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Updated documentation to resolve some Doxygen warnings

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This commit is contained in:
Ray Speth 2012-06-14 21:06:30 +00:00
parent 61fce224af
commit 0f04aaf0be
31 changed files with 66 additions and 415 deletions
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2
include/cantera/Interface.h
View file

@ -29,7 +29,7 @@ public:
/*!
* Construct an Interface instance from a specification in an input file.
*
* @param infile. Cantera input file in CTI or CTML format.
* @param infile Cantera input file in CTI or CTML format.
* @param id Identification string to distinguish between
* multiple definitions within one input file.
* @param otherPhases Neighboring phases that may participate in the

3
include/cantera/base/xml.h
View file

@ -746,10 +746,9 @@ private:
* on. This is fixed up in the public method. A method to only write out a limited
* amount of the xml tree has been added.
*
*
* @param s ostream to write to
* @param level Indentation level to work from
* @param numRecurvivesAllowed Number of recursive calls allowed
* @param numRecursivesAllowed Number of recursive calls allowed
*/
void write_int(std::ostream& s, int level = 0, int numRecursivesAllowed = 60000) const;

3
include/cantera/equil/equil.h
View file

@ -63,9 +63,7 @@ namespace Cantera
* Return variable is equal to the number of subroutine attempts
* it took to equilibrate the system.
*
*
* @ingroup equilfunctions
* @ingroup equil
*/
int equilibrate(thermo_t& s, const char* XY,
int solver = -1, doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS,
@ -94,7 +92,6 @@ int equilibrate(thermo_t& s, const char* XY,
* it took to equilibrate the system.
*
* @ingroup equilfunctions
* @ingroup equil
*/
doublereal equilibrate(MultiPhase& s, const char* XY,
doublereal rtol = 1.0e-9, int maxsteps = 5000, int maxiter = 100,

10
include/cantera/equil/vcs_IntStarStar.h
View file

@ -1,5 +1,5 @@
/**
* @file IntStarStar.h
* @file vcs_IntStarStar.h
*
* Header file for class IntStarStar
*/
@ -44,13 +44,13 @@ public:
//! Copy constructor
/*!
* @param y Object to be copied
*/
*/
IntStarStar(const IntStarStar& y);
//! Assignment operator
/*!
* @param y Object to be copied
*/
*/
IntStarStar& operator=(const IntStarStar& y);
//! Resize the array, and fill the new entries with 'v'
@ -91,13 +91,13 @@ private:
//! Storage area for the matrix, layed out in Fortran style, row-inner, column outer format
/*!
* Length = m_nrows * m_ncols
*/
*/
std::vector<int> m_data;
//! Vector of column addresses
/*!
* Length = number of columns = m_ncols
*/
*/
std::vector<int*> m_colAddr;
//! number of rows

