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Remove deprecated code with functional alternatives

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This commit is contained in:
Ray Speth 2015-07-13 18:45:58 -04:00
parent 9e8b8e4f63
commit 546289f737
96 changed files with 91 additions and 8713 deletions
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3
doc/sphinx/cti/reactions.rst
View file

@ -58,9 +58,6 @@ which is defined with an :class:`Arrhenius` entry::
rate_coeff = Arrhenius(A=1.0e13, b=0, E=(7.3, 'kcal/mol'))
rate_coeff = Arrhenius(1.0e13, 0, (7.3, 'kcal/mol'))
Note: the usage of ``n`` as the temperature exponent has been deprecated. It is
still available in version 2.2 but will be removed.
As a shorthand, if the ``rate_coeff`` field is assigned a sequence of three numbers, these are assumed to be :math:`(A, b, E)` in the modified Arrhenius function::
rate_coeff = [1.0e13, 0, (7.3, 'kcal/mol')] # equivalent to above

19
include/cantera/base/ctml.h
View file

@ -742,25 +742,6 @@ void getNamedStringValue(const XML_Node& node, const std::string& nameString, st
std::string getChildValue(const XML_Node& parent,
const std::string& nameString);
//! Read an ctml file from a file and fill up an XML tree
/*!
* This is the main routine that reads a ctml file and puts it into
* an XML_Node tree
*
* @param node Root of the tree
* @param file Name of the file
* @param debug Turn on debugging printing
* @deprecated To be removed after Cantera 2.2. Use get_XML_File() instead.
*/
void get_CTML_Tree(XML_Node* node, const std::string& file,
const int debug = 0);
//! Read an ctml file from a file and fill up an XML tree.
//! @param file Name of the file
//! @return Root of the tree
//! @deprecated To be removed after Cantera 2.2. Use get_XML_File() instead.
XML_Node getCtmlTree(const std::string& file);
//! Convert a cti file into a ctml file
/*!
* @param file Pointer to the file

19
include/cantera/base/xml.h
View file

@ -222,13 +222,6 @@ public:
*/
std::string value() const;
//! Overloaded parenthesis operator returns the value of the Node
/*!
* @return Returns the value of the node as a string.
* @deprecated Use value() instead.
*/
std::string operator()() const;
//! Return the value of an XML child node as a string
/*!
* @param cname Name of the child node to the current
@ -559,18 +552,6 @@ public:
*/
XML_Node* findByName(const std::string& nm, int depth = 100000);
//! Get a vector of pointers to XML_Node containing all of the children
//! of the current node which matches the input name
/*!
* @param name Name of the XML_Node children to search on
*
* @param children output vector of pointers to XML_Node children
* with the matching name
* @deprecated To be removed after Cantera 2.2. Use the version that returns
* the vector of child nodes
*/
void getChildren(const std::string& name, std::vector<XML_Node*>& children) const;
//! Get a vector of pointers to XML_Node containing all of the children
//! of the current node which match the given name
/*!

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

@ -799,13 +799,11 @@ size_t BasisOptimize(int* usedZeroedSpecies, bool doFormRxn,
* elements that is necessary for calculation of the formula matrix.
*
* @ingroup equilfunctions
* @deprecated - The return value for this function is deprecated. After
* Cantera 2.2, this function will return void.
*/
size_t ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
MultiPhase* mphase,
std::vector<size_t>& orderVectorSpecies,
std::vector<size_t>& orderVectorElements);
void ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
MultiPhase* mphase,
std::vector<size_t>& orderVectorSpecies,
std::vector<size_t>& orderVectorElements);
//! External int that is used to turn on debug printing for the
//! BasisOptimze program.

88
include/cantera/equil/equil.h
View file

@ -1,88 +0,0 @@
/**
* @file equil.h
* This file contains the definition of some high level general equilibration
* routines.
* @deprecated All functions defined in this file are deprecated. To be removed
* after Cantera 2.2.
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_KERNEL_EQUIL_H
#define CT_KERNEL_EQUIL_H
#pragma message("cantera/equil/equil.h is deprecated")
#include "MultiPhase.h"
#include "vcs_defs.h"
namespace Cantera
{
/*!
* @defgroup equilfunctions Equilibrium Solver Capability
*
* Cantera has several different equilibrium routines.
*/
//! Equilibrate a ThermoPhase object
/*!
* Set a single-phase chemical solution to chemical equilibrium. This is a
* convenience function that uses one or the other of the two chemical
* equilibrium solvers. The XY parameter indicates what two thermodynamic
* quantities, other than element composition, are to be held constant during
* the equilibration process.
*
* @param s ThermoPhase object that will be equilibrated.
* @param XY String representation of what two properties
* are being held constant
* @param solver ID of the solver to be used to equilibrate the phase.
* If solver = 0, the ChemEquil solver will be used,
* and if solver = 1, the
* MultiPhaseEquil solver will be used (slower than ChemEquil,
* but more stable). If solver < 0 (default, then ChemEquil will
* be tried first, and if it fails MultiPhaseEquil will be tried.
* @param rtol Relative tolerance
* @param maxsteps Maximum number of steps to take to find the solution
* @param maxiter For the MultiPhaseEquil solver only, this is
* the maximum number of outer temperature or pressure iterations
* to take when T and/or P is not held fixed.
* @param loglevel loglevel Controls amount of diagnostic output. loglevel
* = 0 suppresses diagnostics, and increasingly-verbose messages
* are written as loglevel increases.
*
* @return The number of iterations it took to equilibrate the system.
* @deprecated Use ThermoPhase::equilibrate instead. To be removed after Cantera 2.2.
* @ingroup equilfunctions
*/
int equilibrate(thermo_t& s, const char* XY,
int solver = -1, doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS,
int maxiter = 100, int loglevel = -99);
//! Equilibrate a MultiPhase object
/*!
* Equilibrate a MultiPhase object. The XY parameter indicates what two
* thermodynamic quantities, other than element composition, are to be held
* constant during the equilibration process.
*
* This is the top-level driver for multiphase equilibrium. It doesn't do
* much more than call the equilibrate method of class MultiPhase, except
* that it adds some messages to the logfile, if loglevel is set > 0.
*
* @param s MultiPhase object that will be equilibrated.
* @param XY String representation of what is being held constant
* @param rtol Relative tolerance
* @param maxsteps Maximum number of steps
* @param maxiter Maximum iterations
* @param loglevel loglevel
*
* @return The number of iterations it took to equilibrate the system.
* @deprecated Use MultiPhase::equilibrate instead. To be removed after Cantera 2.2.
* @ingroup equilfunctions
*/
doublereal equilibrate(MultiPhase& s, const char* XY,
doublereal rtol = 1.0e-9, int maxsteps = 5000, int maxiter = 100,
int loglevel = -99);
}
#endif

147
include/cantera/equil/vcs_MultiPhaseEquil.h
View file

@ -11,153 +11,6 @@
namespace Cantera
{
//! Set a single-phase chemical solution to chemical equilibrium.
/*!
* The function uses the element abundance vector that is currently
* consistent with the composition within the phase itself. Two other
* thermodynamic quantities, determined by the XY string, are held constant
* during the equilibration. This is a convenience function that uses one or
* the other of the two chemical equilibrium solvers.
*
* @param s The object to set to an equilibrium state
* @param XY An integer specifying the two properties to be held constant.
* @param estimateEquil integer indicating whether the solver
* should estimate its own initial condition.
* - If 0, the initial mole fraction vector in the
* ThermoPhase object is used as the initial condition.
* - If 1, the initial mole fraction vector is used if the
* element abundances are satisfied.
* - if -1, the initial mole fraction vector is thrown out,
* and an estimate is formulated.
* @param printLvl Determines the amount of printing that gets sent to stdout
* from the vcs package (Note, you may have to compile with
* debug flags to get some printing).
* @param solver The equilibrium solver to use. If solver = 0, the ChemEquil
* solver will be used, and if solver = 1, the
* vcs_MultiPhaseEquil solver will be used (slower than
* ChemEquil, but more stable). If solver < 0 (default, then
* ChemEquil will be tried first, and if it fails
* vcs_MultiPhaseEquil will be tried.
* @param rtol Relative tolerance of the solve. Defaults to 1.0E-9.
* @param maxsteps The maximum number of steps to take to find the solution.
* @param maxiter For the MultiPhaseEquil solver only, this is the maximum
* number of outer temperature or pressure iterations to take
* when T and/or P is not held fixed.
* @param loglevel Controls amount of diagnostic output. loglevel
* = 0 suppresses diagnostics, and increasingly-verbose
* messages are written as loglevel increases.
* @deprecated Use ThermoPhase::equilibrate instead. To be removed after
* Cantera 2.2.
* @ingroup equilfunctions
*/
int vcs_equilibrate(thermo_t& s, const char* XY,
int estimateEquil = 0, int printLvl = 0,
int solver = -1, doublereal rtol = 1.0e-9,
int maxsteps = VCS_MAXSTEPS,
int maxiter = 100, int loglevel = -99);
//! Set a multi-phase chemical solution to chemical equilibrium.
/*!
* This function uses the vcs_MultiPhaseEquil interface to the vcs solver.
* The function uses the element abundance vector that is currently
* consistent with the composition within the phases themselves. Two other
* thermodynamic quantities, determined by the XY string, are held constant
* during the equilibration.
*
* @param s The object to set to an equilibrium state
* @param XY A character string representing the unknowns to be held constant
* @param estimateEquil integer indicating whether the solver
* should estimate its own initial condition.
* - If 0, the initial mole fraction vector in the
* ThermoPhase object is used as the initial condition.
* - If 1, the initial mole fraction vector is used if the
* element abundances are satisfied.
* - If -1, the initial mole fraction vector is thrown out,
* and an estimate is formulated.
* @param printLvl Determines the amount of printing that gets sent to stdout
* from the vcs package (Note, you may have to compile with
* debug flags to get some printing).
* @param solver Determines which solver is used.
* - 1 MultiPhaseEquil solver
* - 2 VCSnonideal Solver (default)
* @param rtol Relative tolerance of the solve. Defaults to 1.0E-9.
* @param maxsteps The maximum number of steps to take to find the solution.
* @param maxiter For the MultiPhaseEquil solver only, this is the maximum
* number of outer temperature or pressure iterations to take
* when T and/or P is not held fixed.
* @param loglevel Controls amount of diagnostic output. loglevel
* = 0 suppresses diagnostics, and increasingly-verbose
* messages are written as loglevel increases.
* @deprecated Use MultiPhase::equilibrate instead. To be removed after
* Cantera 2.2.
* @ingroup equilfunctions
*/
int vcs_equilibrate(MultiPhase& s, const char* XY,
int estimateEquil = 0, int printLvl = 0,
int solver = 2,
doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS,
int maxiter = 100, int loglevel = -99);
//! Set a multi-phase chemical solution to chemical equilibrium.
/*!
* This function uses the vcs_MultiPhaseEquil interface to the vcs solver.
* The function uses the element abundance vector that is currently
* consistent with the composition within the phases themselves. Two other
* thermodynamic quantities, determined by the XY string, are held constant
* during the equilibration.
*
* @param s The MultiPhase object to be set to an equilibrium state
* @param ixy An integer specifying the two properties to be held constant.
* @param estimateEquil integer indicating whether the solver
* should estimate its own initial condition.
* - If 0, the initial mole fraction vector in the
* ThermoPhase object is used as the initial condition.
* - If 1, the initial mole fraction vector is used if the
* element abundances are satisfied.
* - if -1, the initial mole fraction vector is thrown out,
* and an estimate is formulated.
* @param printLvl Determines the amount of printing that gets sent to stdout
* from the vcs package (Note, you may have to compile with
* debug flags to get some printing).
* @param solver Determines which solver is used.
* - 1 MultiPhaseEquil solver
* - 2 VCSnonideal Solver (default)
* @param rtol Relative tolerance of the solve. Defaults to 1.0E-9.
* @param maxsteps The maximum number of steps to take to find the solution.
* @param maxiter For the MultiPhaseEquil solver only, this is
* the maximum number of outer temperature or
* pressure iterations to take when T and/or P is
* not held fixed.
* @param loglevel Controls amount of diagnostic output. loglevel
* = 0 suppresses diagnostics, and increasingly-verbose
* messages are written as loglevel increases.
* @deprecated Use MultiPhase::equilibrate instead. To be removed after
* Cantera 2.2.
* @ingroup equilfunctions
*/
int vcs_equilibrate_1(MultiPhase& s, int ixy,
int estimateEquil = 0, int printLvl = 0,
int solver = 2,
doublereal rtol = 1.0e-9, int maxsteps = VCS_MAXSTEPS,
int maxiter = 100, int loglevel = -99);
//! Determine the phase stability of a single phase given the current conditions
//! in a MultiPhase object
/*!
* @param s The MultiPhase object to be set to an equilibrium state
* @param iphase Phase index within the multiphase object to be
* tested for stability.
* @param funcStab Function value that tests equilibrium. > 0 indicates stable
* < 0 indicates unstable
* @param printLvl Determines the amount of printing that gets sent to
* stdout from the vcs package (Note, you may have to compile
* with debug flags to get some printing).
* @param loglevel Controls amount of diagnostic output. loglevel
* = 0 suppresses diagnostics, and increasingly-verbose
* messages are written as loglevel increases.
*/
int vcs_determine_PhaseStability(MultiPhase& s, int iphase,
double& funcStab, int printLvl, int loglevel);
//! Translate a MultiPhase object into a VCS_PROB problem definition object
/*!

