doxygen update:

Added EdgePhase
Worked on test suite:
   HMW_Test_1 passes now whether Debug_Mode is turned on or not.

Cantera/src/EdgePhase.h

@@ -1,7 +1,7 @@
 /**
  *
  *  @file EdgePhase.h
- *
+ *       Declarations for the EdgePhase thermodynamic object.
  */
 
 /*  $Author$
@@ -12,7 +12,6 @@
  *
  */
 
-
 #ifndef CT_EDGEPHASE_H
 #define CT_EDGEPHASE_H
 
@@ -22,15 +21,58 @@
 
 namespace Cantera {
 
-    class EdgePhase : public SurfPhase  {
+  //! A thermodynamic %Phase representing a one dimensional edge between two surfaces
+  /*!
+   * This thermodynamic function is largely a wrapper around the SurfPhase
+   * thermodynamic object.
+   *
+   * All of the equations and formulations carry through from SurfPhase to this
+   * EdgePhase object.
+   * It should be noted however, that dimensional object with length dimensions,
+   * have their dimensions reduced by one.
+   *
+   * @ingroup thermoprops
+   */
+  class EdgePhase : public SurfPhase  {
+    
+  public:
+    
+    //! Constructor
+    /*!
+     * @param n0  Surface site density (kmol m-1).
+     */
+    EdgePhase(doublereal n0 = 0.0);
 
-    public:
+    //! Destructor
+    virtual ~EdgePhase() {}
 
-        EdgePhase(doublereal n0 = 0.0);
+    //! returns the equation of state type
-        virtual ~EdgePhase() {}
+    virtual int eosType() const { return cEdge; }
-        virtual int eosType() const { return cEdge; }
+
-        virtual void setParametersFromXML(const XML_Node& eosdata);
+
-    };
+    //! Set the Equation-of-State parameters by reading an XML Node Input
+    /*!
+     *
+     * The Equation-of-State data consists of one item, the site density.
+     *
+     * @param thermoData   Reference to an XML_Node named thermo
+     *                     containing the equation-of-state data. The
+     *                     XML_Node is within the phase XML_Node describing
+     *                     the %EdgePhase object.
+     *
+     * An example of the contents of the thermoData XML_Node is provided
+     * below. The units attribute is used to supply the units of the
+     * site density in any convenient form. Internally it is changed
+     * into MKS form.
+     *
+     * @code
+     *    <thermo model="Edge">
+     *       <site_density units="mol/cm"> 3e-15 </site_density>
+     *    </thermo>
+     * @endcode
+     */
+    virtual void setParametersFromXML(const XML_Node& thermoData);
+  };
 }
         
 #endif

Cantera/src/ThermoPhase.h

@@ -89,6 +89,7 @@ namespace Cantera {
    *    - IdealGasPhase       in IdealGasPhase.h
    *    - StoichSubstance     in StoichSubstance.h
    *    - SurfPhase           in SurfPhase.h
+   *    - EdgePhase           in EdgePhase.h
    *    - LatticePhase        in LatticePhase.h
    *    - LatticeSolidPhase   in LatticeSolidPhase.h
    *    - ConstDensityThermo  in ConstDensityThermo.h

Cantera/src/thermo/HMWSoln.cpp

@@ -5252,6 +5252,13 @@ namespace Cantera {
     }
   }
 
+  int HMWSoln::debugPrinting() {
+#ifdef DEBUG_MODE
+   return m_debugCalc;
+#else
+   return 0;
+#endif
+  }
  
   /*****************************************************************************/
 }

Cantera/src/thermo/HMWSoln.h

@@ -1447,11 +1447,16 @@ namespace Cantera {
 
 
   public:
-    /*
+    /*!
-     * Turn on copious debug printing
+     * Turn on copious debug printing when this
+     * is true and DEBUG_MODE is turned on.
      */
     mutable int m_debugCalc;
-
+    //! Return int specifying the amount of debug printing
+    /*!
+     *  This will return 0 if DEBUG_MODE is not turned on
+     */
+    int debugPrinting();
   };
 