63
include/cantera/equil/vcs_VolPhase.h
View file

@ -190,22 +190,20 @@ public:
* This function takes as input the mole numbers in vcs format, and
* then updates this object with their values. This is essentially
* a gather routine.
*
* Additionally it checks to see that the total moles value in
* TPhMoles[iplace] is equal to the internally computed value.
* If this isn't the case, an error exit is carried out.
*
*
* @param vcsStateStatus State calc value either VCS_STATECALC_OLD
* or VCS_STATECALC_NEW. With any other value nothing is done.
* @param molesSpeciesVCS array of mole numbers. Note, the indices
* for species in
* this array may not be contiguous. IndSpecies[] is needed
* to gather the species into the local contiguous vector
* format.
* @param TPhMoles VCS's array containing the number of moles
* in each phase.
* @param iphase index of the current phase.
*
* for species in this array may not be contiguous. IndSpecies[] is
* needed to gather the species into the local contiguous vector
* format.
* @param TPhMoles VCS's array containing the number of moles in each phase.
*/
void setMolesFromVCSCheck(const int stateCalc,
void setMolesFromVCSCheck(const int vcsStateStatus,
const double* molesSpeciesVCS,
const double* const TPhMoles);
@ -252,12 +250,8 @@ public:
* Calculate the Gibbs free energies for the standard state
* of the kth species.
* The results are held internally within the object.
* The kth species standard state G is returned
*
* @param kspec Species number (within the phase)
* @param TKelvin Current temperature
* @param pres Current pressure
*
* @return Gstar[kspec] returns the gibbs free energy for the
* standard state of the kth species.
*/
@ -267,26 +261,19 @@ public:
//! of a species, return a value for one species
/*!
* @param kspec species index
* @param TKelvin temperature
*
* @return return value of the gibbs free energy
*/
double G0_calc_one(size_t kspec) const;
//! Molar volume calculation for standard state of one species
/*!
* Calculate the molar volume for the standard states
* The results are held internally within the object.
* Return the molar volume for one species
* Calculate the molar volume for the standard states. The results are held
* internally within the object. Return the molar volume for one species.
*
* @param kspec Species number (within the phase)
* @param TKelvin Current temperature
* @param pres Current pressure
*
* @return molar volume of the kspec species's standard
* state (m**3/kmol)
* @return molar volume of the kspec species's standard state (m**3/kmol)
*/
double VolStar_calc_one(size_t kglob) const;
double VolStar_calc_one(size_t kspec) const;
//! Fill in the partial molar volume vector for VCS
/*!
@ -309,6 +296,8 @@ public:
* @param VolPM vector of partial molar volumes for all of the species
* in all of the phases in a VCS problem. Only the
* entries for the current phase are filled in.
*
* @todo This function's documentation is incorrect.
*/
void sendToVCS_GStar(double* const gstar) const;
@ -601,28 +590,17 @@ private:
/*!
* Calculate the Gibbs free energies for the standard states
* The results are held internally within the object.
*
* @param TKelvin Current temperature
* @param pres Current pressure
*/
void _updateGStar() const;
//! Gibbs free energy calculation at a temperature for the reference state
//! of each species
/*!
*
*/
void _updateG0() const;
//! Molar volume calculation for standard states
/*!
* Calculate the molar volume for the standard states
* The results are held internally within the object.
*
* @param TKelvin Current temperature
* @param pres Current pressure
*
* Units are in m**3/kmol
* Calculate the molar volume for the standard states. The results are held
* internally within the object. Units are in m**3/kmol.
*/
void _updateVolStar() const;
@ -641,12 +619,9 @@ private:
* with respect to mole number of jth species.
* (temp, pressure, and other mole numbers held constant)
*
* We employ a finite difference derivative approach here.
* Because we have to change the mole numbers, this is not
* a const function, even though the paradigm would say that
* it should be.
*
* @param moleNumbers Mole numbers are input.
* We employ a finite difference derivative approach here. Because we have
* to change the mole numbers, this is not a const function, even though
* the paradigm would say that it should be.
*/
void _updateLnActCoeffJac();

18
include/cantera/equil/vcs_solve.h
View file

@ -171,7 +171,7 @@ public:
*
* Input
* ---------
* @param doJustCompoents If true, the m_stoichCoeffRxnMatrix[][] and
* @param doJustComponents If true, the m_stoichCoeffRxnMatrix[][] and
* m_deltaMolNumPhase[] are not calculated.
*
* @param aw Vector of mole fractions which will be used to construct an
@ -219,8 +219,8 @@ public:
* This is 1 if the phase, iphase, participates in the
* formation reaction, irxn, and zero otherwise.
*
* @return Returns VCS_SUCCESS if everything went ok. Returns something else if
* there is a problem.
* @return Returns VCS_SUCCESS if everything went ok. Returns
* VCS_FAILED_CONVERGENCE if there is a problem.
*/
int vcs_basopt(const bool doJustComponents, double aw[], double sa[], double sm[],
double ss[], double test, bool* const usedZeroedSpecies);
@ -497,7 +497,7 @@ public:
//! Print out a table of chemical potentials
/*!
* @param vcsState Determines where to get the mole numbers from.
* @param stateCalc Determines where to get the mole numbers from.
* - VCS_STATECALC_OLD -> from m_molNumSpecies_old
* - VCS_STATECALC_NEW -> from m_molNumSpecies_new
*/
@ -506,7 +506,7 @@ public:
//! This routine uploads the state of the system into all of the
//! vcs_VolumePhase objects in the current problem.
/*!
* @param vcsState Determines where to get the mole numbers from.
* @param stateCalc Determines where to get the mole numbers from.
* - VCS_STATECALC_OLD -> from m_molNumSpecies_old
* - VCS_STATECALC_NEW -> from m_molNumSpecies_new
*/
@ -574,7 +574,7 @@ public:
* Special branching occurs sometimes. This causes the component basis
* to be reevaluated
*
* @param forceComponentRecalc integer flagging whether a component recalculation needs
* @param forceComponentCalc integer flagging whether a component recalculation needs
* to be carried out.
* @param kSpecial species number of phase being zeroed.
*
@ -1256,7 +1256,7 @@ private:
* 2) Vphase->IndSpecies is up to date
* 3) m_deltaGRxn_old[irxn] is up to date
*/
bool recheck_deleted_phase(const int iph);
bool recheck_deleted_phase(const int iphase);
//! Minor species alternative calculation
/*!
@ -1298,8 +1298,6 @@ private:
* @param do_delete: BOOLEAN which if true on return, then we branch
* to the section that deletes a species from the
* current set of active species.
*
* @param dx The change in mole number
*/
double vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete
#ifdef DEBUG_MODE
@ -1349,7 +1347,7 @@ private:
/*!
* Positive DG for species which don't exist are ignored.
*
* @param dgLocal Vector of local delta G's.
* @param dg Vector of local delta G's.
*/
double l2normdg(double dg[]) const;