17
include/cantera/equilibrium.h
View file

@ -1,17 +0,0 @@
/**
* @file equilibrium.h
* cxx layer - Header file providing support for chemical equilibrium calculations
* (see \ref equilfunctions)
* @deprecated Equilibrium solvers are directly available through class
* Cantera::ThermoPhase and class Cantera::MultiPhase
*/
#ifndef CT_EQUIL_INCL
#define CT_EQUIL_INCL
#pragma message("cantera/equilibrium.h is deprecated")
#include "equil/equil.h"
#include "equil/ChemEquil.h"
#include "equil/MultiPhaseEquil.h"
#include "equil/vcs_MultiPhaseEquil.h"
#endif

1
include/cantera/kinetics/AqueousKinetics.h
View file

@ -55,7 +55,6 @@ public:
//! Update the equilibrium constants in molar units.
void updateKc();
virtual void addReaction(ReactionData& r);
virtual bool addReaction(shared_ptr<Reaction> r);
virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);
};

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

@ -34,7 +34,6 @@ public:
virtual void getRevRateConstants(doublereal* krev,
bool doIrreversible = false);
virtual void addReaction(ReactionData& r);
virtual bool addReaction(shared_ptr<Reaction> r);
virtual void init();
virtual void finalize();
@ -44,7 +43,6 @@ public:
protected:
virtual void addElementaryReaction(ReactionData& r);
virtual void addElementaryReaction(ElementaryReaction& r);
virtual void modifyElementaryReaction(size_t i, ElementaryReaction& rNew);

4
include/cantera/kinetics/ElectrodeKinetics.h
View file

@ -75,10 +75,6 @@ public:
*/
virtual void updateROP();
virtual void determineFwdOrdersBV(ReactionData& rdata, std::vector<doublereal>& fwdFullorders);
//void addGlobalReaction(ReactionData& r);
double calcForwardROP_BV(size_t irxn, size_t iBeta, double ioc, double nStoich, double nu, doublereal ioNet);
double calcForwardROP_BV_NoAct(size_t irxn, size_t iBeta, double ioc, double nStoich, double nu, doublereal ioNet);

65
include/cantera/kinetics/Enhanced3BConc.h
View file

@ -1,65 +0,0 @@
/**
* @file Enhanced3BConc.h
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_ENH_CONC_H
#define CT_ENH_CONC_H
#include "cantera/base/ct_defs.h"
#include "cantera/base/global.h"
namespace Cantera
{
/**
* Computes enhanced third-body concentrations.
* @deprecated Replaced by ThirdBodyCalc. To be removed after Cantera 2.2.
* @see GasKinetics
*/
class Enhanced3BConc
{
public:
Enhanced3BConc() : m_deflt(1.0) {
warn_deprecated("class Enhanced3BConc",
"To be removed after Cantera 2.2.");
}
Enhanced3BConc(const std::map<size_t, doublereal>& enhanced,
doublereal deflt = 1.0) {
warn_deprecated("class Enhanced3BConc",
"To be removed after Cantera 2.2.");
std::map<size_t, doublereal>::const_iterator iter;
for (iter = enhanced.begin(); iter != enhanced.end(); ++iter) {
m_index.push_back(iter->first);
m_eff.push_back(iter->second - deflt);
}
m_deflt = deflt;
}
doublereal update(const vector_fp& c, doublereal ctot) const {
doublereal sum = 0.0;
for (size_t i = 0; i < m_eff.size(); i++) {
sum += m_eff[i] * c[m_index[i]];
}
return m_deflt * ctot + sum;
}
void getEfficiencies(vector_fp& eff) const {
for (size_t i = 0; i < m_eff.size(); i++) {
eff[m_index[i]] = m_eff[i] + m_deflt;
}
}
private:
std::vector<size_t> m_index;
vector_fp m_eff;
doublereal m_deflt;
};
}
#endif

18
include/cantera/kinetics/FalloffMgr.h
View file

@ -30,24 +30,6 @@ public:
//else m_factory = f;
}
//! Install a new falloff function calculator.
/*
* @param rxn Index of the falloff reaction. This will be used to
* determine which array entry is modified in method pr_to_falloff.
* @param falloffType of falloff function to install.
* @param reactionType Either `FALLOFF_RXN` or `CHEMACT_RXN`
* @param c vector of coefficients for the falloff function.
* @deprecated Use install(size_t, int, shared_ptr<Falloff>). To be removed
* after Cantera 2.2.
*/
void install(size_t rxn, int falloffType, int reactionType,
const vector_fp& c) {
warn_deprecated("FalloffMgr::install(size_t, int, int, const vector_fp&)",
"Use install(size_t, int, shared_ptr<Falloff>). To be removed after Cantera 2.2.");
shared_ptr<Falloff> f(m_factory->newFalloff(falloffType,c));
install(rxn, reactionType, f);
}
//! Install a new falloff function calculator.
/*
* @param rxn Index of the falloff reaction. This will be used to

6
include/cantera/kinetics/GasKinetics.h
View file

@ -52,7 +52,6 @@ public:
//! @name Reaction Mechanism Setup Routines
//! @{
virtual void init();
virtual void addReaction(ReactionData& r);
virtual bool addReaction(shared_ptr<Reaction> r);
virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);
virtual void finalize();
@ -111,11 +110,6 @@ protected:
void processFalloffReactions();
void addThreeBodyReaction(ReactionData& r);
void addFalloffReaction(ReactionData& r);
void addPlogReaction(ReactionData& r);
void addChebyshevReaction(ReactionData& r);
void addThreeBodyReaction(ThreeBodyReaction& r);
void addFalloffReaction(FalloffReaction& r);
void addPlogReaction(PlogReaction& r);

12
include/cantera/kinetics/InterfaceKinetics.h
View file

@ -210,7 +210,6 @@ public:
virtual void addPhase(thermo_t& thermo);
virtual void init();
virtual void addReaction(ReactionData& r);
virtual bool addReaction(shared_ptr<Reaction> r);
virtual void modifyReaction(size_t i, shared_ptr<Reaction> rNew);
virtual void finalize();
@ -292,16 +291,6 @@ public:
*/
virtual void updateMu0();
//! Number of reactions in the mechanism
/*!
* @deprecated This is a duplicate of Kinetics::nReactions()
*/
size_t reactionNumber() const {
warn_deprecated("InterfaceKinetics::reactionNumber",
"To be removed after Cantera 2.2. Duplicate of nReactions().");
return m_ii;
}
//! Update the equilibrium constants and stored electrochemical potentials
//! in molar units for all reversible reactions and for all species.
/*!
@ -391,7 +380,6 @@ public:
*/
int phaseStability(const size_t iphase) const;
virtual void determineFwdOrdersBV(ReactionData& rdata, vector_fp& fwdFullorders);
virtual void determineFwdOrdersBV(ElectrochemicalReaction& r, vector_fp& fwdFullorders);
protected:

19
include/cantera/kinetics/Kinetics.h
View file

@ -19,8 +19,6 @@
namespace Cantera
{
// forward references
class ReactionData;
class Reaction;
/**
@ -787,17 +785,6 @@ public:
*/
virtual void finalize();
/**
* Add a single reaction to the mechanism. This routine
* must be called after init() and before finalize(). Derived classes
* should call the base class method in addition to handling their
* own specialized behavior.
*
* @param r Reference to the ReactionData object for the reaction
* to be added.
*/
virtual void addReaction(ReactionData& r);
/**
* Add a single reaction to the mechanism. Derived classes should call the
* base class method in addition to handling their own specialized behavior.
@ -839,12 +826,6 @@ public:
m_skipUndeclaredThirdBodies = skip;
}
//! @deprecated To be removed after Cantera 2.2. No longer called as part
//! of addReaction.
virtual void installReagents(const ReactionData& r) {
throw NotImplementedError("Kinetics::installReagents");
}
virtual void installGroups(size_t irxn, const std::vector<grouplist_t>& r,
const std::vector<grouplist_t>& p);

21
include/cantera/kinetics/RateCoeffMgr.h
View file

@ -25,27 +25,6 @@ public:
Rate1() {}
virtual ~Rate1() {}
/**
* Install a rate coefficient calculator.
* @param rxnNumber the reaction number
* @param rdata rate coefficient specification for the reaction
*/
size_t install(size_t rxnNumber, const ReactionData& rdata) {
/*
* Check to see if the current reaction rate type is the same as the
* type of this class. If not, throw an error condition.
*/
if (rdata.rateCoeffType != R::type())
throw CanteraError("Rate1::install",
"incorrect rate coefficient type: "+int2str(rdata.rateCoeffType) + ". Was Expecting type: "+ int2str(R::type()));
// Install a rate calculator and return the index of the calculator.
m_rxn.push_back(rxnNumber);
m_rates.push_back(R(rdata));
m_indices[rxnNumber] = m_rxn.size() - 1;
return m_rates.size() - 1;
}
/**
* Install a rate coefficient calculator.
* @param rxnNumber the reaction number

