XML file containing the description of the phase
+      *
+      * @param id  Optional parameter identifying the name of the
+      *            phase. If none is given, the first XML
+      *            phase element will be used.
+      */
+     void constructPhaseFile(std::string inputFile, std::string id);
+
+     //!   Import and initialize a HMWSoln phase specification in an XML tree into the current object.
+     /*!
+      *   Here we read an XML description of the phase.
+      *   We import descriptions of the elements that make up the
+      *   species in a phase.
+      *   We import information about the species, including their
+      *   reference state thermodynamic polynomials. We then freeze
+      *   the state of the species.
+      *
+      *   Then, we read the species molar volumes from the xml
+      *   tree to finish the initialization.
+      *
+      * @param phaseNode This object must be the phase node of a complete XML tree
+      *             description of the phase, including all of the
+      *             species data. In other words while "phase" must
+      *             point to an XML phase object, it must have
+      *             sibling nodes "speciesData" that describe
+      *             the species in the phase.
+      *
+      * @param id   ID of the phase. If nonnull, a check is done
+      *             to see if phaseNode is pointing to the phase
+      *             with the correct id.
+      */
+     void constructPhaseXML(XML_Node& phaseNode, std::string id);
+
     /**
      * @name  Utilities
      * @{

include/cantera/thermo/IonsFromNeutralVPSSTP.h

@@ -159,6 +159,50 @@ public:
      */
     virtual ThermoPhase* duplMyselfAsThermoPhase() const;
 
+    /// The following methods are used in the process of constructing
+    /// the phase and setting its parameters from a specification in an
+    /// input file.
+
+    //! Initialization of an IonsFromNeutralVPSSTP phase using an xml file
+    /*!
+     * This routine is a precursor to initThermo(XML_Node*)
+     * routine, which does most of the work.
+     *
+     * @param inputFile XML file containing the description of the phase
+     *
+     * @param id  Optional parameter identifying the name of the
+     *            phase. If none is given, the first XML
+     *            phase element will be used.
+     */
+    void constructPhaseFile(std::string inputFile, std::string id);
+
+    //!   Import and initialize an IonsFromNeutralVPSSTP phase
+    //!   specification in an XML tree into the current object.
+    /*!
+     *   Here we read an XML description of the phase.
+     *   We import descriptions of the elements that make up the
+     *   species in a phase.
+     *   We import information about the species, including their
+     *   reference state thermodynamic polynomials. We then freeze
+     *   the state of the species.
+     *
+     *   Then, we read the species molar volumes from the xml
+     *   tree to finish the initialization.
+     *
+     * @param phaseNode This object must be the phase node of a complete XML tree
+     *             description of the phase, including all of the
+     *             species data. In other words while "phase" must
+     *             point to an XML phase object, it must have
+     *             sibling nodes "speciesData" that describe
+     *             the species in the phase.
+     *
+     * @param id   ID of the phase. If nonnull, a check is done
+     *             to see if phaseNode is pointing to the phase
+     *             with the correct id.
+     */
+    void constructPhaseXML(XML_Node& phaseNode, std::string id);
+
+
     /**
      *
      * @name  Utilities

platform/posix/SConscript

@@ -107,6 +107,9 @@ if not localenv['build_with_f2c']:
 else:
     localenv['mak_syslibs'] = ''
 
+# print localenv.Dump()
+# exit(0)
+
 mak = build(localenv.SubstFile('Cantera.mak', 'Cantera.mak.in'))
 install('$inst_incdir', mak)
 