7
include/cantera/kinetics/FalloffMgr.h
View file

@ -21,12 +21,7 @@ class FalloffMgr
{
public:
/**
* Constructor.
* @param f If supplied, this factory will be used to construct
* falloff function calculators. If omitted, the standard factory
* will be used.
*/
//! Constructor.
FalloffMgr(/*FalloffFactory* f = 0*/) :
m_n(0), m_n0(0), m_worksize(0) {
//if (f == 0)

2
include/cantera/kinetics/InterfaceKinetics.h
View file

@ -616,7 +616,7 @@ public:
* which are observed.
*
* @param iphase Index of the phase. This is the order within the internal thermo vector object
* @param exists Boolean indicating whether the phase exists or not
* @param isStable Flag indicating whether the phase is stable or not
*/
void setPhaseStability(const int iphase, const int isStable);

2
include/cantera/kinetics/RateCoeffMgr.h
View file

@ -34,8 +34,6 @@ public:
* Install a rate coefficient calculator.
* @param rxnNumber the reaction number
* @param rdata rate coefficient specification for the reaction
* @param useAux flag to indicate that auxiliary rate information from
* rdata should be used.
*/
size_t install(size_t rxnNumber, const ReactionData& rdata) {
/*

2
include/cantera/kinetics/importKinetics.h
View file

@ -113,7 +113,7 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp,
* @param kf XML_Node containing information about the rate coefficients.
* @param kin kinetics manager
* @param rdata ReactionData reference
* @param negA Boolean indicating whether negative A's are ok.
* @param rules Rules for parsing and installing reactions
*
* Trigger an exception for negative A unless specifically authorized.
*

6
include/cantera/numerics/ctlapack.h
View file

@ -441,11 +441,7 @@ inline doublereal ct_dtrcon(const char* norm, ctlapack::upperlower_t uplot, con
return rcond;
}
//====================================================================================================================
//!
/*!
* @param work Must be dimensioned equal to greater than 3N
* @param iwork Must be dimensioned equal to or greater than N
*/
inline void ct_dpotrf(ctlapack::upperlower_t uplot, size_t n, doublereal* a, size_t lda, int& info)
{
char uplo = upper_lower[uplot];

1
include/cantera/spectra/LineBroadener.h
View file

@ -94,7 +94,6 @@ public:
/**
* Constructor.
* @param FWHM Full width at half-maximum.
*/
GaussianProfile(doublereal sigma);
virtual doublereal profile(doublereal deltaFreq);

4
include/cantera/thermo/Crystal.h
View file

@ -29,8 +29,8 @@ public:
const vector_fp& latticeSiteDensity);
/// Add a phase to the mixture.
/// @param p pointer to the phase object
/// @param moles total number of moles of all species in this phase
/// @param lattice pointer to the phase object
/// @param siteDensity total density of sites in this phase
void addLattice(LatticePhase* lattice, doublereal siteDensity) {
MultiPhase::addPhase(lattice, siteDensity);
}

5
include/cantera/thermo/GibbsExcessVPSSTP.h
View file

@ -327,14 +327,13 @@ public:
*/
virtual void getActivities(doublereal* ac) const;
//! Get the array of non-dimensional molar-based ln activity coefficients at
//! Get the array of non-dimensional molar-based activity coefficients at
//! the current solution temperature, pressure, and solution concentration.
/*!
* @param lnac Output vector of ln activity coefficients. Length: m_kk.
* @param ac Output vector of activity coefficients. Length: m_kk.
*/
virtual void getActivityCoefficients(doublereal* ac) const;
//! Get the array of temperature derivatives of the log activity coefficients
/*!
* This function is a virtual class, but it first appears in GibbsExcessVPSSTP

2
include/cantera/thermo/MargulesVPSSTP.h
View file

@ -495,7 +495,7 @@ public:
//! Get the array of non-dimensional molar-based ln activity coefficients at
//! the current solution temperature, pressure, and solution concentration.
/*!
* @param ac Output vector of ln activity coefficients. Length: m_kk.
* @param lnac Output vector of ln activity coefficients. Length: m_kk.
*/
virtual void getLnActivityCoefficients(doublereal* lnac) const;