226
include/cantera/kinetics/ReactionData.h
View file

@ -1,226 +0,0 @@
/**
* @file ReactionData.h
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_REACTION_DATA_H
#define CT_REACTION_DATA_H
#include "cantera/kinetics/reaction_defs.h"
#include "cantera/base/utilities.h"
namespace Cantera
{
//! Intermediate class which stores data about a reaction and its rate
//! parameterization before adding the reaction to a Kinetics object.
/*!
* All data in this class is public.
* @deprecated Use class Reaction and its children. To be removed after
* Cantera 2.2.
*/
class ReactionData
{
public:
ReactionData() :
reactionType(ELEMENTARY_RXN),
validate(false),
number(0),
rxn_number(0),
filmResistivity(0.0),
equilibriumConstantPower(1.0),
affinityPower(1.0),
reversible(true),
duplicate(false),
rateCoeffType(ARRHENIUS_REACTION_RATECOEFF_TYPE),
falloffType(NONE),
error(0),
equation(""),
default_3b_eff(1.0),
global(false),
isReversibleWithFrac(false),
beta(0.0),
chebTmin(-1.0),
chebTmax(-1.0),
chebPmin(-1.0),
chebPmax(-1.0),
chebDegreeT(0),
chebDegreeP(0)
{
warn_deprecated("class ReactionData",
"To be removed after Cantera 2.2.");
}
virtual ~ReactionData() {}
//! Type of the reaction. The valid types are listed in the file,
//! reaction_defs.h, with constants ending in `RXN`.
int reactionType;
bool validate; //!< Perform validation of the rate coefficient data
int number; //!< Index of this reaction within the mechanism
int rxn_number; //!< @deprecated duplicate of #number
std::vector<size_t> reactants; //!< Indices of reactant species
std::vector<size_t> products; //!< Indices of product species
//! Reaction order with respect to each reactant species, in the order
//! given by #reactants. Usually the same as the stoichiometric coefficients.
/*!
* Length is equal to the number of reactants defined in the reaction
* The order of species is given by the reactants vectors.
*/
vector_fp rorder;
//! Reaction order of the reverse reaction with respect to each product
//! species, in the order given by #products. Usually the same as the stoichiometric coefficients.
/*!
* Length is equal to the number of products defined in the reaction.
* The order of species is given by the products vectors.
*/
vector_fp porder;
//! Reaction order for the forward direction of the reaction
/*!
* Length is equal to the number of kinetic species defined in the kinetics object
* The order of species is given by kinetics species vector.
*/
vector_fp forwardFullOrder_;
//! Reactant stoichiometric coefficients, in the order given by #reactants.
/*!
* Length is equal to the number of products defined in the reaction.
* The order of species is given by the products vectors.
*/
vector_fp rstoich;
//! Product stoichiometric coefficients, in the order given by #products.
/*!
* Length is equal to the number of products defined in the reaction.
* The order of species is given by the products vectors.
*/
vector_fp pstoich;
std::vector<grouplist_t> rgroups; //!< Optional data used in reaction path diagrams
std::vector<grouplist_t> pgroups; //!< Optional data used in reaction path diagrams
//! Map of species index to third body efficiency
std::map<size_t, doublereal> thirdBodyEfficiencies;
//! Net stoichiometric coefficients for participating species. Used for
//! duplicate reaction detection. Key is `-1-k` for reactants, `1+k` for
//! products.
std::map<int, doublereal> net_stoich;
//! Film Resistivity value
/*!
* Only valid for Butler-Volmer formulations.
* Units are in ohms m2.
* default = 0.0 ohms m2
*/
doublereal filmResistivity;
//! Power of the equilibrium constant within the Affinity representation
/*!
* Only valid for Affinity representation.
* default = 1.0
*/
doublereal equilibriumConstantPower;
//! Power of the "One minus Affinity" term within the Affinity representation
/*!
* Only value for Affinity representation
* default = 1.0
*/
doublereal affinityPower;
//! True if the current reaction is reversible. False otherwise
bool reversible;
//! True if the current reaction is marked as duplicate
bool duplicate;
//! Type of the rate coefficient for the forward rate constant
/*!
* The valid types are listed in the file, reaction_defs.h and they
* all end in RATECOEFF_TYPE
*/
int rateCoeffType;
//! Vector of rate coefficient parameters. For elementary reactions, these
//! are the pre- exponential factor, temperature exponent, and activation
//! energy in the Arrhenius expression.
vector_fp rateCoeffParameters;
//! Vector of auxiliary rate coefficient parameters. This is used for
//! the alternate Arrhenius parameters used in falloff and chemically
//! activated reactions.
vector_fp auxRateCoeffParameters;
//! Type of falloff parameterization to use. Values are defined in
//! reaction_defs.h, with names ending in `FALLOFF`.
int falloffType;
//! Values used in the falloff parameterization. Meaning of each parameter
//! depends on #falloffType.
vector_fp falloffParameters;
int error; //!< @deprecated unused. To be removed after Cantera 2.2.
//! The reaction equation. Used only for display purposes.
std::string equation;
//! The reactants half of the reaction equation, used for display purposes.
std::string reactantString;
//! The products half of the reaction equation, used for display purposes.
std::string productString;
//! The default third body efficiency for species not listed in
//! #thirdBodyEfficiencies.
doublereal default_3b_eff;
//! Adjustments to the Arrhenius rate expression dependent on surface
//! species coverages. Contains 4 elements for each coverage dependency:
//! the species index, and the three coverage parameters (a, E, m). See
//! SurfaceArrhenius for details on the parameterization.
vector_fp cov;
//! True for "global" reactions which do not follow elementary mass action
//! kinetics, i.e. reactions for which the reaction order is not given by
//! the stoichiometric coefficients.
bool global;
//! Some reactions can be elementary reactions but have fractional
//! stoichiometries with respect to some products and reactants. An
//! example of these are solid reactions involving phase transformations.
//! Species with fractional stoichiometries must be from single-species
//! phases with unity activities.
bool isReversibleWithFrac;
//! Forward value of the apparent Electrochemical transfer coefficient
doublereal beta;
//! Arrhenius parameters for P-log reactions.
//! The keys are the pressures corresponding to each Arrhenius expression.
//! Multiple sets of Arrhenius parameters may be specified at a given
//! pressure.
std::multimap<double, vector_fp> plogParameters;
double chebTmin; //!< Minimum temperature for Chebyshev fit
double chebTmax; //!< Maximum temperature for Chebyshev fit
double chebPmin; //!< Minimum pressure for Chebyshev fit
double chebPmax; //!< Maximum pressure for Chebyshev fit
size_t chebDegreeT; //!< Degree of Chebyshev fit in T
size_t chebDegreeP; //!< Degree of Chebyshev fit in P
//! Chebyshev coefficients. length chebDegreeT * chebDegreeP
vector_fp chebCoeffs;
//! Get the actual third-body efficiency for species *k*
double efficiency(size_t k) const {
return getValue(thirdBodyEfficiencies, k, default_3b_eff);
}
};
}
#endif

223
include/cantera/kinetics/ReactionStoichMgr.h
View file

@ -1,223 +0,0 @@
/**
* @file ReactionStoichMgr.h
*
* Header file declaring class ReactionStoichMgr.
*/
#ifndef CT_RXN_STOICH
#define CT_RXN_STOICH
#include "cantera/kinetics/StoichManager.h"
namespace Cantera
{
class ReactionData;
class Reaction;
/**
* Reaction mechanism stoichiometry manager. This is an internal class used
* by kinetics manager classes, and is not meant for direct use in
* user programs.
*
* Class ReactionStoichMgr handles the calculation of quantities involving
* the stoichiometry of a set of reactions. The reactions may have integer
* or non-integer stoichiometric coefficients. Specifically, its methods compute
* - species creation rates
* - species destruction rates
* - species net production rates
* - the change in molar species properties in the reactions
* - concentration products
*
* To use this class, method add() is first used to add each reaction.
* Once all reactions have been added, the methods that compute various
* quantities may be called.
*
* The nomenclature used below to document the methods is as follows.
*
* - \f$ N_r \f$
* Integer reactant stoichiometric coefficient matrix. The (k,i)
* element of this matrix is the stoichiometric coefficient of
* species \e k as a reactant in reaction \e i.
* - \f$ N_p \f$
* Integer product stoichiometric coefficient matrix. The (k,i)
* element of this matrix is the stoichiometric coefficient of
* species \e k as a product in reaction \e i.
* - \f$ Q_{\rm fwd} \f$
* Vector of length I of forward rates of progress.
* - \f$ Q_{\rm rev} \f$
* Vector of length I of reverse rates of progress.
* - \f$ C \f$
* Vector of K species creation rates.
* - \f$ D \f$
* Vector of K species destruction rates.
* - \f$ W = C - D \f$
* Vector of K species net production rates.
* @deprecated Unused; Functionality merged into class Kinetics. To be removed
* after Cantera 2.2.
*/
class ReactionStoichMgr
{
public:
/// Constructor.
ReactionStoichMgr();
/// Destructor.
virtual ~ReactionStoichMgr() {}
ReactionStoichMgr(const ReactionStoichMgr& right);
ReactionStoichMgr& operator=(const ReactionStoichMgr& right);
//! Add a reaction with mass-action kinetics.
/*!Vectors
* 'reactants' and 'products' contain the integer species
* indices of the reactants and products, respectively. Note
* that if more than one molecule of a given species is
* involved in the reaction, then its index is repeated.
*
* For example, suppose a reaction mechanism involves the
* species N2, O2, O, N, NO. N2 is assigned index number 0, O2
* number 1, and so on through NO with number 4. Then the
* representation of the following reactions is as shown here.
*
* - N + O = NO
* - reactants: (3, 2)
* - products: (4)
*
* - O + O = O2
* - reactants: (2, 2) [ note repeated index ]
* - products: (1)
*
* @param rxn Reaction number. This number will be used as the index
* into the rate of progress vector in the methods below.
* @param reactants Vector of integer reactant indices
* @param products Vector of integer product indices
* @param reversible True if the reaction is reversible, false otherwise
*/
virtual void add(size_t rxn, const std::vector<size_t>& reactants,
const std::vector<size_t>& products, bool reversible);
/**
* Add a reaction with specified, possibly non-integral, reaction orders.
* @param rxn Reaction number
* @param r Data structure containing reactant and product vectors, etc.
*/
virtual void add(size_t rxn, const ReactionData& r);
/**
* Species creation rates. Given the arrays of the forward and reverse
* rates of progress for all reactions, compute the species creation
* rates, given by
* \f[
* C = N_p Q_f + N_r Q_r.
* \f]
*/
virtual void getCreationRates(size_t nSpecies,
const doublereal* fwdRatesOfProgress,
const doublereal* revRatesOfProgress,
doublereal* creationRates);
/**
* Species destruction rates. Given the arrays of the forward and reverse
* rates of progress for all reactions, compute the species destruction
* rates, given by
* \f[
* D = N_r Q_f + N_p Q_r,
* \f]
* Note that the stoichiometric coefficient matrices are very sparse, integer
* matrices.
*/
virtual void getDestructionRates(size_t nSpecies,
const doublereal* fwdRatesOfProgress,
const doublereal* revRatesOfProgress,
doublereal* destructionRates);
/**
* Species net production rates. Given the array of the net rates of
* progress for all reactions, compute the species net production rates,
* given by
* \f[
* W = (N_r - N_p) Q_{\rm net},
* \f]
*/
virtual void getNetProductionRates(size_t nsp, const doublereal* ropnet, doublereal* w);
//! Calculates the change of a molar species property in a reaction.
/*!
* Given an array of species properties 'g', return in array 'dg' the
* change in this quantity in the reactions. Array 'g' must have a length
* at least as great as the number of species, and array 'dg' must have a
* length as great as the total number of reactions.
* \f[
* \delta g_i = \sum_k{\nu_{i,k} g_k }
* \f]
*
* @param nReactions Number of reactions
* @param g Molar property of the species.
* An example would be the partial molar enthalpy
* Length is equal to number of kinetic species
* @param dg Calculated property change of the reaction.
* An example would be the delta change in enthalpy,
* i.e., the enthalpy of reaction.
*/
virtual void getReactionDelta(size_t nReactions,
const doublereal* g,
doublereal* dg);
/**
* Given an array of species properties 'g', return in array 'dg' the
* change in this quantity in the reversible reactions. Array 'g' must
* have a length at least as great as the number of species, and array
* 'dg' must have a length as great as the total number of reactions.
* This method only computes 'dg' for the reversible reactions, and the
* entries of 'dg' for the irreversible reactions are unaltered. This is
* primarily designed for use in calculating reverse rate coefficients
* from thermochemistry for reversible reactions.
*/
virtual void getRevReactionDelta(size_t nr, const doublereal* g, doublereal* dg);
/**
* Given an array of concentrations C, multiply the entries in array R by
* the concentration products for the reactants.
* \f[
* R_i = R_i * \prod_k C_k^{o_{k,i}}
* \f]
*
* Here \f$ o_{k,i} \f$ is the reaction order of species k in reaction i.
*/
virtual void multiplyReactants(const doublereal* C, doublereal* R);
/**
* Given an array of concentrations C, multiply the entries in array R by
* the concentration products for the products.
* \f[
* R_i = R_i * \prod_k C_k^{\nu^{(p)}_{k,i}}
* \f]
* Here \f$ \nu^{(p)}_{k,i} \f$ is the product stoichiometric coefficient
* of species k in reaction i.
*/
virtual void multiplyRevProducts(const doublereal* c, doublereal* r);
//! @deprecated To be removed after Cantera 2.2
virtual void write(const std::string& filename);
protected:
//! @deprecated To be removed after Cantera 2.2
void writeCreationRates(std::ostream& f);
//! @deprecated To be removed after Cantera 2.2
void writeDestructionRates(std::ostream& f);
//! @deprecated To be removed after Cantera 2.2
void writeNetProductionRates(std::ostream& f);
//! @deprecated To be removed after Cantera 2.2
void writeMultiplyReactants(std::ostream& f);
//! @deprecated To be removed after Cantera 2.2
void writeMultiplyRevProducts(std::ostream& f);
StoichManagerN m_reactants;
StoichManagerN m_revproducts;
StoichManagerN m_irrevproducts;
vector_fp m_dummy;
};
}
#endif