src/thermo/HMWSoln_input.cpp

@@ -1047,6 +1047,206 @@ void HMWSoln::initThermo()
     initLengths();
 }
 
+ /*
+  *   Import, construct, and initialize a HMWSoln phase
+  *   specification from an XML tree into the current object.
+  *
+  * This routine is a precursor to constructPhaseXML(XML_Node*)
+  * routine, which does most of the work.
+  *
+  * @param infile XML file containing the description of the
+  *        phase
+  *
+  * @param id  Optional parameter identifying the name of the
+  *            phase. If none is given, the first XML
+  *            phase element will be used.
+  */
+ void HMWSoln::constructPhaseFile(std::string inputFile, std::string id) {
+
+   if (inputFile.size() == 0) {
+     throw CanteraError("HMWSoln:constructPhaseFile",
+                        "input file is null");
+   }
+   string path = findInputFile(inputFile);
+   std::ifstream fin(path.c_str());
+   if (!fin) {
+     throw CanteraError("HMWSoln:constructPhaseFile","could not open "
+                        +path+" for reading.");
+   }
+   /*
+    * 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);
+   constructPhaseXML(*fxml_phase, id);
+   delete fxml;
+ }
+
+ /*
+  *   Import, construct, and initialize a HMWSoln phase
+  *   specification from an XML tree into the current object.
+  *
+  *   Most of the work is carried out by the cantera base
+  *   routine, importPhase(). That routine imports all of the
+  *   species and element data, including the standard states
+  *   of the species.
+  *
+  *   Then, In this routine, we read the information
+  *   particular to the specification of the activity
+  *   coefficient model for the Pitzer parameterization.
+  *
+  *   We also read information about the molar volumes of the
+  *   standard states if present in the XML file.
+  *
+  * @param phaseNode This object must be the phase node of a
+  *             complete XML tree
+  *             description of the phase, including all of the
+  *             species data. In other words while "phase" must
+  *             point to an XML phase object, it must have
+  *             sibling nodes "speciesData" that describe
+  *             the species in the phase.
+  * @param id   ID of the phase. If nonnull, a check is done
+  *             to see if phaseNode is pointing to the phase
+  *             with the correct id.
+  */
+ void HMWSoln::constructPhaseXML(XML_Node& phaseNode, std::string id) {
+   string stemp;
+   if (id.size() > 0) {
+     string idp = phaseNode.id();
+     if (idp != id) {
+       throw CanteraError("HMWSoln::constructPhaseXML",
+                          "phasenode and Id are incompatible");
+     }
+   }
+
+   /*
+    * Find the Thermo XML node
+    */
+   if (!phaseNode.hasChild("thermo")) {
+     throw CanteraError("HMWSoln::constructPhaseXML",
+                        "no thermo XML node");
+   }
+   XML_Node& thermoNode = phaseNode.child("thermo");
+
+   /*
+    * Possibly change the form of the standard concentrations
+    */
+   if (thermoNode.hasChild("standardConc")) {
+     XML_Node& scNode = thermoNode.child("standardConc");
+     m_formGC = 2;
+     stemp = scNode.attrib("model");
+     string formString = lowercase(stemp);
+     if (formString != "") {
+       if (formString == "unity") {
+         m_formGC = 0;
+         printf("exit standardConc = unity not done\n");