10
include/cantera/thermo/MixtureFugacityTP.h
View file

@ -277,7 +277,7 @@ public:
//! Get the pure Gibbs free energies of each species.
//! Species are assumed to be in their standard states. This is the same
//! as getStandardChemPotentials().
//! @param gpure[out] Array of standard state Gibbs free energies.
//! @param[out] gpure Array of standard state Gibbs free energies.
//! length = m_kk. units are J/kmol.
void getPureGibbs(doublereal* gpure) const;
@ -389,7 +389,7 @@ public:
//! Set the internally stored temperature (K) and density (kg/m^3)
/*!
* @param t Temperature in kelvin
* @param T Temperature in kelvin
* @param rho Density (kg/m^3)
*/
virtual void setState_TR(doublereal T, doublereal rho);
@ -793,10 +793,10 @@ protected:
* @param pres pressure (Pascal)
* @param densLiq Output density of liquid
* @param densGas output density of gas
* @param delGRT output delGRT
* @param gasGRT output delGRT
*/
int corr0(doublereal TKelvin, doublereal pre, doublereal& densLiq,
doublereal& densGas, doublereal& liqGRT, doublereal& gasGRT);
int corr0(doublereal TKelvin, doublereal pres, doublereal& densLiq,
doublereal& densGas, doublereal& liqGRT, doublereal& gasGRT);
public:
//! Returns the Phase State flag for the current state of the object
/*!

2
include/cantera/thermo/MolarityIonicVPSSTP.h
View file

@ -232,7 +232,7 @@ public:
/*!
* @param lnac Output vector of ln activity coefficients. Length: m_kk.
*/
virtual void getLnActivityCoefficients(doublereal* ac) const;
virtual void getLnActivityCoefficients(doublereal* lnac) const;
//@}
/// @name Partial Molar Properties of the Solution

2
include/cantera/thermo/RedlichKisterVPSSTP.h
View file

@ -493,7 +493,7 @@ public:
/*!
* @param lnac Output vector of ln activity coefficients. Length: m_kk.
*/
virtual void getLnActivityCoefficients(doublereal* ac) const;
virtual void getLnActivityCoefficients(doublereal* lnac) const;
//@}
/// @name Partial Molar Properties of the Solution

6
include/cantera/thermo/RedlichKwongMFTP.h
View file

@ -59,7 +59,7 @@ public:
* the routine initThermo(), with a reference to the
* XML database to get the info for the phase.
*
* @param inputFile Name of the input file containing the phase XML data
* @param infile Name of the input file containing the phase XML data
* to set up the object
* @param id ID of the phase in the input file. Defaults to the empty string.
*/
@ -558,7 +558,7 @@ private:
/*!
* @param pureFluidParam XML_Node for the pure fluid parameters
*/
void readXMLPureFluid(XML_Node& PureFluidParam);
void readXMLPureFluid(XML_Node& pureFluidParam);
//! Apply mixing rules for a coefficients
@ -569,7 +569,7 @@ private:
/*!
* @param pureFluidParam XML_Node for the cross fluid parameters
*/
void readXMLCrossFluid(XML_Node& PureFluidParam);
void readXMLCrossFluid(XML_Node& pureFluidParam);

3
src/converters/CKParser.cpp
View file

@ -583,9 +583,6 @@ next:
* @param names List of species names (input).
* @param species Table of species objects holding data from records
* in THERMO section (output).
* @param allowExtThermoData True if 'THERMO' specified, false if
* 'THERMO ALL' specified.
*
*/
bool CKParser::readThermoSection(std::vector<std::string>& names,

4
src/converters/CKReader.cpp
View file

@ -28,15 +28,13 @@ using namespace std;
namespace ckr
{
/**
* read and optionally validate an input file in Chemkin format.
* @param inputFile path to the input file
* @param thermoDatabase path to the species database file
* @param log path to the file where log messages should be written
* @param logfile path to the file where log messages should be written
* @return true if no errors were encountered, false otherwise
*/
bool CKReader::read(const std::string& inputFile, const std::string& thermoDatabase,
const std::string& logfile)
{