103
include/cantera/kinetics/RxnRates.h
View file

@ -8,7 +8,7 @@
#ifndef CT_RXNRATES_H
#define CT_RXNRATES_H
#include "ReactionData.h"
#include "cantera/kinetics/reaction_defs.h"
#include "cantera/base/ctexceptions.h"
#include "cantera/base/stringUtils.h"
@ -39,9 +39,6 @@ public:
//! Default constructor.
Arrhenius();
//! Constructor from ReactionData.
explicit Arrhenius(const ReactionData& rdata);
/// Constructor.
/// @param A pre-exponential. The unit system is
/// (kmol, m, s). The actual units depend on the reaction
@ -152,7 +149,6 @@ public:
SurfaceArrhenius();
explicit SurfaceArrhenius(double A, double b, double Ta);
explicit SurfaceArrhenius(const ReactionData& rdata);
//! Add a coverage dependency for species *k*, with pre-exponential
//! dependence *a*, temperature exponent dependence *m* and activation
@ -223,97 +219,6 @@ protected:
};
//! Arrhenius reaction rate type depends only on temperature
/**
* A reaction rate coefficient of the following form.
*
* \f[
* k_f = A T^b \exp (-E/RT)
* \f]
*
* @deprecated Duplicate of class Arrhenius. To be removed after Cantera 2.2.
*/
class ExchangeCurrent
{
public:
//! return the rate coefficient type.
static int type() {
return EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
}
//! Default constructor.
ExchangeCurrent();
//! Constructor with Arrhenius parameters from a ReactionData struct.
explicit ExchangeCurrent(const ReactionData& rdata);
/// Constructor.
/// @param A pre-exponential. The unit system is
/// (kmol, m, s). The actual units depend on the reaction
/// order and the dimensionality (surface or bulk).
/// @param b Temperature exponent. Non-dimensional.
/// @param E Activation energy in temperature units. Kelvin.
ExchangeCurrent(doublereal A, doublereal b, doublereal E);
//! Update concentration-dependent parts of the rate coefficient.
/*!
* For this class, there are no
* concentration-dependent parts, so this method does nothing.
*/
void update_C(const doublereal* c) {
}
/**
* Update the value of the logarithm of the rate constant.
*
* Note, this function should never be called for negative A values.
* If it does then it will produce a negative overflow result, and
* a zero net forwards reaction rate, instead of a negative reaction
* rate constant that is the expected result.
* @deprecated. To be removed after Cantera 2.2
*/
doublereal update(doublereal logT, doublereal recipT) const {
return m_logA + m_b*logT - m_E*recipT;
}
/**
* Update the value the rate constant.
*
* This function returns the actual value of the rate constant.
* It can be safely called for negative values of the pre-exponential
* factor.
*/
doublereal updateRC(doublereal logT, doublereal recipT) const {
return m_A * std::exp(m_b*logT - m_E*recipT);
}
//! @deprecated. To be removed after Cantera 2.2
void writeUpdateRHS(std::ostream& s) const {
s << " exp(" << m_logA;
if (m_b != 0.0) {
s << " + " << m_b << " * tlog";
}
if (m_E != 0.0) {
s << " - " << m_E << " * rt";
}
s << ");" << std::endl;
}
//! @deprecated. To be removed after Cantera 2.2
doublereal activationEnergy_R() const {
return m_E;
}
//! @deprecated. To be removed after Cantera 2.2
static bool alwaysComputeRate() {
return false;
}
protected:
doublereal m_logA, m_b, m_E, m_A;
};
//! Pressure-dependent reaction rate expressed by logarithmically interpolating
//! between Arrhenius rate expressions at various pressures.
class Plog
@ -327,9 +232,6 @@ public:
//! Default constructor.
Plog() {}
//! Constructor from ReactionData.
explicit Plog(const ReactionData& rdata);
//! Constructor from Arrhenius rate expressions at a set of pressures
explicit Plog(const std::multimap<double, Arrhenius>& rates);
@ -451,9 +353,6 @@ public:
//! Default constructor.
ChebyshevRate() {}
//! Constructor from ReactionData.
explicit ChebyshevRate(const ReactionData& rdata);
//! Constructor directly from coefficient array
/*
* @param Tmin Minimum temperature [K]

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

@ -670,7 +670,7 @@ inline static void _writeMultiply(InputIter begin, InputIter end,
* This class handles operations involving the stoichiometric
* coefficients on one side of a reaction (reactant or product) for
* a set of reactions comprising a reaction mechanism. This class is
* used by class ReactionStoichMgr, which contains three instances
* used by class Kinetics, which contains three instances
* of this class (one to handle operations on the reactions, one for
* the products of reversible reactions, and one for the products of
* irreversible reactions).

62
include/cantera/kinetics/ThirdBodyMgr.h
View file

@ -1,62 +0,0 @@
/**
* @file ThirdBodyMgr.h
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_THIRDBODY_MGR_H
#define CT_THIRDBODY_MGR_H
#include "cantera/base/utilities.h"
#include "Enhanced3BConc.h"
namespace Cantera
{
//! @deprecated Replaced by ThirdBodyCalc. To be removed after Cantera 2.2.
template<class _E>
class ThirdBodyMgr
{
public:
ThirdBodyMgr() {
warn_deprecated("class ThirdBodyMgr", "To be removed after Cantera 2.2.");
}
void install(size_t rxnNumber, const std::map<size_t, doublereal>& enhanced,
doublereal dflt=1.0) {
m_reaction_index.push_back(rxnNumber);
m_concm.push_back(_E(enhanced, dflt));
}
void update(const vector_fp& conc, doublereal ctot, doublereal* work) {
typename std::vector<_E>::const_iterator b = m_concm.begin();
for (; b != m_concm.end(); ++b, ++work) {
*work = b->update(conc, ctot);
}
}
void multiply(doublereal* output, const doublereal* work) {
scatter_mult(work, work + m_reaction_index.size(),
output, m_reaction_index.begin());
}
size_t workSize() {
return m_concm.size();
}
bool contains(int rxnNumber) {
return (find(m_reaction_index.begin(),
m_reaction_index.end(), rxnNumber)
!= m_reaction_index.end());
}
protected:
std::vector<size_t> m_reaction_index;
std::vector<_E> m_concm;
};
}
#endif

85
include/cantera/kinetics/importKinetics.h
View file

@ -28,91 +28,6 @@ struct ReactionRules {
bool allowNegativeA;
};
//!This function returns a ratio if two reactions are duplicates of
//!one another, and 0.0 otherwise.
/*!
* The input arguments are two maps from species number to stoichiometric
* coefficient, one for each reaction. The reactions are considered duplicates
* if their stoichiometric coefficients have the same ratio for all species.
*
* @param r1 map 1
* @param r2 map 2
*
* @return
* Returns 0.0 if the reactions are not the same.
* If the reactions are the same, it returns the ratio of the
* stoichiometric coefficients.
*
* @ingroup kineticsmgr
* @deprecated Now handled by Kinetics::checkDuplicateStoich. To be removed
* after Cantera 2.2.
*/
doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
std::map<int, doublereal>& r2);
//! This function will check a specific reaction to see if the elements balance.
/*!
* @param kin Kinetics object
* @param rdata Object containing the information about one reaction
* @param errorTolerance double containing the error tolerance.
*
* @ingroup kineticsmgr
* @deprecated Now handled by Kinetics::checkReactionBalance. To be removed
* after Cantera 2.2.
*/
void checkRxnElementBalance(Kinetics& kin,
const ReactionData& rdata,
doublereal errorTolerance = 1.0e-3);
/**
* Get the reactants or products of a reaction. The information is returned in
* the spnum, stoich, and order vectors. The length of the vectors is the
* number of different types of reactants or products found for the reaction.
*
* @param[in] rxn XML node pointing to the reaction element in the XML tree.
* @param[in] kin Reference to the kinetics object to install the information
* into.
* @param[in] rp 1 -> Go get the reactants for a reaction; -1 -> Go get the
* products for a reaction
* @param[in] default_phase Name for the default phase to loop up species in.
* @param[out] spnum vector of species numbers found. Length is number of
* reactants or products.
* @param[out] stoich stoichiometric coefficient of the reactant or product.
* Length is number of reactants or products.
* @param[out] order Order of the reactant and product in the reaction rate
* expression.
* @param[in] rules If rules.skipUndeclaredSpecies is set and we fail to find
* a species we simply return false, allowing the calling
* routine to skip this reaction and continue. Otherwise, we
* will throw an error.
* @deprecated Now handled through newReaction() and its support functions. To
* be removed after Cantera 2.2.
*/
bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp, std::string default_phase,
std::vector<size_t>& spnum, vector_fp& stoich,
vector_fp& order, const ReactionRules& rules);
//! Read the rate coefficient data from the XML file.
/*!
* Extract the rate coefficient for a reaction from the XML node, kf.
* kf should point to a XML element named "rateCoeff".
* rdata is the partially filled ReactionData object for the reaction.
* This function will fill in more fields in the ReactionData object.
*
* @param kf XML_Node containing information about the rate coefficients.
* @param kin kinetics manager
* @param rdata ReactionData reference
* @param rules Rules for parsing and installing reactions
*
* Trigger an exception for negative A unless specifically authorized.
*
* @deprecated Now handled through newReaction() and its support functions. To
* be removed after Cantera 2.2.
*
* @ingroup kineticsmgr
*/
void getRateCoefficient(const XML_Node& kf, Kinetics& kin, ReactionData& rdata,
const ReactionRules& rules);
//! Install information about reactions into the kinetics object, kin.
/*!

28
include/cantera/thermo/AdsorbateThermo.h
View file

@ -35,25 +35,6 @@ public:
m_nFreqs(0) {
}
//! Full Constructor
/*!
* @param n Species index
* @param tlow output - Minimum temperature
* @param thigh output - Maximum temperature
* @param pref output - reference pressure (Pa).
* @deprecated Use the constructor which does not require the species index.
* To be removed after Cantera 2.2.
*/
Adsorbate(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs)
: SpeciesThermoInterpType(n, tlow, thigh, pref)
{
m_nFreqs = int(coeffs[0]);
m_be = coeffs[1];
m_freq.resize(m_nFreqs);
std::copy(coeffs+2, coeffs + 2 + m_nFreqs, m_freq.begin());
}
//! Full Constructor
/*!
* @param tlow output - Minimum temperature
@ -82,17 +63,16 @@ public:
doublereal* cp_R,
doublereal* h_RT,
doublereal* s_R) const {
h_RT[m_index] = _energy_RT(temp);
cp_R[m_index] = (temp*h_RT[m_index]
- (temp-0.01)*_energy_RT(temp-0.01))/0.01;
s_R[m_index] = h_RT[m_index] - _free_energy_RT(temp);
*h_RT = _energy_RT(temp);
*cp_R = (temp**h_RT - (temp-0.01)*_energy_RT(temp-0.01))/0.01;
*s_R = *h_RT - _free_energy_RT(temp);
}
void reportParameters(size_t& n, int& type,
doublereal& tlow, doublereal& thigh,
doublereal& pref,
doublereal* const coeffs) const {
n = m_index;
n = 0;
type = ADSORBATE;
tlow = m_lowT;
thigh = m_highT;

