From 96cf312ec6e765e174e1fc5b1403682158c02ccb Mon Sep 17 00:00:00 2001
From: Ray Speth <speth@mit.edu>
Date: Sat, 18 Apr 2015 16:19:00 -0400
Subject: [PATCH] [Thermo] Always add species using Species objects

Deprecate the non-Species-based addSpecies and addUniqueSpecies
functions.
---
 include/cantera/thermo/Phase.h   |  4 ++++
 src/thermo/FixedChemPotSSTP.cpp  | 14 ++++----------
 src/thermo/LatticeSolidPhase.cpp | 23 +----------------------
 src/thermo/Phase.cpp             |  6 ++++++
 4 files changed, 15 insertions(+), 32 deletions(-)

diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h
index caec1b758..2b70d1fdb 100644
--- a/include/cantera/thermo/Phase.h
+++ b/include/cantera/thermo/Phase.h
@@ -763,6 +763,8 @@ public:
     //! @see ignoreUndefinedElements addUndefinedElements throwUndefinedElements
     virtual bool addSpecies(shared_ptr<Species> spec);
 
+    //! @deprecated Use AddSpecies(shared_ptr<Species> spec) instead. To be
+    //! removed after Cantera 2.2.
     void addSpecies(const std::string& name, const doublereal* comp,
                     doublereal charge = 0.0, doublereal size = 1.0);
 
@@ -774,6 +776,8 @@ public:
     //! species.
     //!     @param charge  Charge of the species. Defaults to zero.
     //!     @param size    Size of the species (meters). Defaults to 1 meter.
+    //! @deprecated Use addSpecies(shared_ptr<Species> spec) instead. To be
+    //!     removed after Cantera 2.2.
     void addUniqueSpecies(const std::string& name, const doublereal* comp,
                           doublereal charge = 0.0,
                           doublereal size = 1.0);
diff --git a/src/thermo/FixedChemPotSSTP.cpp b/src/thermo/FixedChemPotSSTP.cpp
index b4d5a0671..a55801cad 100644
--- a/src/thermo/FixedChemPotSSTP.cpp
+++ b/src/thermo/FixedChemPotSSTP.cpp
@@ -84,18 +84,12 @@ FixedChemPotSSTP::FixedChemPotSSTP(const std::string& Ename, doublereal val) :
     setName(pname);
     setNDim(3);
     addElement(Ename);
-    vector_fp ecomp(nElements(), 0.0);
-    ecomp[0] = 1.0;
-    double chrg = 0.0;
-    addUniqueSpecies(pname, &ecomp[0], chrg, 0.0);
-    double c[4];
-    c[0] = 298.15;
-    c[1] = val;
-    c[2] = 0.0;
-    c[3] = 0.0;
+    shared_ptr<Species> sp(new Species(pname, parseCompString(Ename + ":1.0")));
+    double c[4] = {298.15, val, 0.0, 0.0};
     shared_ptr<SpeciesThermoInterpType> stit(
             newSpeciesThermoInterpType("const_cp", 0.1, 1e30, OneAtm, c));
-    m_spthermo->install_STIT(0, stit);
+    sp->thermo = stit;
+    addSpecies(sp);
     initThermo();
     m_p0 = OneAtm;
     m_tlast = 298.15;
diff --git a/src/thermo/LatticeSolidPhase.cpp b/src/thermo/LatticeSolidPhase.cpp
index 478c026a9..568eed052 100644
--- a/src/thermo/LatticeSolidPhase.cpp
+++ b/src/thermo/LatticeSolidPhase.cpp
@@ -341,31 +341,10 @@ void LatticeSolidPhase::installSlavePhases(Cantera::XML_Node* phaseNode)
             addElement(lp->elementName(es), aws[es], lp->atomicNumber(es),
                        lp->entropyElement298(es), lp->elementType(es));
         }
-        const std::vector<const XML_Node*> & spNode =  lp->speciesData();
         kstart = kk;
 
-
         for (size_t k = 0; k < lp->nSpecies(); k++) {
-            std::map<std::string, double> comp;
-            lp->getAtoms(k, DATA_PTR(constArr));
-            vector_fp ecomp(nElements(), 0.0);
-            for (size_t m = 0; m < lp->nElements(); m++) {
-                if (constArr[m] != 0.0) {
-                    size_t newIndex = elementIndex(lp->elementName(m));
-                    if (newIndex == npos) {
-                        throw CanteraError("LatticeSolidPhase::installSlavePhases",
-                                           "element not found");
-                    }
-                    ecomp[newIndex] = constArr[m];
-                }
-            }
-            addUniqueSpecies(lp->speciesName(k), &ecomp[0], lp->charge(k),
-                             lp->size(k));
-            shared_ptr<SpeciesThermoInterpType> stit(
-                newSpeciesThermoInterpType(spNode[k]->child("thermo")));
-            stit->validate(spNode[k]->attrib("name"));
-            m_spthermo->install_STIT(kk, stit);
-            m_speciesData.push_back(new XML_Node(*(spNode[k])));
+            addSpecies(lp->species(k));
             kk++;
         }
         /*
diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp
index 2c59ebbe4..9254ee30f 100644
--- a/src/thermo/Phase.cpp
+++ b/src/thermo/Phase.cpp
@@ -926,6 +926,9 @@ bool Phase::addSpecies(shared_ptr<Species> spec) {
 void Phase::addSpecies(const std::string& name_, const doublereal* comp,
                        doublereal charge_, doublereal size_)
 {
+    warn_deprecated("Phase::addSpecies(string, double*, double, double)",
+        "Use AddSpecies(shared_ptr<Species> spec) instead. To be removed "
+        "after Cantera 2.2.");
     compositionMap cmap;
     for (size_t i = 0; i < nElements(); i++) {
         if (comp[i]) {
@@ -939,6 +942,9 @@ void Phase::addSpecies(const std::string& name_, const doublereal* comp,
 void Phase::addUniqueSpecies(const std::string& name_, const doublereal* comp,
                              doublereal charge_, doublereal size_)
 {
+    warn_deprecated("Phase::addUniqueSpecies",
+        "Use AddSpecies(shared_ptr<Species> spec) instead. To be removed "
+        "after Cantera 2.2.");
     for (size_t k = 0; k < m_kk; k++) {
         if (m_speciesNames[k] == name_) {
             // We have found a match. Do some compatibility checks.