21
src/converters/NASA9Parser.cpp
View file

@ -103,24 +103,6 @@ static double de_atof(std::string s)
return rval;
}
/**
* Check validity of the three temperatures defining the two
* temperature ranges for the NASA polynomial species thermodynamic
* property fits.
* @param log log file output stream
* @param tmin minimum temperature
* @param tmid intermediate temperature
* @param tmax maximum temperature
*/
// static void checkTemps(std::ostream& log, double tmin,
// double tmid, double tmax)
// {
// if (tmin == 0.0 || tmid == 0.0 || tmax == 0.0) {
// throw CK_SyntaxError(log,
// "error reading Tmin, Tmid, or Tmax");
// }
//}
static double getNumberFromString(std::string s)
{
bool inexp = false;
@ -165,8 +147,6 @@ static int de_atoi(std::ostream& log, std::string s, int line = -1)
* @param temp Devault vector of temperature region boundaries
* There are one more temperatures than there are
* temperature regions.
* @param allowExtThermoData True if 'THERMO' specified, false if
* 'THERMO ALL' specified.
*
* @return True, if the THERMO section exists and the species
* have all been successfully processed. False, if
@ -249,7 +229,6 @@ bool CKParser::readNASA9ThermoSection(std::vector<string>& names,
<< " of " << m_ckfilename;
writeSpeciesData(log, spec);
}
//checkTemps(log, spec.tlow, spec.tmid, spec.thigh);
if (getAllSpecies) {
names.push_back(spec.name);
nsp = static_cast<int>(names.size());

81
src/equil/vcs_VolPhase.cpp
View file

@ -405,14 +405,6 @@ void vcs_VolPhase::_updateG0() const
}
/***************************************************************************/
// Gibbs free energy calculation at a temperature for the reference state
// of a species, return a value for one species
/*
* @param kspec species index
* @param TKelvin temperature
*
* @return return value of the gibbs free energy
*/
double vcs_VolPhase::G0_calc_one(size_t kspec) const
{
if (!m_UpToDate_G0) {
@ -422,14 +414,6 @@ double vcs_VolPhase::G0_calc_one(size_t kspec) const
}
/***************************************************************************/
// Gibbs free energy calculation for standard states
/*
* Calculate the Gibbs free energies for the standard states
* The results are held internally within the object.
*
* @param TKelvin Current temperature
* @param pres Current pressure (pascal)
*/
void vcs_VolPhase::_updateGStar() const
{
if (m_useCanteraCalls) {
@ -448,18 +432,6 @@ void vcs_VolPhase::_updateGStar() const
}
/***************************************************************************/
// Gibbs free energy calculation for standard state of one species
/*
* Calculate the Gibbs free energies for the standard state
* of the kth species.
* The results are held internally within the object.
* The kth species standard state G is returned
*
* @param kspec Species number (within the phase)
*
* @return Gstar[kspec] returns the gibbs free energy for the
* standard state of the kspec species.
*/
double vcs_VolPhase::GStar_calc_one(size_t kspec) const
{
if (!m_UpToDate_GStar) {
@ -704,22 +676,6 @@ void vcs_VolPhase::setMolesFromVCS(const int stateCalc,
}
/***************************************************************************/
// Set the moles within the phase
/*
* This function takes as input the mole numbers in vcs format, and
* then updates this object with their values. This is essentially
* a gather routine.
*
* @param vcsStateStatus State calc value either VCS_STATECALC_OLD
* or VCS_STATECALC_NEW. With any other value
* nothing is done.
*
* @param molesSpeciesVCS array of mole numbers. Note,
* the indices for species in
* this array may not be contiguous. IndSpecies[] is needed
* to gather the species into the local contiguous vector
* format.
*/
void vcs_VolPhase::setMolesFromVCSCheck(const int vcsStateStatus,
const double* molesSpeciesVCS,
const double* const TPhMoles)
@ -813,16 +769,6 @@ double vcs_VolPhase::sendToVCS_VolPM(double* const VolPM) const
}
/***************************************************************************/
// Fill in the partial molar volume vector for VCS
/*
* This routine will calculate the partial molar volumes for the
* current phase (if needed), and fill in the corresponding entries in the
* VCS partial molar volumes vector.
*
* @param VolPM vector of partial molar volumes for all of the species
* in all of the phases in a VCS problem. Only the
* entries for the current phase are filled in.
*/
void vcs_VolPhase::sendToVCS_GStar(double* const gstar) const
{
if (!m_UpToDate_GStar) {
@ -902,16 +848,6 @@ void vcs_VolPhase::setState_T(const double temp)
}
/***************************************************************************/
// Molar volume calculation for standard states
/*
* Calculate the molar volume for the standard states
* The results are held internally within the object.
*
* @param TKelvin Current temperature
* @param pres Current pressure (pascal)
*
* Calculations are in m**3 / kmol
*/
void vcs_VolPhase::_updateVolStar() const
{
if (m_useCanteraCalls) {
@ -928,19 +864,6 @@ void vcs_VolPhase::_updateVolStar() const
}
/***************************************************************************/
// Molar volume calculation for standard state of one species
/*
* Calculate the molar volume for the standard states
* The results are held internally within the object.
* Return the molar volume for one species
*
* @param kspec Species number (within the phase)
* @param TKelvin Current temperature
* @param pres Current pressure (pascal)
*
* @return molar volume of the kspec species's standard
* state
*/
double vcs_VolPhase::VolStar_calc_one(size_t kspec) const
{
if (!m_UpToDate_VolStar) {
@ -993,10 +916,6 @@ double vcs_VolPhase::_updateVolPM() const
}
/***************************************************************************/
/*
* _updateLnActCoeffJac():
*
*/
void vcs_VolPhase::_updateLnActCoeffJac()
{
/*