 }

test_problems/ChemEquil_gri_matrix/.cvsignore

@@ -5,3 +5,5 @@ gri_matrix
 output.txt
 outputa.txt
 tmp
+.depends
+*.d

test_problems/ChemEquil_gri_pairs/.cvsignore

@@ -4,3 +4,5 @@ diff_test.out
 gri_pairs
 outputa.txt
 csvCode.txt
+.depends
+*.d

test_problems/ChemEquil_ionizedGas/.cvsignore

@@ -5,3 +5,5 @@ output.txt
 csvCode.txt
 ct2ctml.log
 diff_test.out
+.depends
+*.d

test_problems/ChemEquil_red1/.cvsignore

@@ -3,3 +3,5 @@ Makefile
 output.txt
 csvCode.txt
 diff_test.out
+.depends
+*.d

test_problems/Makefile.in

@@ -42,17 +42,17 @@ test:
 	@ cd ChemEquil_ionizedGas; @MAKE@ -s test
 	@ cd ChemEquil_red1; @MAKE@ -s test
 ifeq ($(test_ck),1)
-	@ cd ck2cti_test;  @MAKE@ test
+	@ cd ck2cti_test;  @MAKE@ -s test
 endif
 ifeq ($(test_python),1)
-	cd min_python;   @MAKE@ test
+	cd min_python;   @MAKE@ -s test
 endif
 ifeq ($(test_python),2)
-	cd min_python;   @MAKE@ test
+	cd min_python;   @MAKE@ -s test
-	cd python;       @MAKE@ test
+	cd python;       @MAKE@ -s test
 endif
 ifeq ($(test_cathermo),1)
-	cd cathermo;     @MAKE@ test
+	cd cathermo;     @MAKE@ -s test
 endif
 
 clean:

test_problems/cathermo/HMW_test_1/.cvsignore

@@ -8,3 +8,5 @@ HMW_test_1.d
 diff_test.out
 table.csv
 csvCode.txt
+CheckDebug.txt
+output_bc.txt

test_problems/cathermo/HMW_test_1/HMW_test_1.cpp

@@ -56,14 +56,20 @@ int main(int argc, char **argv)
 
    try {
   
-#ifdef DEBUG_MODE
-       CHECK_DEBUG_MODE = 1;
-#endif
-     if (CHECK_DEBUG_MODE != 1) {
-       printf("Check can only be done if DEBUG_MODE is defined\n");
-       exit(-1);
-     }
      HMWSoln *HMW = new HMWSoln(1);
+
+#ifdef DEBUG_MODE
+     CHECK_DEBUG_MODE = 1;
+#endif
+     if (CHECK_DEBUG_MODE == 1) {
+       HMW->m_debugCalc = 1;
+       if (HMW->debugPrinting()) {
+         FILE *ff = fopen("CheckDebug.txt", "w");
+         fprintf(ff,"%1d\n", 1);
+         fclose(ff);
+       }
+       HMW->m_debugCalc = 0;
+     }
      
      int nsp = HMW->nSpecies();
     

