From 3ea77c5187842a212f70b7e37d1cf53ae68a3e10 Mon Sep 17 00:00:00 2001
From: Harry Moffat <hkmoffa@sandia.gov>
Date: Thu, 31 May 2007 23:51:49 +0000
Subject: [PATCH] Fixed a UMR in Reaction.h that was causing optimized versions
 of ck2cti to hang or seg fault sometimes.

Added some exceptions that captures cases where the thermo
parameters for a molecule were not found in the database.
Now, an error exit occurs, instead of before, where misc
garbage but written to the output file.
---
 Cantera/src/converters/Reaction.h   | 11 ++++++++---
 Cantera/src/converters/RxnSpecies.h |  2 ++
 Cantera/src/converters/ck2ct.cpp    | 28 ++++++++++++++++++++++++----
 Cantera/src/converters/ckr_defs.h   |  2 ++
 4 files changed, 36 insertions(+), 7 deletions(-)

diff --git a/Cantera/src/converters/Reaction.h b/Cantera/src/converters/Reaction.h
index 077419fa9..c626ea87e 100755
--- a/Cantera/src/converters/Reaction.h
+++ b/Cantera/src/converters/Reaction.h
@@ -93,13 +93,18 @@ namespace ckr {
 
 
     //////////////////////////////////////////////////////////////////////////
-    
+   
+    //! Specifies the Units for all reactions 
     /**
-     *   Specifies the units for all reactions.  
+     *   The default units are Cal per gmol for the activivation units
+     *   and the default number type is assumed to be gmol.
      */
-    
     class ReactionUnits {
     public:
+        ReactionUnits() :
+           ActEnergy(ckr::Cal_per_Mole),
+           Quantity(ckr::Moles) { }
+           
         int ActEnergy;    ///< Activation energy unit flag 
         int Quantity;     ///< Moles or molecules unit flag
     };
diff --git a/Cantera/src/converters/RxnSpecies.h b/Cantera/src/converters/RxnSpecies.h
index 1725ebc33..e49b46a79 100755
--- a/Cantera/src/converters/RxnSpecies.h
+++ b/Cantera/src/converters/RxnSpecies.h
@@ -27,6 +27,8 @@ namespace ckr {
  */
 class RxnSpecies {
 public:
+    RxnSpecies() :
+      number(0) {}
     string         name;        //!< The name of the object.
     double         number;      //!< The number of units (molecules, etc.).
     grouplist_t    groups;
diff --git a/Cantera/src/converters/ck2ct.cpp b/Cantera/src/converters/ck2ct.cpp
index 555da827c..be2d65d2d 100644
--- a/Cantera/src/converters/ck2ct.cpp
+++ b/Cantera/src/converters/ck2ct.cpp
@@ -190,11 +190,15 @@ namespace pip {
     }
 
     /**
-     * addSpecies():
+     * Write out a species cti block to the output file.
      *
      */
     static void addSpecies(FILE* f, string idtag, const ckr::Species& sp) {
         string spname = sp.name;
+	if (spname.size() == 0) {
+	  throw CanteraError("addSpecies", 
+			     "Species name is empty");
+	}
         fprintf(f,"\nspecies(name = \"%s\",\n",spname.c_str());
         int nel = static_cast<int>(sp.elements.size());
         int m, num;
@@ -226,6 +230,18 @@ namespace pip {
         }
 
         fprintf(f,"    atoms = \"%s\",\n", str.c_str());
+	if (sp.lowCoeffs.size() == 0) {
+	  throw CanteraError("addSpecies", 
+			     "Low Nasa Thermo Polynomial was not found");
+	}
+	if (sp.highCoeffs.size() == 0) {
+	  throw CanteraError("addSpecies", 
+			     "High Nasa Thermo Polynomial was not found");
+	}
+	if (sp.tlow >= sp.thigh) {
+	  throw CanteraError("addSpecies", 
+			     "Low temp limit is greater or equal to high temp limit");
+	}
         addNASA(f, sp.lowCoeffs, sp.highCoeffs, 
             sp.tlow, sp.tmid, sp.thigh);
 
@@ -277,7 +293,10 @@ namespace pip {
         else {
             if (rxn.kf.type == ckr::Arrhenius) {
                 fprintf(f,"  [%10.5E, %g, %g]", rxn.kf.A, rxn.kf.n, rxn.kf.E);
-            }
+            } else {
+	      throw CanteraError("addReaction",
+				 "unknown kf_type to reaction: " + int2str(rxn.kf.type));
+	    }
         }
     
         // reaction orders
@@ -346,7 +365,7 @@ namespace pip {
         doublereal version = 1.0;
 
         fprintf(f,  "units(length = \"cm\", time = \"s\", quantity = \"mol\", ");
-        string e_unit;
+        string e_unit = " ";
         int eunit = r.units.ActEnergy;
         if (eunit == ckr::Cal_per_Mole)
             e_unit = "cal/mol";
@@ -443,7 +462,7 @@ namespace pip {
         }
     }
 
-
+/*
     static int fixtext(string infile, string outfile) {
         ifstream fin(infile.c_str());
         ofstream fout(outfile.c_str());
@@ -474,6 +493,7 @@ namespace pip {
         fout.close();
         return 0;
     }
+*/
 
     int convert_ck(const char* in_file, const char* db_file,
         const char* tr_file, const char* id_tag, bool debug, bool validate) {
diff --git a/Cantera/src/converters/ckr_defs.h b/Cantera/src/converters/ckr_defs.h
index b2475151d..5d00622ed 100755
--- a/Cantera/src/converters/ckr_defs.h
+++ b/Cantera/src/converters/ckr_defs.h
@@ -67,6 +67,8 @@ namespace ckr {
     /** @name Activation Energy Units 
      *  These constants specify the supported units for the activation energy of
      *  a reaction
+     *  The default is to assume Cal_per_Mole for unspecified units in the activation energy
+     *  as this was the original default
      */
     //@{
     const int Cal_per_Mole = 1,