174
src/equil/vcs_solve_TP.cpp
View file

@ -2032,49 +2032,6 @@ L_RETURN_BLOCK_B:
}
/*********************************************************************************/
// Minor species alternative calculation
/*
* This is based upon the following approximation:
* The mole fraction changes due to these reactions don't affect
* the mole numbers of the component species. Therefore the following
* approximation is valid for a small component of an ideal phase:
*
* 0 = m_deltaGRxn_old(I) + log(molNum_new(I)/molNum_old(I))
*
* m_deltaGRxn_old contains the contribution from
*
* m_feSpecies_old(I) =
* m_SSfeSpecies(I) +
* log(ActCoeff[i] * molNum_old(I) / m_tPhaseMoles_old(iph))
* Thus,
*
* molNum_new(I)= molNum_old(I) * EXP(-m_deltaGRxn_old(I))
*
* Most of this section is mainly restricting the update to reasonable
* values.
* We restrict the update a factor of 1.0E10 up and 1.0E-10 down
* because we run into trouble with the addition operator due to roundoff
* if we go larger than ~1.0E15. Roundoff will then sometimes produce
* zero mole fractions.
*
* Note: This routine was generalized to incorporate
* nonideal phases and phases on the molality basis
*
* Input:
* ------
* @param kspec The current species and corresponding formation
* reaction number.
* @param irxn The current species and corresponding formation
* reaction number.
*
* Output:
* ---------
* @param do_delete: BOOLEAN which if true on return, then we branch
* to the section that deletes a species from the
* current set of active species.
*
* @param dx The change in mole number
*/
double VCS_SOLVE::vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete
#ifdef DEBUG_MODE
, char* ANOTE
@ -2777,46 +2734,6 @@ int VCS_SOLVE::vcs_recheck_deleted()
}
/***********************************************************************************/
// Recheck deletion condition for multispecies phases.
/*
* We assume here that DG_i_0 has been calculated for deleted species correctly
*
*
* m_feSpecies(I) = m_SSfeSpecies(I)
* + ln(ActCoeff[I])
* - ln(Mnaught * m_units)
* + m_chargeSpecies[I] * Faraday_dim * m_phasePhi[iphase];
*
* sum_u = sum_j_comp [ sigma_i_j * u_j ]
* = u_i_O + log((AC_i * W_i)/m_tPhaseMoles_old)
*
* DG_i_0 = m_feSpecies(I) - sum_m{ a_i_m DG_m }
*
*
* by first evaluating:
*
* DG_i_O = u_i_O - sum_u.
*
* Then, the phase pops into existence iff
*
* phaseDG = 1.0 - sum_i{exp(-DG_i_O)} < 0.0
*
* This formula works for both single species phases and for multispecies
* phases. It's an overkill for single species phases.
*
* @param iphase Phase index number
*
* @return Returns true if the phase is currently deleted
* but should be reinstated. Returns false otherwise.
*
* NOTE: this routine is currently not used in the code, and
* contains some basic changes that are incompatible.
*
* assumptions:
* 1) Vphase Existence is up to date
* 2) Vphase->IndSpecies is up to date
* 3) m_deltaGRxn_old[irxn] is up to date
*/
bool VCS_SOLVE::recheck_deleted_phase(const int iphase)
{
@ -3141,77 +3058,6 @@ bool VCS_SOLVE::vcs_globStepDamp()
}
/****************************************************************************************/
// Choose the optimum species basis for the calculations
/*
* Choose the optimum component species basis for the calculations.
* This is done by choosing the species with the largest mole fraction
* not currently a linear combination of the previous components.
* Then, calculate the stoichiometric coefficient matrix for that
* basis.
*
* Rearranges the solution data to put the component data at the
* front of the species list.
*
* Then, calculates M_STOICHCOEFFRXNMATRIX(J,I) the formation reactions
* for all noncomponent species in the mechanism.
* Also calculates DNG(I) and DNL(I), the net mole change for each
* formation reaction.
* Also, initializes IR(I) to the default state.
*
* Input
* ---------
* @param doJustCompoents If true, the m_stoichCoeffRxnMatrix[][] and
* m_deltaMolNumPhase[] are not calculated.
*
* @param aw Vector of mole fractions which will be used to construct an