+         exit(EXIT_FAILURE);
+       } else if (formString == "molar_volume") {
+         m_formGC = 1;
+         printf("exit standardConc = molar_volume not done\n");
+         exit(EXIT_FAILURE);
+       } else if (formString == "solvent_volume") {
+         m_formGC = 2;
+       } else {
+         throw CanteraError("HMWSoln::constructPhaseXML",
+                            "Unknown standardConc model: " + formString);
+       }
+     }
+   }
+   /*
+    * Get the Name of the Solvent:
+    *      <solvent> solventName </solvent>
+    */
+   string solventName = "";
+   if (thermoNode.hasChild("solvent")) {
+     XML_Node& scNode = thermoNode.child("solvent");
+     vector<string> nameSolventa;
+     getStringArray(scNode, nameSolventa);
+     int nsp = static_cast<int>(nameSolventa.size());
+     if (nsp != 1) {
+       throw CanteraError("HMWSoln::constructPhaseXML",
+                          "badly formed solvent XML node");
+     }
+     solventName = nameSolventa[0];
+   }
+
+   /*
+    * Determine the form of the Pitzer model,
+    *   We will use this information to size arrays below.
+    */
+   if (thermoNode.hasChild("activityCoefficients")) {
+     XML_Node& scNode = thermoNode.child("activityCoefficients");
+     stemp = scNode.attrib("model");
+     string formString = lowercase(stemp);
+     if (formString != "") {
+       if        (formString == "pitzer" || formString == "default") {
+         m_formPitzer = PITZERFORM_BASE;
+       } else if (formString == "base") {
+         m_formPitzer = PITZERFORM_BASE;
+       } else {
+         throw CanteraError("HMWSoln::constructPhaseXML",
+                            "Unknown Pitzer ActivityCoeff model: "
+                            + formString);
+       }
+     }
+     /*
+      * Determine the form of the temperature dependence
+      * of the Pitzer activity coefficient model.
+      */
+     stemp = scNode.attrib("TempModel");
+     formString = lowercase(stemp);
+     if (formString != "") {
+       if (formString == "constant" || formString == "default") {
+         m_formPitzerTemp = PITZER_TEMP_CONSTANT;
+       } else if (formString == "linear") {
+         m_formPitzerTemp = PITZER_TEMP_LINEAR;
+       } else if (formString == "complex" || formString == "complex1") {
+         m_formPitzerTemp = PITZER_TEMP_COMPLEX1;
+       } else {
+         throw CanteraError("HMWSoln::constructPhaseXML",
+                            "Unknown Pitzer ActivityCoeff Temp model: "
+                            + formString);
+       }
+     }
+
+     /*
+      * Determine the reference temperature
+      * of the Pitzer activity coefficient model's temperature
+      * dependence formulation: defaults to 25C
+      */
+     stemp = scNode.attrib("TempReference");
+     formString = lowercase(stemp);
+     if (formString != "") {
+       m_TempPitzerRef = atofCheck(formString.c_str());
+     } else {
+       m_TempPitzerRef = 273.15 + 25;
+     }
+
+   }
+
+   /*
+    * Call the Cantera importPhase() function. This will import
+    * all of the species into the phase. This will also handle
+    * all of the solvent and solute standard states
+    */
+   bool m_ok = importPhase(phaseNode, this);
+   if (!m_ok) {
+     throw CanteraError("HMWSoln::constructPhaseXML","importPhase failed ");
+   }
+
+ }
+
+
+
 /**
  * Process the XML file after species are set up.
  *

