Cleaned up documentation and comments for class Phase
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Ray Speth
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2 changed files with 433 additions and 879 deletions
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@ -1,8 +1,6 @@
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/**
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* @file Phase.cpp
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* Definition file for class, Phase, which contains functions for setting the
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* state of a phase, and for referencing species by name
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* (see \ref phases and class \link Cantera::Phase Phase\endlink).
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* Definition file for class Phase.
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*/
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// Copyright 2001 California Institute of Technology
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@ -33,16 +31,10 @@ Phase::Phase() :
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m_Elements->subscribe();
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}
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/*
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* Copy Constructor
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*
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* This function just does the default initialization, and
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* then calls the assignment operator.
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*/
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Phase::Phase(const Phase& right) :
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m_kk(0),
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m_ndim(3),
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m_xml(new XML_Node("phase")),
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m_xml(0),
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m_id("<phase>"),
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m_name(""),
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m_temp(0.0),
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@ -52,9 +44,7 @@ Phase::Phase(const Phase& right) :
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m_speciesFrozen(false) ,
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m_Elements(0)
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{
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/*
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* Call the assignment operator.
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*/
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// Use the assignment operator to do the actual copying
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*this = operator=(right);
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}
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@ -66,18 +56,17 @@ Phase& Phase::operator=(const Phase& right)
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}
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// Handle our own data
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m_kk = right.m_kk;
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m_ndim = right.m_ndim;
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m_data = right.m_data;
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m_temp = right.m_temp;
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m_dens = right.m_dens;
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m_mmw = right.m_mmw;
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m_ym = right.m_ym;
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m_y = right.m_y;
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m_molwts = right.m_molwts;
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m_rmolwts = right.m_rmolwts;
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m_kk = right.m_kk;
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m_ndim = right.m_ndim;
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m_temp = right.m_temp;
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m_dens = right.m_dens;
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m_mmw = right.m_mmw;
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m_ym = right.m_ym;
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m_y = right.m_y;
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m_molwts = right.m_molwts;
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m_rmolwts = right.m_rmolwts;
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m_stateNum = -1;
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m_speciesFrozen = right.m_speciesFrozen;
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m_speciesFrozen = right.m_speciesFrozen;
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if (m_Elements) {
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int nleft = m_Elements->unsubscribe();
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if (nleft <= 0) {
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@ -92,14 +81,14 @@ Phase& Phase::operator=(const Phase& right)
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delete m_Elements;
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}
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}
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m_Elements = right.m_Elements;
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m_Elements = right.m_Elements;
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if (m_Elements) {
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m_Elements->subscribe();
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}
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m_speciesNames = right.m_speciesNames;
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m_speciesComp = right.m_speciesComp;
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m_speciesCharge = right.m_speciesCharge;
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m_speciesSize = right.m_speciesSize;
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m_speciesNames = right.m_speciesNames;
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m_speciesComp = right.m_speciesComp;
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m_speciesCharge = right.m_speciesCharge;
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m_speciesSize = right.m_speciesSize;
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/*
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* This is a little complicated. -> Because we delete m_xml
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@ -112,7 +101,7 @@ Phase& Phase::operator=(const Phase& right)
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m_xml = 0;
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}
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if (right.m_xml) {
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m_xml = new XML_Node();
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m_xml = new XML_Node();
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(right.m_xml)->copy(m_xml);
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}
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m_id = right.m_id;
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@ -248,27 +237,6 @@ void Phase::getAtoms(size_t k, double* atomArray) const
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}
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}
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// Returns the index of a species named 'name' within the Phase object
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/*
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* The first species in the phase will have an index 0, and the last one in the
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* phase will have an index of nSpecies() - 1.
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*
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*
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* A species name may be referred to via three methods:
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*
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* - "speciesName"
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* - "PhaseId:speciesName"
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* - "phaseName:speciesName"
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* .
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*
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* The first two methods of naming may not yield a unique species within
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* complicated assemblies of Cantera Phases.
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*
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* @param nameStr String name of the species. It may also be the phase name
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* species name combination, separated by a colon.
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* @return Returns the index of the species. If the name is not found,
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* the value of -1 is returned.