* optimal basis from.
*
* @param sa Gramm-Schmidt orthog work space (nc in length) sa[j]
* @param ss Gramm-Schmidt orthog work space (nc in length) ss[j]
* @param sm QR matrix work space (nc*ne in length) sm[i+j*ne]
* @param test This is a small negative number dependent upon whether
* an estimate is supplied or not.
*
* Output
* ---------
* @param usedZeroedSpecies = If true, then a species with a zero concentration
* was used as a component. The problem may be
* converged. Or, the problem may have a range space
* error and may not have a proper solution.
*
* Internal Variables calculated by this routine:
* -----------------------------------------------
*
* m_numComponents
* Number of component species
*
* component species
* This routine calculates the m_numComponent species. It switches
* their positions in the species vector so that they occupy
* the first m_numComponent spots in the species vector.
*
* m_stoichCoeffRxnMatrix[irxn][jcomp]
* Stoichiometric coefficient matrix for the reaction mechanism
* expressed in Reduced Canonical Form.
* j refers to the component number, and irxn
* refers to the irxn_th non-component species.
*
* m_deltaMolNumPhase[irxn]
* Change in the number of total number of moles of species in all phases
* due to the noncomponent formation reaction, irxn.
*
* m_deltaMolNumPhase[irxn][iphase]
* Change in the number of moles in phase, iphase, due to the
* noncomponent formation reaction, irxn.
*
* m_phaseParticipation[irxn]
* This is 1 if the phase, iphase, participates in the
* formation reaction, irxn, and zero otherwise.
*
* @return Returns VCS_SUCCESS if everything went ok. Returns
* VCS_FAILED_CONVERGENCE if there is a problem.
*/
int VCS_SOLVE::vcs_basopt(const bool doJustComponents, double aw[], double sa[], double sm[],
double ss[], double test, bool* const usedZeroedSpecies)
{
@ -4604,12 +4450,7 @@ void VCS_SOLVE::vcs_dfe(const int stateCalc,
}
//====================================================================================================================
// Print out a table of chemical potentials
/*
* @param vcsState Determines where to get the mole numbers from.
* - VCS_STATECALC_OLD -> from m_molNumSpecies_old
* - VCS_STATECALC_NEW -> from m_molNumSpecies_new
*/
void VCS_SOLVE::vcs_printSpeciesChemPot(const int stateCalc) const
{
double mfValue = 1.0;
@ -4730,12 +4571,6 @@ void VCS_SOLVE::prneav() const
#endif
/*****************************************************************************/
// Calculate the norm of a deltaGibbs free energy vector
/*
* Positive DG for species which don't exist are ignored.
*
* @param dgLocal Vector of local delta G's.
*/
double VCS_SOLVE::l2normdg(double dgLocal[]) const
{
double tmp;
@ -4816,13 +4651,6 @@ void VCS_SOLVE::check_tmoles() const
#endif
/*****************************************************************************/
// This routine uploads the state of the system into all of the
// vcs_VolPhase objects in the current problem.
/*
* @param vcsState Determines where to get the mole numbers from.
* - VCS_STATECALC_OLD -> from m_molNumSpecies_old
* - VCS_STATECALC_NEW -> from m_molNumSpecies_new
*/
void VCS_SOLVE::vcs_updateVP(const int vcsState)
{
vcs_VolPhase* Vphase;

6
src/kinetics/importKinetics.cpp
View file

@ -663,11 +663,11 @@ next:
* points directly to a ctml element named "reaction". i refers
* to the number id of the reaction in the kinetics object.
*
* @param i Reaction number.
* @param iRxn Reaction number.
* @param r XML_Node containing reaction data.
* @param k Kinetics manager to which reaction will be added.
* @param kin Kinetics manager to which reaction will be added.
* @param default_phase Default phase for locating a species
* @param rule Rule for handling reactions with missing species
* @param rules Rule for handling reactions with missing species
* (skip or flag as error)
* @param validate_rxn If true, check that this reaction is not a
* duplicate of one already entered, and check that the reaction