src/thermo/IonsFromNeutralVPSSTP.cpp

@@ -240,6 +240,146 @@ IonsFromNeutralVPSSTP::duplMyselfAsThermoPhase() const
     return new IonsFromNeutralVPSSTP(*this);
 }
 
+/*
+ *   Import, construct, and initialize a phase
+ *   specification from an XML tree into the current object.
+ *
+ * This routine is a precursor to constructPhaseXML(XML_Node*)
+ * routine, which does most of the work.
+ *
+ * @param infile XML file containing the description of the
+ *        phase
+ *
+ * @param id  Optional parameter identifying the name of the
+ *            phase. If none is given, the first XML
+ *            phase element will be used.
+ */
+void IonsFromNeutralVPSSTP::constructPhaseFile(std::string inputFile, std::string id) {
+
+  if (inputFile.size() == 0) {
+    throw CanteraError("MargulesVPSSTP:constructPhaseFile",
+                       "input file is null");
+  }
+  string path = findInputFile(inputFile);
+  std::ifstream fin(path.c_str());
+  if (!fin) {
+    throw CanteraError("MargulesVPSSTP:constructPhaseFile","could not open "
+                       +path+" for reading.");
+  }
+  /*
+   * 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("MargulesVPSSTP:constructPhaseFile",
+                       "ERROR: Can not find phase named " +
+                       id + " in file named " + inputFile);
+  }
+  fxml_phase->copy(&phaseNode_XML);
+  constructPhaseXML(*fxml_phase, id);
+  delete fxml;
+}
+
+/*
+ *   Import, construct, and initialize a HMWSoln phase
+ *   specification from an XML tree into the current object.
+ *
+ *   Most of the work is carried out by the cantera base
+ *   routine, importPhase(). That routine imports all of the
+ *   species and element data, including the standard states
+ *   of the species.
+ *
+ *   Then, In this routine, we read the information
+ *   particular to the specification of the activity
+ *   coefficient model for the Pitzer parameterization.
+ *
+ *   We also read information about the molar volumes of the
+ *   standard states if present in the XML file.
+ *
+ * @param phaseNode This object must be the phase node of a
+ *             complete XML tree
+ *             description of the phase, including all of the
+ *             species data. In other words while "phase" must
+ *             point to an XML phase object, it must have
+ *             sibling nodes "speciesData" that describe
+ *             the species in the phase.
+ * @param id   ID of the phase. If nonnull, a check is done
+ *             to see if phaseNode is pointing to the phase
+ *             with the correct id.
+ */
+
+void IonsFromNeutralVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id) {
+   string stemp;
+   if (id.size() > 0) {
+     string idp = phaseNode.id();
+     if (idp != id) {
+       throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                          "phasenode and Id are incompatible");
+     }
+   }
+
+   /*
+    * Find the thermo XML node
+    */
+   if (!phaseNode.hasChild("thermo")) {
+     throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                        "no thermo XML node");
+   }
+   XML_Node& thermoNode = phaseNode.child("thermo");
+
+
+
+   /*
+    * Make sure that the thermo model is IonsFromNeutralMolecule
+    */
+   stemp = thermoNode.attrib("model");
+   string formString = lowercase(stemp);
+   if (formString != "ionsfromneutralmolecule") {
+     throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                        "model name isn't IonsFromNeutralMolecule: " + formString);
+   }
+
+   /*
+    * Find the Neutral Molecule Phase
+    */
+   if (!thermoNode.hasChild("neutralMoleculePhase")) {
+     throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                        "no neutralMoleculePhase XML node");
+   }
+   XML_Node& neutralMoleculeNode = thermoNode.child("neutralMoleculePhase");
+
+   string nsource = neutralMoleculeNode["datasrc"];
+   XML_Node *neut_ptr = get_XML_Node(nsource, 0);
+   if (!neut_ptr) {
+     throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                        "neut_ptr = 0");
+   }
+
+   /*
+    *  Create the neutralMolecule ThermoPhase if we haven't already
+    */
+   if (!neutralMoleculePhase_) {
+     neutralMoleculePhase_  = newPhase(*neut_ptr);
+   }
+
+   /*
+    * Call the Cantera importPhase() function. This will import
+    * all of the species into the phase. This will also handle
+    * all of the solvent and solute standard states
+    */
+   bool m_ok = importPhase(phaseNode, this);
+   if (!m_ok) {
+     throw CanteraError("IonsFromNeutralVPSSTP::constructPhaseXML",
+                        "importPhase failed ");
+   }
+
+ }
+
+
 /*
  *  -------------- Utilities -------------------------------
  */

src/thermo/ThermoFactory.cpp

@@ -247,7 +247,22 @@ ThermoPhase* newPhase(XML_Node& xmlphase)
     const XML_Node& th = xmlphase.child("thermo");
     string model = th["model"];
     ThermoPhase* t = newThermoPhase(model);
-    importPhase(xmlphase, t);
+    if (model == "singing cows") {
+      throw CanteraError("ThermoPhase::newPhase", "Cows don't sing");
+    }
+    else if (model == "HMW") {
+      HMWSoln* p = dynamic_cast<HMWSoln*>(t);
+      p->constructPhaseXML(xmlphase,"");
+    }
+    else if (model == "IonsFromNeutralMolecule") {
+      IonsFromNeutralVPSSTP* p = dynamic_cast<IonsFromNeutralVPSSTP*>(t);
+      p->constructPhaseXML(xmlphase,"");
+    }
+    else {
+      importPhase(xmlphase, t);
+    }
+    //return t;
+    //importPhase(xmlphase, t);
     return t;
 }