test_problems/cathermo/HMW_test_1/output_noD_blessed.txt

@@ -0,0 +1,58 @@
+Index  Name                  MoleF      Molality      Charge
+ 0     H2O(L)            8.1992706e-01  5.5508435e+01   0.0 
+ 1     Cl-               9.0036447e-02  6.0953986e+00  -1.0 
+ 2     H+                3.1947185e-11  2.1628000e-09   1.0 
+ 3     Na+               9.0036468e-02  6.0954000e+00   1.0 
+ 4     OH-               2.0645728e-08  1.3977000e-06  -1.0 
+
+ Species          Species            beta0MX  beta1MX   beta2MX   CphiMX    alphaMX thetaij    
+ Cl-              H+                 0.17750   0.29450   0.00000   0.00080   2.00000   0.00000 
+ Cl-              Na+                0.07650   0.26640   0.00000   0.00127   2.00000   0.00000 
+ Cl-              OH-                0.00000   0.00000   0.00000   0.00000   0.00000  -0.05000 
+ H+               Na+                0.00000   0.00000   0.00000   0.00000   0.00000   0.03600 
+ H+               OH-                0.00000   0.00000   0.00000   0.00000   0.00000   0.00000 
+ Na+              OH-                0.08640   0.25300   0.00000   0.00440   2.00000   0.00000 
+
+ Species          Species          Species       psi   
+ Cl-              H+               Na+               -0.00400 
+ Cl-              Na+              H+                -0.00400 
+ Cl-              Na+              OH-               -0.00600 
+ Cl-              OH-              Na+               -0.00600 
+ H+               Cl-              Na+               -0.00400 
+ H+               Na+              Cl-               -0.00400 
+ Na+              Cl-              H+                -0.00400 
+ Na+              Cl-              OH-               -0.00600 
+ Na+              H+               Cl-               -0.00400 
+ Na+              OH-              Cl-               -0.00600 
+ OH-              Cl-              Na+               -0.00600 
+ OH-              Na+              Cl-               -0.00600 
+a1 = 3.04284e-10
+a2 = 3.04284e-10
+            Name      Activity  ActCoeffMolal    MoleFract      Molality
+          H2O(L)      0.754581       0.92042      0.819823       55.5084
+             Cl-       6.09579      0.999359     0.0900885        6.0997
+              H+   1.00009e-08       4.62404   3.19431e-11    2.1628e-09
+             Na+       6.09579      0.999359     0.0900885        6.0997
+             OH-    7.5986e-07       0.54365   2.06431e-08    1.3977e-06
+           Species   Standard chemical potentials (kJ/gmol) 
+------------------------------------------------------------
+          H2O(L)      -306.685777
+             Cl-      -131.064852
+              H+        0.0017225
+             Na+      -311.160543
+             OH-      -226.880122
+------------------------------------------------------------
+ Some DeltaSS values:               Delta(mu_0)
+ NaCl(S): Na+ + Cl- -> NaCl(S):       9.594995 kJ/gmol 
+                                :       3.870573 (dimensionless) 
+                                :       1.680969 (dimensionless/ln10) 
+            G0(NaCl(S)) =      -432.6304 (fixed)
+            G0(Na+)     =      -311.1605
+            G0(Cl-)     =      -131.0649
+ OH-: H2O(L) - H+ -> OH-:       79.80738 kJ/gmol 
+                                :        32.1939 (dimensionless) 
+                                :       13.98163 (dimensionless/ln10) 
+            G0(OH-)    =      -226.8801
+            G0(H+)     =      0.0017225
+            G0(H2O(L)) =      -306.6858
+------------------------------------------------------------

test_problems/cathermo/HMW_test_1/runtest

@@ -12,6 +12,7 @@ if test ! -x $prog ; then
 fi
 ##########################################################################
 /bin/rm -f test.out test.diff   output.txt
+/bin/rm -f CheckDebug.txt output_bc.txt
 
 #################################################################
 #
@@ -29,7 +30,14 @@ then
 fi
 
 $CANTERA_BIN/exp3to2.sh output.txt > outputa.txt
-diff -w outputa.txt output_blessed.txt > diff_test.out
+if [ -f CheckDebug.txt ]
+then
+  cp output_blessed.txt output_bc.txt
+else
+  cp output_noD_blessed.txt output_bc.txt
+fi
+
+diff -w outputa.txt output_bc.txt > diff_test.out
 retnStat=$?
 if [ $retnStat = "0" ]
 then

test_problems/min_python/negATest/.cvsignore

@@ -21,3 +21,4 @@ testdest2.xml
 negATest
 diff_xml.out
 noxNeg.xml
+.ctt*

test_problems/python/.cvsignore

@@ -12,3 +12,4 @@ frac_test.out
 *.txt
 *.log
 flame1_blessed_tmp.csv
+.ctt*

tools/doc/Cantera.cfg.in

@@ -102,7 +102,7 @@ FILE_PATTERNS          = Kinetics.h Kinetics.cpp \
                          importCTML.cpp importCTML.h \
                          ThermoFactory.h ThermoFactory.cpp \
                          IdealGasPhase.h IdealGasPhase.cpp \
-                         SurfPhase.h SurfPhase.cpp \
+                         SurfPhase.h EdgePhase.h SurfPhase.cpp \
                          SpeciesThermoFactory.h SpeciesThermoFactory.cpp \
                          speciesThermoTypes.h SpeciesThermoMgr.h SpeciesThermo.h SpeciesThermoInterpTypes.h \
                          NasaThermo.h NasaPoly1.h NasaPoly2.h \