6
src/thermo/GibbsExcessVPSSTP.cpp
View file

@ -248,12 +248,6 @@ void GibbsExcessVPSSTP::getActivities(doublereal* ac) const
}
}
//====================================================================================================================
// Get the array of non-dimensional molar-based activity coefficients at
// the current solution temperature, pressure, and solution concentration.
/*
* @param ac Output vector of activity coefficients. Length: m_kk.
*/
void GibbsExcessVPSSTP::getActivityCoefficients(doublereal* const ac) const
{

12
src/thermo/MixtureFugacityTP.cpp
View file

@ -981,19 +981,7 @@ int MixtureFugacityTP::spinodalFunc::evalSS(const doublereal t, const doublereal
return status;
}
//====================================================================================================================
// Utility routine in the calculation of the saturation pressure
/*
* Private routine
*
* @param TKelvin temperature (kelvin)
* @param pres pressure (Pascal)
* @param densLiq Output density of liquid
* @param densGas output density of gas
* @param delGRT output delGRT
*
* @return Returns zero if both the gas and the liquid states are found for a given pressure.
*/
int MixtureFugacityTP::corr0(doublereal TKelvin, doublereal pres, doublereal& densLiqGuess,
doublereal& densGasGuess, doublereal& liqGRT, doublereal& gasGRT)
{

6
src/thermo/MolarityIonicVPSSTP.cpp
View file

@ -290,11 +290,7 @@ void MolarityIonicVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id)
* - Activities, Standard States, Activity Concentrations -----------
*/
//====================================================================================================================
// Get the array of non-dimensional molar-based activity coefficients at
// the current solution temperature, pressure, and solution concentration.
/*
* @param ac Output vector of activity coefficients. Length: m_kk.
*/
void MolarityIonicVPSSTP::getLnActivityCoefficients(doublereal* lnac) const
{
/*

6
src/thermo/RedlichKisterVPSSTP.cpp
View file

@ -347,11 +347,7 @@ void RedlichKisterVPSSTP::constructPhaseXML(XML_Node& phaseNode, std::string id)
* - Activities, Standard States, Activity Concentrations -----------
*/
//====================================================================================================================
// Get the array of non-dimensional molar-based activity coefficients at
// the current solution temperature, pressure, and solution concentration.
/*
* @param ac Output vector of activity coefficients. Length: m_kk.
*/
void RedlichKisterVPSSTP::getLnActivityCoefficients(doublereal* lnac) const
{
/*

10
src/thermo/RedlichKwongMFTP.cpp
View file

@ -1021,10 +1021,10 @@ void RedlichKwongMFTP::initThermoXML(XML_Node& phaseNode, std::string id)
}
//====================================================================================================================
void RedlichKwongMFTP::readXMLPureFluid(XML_Node& PureFluidParam)
void RedlichKwongMFTP::readXMLPureFluid(XML_Node& pureFluidParam)
{
vector_fp vParams;
string xname = PureFluidParam.name();
string xname = pureFluidParam.name();
if (xname != "pureFluidParameters") {
throw CanteraError("RedlichKwongMFTP::readXMLPureFluid",
"Incorrect name for processing this routine: " + xname);
@ -1034,7 +1034,7 @@ void RedlichKwongMFTP::readXMLPureFluid(XML_Node& PureFluidParam)
* Read the species
* Find the index of the species in the current phase. It's not an error to not find the species
*/
string iName = PureFluidParam.attrib("species");
string iName = pureFluidParam.attrib("species");
if (iName == "") {
throw CanteraError("RedlichKwongMFTP::readXMLPureFluid", "no species attribute");
}
@ -1044,9 +1044,9 @@ void RedlichKwongMFTP::readXMLPureFluid(XML_Node& PureFluidParam)
}
size_t counter = iSpecies + m_kk * iSpecies;
size_t nParamsExpected, nParamsFound;
size_t num = PureFluidParam.nChildren();
size_t num = pureFluidParam.nChildren();
for (size_t iChild = 0; iChild < num; iChild++) {
XML_Node& xmlChild = PureFluidParam.child(iChild);
XML_Node& xmlChild = pureFluidParam.child(iChild);
string stemp = xmlChild.name();
string nodeName = lowercase(stemp);

2
src/thermo/SpeciesThermoFactory.cpp
View file

@ -674,7 +674,7 @@ static void installNasa9ThermoFromXML(std::string speciesName,
* @param speciesName String name of the species
* @param sp SpeciesThermo object that will receive the nasa polynomial object
* @param k Species index within the phase
* @param tp Vector of XML Nodes that make up the parameterization
* @param f XML Node that contains the parameterization
*/
static void installAdsorbateThermoFromXML(std::string speciesName,
SpeciesThermo& sp, size_t k,