24
include/cantera/thermo/ConstCpPoly.h
View file

@ -38,10 +38,6 @@ namespace Cantera
* - c[2] = \f$ S_k^o(T_0, p_{ref}) \f$ (J/kmol K)
* - c[3] = \f$ {Cp}_k^o(T_0, p_{ref}) \f$ (J(kmol K)
*
* The multispecies SimpleThermo class makes the same assumptions as
* this class does.
*
* @see SimpleThermo
* @ingroup spthermo
*/
class ConstCpPoly: public SpeciesThermoInterpType
@ -50,26 +46,6 @@ public:
//! empty constructor
ConstCpPoly();
//! Constructor used in templated instantiations
/*!
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the
* parameters for the standard state for species n.
* There are 4 coefficients for the ConstCpPoly parameterization.
* - c[0] = \f$ T_0 \f$(Kelvin)
* - c[1] = \f$ H_k^o(T_0, p_{ref}) \f$ (J/kmol)
* - c[2] = \f$ S_k^o(T_0, p_{ref}) \f$ (J/kmol K)
* - c[3] = \f$ {Cp}_k^o(T_0, p_{ref}) \f$ (J(kmol K)
* @deprecated Use the constructor which does not take the species index. To
* be removed after Cantera 2.2.
*/
ConstCpPoly(size_t n, doublereal tlow, doublereal thigh,
doublereal pref,
const doublereal* coeffs);
//! Normal constructor
/*!
* @param tlow Minimum temperature

320
include/cantera/thermo/Elements.h
View file

@ -95,326 +95,6 @@ namespace Cantera
//! @exception CanteraError If a match is not found, throws a CanteraError
double LookupWtElements(const std::string& ename);
class XML_Node;
//! Object containing the elements that make up species in a phase.
/*!
* Class Elements manages the elements that are part of a
* chemistry specification. This class may support calculations
* employing Multiple phases. In this case, a single Elements object may
* be shared by more than one Constituents class. Reactions between
* the phases may then be described using stoichiometry base on the
* same Elements class object.
*
* The member functions return information about the elements described
* in a particular instantiation of the class.
*
* @ingroup phases
* @deprecated. Functionality is now part of class Phase. To be removed after
* Cantera 2.2.
*/
class Elements
{
public:
//! Default constructor for the elements class
Elements();
//! Default destructor for the elements class
~Elements();
//! copy constructor
/*!
* This copy constructor just calls the assignment operator for this
* class. It sets the number of subscribers to zer0.
*
* @param right Reference to the object to be copied.
*/
Elements(const Elements& right);
//! Assignment operator
/*!
* This is the assignment operator for the Elements class.
* Right now we pretty much do a straight uncomplicated
* assignment. However, subscribers are not mucked with, as they
* have to do with the address of the object to be subscribed to
*
* @param right Reference to the object to be copied.
*/
Elements& operator=(const Elements& right);
//! Static function to look up an atomic weight
/*!
* This static function looks up the argument string in the
* database above and returns the associated molecular weight.
* The data are from the periodic table.
*
* Note: The idea behind this function is to provide a unified
* source for the element atomic weights. This helps to
* ensure that mass is conserved.
*
* @param ename String, Only the first 3 characters are significant
*
* @return
* Return value contains the atomic weight of the element
* If a match for the string is not found, a value of -1.0 is
* returned.
*
* @exception CanteraError
* If a match is not found, a CanteraError is thrown as well
*/
static double LookupWtElements(const std::string& ename);
/// Atomic weight of element m.
/*!
* @param m element index
*/
doublereal atomicWeight(int m) const {
return m_atomicWeights[m];
}
/// Atomic number of element m.
/*!
* @param m element index
*/
int atomicNumber(int m) const {
return m_atomicNumbers[m];
}
//! Entropy at 298.15 K and 1 bar of stable state
//! of the element
/*!
* units J kmol-1 K-1
*
* @param m Element index
*/
doublereal entropyElement298(int m) const;
//! Return the element constraint type
/*!
* Possible types include:
*
* CT_ELEM_TYPE_ABSPOS 0
* CT_ELEM_TYPE_ELECTRONCHARGE 1
* CT_ELEM_TYPE_CHARGENEUTRALITY 2
* CT_ELEM_TYPE_LATTICERATIO 3
* CT_ELEM_TYPE_KINETICFROZEN 4
* CT_ELEM_TYPE_SURFACECONSTRAINT 5
* CT_ELEM_TYPE_OTHERCONSTRAINT 6
*
* The default is CT_ELEM_TYPE_ABSPOS
*
* @param m Element index
*
* @return Returns the element type
*/
int elementType(int m) const;
//! Change the element type of the mth constraint
/*!
* Reassigns an element type
*
* @param m Element index
* @param elem_type New elem type to be assigned
*
* @return Returns the old element type
*/
int changeElementType(int m, int elem_type);
/// vector of element atomic weights
const vector_fp& atomicWeights() const {
return m_atomicWeights;
}
/**
* Inline function that returns the number of elements in the object.
*
* @return
* \c int: The number of elements in the object.
*/
int nElements() const {
return m_mm;
}
//! Function that returns the index of an element.
/*!
* Index of element named \c name. The index is an integer
* assigned to each element in the order it was added,
* beginning with 0 for the first element. If \c name is not
* the name of an element in the set, then the value -1 is
* returned.
*
* @param name String containing the index.
*/
int elementIndex(const std::string& name) const;
//! Name of the element with index \c m.
/*!
* @param m Element index. If m < 0 or m >= nElements() an exception is thrown.
*/
std::string elementName(int m) const;
//! Returns a string vector containing the element names
/*!
* Returns a read-only reference to the vector of element names.
* @return <tt> const vector<string>& </tt>: The vector contains
* the element names in their indexed order.
*/
const std::vector<std::string>& elementNames() const {
return m_elementNames;
}
//! Add an element to the current set of elements in the current object.
/*!
* The default weight is a special value, which will cause the
* routine to look up the actual weight via a string lookup.
*
* There are two interfaces to this routine. The XML interface
* looks up the required parameters for the regular interface
* and then calls the base routine.
*
* @param symbol string symbol for the element.
* @param weight Atomic weight of the element. If no argument
* is provided, a lookup is attempted.
*/
void addElement(const std::string& symbol,
doublereal weight = -12345.0);
//! Add an element to the current set of elements in the current object.
/*!
* @param e Reference to the XML_Node containing the element information
* The node name is the element symbol and the atomWt attribute
* is used as the atomic weight.
*/
void addElement(const XML_Node& e);
//! Add an element only if the element hasn't been added before.
/*!
* This is accomplished via a string match on symbol.
*
* @param symbol string symbol for the element.
* @param weight Atomic weight of the element. If no argument
* is provided, a lookup is attempted.
* @param atomicNumber defaults to 0
* @param entropy298 Value of the entropy at 298 and 1 bar of the
* element in its most stable form.
* The default is to specify an ENTROPY298_UNKNOWN value,
* which will cause a throw error if its ever
* needed.
* @param elem_type New elem type to be assigned.
* The default is a regular element, CT_ELEM_TYPE_ABSPOS
*/
void addUniqueElement(const std::string& symbol,
doublereal weight = -12345.0, int atomicNumber = 0,
doublereal entropy298 = ENTROPY298_UNKNOWN, int elem_type = CT_ELEM_TYPE_ABSPOS);
//! Add an element to the current set of elements in the current object.
/*!
* @param e Reference to the XML_Node containing the element information
* The node name is the element symbol and the atomWt attribute
* is used as the atomic weight.
*/
void addUniqueElement(const XML_Node& e);
//! Add multiple elements from a XML_Node phase description
/*!
* @param phase XML_Node reference to a phase
*/
void addElementsFromXML(const XML_Node& phase);
//! Prohibit addition of more elements, and prepare to add species.
void freezeElements();
//! True if freezeElements has been called.
bool elementsFrozen() const;
/// Remove all elements
void clear();
/// True if both elements and species have been frozen
bool ready() const;
//! subscribe to this object
/*!
* Increment by one the number of subscriptions to this object.
*/
void subscribe();
//! unsubscribe to this object
/*!
* decrement by one the number of subscriptions to this object.
*/
int unsubscribe();
//! report the number of subscriptions
int reportSubscriptions() const;
protected:
/******************************************************************/
/* Description of DATA in the Object */
/******************************************************************/
//! Number of elements.
int m_mm;
/* m_elementsFrozen: */
/** boolean indicating completion of object
*
* If this is true, then no elements may be added to the
* object.
*/
bool m_elementsFrozen;
/**
* Vector of element atomic weights:
*
* units = kg / kmol
*/
vector_fp m_atomicWeights;
/**
* Vector of element atomic numbers:
*
*/
vector_int m_atomicNumbers;
/** Vector of strings containing the names of the elements
*
* Note, a string search is the primary way to identify elements.
*/
std::vector<std::string> m_elementNames;
//! Entropy at 298.15 K and 1 bar of stable state
/*!
* units J kmol-1
*/
vector_fp m_entropy298;
//! Vector of element types
vector_int m_elem_type;
/**
* Number of Constituents Objects that use this object
*
* Number of Constituents Objects that require this Elements object
* to complete its definition.
* The destructor checks to see that this is equal to zero.
* when the element object is released.
*/
int numSubscribers;
/********* GLOBAL STATIC SECTION *************/
public:
/** Vector of pointers to Elements Objects
*
*/
static std::vector<Elements*> Global_Elements_List;
friend class Constituents;
};
} // namespace
#endif

35
include/cantera/thermo/GeneralSpeciesThermo.h
View file

@ -9,7 +9,7 @@
#ifndef CT_GENERALSPECIESTHERMO_H
#define CT_GENERALSPECIESTHERMO_H
#include "SpeciesThermoMgr.h"
#include "SpeciesThermo.h"
#include "SpeciesThermoInterpType.h"
namespace Cantera
@ -45,39 +45,6 @@ public:
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const ;
//! Install a new species thermodynamic property
//! parameterization for one species.
/*!
* Install a SpeciesThermoInterpType object for the species, index.
* This routine contains an internal list of SpeciesThermoInterpType
* objects that it knows about. A factory-type lookup is done
* to create the object.
*
* @param name Name of the species
* @param index The 'update' method will update the property
* values for this species
* at position i index in the property arrays.
* @param type int flag specifying the type of parameterization to be
* installed.
* @param c vector of coefficients for the parameterization.
* This vector is simply passed through to the
* parameterization constructor. Its length depends upon
* the parameterization.
* @param minTemp minimum temperature for which this parameterization
* is valid.
* @param maxTemp maximum temperature for which this parameterization
* is valid.
* @param refPressure standard-state pressure for this parameterization.
* @see speciesThermoTypes.h
*
* @deprecated Use newSpeciesThermoInterpType and
* GeneralSpeciesThermo::install_STIT. To be removed after Cantera 2.2.
*/
virtual void install(const std::string& name, size_t index, int type,
const doublereal* c,
doublereal minTemp, doublereal maxTemp,
doublereal refPressure);
virtual void install_STIT(size_t index,
shared_ptr<SpeciesThermoInterpType> stit_ptr);

31
include/cantera/thermo/Mu0Poly.h
View file

@ -74,37 +74,6 @@ public:
//! Constructor
Mu0Poly();
//! Constructor used in templated instantiations
/*!
* In the constructor, we calculate and store the
* piecewise linear approximation to the thermodynamic
* functions.
*
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the
* parameters for the standard state for species n.
* There are \f$ 2+npoints*2 \f$ coefficients, where
* \f$ npoints \f$ are the number of temperature points.
* Their identity is further broken down:
* - coeffs[0] = number of points (integer)
* - coeffs[1] = \f$ h^o(298.15 K) \f$ (J/kmol)
* - coeffs[2] = \f$ T_1 \f$ (Kelvin)
* - coeffs[3] = \f$ \mu^o(T_1) \f$ (J/kmol)
* - coeffs[4] = \f$ T_2 \f$ (Kelvin)
* - coeffs[5] = \f$ \mu^o(T_2) \f$ (J/kmol)
* - coeffs[6] = \f$ T_3 \f$ (Kelvin)
* - coeffs[7] = \f$ \mu^o(T_3) \f$ (J/kmol)
* - ........
* .
* @deprecated Use the constructor which does not require the species index.
* To be removed after Cantera 2.2.
*/
Mu0Poly(size_t n, doublereal tlow, doublereal thigh,
doublereal pref, const doublereal* coeffs);
//! Normal constructor
/*!
* In the constructor, we calculate and store the piecewise linear

14
include/cantera/thermo/Nasa9Poly1.h
View file

@ -74,20 +74,6 @@ public:
//! Empty constructor
Nasa9Poly1();
//! constructor used in templated instantiations
/*!
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the
* parameters for the standard state.
* @deprecated Use the constructor whic hdoes not require the species
* index. To be removed after Cantera 2.2.
*/
Nasa9Poly1(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs);
//! Normal constructor
/*!
* @param tlow Minimum temperature

