[docs] Use doxygen cite command

Cantera · Jul 28, 2023 · d60383d · d60383d
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diff --git a/doc/doxygen/Doxyfile b/doc/doxygen/Doxyfile
@@ -775,7 +775,7 @@ LAYOUT_FILE            = doc/doxygen/DoxygenLayout.xml
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
 
-CITE_BIB_FILES         =
+CITE_BIB_FILES         = doc/doxygen/cantera.bib
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages
@@ -899,6 +899,7 @@ FILE_PATTERNS          = *.h \
                          *.cpp \
                          *.txt \
                          *.md \
+                         *.bib \
                          *.dox
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should

diff --git a/doc/doxygen/cantera.bib b/doc/doxygen/cantera.bib
@@ -0,0 +1,12 @@
+@book{kee2003,
+	author = {Robert~J.~Kee and Michael.~E.~Coltrin and Peter~Glarborg},
+	publisher = {John Wiley & Sons},
+	title = {Chemically Reacting Flow: Theory and Practice},
+	year = {2003}}
+@book{kee2017,
+	author = {Robert~J.~Kee and Michael.~E.~Coltrin and Peter~Glarborg and Huayang~Zhu},
+	publisher = {John Wiley & Sons},
+	title = {Chemically Reacting Flow: Theory and Practice},
+    edition = {2nd},
+    doi = {10.1002/9781119186304},
+	year = {2017}}
diff --git a/include/cantera/kinetics/InterfaceRate.h b/include/cantera/kinetics/InterfaceRate.h
@@ -63,9 +63,8 @@ struct InterfaceData : public BlowersMaselData
 //! Base class for rate parameterizations that involve interfaces
 /**
  * Rate expressions defined for interfaces may include coverage dependent terms,
- * where an example is given by [Kee, R. J., Coltrin, M. E., & Glarborg, P.(2003).
- * Chemically reacting flow: theory and practice. John Wiley & Sons. Eq 11.113].
- * Using Cantera nomenclature, this expression can be rewritten as
+ * where an example is given by Kee, et al. \cite kee2003, Eq 11.113.
+ * Using %Cantera nomenclature, this expression can be rewritten as
  *  \f[
  *      k_f = A T^b \exp \left( - \frac{E_a}{RT} \right)
  *          \prod_k 10^{a_k \theta_k} \theta_k^{m_k}

diff --git a/include/cantera/transport/GasTransport.h b/include/cantera/transport/GasTransport.h
@@ -19,12 +19,7 @@ class MMCollisionInt;
 //! Class GasTransport implements some functions and properties that are
 //! shared by the MixTransport and MultiTransport classes.
 //!
-//! ### References
-//!
-//! * [Kee2003] R. J. Kee, M. E. Coltrin, and P. Glarborg. Chemically Reacting
-//!       Flow: Theory and Practice. 1st Ed. John Wiley and Sons, 2003.
-//! * [Kee2017] R. J. Kee, M. E. Coltrin, P. Glarborg, and H. Zhu. Chemically
-//!       Reacting Flow: Theory and Practice. 2nd Ed. John Wiley and Sons, 2017.
+//! For details, see Kee, et al. \cite kee2003 and \cite kee2017.
 //!
 //! @ingroup tranprops
 class GasTransport : public Transport

diff --git a/include/cantera/transport/MixTransport.h b/include/cantera/transport/MixTransport.h
@@ -19,9 +19,7 @@ namespace Cantera
 //! Class MixTransport implements mixture-averaged transport properties for
 //! ideal gas mixtures.
 /*!
- * The model is based on that described in: R. J. Kee, M. J. Coltrin, and P.
- * Glarborg, "Chemically Reacting Flow: Theory & Practice", John Wiley & Sons,
- * 2003.
+ * The model is based on that described in Kee, et al. \cite kee2003.
  *
  * The viscosity is computed using the Wilke mixture rule (kg /m /s)
  *

diff --git a/include/cantera/transport/MultiTransport.h b/include/cantera/transport/MultiTransport.h
@@ -17,9 +17,8 @@ namespace Cantera
 //! Class MultiTransport implements multicomponent transport properties for
 //! ideal gas mixtures.
 /*!
- * The implementation generally follows the procedure outlined in: R. J. Kee, M.
- * J. Coltrin, and P. Glarborg, "Chemically Reacting Flow: Theory & Practice",
- * John Wiley & Sons, 2003.
+ * The implementation generally follows the procedure outlined in Kee, et al.
+ * \cite kee2003.
  *
  * @ingroup tranprops
  */

diff --git a/src/base/application.h b/src/base/application.h
@@ -374,17 +374,18 @@ class Application
     //! Set definition used for rate constant calculation.
     //! @see Kinetics::getFwdRateConstants()
     /*!
-     * If set to 'false' (default value), rate constants of three-body reactions are
-     * consistent with conventional definitions (for example Eq. 9.75 in Kee, Coltrin
-     * and Glarborg, 'Chemically Reacting Flow', Wiley Interscience, 2003). If set to
-     * 'true', output for rate constants of three-body reactions is multiplied by
-     * third-body concentrations, consistent with Cantera's behavior prior to version 3.0.
+     * If set to `false` (default value), rate constants of three-body reactions are
+     * consistent with conventional definitions (for example Eq. 9.75 in Kee, et al.
+     * @cite kee2003).
+     * If set to `true`, output for rate constants of three-body reactions is
+     * multiplied by third-body concentrations, consistent with %Cantera's behavior
+     * prior to version 3.0.
      */
     void use_legacy_rate_constants(bool legacy=true) {
         m_use_legacy_rate_constants = legacy;
     }
 
-    //! Returns `true` if legacy rate constant definition should be used
+    //! Returns `true` if legacy rate constant definition is used
     bool legacy_rate_constants_used() {
         return m_use_legacy_rate_constants;
     }