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Updated doxygen make generation capability.

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Started to modify doxygen content to get rid of the large number of warnings.
This commit is contained in:
Harry Moffat 2014-08-21 00:48:04 +00:00
parent 81556ea8aa
commit 0d9b7d7868
3 changed files with 55 additions and 16 deletions
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2
bin/make_doxygen
View file

@ -4,7 +4,7 @@
CUR=`pwd`
CANTERA_SRC_ROOT=${CANTERA_SRC_ROOT:="$CUR"}
# /bin/rm -rf build/docs/doxygen
/bin/rm -rf build/docs/doxygen
cd $CANTERA_SRC_ROOT
#doxygen doc/doxygen/Doxyfile
doxygen doc/doxygen/Doxyfile.tested

19
doc/doxygen/Doxyfile.tested
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@ -545,7 +545,7 @@ WARN_IF_DOC_ERROR = YES
# wrong or incomplete parameter documentation, but not about the absence of
# documentation.
WARN_NO_PARAMDOC = NO
WARN_NO_PARAMDOC = YES
# The WARN_FORMAT tag determines the format of the warning messages that
# doxygen can produce. The string should contain the $file, $line, and $text
@ -570,12 +570,21 @@ WARN_LOGFILE =
# documented source files. You may enter file names like "myfile.cpp" or
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
# src/base \
include/base \
include/thermo \
# src/thermo \
INPUT = \
src/base \
src/kinetics \
src/thermo \
include \
include/cantera/thermo/ThermoPhase.h \
include/cantera/thermo/Phase.h \
include/cantera/kinetics/Kinetics.h \
src/kinetics/Kinetics.cpp \
include/cantera/kinetics/ReactionData.h \
include/cantera/kinetics/ExtraGlobalRxn.h \
src/thermo/ThermoPhase.cpp \
src/thermo/Phase.cpp \
src/kinetics/ExtraGlobalRxn.cpp \
doc/doxygen
# This tag can be used to specify the character encoding of the source files

50
include/cantera/thermo/Phase.h
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@ -40,12 +40,11 @@ public:
: CanteraError(func, "Elements cannot be added after species.") {}
};
//! Base class for phases of matter
//! Class %Phase is the base class for phases of matter, managing the species and elements in a phase, as well as the
//! independent variables of temperature, mass density, species mass/mole fraction,
//! and other generalized forces and intrinsic properties (such as electric potential)
//! that define the thermodynamic state.
/*!
*
* Class Phase manages the species and elements in a phase, as well as the
* independent variables of temperature, mass density, and species mass/mole
* fraction that define the thermodynamic state.
*
* Class Phase provides information about the elements and species in a
* phase - names, index numbers (location in arrays), atomic or molecular
@ -88,10 +87,19 @@ public:
* The first two methods of naming may not yield a unique species within
* complicated assemblies of %Cantera Phases.
*
* @todo Make the concept of saving state vectors more general, so that it can
* @todo
* Make the concept of saving state vectors more general, so that it can
* handle other cases where there are additional internal state variables, such
* as the voltage, a potential energy, or a strain field.
*
* Specify that the input mole, mass, and volume fraction vectors must sum to one on entry to the set state routines.
* Non-conforming mole/mass fraction vectors are not thermodynamically consistent.
* Moreover, ynless we do this, the calculation of jacobians will be altered whenever the treatment of non-conforming mole
* fractions is changed. Add setState functions corresponding to specifying mole numbers, which is actually what
* is being done (well one of the options, there are many) when non-conforming mole fractions are input.
* Note, we realize that most numerical jacobian and some analytical jacobians use non-conforming calculations.
* These can easily be changed to the set mole number setState functions.
*
* @ingroup phases
*/
class Phase
@ -488,15 +496,22 @@ public:
virtual void setMassFractions_NoNorm(const doublereal* const y);
//! Get the species concentrations (kmol/m^3).
//! @param[out] c Array of species concentrations Length must be
//! greater than or equal to the number of species.
/*!
* @param[out] c The vector of species concentrations. Units are kmol/m^3. The length of
* the vector must be greater than or equal to the number of species within the phase.
*/
void getConcentrations(doublereal* const c) const;
//! Concentration of species k.
//! If k is outside the valid range, an exception will be thrown.
//! @param k Index of species
/*!
* @param[in] k Index of the species within the phase.
*
* @return Returns the concentration of species k (kmol m-3).
*/
doublereal concentration(const size_t k) const;
//! Set the concentrations to the specified values within the phase.
//! We set the concentrations here and therefore we set the overall density
//! of the phase. We hold the temperature constant during this operation.
@ -700,6 +715,10 @@ public:
doublereal size = 1.0);
//!@} end group adding species and elements
//! Returns a bool indicating wether the object is ready for use
/*!
* @return returns true if the object is ready for calculation, false otherwise.
*/
virtual bool ready() const;
//! Return the State Mole Fraction Number
@ -708,6 +727,12 @@ public:
}
protected:
//! Cached for saved calculations within each ThermoPhase.
/*!
* For more information on how to use this, see examples within the source code and documentation
* for this within ValueCache class itself.
*/
mutable ValueCache m_cache;
//! Set the molecular weight of a single species to a given value
@ -760,7 +785,12 @@ private:
//! weight of mixture.
mutable vector_fp m_ym;
mutable vector_fp m_y; //!< species mass fractions
//! Mass fractions of the species
/*!
* Note, this vector
* Length is m_kk
*/
mutable vector_fp m_y;
vector_fp m_molwts; //!< species molecular weights (kg kmol-1)