2
include/cantera/thermo/Nasa9PolyMultiTempRegion.h
View file

@ -72,8 +72,6 @@ public:
virtual int reportType() const;
virtual void setIndex(size_t index);
virtual size_t temperaturePolySize() const { return 7; }
virtual void updateTemperaturePoly(double T, double* T_poly) const;

40
include/cantera/thermo/NasaPoly1.h
View file

@ -40,7 +40,6 @@ namespace Cantera
+ \frac{a_3}{3} T^3 + \frac{a_4}{4} T^4 + a_6.
* \f]
*
* This class is designed specifically for use by class NasaThermo.
* @ingroup spthermo
*/
class NasaPoly1 : public SpeciesThermoInterpType
@ -50,29 +49,6 @@ public:
NasaPoly1()
: m_coeff(7, 0.0) {}
//! constructor used in templated instantiations
/*!
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the parameters for the
* standard state, in the order [a5,a6,a0,a1,a2,a3,a4]
* @deprecated Use the constructor which does not take species index. To be
* removed after Cantera 2.2.
*/
NasaPoly1(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_coeff(7)
{
for (size_t i = 0; i < 5; i++) {
m_coeff[i] = coeffs[i+2];
}
m_coeff[5] = coeffs[0];
m_coeff[6] = coeffs[1];
}
//! Normal constructor
/*!
* @param tlow Minimum temperature
@ -142,11 +118,10 @@ public:
s = ct0*tt[5] + ct1 + 0.5*ct2 + 1.0/3.0*ct3
+0.25*ct4 + m_coeff[6]; // last term is a6
// return the computed properties in the location in the output
// arrays for this species
cp_R[m_index] = cp;
h_RT[m_index] = h;
s_R[m_index] = s;
// return the computed properties for this species
*cp_R = cp;
*h_RT = h;
*s_R = s;
//writelog("NASA1: for species "+int2str(m_index)+", h_RT = "+
// fp2str(h)+"\n");
}
@ -163,7 +138,7 @@ public:
doublereal& tlow, doublereal& thigh,
doublereal& pref,
doublereal* const coeffs) const {
n = m_index;
n = 0;
type = NASA1;
tlow = m_lowT;
thigh = m_highT;
@ -195,15 +170,12 @@ public:
double h = h_RT * GasConstant * temp;
if (h298) {
h298[m_index] = h;
*h298 = h;
}
return h;
}
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New) {
if (k != m_index) {
return;
}
double hcurr = reportHf298(0);
double delH = Hf298New - hcurr;
m_coeff[5] += (delH) / GasConstant;

34
include/cantera/thermo/NasaPoly2.h
View file

@ -54,26 +54,6 @@ public:
m_coeff(15, 0.0) {
}
//! Full Constructor
/*!
* @param n Species index
* @param tlow output - Minimum temperature
* @param thigh output - Maximum temperature
* @param pref output - reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the parameters for
* the standard state [Tmid, 7 low-T coeffs, 7 high-T coeffs]
* @deprecated Use constructor without species index. To be removed after
* Cantera 2.2.
*/
NasaPoly2(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_midT(coeffs[0]),
mnp_low(n, tlow, coeffs[0], pref, coeffs +1),
mnp_high(n, tlow, thigh, pref, coeffs + 8),
m_coeff(coeffs, coeffs + 15) {
}
//! Full Constructor
/*!
* @param tlow output - Minimum temperature
@ -103,12 +83,6 @@ public:
return NASA2;
}
virtual void setIndex(size_t index) {
SpeciesThermoInterpType::setIndex(index);
mnp_low.setIndex(index);
mnp_high.setIndex(index);
}
virtual size_t temperaturePolySize() const { return 6; }
virtual void updateTemperaturePoly(double T, double* T_poly) const {
@ -159,7 +133,7 @@ public:
doublereal& tlow, doublereal& thigh,
doublereal& pref,
doublereal* const coeffs) const {
n = m_index;
n = 0;
type = NASA2;
tlow = m_lowT;
thigh = m_highT;
@ -177,16 +151,12 @@ public:
h = mnp_high.reportHf298(0);
}
if (h298) {
h298[m_index] = h;
*h298 = h;
}
return h;
}
void modifyOneHf298(const size_t k, const doublereal Hf298New) {
if (k != m_index) {
return;
}
doublereal h298now = reportHf298(0);
doublereal delH = Hf298New - h298now;
double h = mnp_low.reportHf298(0);

86
include/cantera/thermo/Phase.h
View file

@ -415,13 +415,6 @@ public:
/// @name Composition
//@{
//! Get the mole fractions by name.
//! @param[out] x composition map containing the species mole fractions.
//! @deprecated To be removed after Cantera 2.2. use
//! `compositionMap getMoleFractionsByName(double threshold)`
//! instead.
void getMoleFractionsByName(compositionMap& x) const;
//! Get the mole fractions by name.
//! @param threshold Exclude species with mole fractions less than or
//! equal to this threshold.
@ -698,90 +691,11 @@ public:
int atomicNumber=0, doublereal entropy298=ENTROPY298_UNKNOWN,
int elem_type=CT_ELEM_TYPE_ABSPOS);
//! Add an element from an XML specification.
//! @param e Reference to the XML_Node where the element is described.
//! @deprecated. To be removed after Cantera 2.2.
void addElement(const XML_Node& e);
//! Add an element, checking for uniqueness
//! The uniqueness is checked by comparing the string symbol. If not
//! unique, nothing is done.
//! @param symbol String symbol of the element
//! @param weight Atomic weight of the element (kg kmol-1).
//! @param atomicNumber Atomic number of the element (unitless)
//! @param entropy298 Entropy of the element at 298 K and 1 bar in its
//! most stable form. The default is the value ENTROPY298_UNKNOWN, which is
//! interpreted as an unknown, and if used will cause %Cantera to throw an
//! error.
//! @param elem_type Specifies the type of the element constraint
//! equation. This defaults to CT_ELEM_TYPE_ABSPOS, i.e., an element.
//! @deprecated. Equivalent to addElement. To be removed after Cantera 2.2.
void addUniqueElement(const std::string& symbol, doublereal weight=-12345.0,
int atomicNumber = 0,
doublereal entropy298 = ENTROPY298_UNKNOWN,
int elem_type = CT_ELEM_TYPE_ABSPOS);
//! Add an element, checking for uniqueness
//! The uniqueness is checked by comparing the string symbol. If not unique,
//! nothing is done.
//! @param e Reference to the XML_Node where the element is described.
//! @deprecated. To be removed after Cantera 2.2.
void addUniqueElement(const XML_Node& e);
//! Add all elements referenced in an XML_Node tree
//! @param phase Reference to the root XML_Node of a phase
//! @deprecated. To be removed after Cantera 2.2.
void addElementsFromXML(const XML_Node& phase);
//! Prohibit addition of more elements, and prepare to add species.
//! @deprecated. To be removed after Cantera 2.2.
void freezeElements();
//! True if freezeElements has been called.
//! @deprecated. To be removed after Cantera 2.2.
bool elementsFrozen();
//! Add an element after elements have been frozen, checking for uniqueness
//! The uniqueness is checked by comparing the string symbol. If not
//! unique, nothing is done.
//! @param symbol String symbol of the element
//! @param weight Atomic weight of the element (kg kmol-1).
//! @param atomicNumber Atomic number of the element (unitless)
//! @param entropy298 Entropy of the element at 298 K and 1 bar in its
//! most stable form. The default is the value ENTROPY298_UNKNOWN, which
//! if used will cause Cantera to throw an error.
//! @param elem_type Specifies the type of the element constraint
//! equation. This defaults to CT_ELEM_TYPE_ABSPOS, i.e., an element.
//! @deprecated. Equivalent to addElement. To be removed after Cantera 2.2.
size_t addUniqueElementAfterFreeze(const std::string& symbol,
doublereal weight, int atomicNumber,
doublereal entropy298 = ENTROPY298_UNKNOWN,
int elem_type = CT_ELEM_TYPE_ABSPOS);
//! Add a Species to this Phase. Returns `true` if the species was
//! successfully added, or `false` if the species was ignored.
//! @see ignoreUndefinedElements addUndefinedElements throwUndefinedElements
virtual bool addSpecies(shared_ptr<Species> spec);
//! @deprecated Use AddSpecies(shared_ptr<Species> spec) instead. To be
//! removed after Cantera 2.2.
void addSpecies(const std::string& name, const doublereal* comp,
doublereal charge = 0.0, doublereal size = 1.0);
//! Add a species to the phase, checking for uniqueness of the name
//! This routine checks for uniqueness of the string name. It only adds the
//! species if it is unique.
//! @param name String name of the species
//! @param comp Array containing the elemental composition of the
//! species.
//! @param charge Charge of the species. Defaults to zero.
//! @param size Size of the species (meters). Defaults to 1 meter.
//! @deprecated Use addSpecies(shared_ptr<Species> spec) instead. To be
//! removed after Cantera 2.2.
void addUniqueSpecies(const std::string& name, const doublereal* comp,
doublereal charge = 0.0,
doublereal size = 1.0);
//! Return the Species object for the named species.
shared_ptr<Species> species(const std::string& name) const;

83
include/cantera/thermo/ShomatePoly.h
View file

@ -59,36 +59,6 @@ public:
//! Empty constructor
ShomatePoly() {}
//! Constructor used in templated instantiations
/*!
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the
* parameters for the standard state for species n.
* There are 7 coefficients for the Shomate polynomial:
* - c[0] = \f$ A \f$
* - c[1] = \f$ B \f$
* - c[2] = \f$ C \f$
* - c[3] = \f$ D \f$
* - c[4] = \f$ E \f$
* - c[5] = \f$ F \f$
* - c[6] = \f$ G \f$
*
* See the class description for the polynomial representation of the
* thermo functions in terms of \f$ A, \dots, G \f$.
*
* @deprecated Use the alternate constructor which does not take the
* species index. To be removed after Cantera 2.2.
*/
ShomatePoly(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_coeff(coeffs, coeffs + 7)
{
}
//! Normal constructor
/*!
* @param tlow Minimum temperature
@ -175,9 +145,9 @@ public:
* the results by dividing by (GasConstant * T),
* where GasConstant has units of J/(kmol * K).
*/
cp_R[m_index] = 1.e3 * cp * tt[5];
h_RT[m_index] = 1.e6 * h * tt[6];
s_R[m_index] = 1.e3 * s * tt[5];
*cp_R = 1.e3 * cp * tt[5];
*h_RT = 1.e6 * h * tt[6];
*s_R = 1.e3 * s * tt[5];
}
virtual void updatePropertiesTemp(const doublereal temp,
@ -192,7 +162,7 @@ public:
doublereal& tlow, doublereal& thigh,
doublereal& pref,
doublereal* const coeffs) const {
n = m_index;
n = 0;
type = SHOMATE;
tlow = m_lowT;
thigh = m_highT;
@ -229,7 +199,7 @@ public:
double hh = 1.e6 * h;
if (h298) {
h298[m_index] = 1.e6 * h;
*h298 = 1.e6 * h;
}
return hh;
}
@ -296,31 +266,6 @@ public:
m_coeff.resize(15);
}
//! Constructor used in templated instantiations
/*!
* @param n Species index
* @param tlow Minimum temperature
* @param thigh Maximum temperature
* @param pref reference pressure (Pa).
* @param coeffs Vector of coefficients used to set the
* parameters for the standard state.
* There are 15 coefficients for the 2-zone Shomate polynomial.
* The first coefficient is the value of Tmid. The next 7
* coefficients are the low temperature range Shomate coefficients.
* The last 7 are the high temperature range Shomate coefficients.
* @deprecated Use the constructor that does not require the species index.
* To be removed after Cantera 2.2.
*/
ShomatePoly2(size_t n, doublereal tlow, doublereal thigh, doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_midT(coeffs[0]),
msp_low(n, tlow, coeffs[0], pref, coeffs+1),
msp_high(n, coeffs[0], thigh, pref, coeffs+8),
m_coeff(coeffs, coeffs + 15)
{
}
//! Normal constructor
/*!
* @param tlow Minimum temperature
@ -347,12 +292,6 @@ public:
return SHOMATE2;
}
virtual void setIndex(size_t index) {
SpeciesThermoInterpType::setIndex(index);
msp_low.setIndex(index);
msp_high.setIndex(index);
}
virtual size_t temperaturePolySize() const { return 7; }
virtual void updateTemperaturePoly(double T, double* T_poly) const {
@ -405,7 +344,7 @@ public:
doublereal& tlow, doublereal& thigh,
doublereal& pref,
doublereal* const coeffs) const {
n = m_index;
n = 0;
type = SHOMATE2;
tlow = m_lowT;
thigh = m_highT;
@ -425,8 +364,8 @@ public:
virtual void modifyParameters(doublereal* coeffs) {
std::copy(coeffs, coeffs + 15, m_coeff.begin());
m_midT = coeffs[0];
msp_low = ShomatePoly(m_index, m_lowT, m_midT, m_Pref, coeffs+1);
msp_high = ShomatePoly(m_index, m_midT, m_highT, m_Pref, coeffs+8);
msp_low = ShomatePoly(m_lowT, m_midT, m_Pref, coeffs+1);
msp_high = ShomatePoly(m_midT, m_highT, m_Pref, coeffs+8);
}
virtual doublereal reportHf298(doublereal* const h298 = 0) const {
@ -437,16 +376,12 @@ public:
h = msp_high.reportHf298(h298);
}
if (h298) {
h298[m_index] = h;
*h298 = h;
}
return h;
}
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New) {
if (k != m_index) {
return;
}
doublereal h298now = reportHf298(0);
doublereal delH = Hf298New - h298now;
double h = msp_low.reportHf298(0);

