From 86be28621a1fe3658d6f76064b2e608bd0097e8a Mon Sep 17 00:00:00 2001
From: Harry Moffat <hkmoffa@sandia.gov>
Date: Tue, 29 Jun 2010 18:28:08 +0000
Subject: [PATCH] Added doxygen input.

---
 .../src/transport/LiquidTranInteraction.cpp   |  2 +-
 Cantera/src/transport/LiquidTransport.cpp     | 23 ++++++++++---------
 Cantera/src/transport/TransportBase.h         | 21 +++++++++++++----
 Cantera/src/transport/WaterTransport.h        |  7 ++++++
 4 files changed, 37 insertions(+), 16 deletions(-)

diff --git a/Cantera/src/transport/LiquidTranInteraction.cpp b/Cantera/src/transport/LiquidTranInteraction.cpp
index 36531da93..e4585f832 100644
--- a/Cantera/src/transport/LiquidTranInteraction.cpp
+++ b/Cantera/src/transport/LiquidTranInteraction.cpp
@@ -709,7 +709,7 @@ namespace Cantera {
       for (i = 0; i < nsp; i++) {
 	if (m_mobRatMixModel[k]) {
 	  m_mobRatMix(i,j) = m_mobRatMixModel[k]->getMixTransProp(m_mobRatSpecies[k] );	
-	  if (m_mobRatMix(i,j) > 0) {
+	  if (m_mobRatMix(i,j) > 0.0) {
             m_mobRatMix(j,i) = 1.0/m_mobRatMix(i,j);
           }
 	}
diff --git a/Cantera/src/transport/LiquidTransport.cpp b/Cantera/src/transport/LiquidTransport.cpp
index 929a23a39..eed8b7c53 100644
--- a/Cantera/src/transport/LiquidTransport.cpp
+++ b/Cantera/src/transport/LiquidTransport.cpp
@@ -231,14 +231,13 @@ namespace Cantera {
 	 }
        }
        for ( int l=0;l < m_nsp2; l++ ){
-         if ( m_mobRatTempDep_Ns[l][k]   ) delete m_mobRatTempDep_Ns[l][k];
+         if (m_mobRatTempDep_Ns[l][k]) delete m_mobRatTempDep_Ns[l][k];
        }
        if ( m_lambdaTempDep_Ns[k] ) delete m_lambdaTempDep_Ns[k];
        if ( m_radiusTempDep_Ns[k] ) delete m_radiusTempDep_Ns[k];
        if ( m_diffTempDep_Ns[k]   ) delete m_diffTempDep_Ns[k];
-     //These are constructed in TransportFactory::newLTI 
-
-       if ( m_selfDiffMixModel[k]   ) delete m_selfDiffMixModel[k];
+       //These are constructed in TransportFactory::newLTI 
+       if (m_selfDiffMixModel[k]) delete m_selfDiffMixModel[k];
      }
 
      for ( int k = 0; k < m_nsp2; k++) {
@@ -548,12 +547,14 @@ namespace Cantera {
     update_T();
     update_C();
 
-    ////// LiquidTranInteraction method
-    if (!m_mobRat_mix_ok){
+    // LiquidTranInteraction method
+    if (!m_mobRat_mix_ok) {
       for (int k = 0; k < m_nsp2; k++){
 	if(m_mobRatMixModel[k]){
-	  m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp( m_mobRatTempDep_Ns[k] );
-	  if ( m_mobRatMix[k] > 0 ) m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway
+	  m_mobRatMix[k] = m_mobRatMixModel[k]->getMixTransProp(m_mobRatTempDep_Ns[k]);
+	  if (m_mobRatMix[k] > 0) {
+            m_mobRatMix[k/m_nsp+m_nsp*(k%m_nsp)] = 1.0/m_mobRatMix[k]; // Also must be off diagonal: k%(1+n)!=0, but then m_mobRatMixModel[k] shouldn't be initialized anyway
+          }
 	}
       }
     }
@@ -576,7 +577,7 @@ namespace Cantera {
     if (!m_mobRat_temp_ok) {
       updateMobilityRatio_T();
     }
-    for (int k=0; k<m_nsp2; k++) {
+    for (int k=0; k < m_nsp2; k++) {
       for (int j=0; j < m_nsp; j++) {
 	mobRat[k][j] = m_mobRatSpecies(k,j); 
       }
@@ -1439,7 +1440,7 @@ namespace Cantera {
 
     for (k = 0; k < m_nsp2; k++) {
       for (j = 0; j < m_nsp; j++) {
-	m_mobRatSpecies(k,j) = m_mobRatTempDep_Ns[k][j]->getSpeciesTransProp() ;
+	m_mobRatSpecies(k,j) = m_mobRatTempDep_Ns[k][j]->getSpeciesTransProp();
       }
     }
     m_mobRat_temp_ok = true;
@@ -1630,7 +1631,7 @@ namespace Cantera {
      * They are still fortran ordered, so that i varies fastest.
      */
 
-    double condSum1, condSum2;
+    double condSum1;
     switch (m_nDim) {
     case 1:  /* 1-D approximation */
 
diff --git a/Cantera/src/transport/TransportBase.h b/Cantera/src/transport/TransportBase.h
index 87d911c95..667190ccc 100644
--- a/Cantera/src/transport/TransportBase.h
+++ b/Cantera/src/transport/TransportBase.h
@@ -329,10 +329,23 @@ namespace Cantera {
     virtual void getSpeciesIonConductivity(doublereal* const ionCond)
     { err("getSpeciesIonConductivity"); }
 
-
-    
-    /**
-     * The mobility ratio. 
+ 
+    //! Returns the pointer to the mobility ratios of the species in the phase
+    /*!
+     *
+     * @param mobRat Returns a matrix of mobility ratios for the current problem.
+     *               The mobility ratio mobRat(i,j) is defined as the ratio of the
+     *               mobility of species i to species j.
+     * 
+     *         mobRat(i,j) = mu_i / mu_j  
+     *
+     *    It is returned in fortran-ordering format. ie. it is returned as mobRat[k], where
+     *
+     *        k = j * nsp + i
+     *
+     *    The size of mobRat must be at least equal to  nsp*nsp
+     *
+     * @deprecated This doesn't seem to be the essential input; it should just be the mobility.
      */
     virtual void mobilityRatio(double* mobRat)
     { err("mobilityRatio"); }
diff --git a/Cantera/src/transport/WaterTransport.h b/Cantera/src/transport/WaterTransport.h
index 6dc61555d..e95fadcda 100644
--- a/Cantera/src/transport/WaterTransport.h
+++ b/Cantera/src/transport/WaterTransport.h
@@ -47,6 +47,13 @@ namespace Cantera {
   public:
 
     //! default constructor
+    /*!
+     *  @param thermo   ThermoPhase object that represents the phase. 
+     *                  Defaults to zero 
+     *
+     *  @param ndim     Number of dimensions of the flux expressions.
+     *                  Defaults to a value of one.
+     */
     WaterTransport(thermo_t* thermo = 0, int ndim = 1);
 
     //!Copy Constructor for the %LiquidThermo object.