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*/
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size_t Phase::speciesIndex(std::string nameStr) const
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{
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std::string pn;
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@ -438,79 +406,65 @@ void Phase::setMassFractionsByName(const std::string& y)
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setMassFractionsByName(yy);
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}
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/** Set the temperature (K), density (kg/m^3), and mole fractions. */
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void Phase::setState_TRX(doublereal t, doublereal dens,
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const doublereal* x)
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void Phase::setState_TRX(doublereal t, doublereal dens, const doublereal* x)
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{
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setMoleFractions(x);
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setTemperature(t);
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setDensity(dens);
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}
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void Phase::setState_TNX(doublereal t, doublereal n,
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const doublereal* x)
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void Phase::setState_TNX(doublereal t, doublereal n, const doublereal* x)
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{
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setMoleFractions(x);
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setTemperature(t);
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setMolarDensity(n);
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}
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/** Set the temperature (K), density (kg/m^3), and mole fractions. */
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void Phase::setState_TRX(doublereal t, doublereal dens,
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compositionMap& x)
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void Phase::setState_TRX(doublereal t, doublereal dens, compositionMap& x)
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{
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setMoleFractionsByName(x);
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setTemperature(t);
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setDensity(dens);
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}
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/** Set the temperature (K), density (kg/m^3), and mass fractions. */
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void Phase::setState_TRY(doublereal t, doublereal dens,
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const doublereal* y)
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void Phase::setState_TRY(doublereal t, doublereal dens, const doublereal* y)
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{
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setMassFractions(y);
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setTemperature(t);
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setDensity(dens);
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}
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/** Set the temperature (K), density (kg/m^3), and mass fractions. */
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void Phase::setState_TRY(doublereal t, doublereal dens,
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compositionMap& y)
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void Phase::setState_TRY(doublereal t, doublereal dens, compositionMap& y)
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{
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setMassFractionsByName(y);
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setTemperature(t);
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setDensity(dens);
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}
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/** Set the temperature (K) and density (kg/m^3) */
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void Phase::setState_TR(doublereal t, doublereal rho)
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{
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setTemperature(t);
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setDensity(rho);
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}
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/** Set the temperature (K) and mole fractions. */
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void Phase::setState_TX(doublereal t, doublereal* x)
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{
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setTemperature(t);
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setMoleFractions(x);
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}
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/** Set the temperature (K) and mass fractions. */
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void Phase::setState_TY(doublereal t, doublereal* y)
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{
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setTemperature(t);
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setMassFractions(y);
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}
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/** Set the density (kg/m^3) and mole fractions. */
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void Phase::setState_RX(doublereal rho, doublereal* x)
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{
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setMoleFractions(x);
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setDensity(rho);
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}
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/** Set the density (kg/m^3) and mass fractions. */
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void Phase::setState_RY(doublereal rho, doublereal* y)
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{
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setMassFractions(y);
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@ -525,9 +479,6 @@ doublereal Phase::molecularWeight(size_t k) const
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return m_molwts[k];
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}
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/*
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* Copy the vector of molecular weights into vector weights.
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*/
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void Phase::getMolecularWeights(vector_fp& weights) const
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{
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const vector_fp& mw = molecularWeights();
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@ -537,10 +488,6 @@ void Phase::getMolecularWeights(vector_fp& weights) const
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copy(mw.begin(), mw.end(), weights.begin());
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}
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/*
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* Copy the vector of molecular weights into array weights.
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* @deprecated
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*/
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void Phase::getMolecularWeights(int iwt, doublereal* weights) const
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{
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const vector_fp& mw = molecularWeights();
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@ -558,9 +505,6 @@ const vector_fp& Phase::molecularWeights() const
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return m_molwts;
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}
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/**
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* Get the mole fractions by name.