363
include/cantera/thermo/SimpleThermo.h
View file

@ -1,363 +0,0 @@
/**
* @file SimpleThermo.h
* Header for the SimpleThermo (constant heat capacity) species reference-state model
* for multiple species in a phase, derived from the
* \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref spthermo and
* \link Cantera::SimpleThermo SimpleThermo\endlink).
*/
#ifndef CT_SIMPLETHERMO_H
#define CT_SIMPLETHERMO_H
#include "SpeciesThermoMgr.h"
#include "speciesThermoTypes.h"
#include "cantera/base/global.h"
#include "cantera/base/utilities.h"
namespace Cantera
{
/*!
* A constant-heat capacity species thermodynamic property manager class. This
* makes the assumption that the heat capacity is a constant. Then, the
* following relations are used to complete the specification of the
* thermodynamic functions for each species in the phase.
*
* \f[
* \frac{c_p(T)}{R} = Cp0\_R
* \f]
* \f[
* \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R)
* \f]
* \f[
* \frac{s^0(T)}{R} = (s0\_R + (log(T) - log(T_0)) * Cp0\_R)
* \f]
*
* This parameterization takes 4 input values. These are:
* - c[0] = \f$ T_0 \f$(Kelvin)
* - c[1] = \f$ H_k^o(T_0, p_{ref}) \f$ (J/kmol)
* - c[2] = \f$ S_k^o(T_0, p_{ref}) \f$ (J/kmol K)
* - c[3] = \f$ {Cp}_k^o(T_0, p_{ref}) \f$ (J(kmol K)
*
* All species must have the same reference pressure.
* The single-species standard-state property Manager ConstCpPoly has the same
* parameterization as the SimpleThermo class does.
*
* @see ConstCpPoly
*
* @ingroup mgrsrefcalc
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo instead.
*/
class SimpleThermo : public SpeciesThermo
{
public:
//! The type of parameterization. Note, this value is used in some
//! template functions. For this object the value is SIMPLE.
const int ID;
//! Constructor
SimpleThermo() :
ID(SIMPLE),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_nspData(0) {
warn_deprecated("class SimpleThermo", "To be removed after "
"Cantera 2.2. Use GeneralSpeciesThermo instead.");
}
//! Copy constructor
/*!
* @param right Object to be copied
*/
SimpleThermo(const SimpleThermo& right) :
SpeciesThermo(right),
ID(SIMPLE),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_nspData(0) {
/*
* Call the assignment operator
*/
*this = right;
}
//! Assignment operator
/*!
* @param right Object to be copied
*/
SimpleThermo& operator=(const SimpleThermo& right) {
/*
* Check for self assignment.
*/
if (this == &right) {
return *this;
}
SpeciesThermo::operator=(right);
m_loc = right.m_loc;
m_index = right.m_index;
m_tlow_max = right.m_tlow_max;
m_thigh_min = right.m_thigh_min;
m_tlow = right.m_tlow;
m_thigh = right.m_thigh;
m_t0 = right.m_t0;
m_logt0 = right.m_logt0;
m_h0_R = right.m_h0_R;
m_s0_R = right.m_s0_R;
m_cp0_R = right.m_cp0_R;
m_p0 = right.m_p0;
m_nspData = right.m_nspData;
return *this;
}
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const {
SimpleThermo* nt = new SimpleThermo(*this);
return (SpeciesThermo*) nt;
}
//! Install a new species thermodynamic property
//! parameterization for one species.
/*!
* @param name String name of the species
* @param index Species index, k
* @param type int flag specifying the type of parameterization to be
* installed.
* @param c Vector of coefficients for the parameterization.
* There are 4 coefficients. The values (and units) are the following
* - c[0] = \f$ T_0 \f$(Kelvin)
* - c[1] = \f$ H_k^o(T_0, p_{ref}) \f$ (J/kmol)
* - c[2] = \f$ S_k^o(T_0, p_{ref}) \f$ (J/kmol K)
* - c[3] = \f$ {Cp}_k^o(T_0, p_{ref}) \f$ (J(kmol K)
*
* @param minTemp_ minimum temperature for which this parameterization
* is valid.
* @param maxTemp_ maximum temperature for which this parameterization
* is valid.
* @param refPressure_ standard-state pressure for this parameterization.
*
* @see ConstCpPoly
*/
virtual void install(const std::string& name, size_t index, int type, const doublereal* c,
doublereal minTemp_, doublereal maxTemp_, doublereal refPressure_) {
if (type != SIMPLE) {
throw CanteraError("SimpleThermo::install",
"Incompatible thermo parameterization: Got " +
int2str(type) + " but " + int2str(SIMPLE) +
" was expected.");
}
m_logt0.push_back(log(c[0]));
m_t0.push_back(c[0]);
m_h0_R.push_back(c[1]/GasConstant);
m_s0_R.push_back(c[2]/GasConstant);
m_cp0_R.push_back(c[3]/GasConstant);
m_index.push_back(index);
m_loc[index] = m_nspData;
m_nspData++;
doublereal tlow = minTemp_;
doublereal thigh = maxTemp_;
m_tlow_max = std::max(tlow, m_tlow_max);
m_thigh_min = std::min(thigh, m_thigh_min);
if (m_tlow.size() < index + 1) {
m_tlow.resize(index + 1, tlow);
m_thigh.resize(index + 1, thigh);
}
m_tlow[index] = tlow;
m_thigh[index] = thigh;
if (m_p0 < 0.0) {
m_p0 = refPressure_;
} else if (fabs(m_p0 - refPressure_) > 0.1) {
std::string logmsg = " WARNING SimpleThermo: New Species, " + name +
", has a different reference pressure, "
+ fp2str(refPressure_) + ", than existing reference pressure, " + fp2str(m_p0) + "\n";
writelog(logmsg);
logmsg = " This is now a fatal error\n";
writelog(logmsg);
throw CanteraError("install()", "Species have different reference pressures");
}
m_p0 = refPressure_;
markInstalled(index);
}
virtual void install_STIT(size_t index,
shared_ptr<SpeciesThermoInterpType> stit_ptr) {
throw CanteraError("install_STIT", "not implemented");
}
virtual void update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const {
size_t k, ki;
doublereal logt = log(t);
doublereal rt = 1.0/t;
for (k = 0; k < m_nspData; k++) {
ki = m_index[k];
cp_R[ki] = m_cp0_R[k];
h_RT[ki] = rt*(m_h0_R[k] + (t - m_t0[k]) * m_cp0_R[k]);
s_R[ki] = m_s0_R[k] + m_cp0_R[k] * (logt - m_logt0[k]);
}
}
//! Like update(), but only updates the single species k.
/*!
* @param k species index
* @param t Temperature (Kelvin)
* @param cp_R Vector of Dimensionless heat capacities. (length m_kk).
* @param h_RT Vector of Dimensionless enthalpies. (length m_kk).
* @param s_R Vector of Dimensionless entropies. (length m_kk).
*/
virtual void update_one(size_t k, doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const {
doublereal logt = log(t);
doublereal rt = 1.0/t;
size_t loc = getValue(m_loc, k);
cp_R[k] = m_cp0_R[loc];
h_RT[k] = rt*(m_h0_R[loc] + (t - m_t0[loc]) * m_cp0_R[loc]);
s_R[k] = m_s0_R[loc] + m_cp0_R[loc] * (logt - m_logt0[loc]);
}
virtual doublereal minTemp(size_t k=npos) const {
if (k == npos) {
return m_tlow_max;
} else {
return m_tlow[getValue(m_loc, k)];
}
}
virtual doublereal maxTemp(size_t k=npos) const {
if (k == npos) {
return m_thigh_min;
} else {
return m_thigh[getValue(m_loc, k)];
}
}
virtual doublereal refPressure(size_t k=npos) const {
return m_p0;
}
virtual int reportType(size_t index) const {
return SIMPLE;
}
/*!
* This utility function reports back the type of parameterization and all
* of the parameters for the species, index.
*
* @param index Species index
* @param type Integer type of the standard type
* @param c Vector of coefficients used to set the
* parameters for the standard state.
* For the SimpleThermo object, there are 4 coefficients.
* @param minTemp_ output - Minimum temperature
* @param maxTemp_ output - Maximum temperature
* @param refPressure_ output - reference pressure (Pa).
*/
virtual void reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp_,
doublereal& maxTemp_,
doublereal& refPressure_) const {
type = reportType(index);
size_t loc = getValue(m_loc, index);
if (type == SIMPLE) {
c[0] = m_t0[loc];
c[1] = m_h0_R[loc] * GasConstant;
c[2] = m_s0_R[loc] * GasConstant;
c[3] = m_cp0_R[loc] * GasConstant;
minTemp_ = m_tlow[loc];
maxTemp_ = m_thigh[loc];
refPressure_ = m_p0;
}
}
virtual doublereal reportOneHf298(const size_t k) const {
throw CanteraError("reportHF298", "unimplemented");
}
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New) {
throw CanteraError("reportHF298", "unimplemented");
}
protected:
//! Mapping between the species index and the vector index where the coefficients are kept
/*!
* This object doesn't have a one-to one correspondence between the species index, kspec,
* and the data location index,indexData, m_cp0_R[indexData].
* This index keeps track of it.
* indexData = m_loc[kspec]
*/
std::map<size_t, size_t> m_loc;
//! Map between the vector index where the coefficients are kept and the species index
/*!
* Length is equal to the number of dataPoints.
* kspec = m_index[indexData]
*/
std::vector<size_t> m_index;
//! Maximum value of the low temperature limit
doublereal m_tlow_max;
//! Minimum value of the high temperature limit
doublereal m_thigh_min;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of data points
*/
vector_fp m_tlow;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of data points
*/
vector_fp m_thigh;
//! Vector of base temperatures (kelvin)
/*!
* Length is equal to the number of species data points
*/
vector_fp m_t0;
//! Vector of base log temperatures (kelvin)
/*!
* Length is equal to the number of species data points
*/
vector_fp m_logt0;
//! Vector of base dimensionless Enthalpies
/*!
* Length is equal to the number of species data points
*/
vector_fp m_h0_R;
//! Vector of base dimensionless Entropies
/*!
* Length is equal to the number of species data points
*/
vector_fp m_s0_R;
//! Vector of base dimensionless heat capacities
/*!
* Length is equal to the number of species data points
*/
vector_fp m_cp0_R;
//! Reference pressure (Pa)
/*!
* all species must have the same reference pressure.
*/
doublereal m_p0;
//! Number of species data points in the object.
/*!
* This is less than or equal to the number of species in the phase.
*/
size_t m_nspData;
};
}
#endif