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*/
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void Phase::getMoleFractionsByName(compositionMap& x) const
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{
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x.clear();
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@ -720,9 +664,11 @@ void Phase::addElement(const XML_Node& e)
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}
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void Phase::addUniqueElement(const std::string& symbol, doublereal weight,
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int atomicNumber, doublereal entropy298, int elem_type)
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int atomicNumber, doublereal entropy298,
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int elem_type)
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{
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m_Elements->addUniqueElement(symbol, weight, atomicNumber, entropy298, elem_type);
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m_Elements->addUniqueElement(symbol, weight, atomicNumber,
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entropy298, elem_type);
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}
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void Phase::addUniqueElement(const XML_Node& e)
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@ -745,7 +691,8 @@ bool Phase::elementsFrozen()
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return m_Elements->elementsFrozen();
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}
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size_t Phase::addUniqueElementAfterFreeze(const std::string& symbol, doublereal weight, int atomicNumber,
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size_t Phase::addUniqueElementAfterFreeze(const std::string& symbol,
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doublereal weight, int atomicNumber,
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doublereal entropy298, int elem_type)
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{
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size_t ii = elementIndex(symbol);
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@ -783,7 +730,8 @@ void Phase::addSpecies(const std::string& name, const doublereal* comp,
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m_speciesCharge.push_back(charge);
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m_speciesSize.push_back(size);
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size_t ne = m_Elements->nElements();
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// Create a changeable copy of the element composition. We now change the charge potentially
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// Create a changeable copy of the element composition. We now change
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// the charge potentially
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vector_fp compNew(ne);
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for (size_t m = 0; m < ne; m++) {
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compNew[m] = comp[m];
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@ -797,14 +745,17 @@ void Phase::addSpecies(const std::string& name, const doublereal* comp,
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if (fabs(charge + ecomp) > 0.001) {
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if (ecomp != 0.0) {
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throw CanteraError("Phase::addSpecies",
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"Input charge and element E compositions differ for species " + name);
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"Input charge and element E compositions differ "
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"for species " + name);
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} else {
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// Just fix up the element E composition based on the input species charge
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// Just fix up the element E composition based on the input
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// species charge
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compNew[eindex] = -charge;
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}
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}
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} else {
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addUniqueElementAfterFreeze("E", 0.000545, 0, 0.0, CT_ELEM_TYPE_ELECTRONCHARGE);
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addUniqueElementAfterFreeze("E", 0.000545, 0, 0.0,
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CT_ELEM_TYPE_ELECTRONCHARGE);
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ne = m_Elements->nElements();
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eindex = m_Elements->elementIndex("E");
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compNew.resize(ne);
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@ -825,11 +776,9 @@ void Phase::addUniqueSpecies(const std::string& name, const doublereal* comp,
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vector<string>::const_iterator it = m_speciesNames.begin();
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for (size_t k = 0; k < m_kk; k++) {
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if (*it == name) {
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/*
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* We have found a match. At this point we could do some
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* compatibility checks. However, let's just return for the
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* moment without specifying any error.
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*/
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// We have found a match. At this point we could do some
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// compatibility checks. However, let's just return for the moment
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// without specifying any error.
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size_t m_mm = m_Elements->nElements();
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for (size_t i = 0; i < m_mm; i++) {
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if (comp[i] != m_speciesComp[m_kk * m_mm + i]) {
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@ -861,10 +810,6 @@ void Phase::freezeSpecies()
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init(molecularWeights());
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size_t kk = nSpecies();
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size_t nv = kk + 2;
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m_data.resize(nv,0.0);
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m_data[0] = 300.0;
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m_data[1] = 0.001;
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m_data[2] = 1.0;
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m_kk = nSpecies();
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}
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@ -881,25 +826,21 @@ void Phase::init(const vector_fp& mw)
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"negative molecular weight for species number "
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+ int2str(k));
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}
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/*
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* Some surface phases may define species representing
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* empty sites that have zero molecular weight. Give them
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* a very small molecular weight to avoid dividing by
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* zero.
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*/
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// Some surface phases may define species representing empty sites
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// hat have zero molecular weight. Give them a very small molecular
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// weight to avoid dividing by zero.
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if (m_molwts[k] < Tiny) {
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m_molwts[k] = Tiny;
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}
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m_rmolwts[k] = 1.0/m_molwts[k];
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}
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/*
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* Now that we have resized the State object, let's fill it with
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* a valid mass fraction vector that sums to one. The State object
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* should never have a mass fraction vector that doesn't sum to one.
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* We will assume that species 0 has a mass fraction of 1.0 and
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* mass fraction of all other species is 0.0.
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*/
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// Now that we have resized the State object, let's fill it with a valid
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// mass fraction vector that sums to one. The Phase object should never
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// have a mass fraction vector that doesn't sum to one. We will assume that
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// species 0 has a mass fraction of 1.0 and mass fraction of all other
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// species is 0.0.
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m_y[0] = 1.0;
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m_ym[0] = m_y[0] * m_rmolwts[0];
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m_mmw = 1.0 / m_ym[0];
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