59
include/cantera/thermo/SpeciesThermo.h
View file

@ -67,37 +67,18 @@ class SpeciesThermoInterpType;
*
* Usually, all of the species in a phase are installed into a SpeciesThermo
* class. However, there is no requirement that a SpeciesThermo
* object handles all of the species in a phase. There are
* two member functions that are called to install each species into
* the SpeciesThermo.
* One routine is called \link SpeciesThermo::install() install()\endlink.
* It is called with the index of the species in the phase,
* an integer type delineating
* the SpeciesThermoInterpType object, and a listing of the
* parameters for that parameterization. A factory routine is called based
* on the integer type. The other routine is called
* \link SpeciesThermo::install_STIT() install_STIT()\endlink.
* It accepts as an argument a pointer to an already formed
* SpeciesThermoInterpType object.
* object handles all of the species in a phase. The member function
* \link SpeciesThermo::install_STIT() install_STIT()\endlink
* is called to install each species into the SpeciesThermo object.
*
* The following classes inherit from SpeciesThermo. Each of these classes
* handle multiple species, usually all of the species in a phase. However,
* there is no requirement that a SpeciesThermo object handles all of the
* species in a phase.
*
* - NasaThermo in file NasaThermo.h
* - This is a two zone model, with each zone consisting of a 7
* coefficient NASA Polynomial format.
* - ShomateThermo in file ShomateThermo.h
* - This is a two zone model, with each zone consisting of a 7
* coefficient Shomate Polynomial format.
* - SimpleThermo in file SimpleThermo.h
* - This is a one-zone constant heat capacity model.
* - GeneralSpeciesThermo in file GeneralSpeciesThermo.h
* - This is a general model. Each species is handled separately
* via a vector over SpeciesThermoInterpType classes.
* - SpeciesThermoDuo in file SpeciesThermoMgr.h
* - This is a combination of two SpeciesThermo types.
*
* The class SpeciesThermoInterpType is a pure virtual base class for
* calculation of thermodynamic functions for a single species
@ -129,12 +110,6 @@ class SpeciesThermoInterpType;
* - This is a multiple zone model, consisting of the 9
* coefficient NASA Polynomial format in each zone.
*
* In particular the NasaThermo SpeciesThermo-derived model has been
* optimized for execution speed. It's the main-stay of gas phase computations
* involving large numbers of species in a phase. It combines the calculation
* of each species, which individually have NasaPoly2 representations, to
* minimize the computational time.
*
* The GeneralSpeciesThermo SpeciesThermo object is completely general. It
* does not try to coordinate the individual species calculations at all and
* therefore is the slowest but most general implementation.
@ -170,34 +145,6 @@ public:
*/
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const = 0;
//! Install a new species thermodynamic property
//! parameterization for one species.
/*!
* @see speciesThermoTypes.h
*
* @param name Name of the species
* @param index The 'update' method will update the property
* values for this species
* at position i index in the property arrays.
* @param type int flag specifying the type of parameterization to be
* installed.
* @param c vector of coefficients for the parameterization.
* This vector is simply passed through to the
* parameterization constructor.
* @param minTemp minimum temperature for which this parameterization
* is valid.
* @param maxTemp maximum temperature for which this parameterization
* is valid.
* @param refPressure standard-state pressure for this
* parameterization.
* @deprecated Use newSpeciesThermoInterpType and
* GeneralSpeciesThermo::install_STIT. To be removed after Cantera 2.2.
*/
virtual void install(const std::string& name, size_t index, int type,
const doublereal* c,
doublereal minTemp, doublereal maxTemp,
doublereal refPressure)=0;
//! Install a new species thermodynamic property
//! parameterization for one species.
/*!

240
include/cantera/thermo/SpeciesThermoFactory.h
View file

@ -1,254 +1,20 @@
/**
* @file SpeciesThermoFactory.h
* Header for factory to build instances of classes that manage the
* Header for factory functions to build instances of classes that manage the
* standard-state thermodynamic properties of a set of species
* (see \ref spthermo and class
* \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink);
* (see \ref spthermo);
*/
// Copyright 2001 California Institute of Technology
#ifndef SPECIESTHERMO_FACTORY_H
#define SPECIESTHERMO_FACTORY_H
#include "SpeciesThermo.h"
#include "cantera/base/ctexceptions.h"
#include "cantera/base/FactoryBase.h"
#include "cantera/base/ct_thread.h"
#include "SpeciesThermoInterpType.h"
namespace Cantera
{
class XML_Node;
class VPStandardStateTP;
class VPSSMgr;
class ThermoPhase;
/**
* Throw a named error for an unknown or missing species thermo model.
*
* @ingroup thermoprops
*/
class UnknownSpeciesThermoModel: public CanteraError
{
public:
//! constructor
/*!
* @param proc Function name error occurred.
* @param spName Species Name that caused the error
* @param speciesThermoModel Unrecognized species thermo model name
*/
UnknownSpeciesThermoModel(const std::string& proc, const std::string& spName,
const std::string& speciesThermoModel) :
CanteraError(proc, "species " + spName +
": Specified speciesThermoPhase model "
+ speciesThermoModel +
" does not match any known type.") {}
};
//! Factory to build instances of classes that manage the
//! standard-state thermodynamic properties of a set of species.
/*!
* This class is responsible for making the decision concerning
* which derivative of SpeciesThermo object to use.
* The SpeciesThermo object is used to calculate
* thermodynamic functions for the reference state.
* It queries the database of species to understand what
* the requirements are for the submodels for all of the
* species in the phase. Then, it picks the SpeciesThermo
* object to use, and passes it back to the calling routine.
* It doesn't load any of the data into the derived
* SpeciesThermo object.
*
* Making the choice of SpeciesThermo types is the only
* thing this class does.
*
* This class is implemented as a singleton -- one in which
* only one instance is needed. The recommended way to access
* the factory is to call this static method, which
* instantiates the class if it is the first call, but
* otherwise simply returns the pointer to the existing
* instance.
*
* @deprecated To be removed after Cantera 2.2. Use class GeneralSpeciesThermo directly
* @ingroup thermoprops
*/
class SpeciesThermoFactory : public FactoryBase
{
public:
//! Static method to return an instance of this class
/*!
* This class is implemented as a singleton -- one in which only one
* instance is needed. The recommended way to access the factory is to
* call this static method, which instantiates the class if it is the
* first call, but otherwise simply returns the pointer to the existing
* instance.
*/
static SpeciesThermoFactory* factory();
//! Delete static instance of this class
/**
* If it is necessary to explicitly delete the factory before
* the process terminates (for example, when checking for
* memory leaks) then this method can be called to delete it.
*/
void deleteFactory();
//! Create a new species property manager for the reference state.
/*!
* @param type the integer type to be created.
* @return Returns the pointer to the newly allocated species property
* manager for the reference state
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo
* directly.
*/
SpeciesThermo* newSpeciesThermo(int type) const;
//! Create a new species thermo property manager given a string
/*!
* @param stype String name for the species thermo type
* @return Returns the pointer to the newly malloced species
* property manager for the reference state
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo
* directly.
*/
SpeciesThermo* newSpeciesThermoManager(const std::string& stype) const;
//! Create a new species property manager for the reference
//! state for a group of species
/*!
* This routine will look through species nodes. It will discover what
* each species needs for its species property managers. Then,
* it will malloc and return the proper species property manager to use.
*
* @param spDataNodeList This vector contains a list of species XML
* nodes that will be in the phase
* @return Returns the pointer to the newly malloced species property
* manager for the reference state
* @deprecated To be removed after Cantera 2.2.
*/
SpeciesThermo* newSpeciesThermo(std::vector<XML_Node*> & spDataNodeList) const;
//! Install a species thermodynamic property parameterization
//! for the reference state for one species into a species thermo manager.
/*!
* @param k Species number
* @param speciesNode Reference to the XML node specifying the species
* standard state information
* @param th_ptr Pointer to the ThermoPhase object for the species
* @param spthermo Species reference state thermo manager
* @param phaseNode_ptr Optional pointer to the XML phase information for
* the phase in which the species resides
*/
void installThermoForSpecies(size_t k, const XML_Node& speciesNode,
ThermoPhase* th_ptr, SpeciesThermo& spthermo,
const XML_Node* phaseNode_ptr = 0) const;
//! Install a species thermodynamic property parameterization
//! for the standard state for one species into a species thermo manager, VPSSMgr
/*!
* This is a wrapper around the createInstallVPSS() function in the
* VPStandardStateTP object.
*
* This serves to install the species into vpss_ptr, create a PDSS file. We also
* read the XML database to extract the constants for these steps.
*
* @param k species number
* @param speciesNode Reference to the XML node specifying the species
* standard state information
* @param vp_ptr variable pressure ThermoPhase object
* @param vpss_ptr Pointer to the Manager for calculating variable
* pressure substances.
* @param spthermo_ptr Species reference state thermo manager
* @param phaseNode_ptr Optional Pointer to the XML phase information for
* the phase in which the species resides
* @deprecated To be removed after Cantera 2.2. Call
* VPStandardStateTP::createInstallVPSS directly instead.
*/
void installVPThermoForSpecies(size_t k, const XML_Node& speciesNode,
VPStandardStateTP* vp_ptr,
VPSSMgr* vpss_ptr,
SpeciesThermo* spthermo_ptr,
const XML_Node* phaseNode_ptr) const;
private:
//! Pointer to the sole instance of this class, which is static
static SpeciesThermoFactory* s_factory;
//! Decl of the static mutex variable that locks the SpeciesThermo factory singleton
static mutex_t species_thermo_mutex;
//! Constructor. This is made private, so that only the static
//! method factory() can instantiate the class.
SpeciesThermoFactory() {}
};
////////////////////// Convenience functions ////////////////////
//
// These functions allow using a different factory class that
// derives from SpeciesThermoFactory.
//
//////////////////////////////////////////////////////////////////
//! Create a new species thermo manager instance, by specifying the type and
//! (optionally) a pointer to the factory to use to create it.
/*!
* This utility program will look through species nodes. It will discover what
* each species needs for its species property managers. Then,
* it will malloc and return the proper species property manager to use.
*
* These functions allow using a different factory class that
* derives from SpeciesThermoFactory.
*
* @param type Species thermo type.
* @param f Pointer to a SpeciesThermoFactory. optional parameter.
* Defaults to NULL.
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo
* directly.
*/
SpeciesThermo* newSpeciesThermoMgr(int type, SpeciesThermoFactory* f=0);
//! Create a new species thermo manager instance, by specifying the type and
//! (optionally) a pointer to the factory to use to create it.
/*!
* This utility program is a basic factory operation for spawning a
* new species reference-state thermo manager
*
* These functions allows for using a different factory class that
* derives from SpeciesThermoFactory. However, no applications of this
* have been done yet.
*
* @param stype String specifying the species thermo type
* @param f Pointer to a SpeciesThermoFactory. optional parameter.
* Defaults to NULL.
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo
* directly.
*/
SpeciesThermo* newSpeciesThermoMgr(const std::string& stype,
SpeciesThermoFactory* f=0);
//! Function to return SpeciesThermo manager
/*!
* This utility program will look through species nodes. It will discover what
* each species needs for its species property managers. Then,
* it will malloc and return the proper species reference state manager to use.
*
* These functions allow using a different factory class that
* derives from SpeciesThermoFactory.
*
* @param spDataNodeList This vector contains a list of species XML nodes that
* will be in the phase
* @param f Pointer to a SpeciesThermoFactory. optional
* parameter. Defaults to NULL.
* @deprecated To be removed after Cantera 2.2.
*/
SpeciesThermo* newSpeciesThermoMgr(std::vector<XML_Node*> spDataNodeList,
SpeciesThermoFactory* f=0);
//! Create a new SpeciesThermoInterpType object given a corresponding constant.
/*!

34
include/cantera/thermo/SpeciesThermoInterpType.h
View file

@ -160,11 +160,6 @@ class SpeciesThermoInterpType
public:
SpeciesThermoInterpType();
//! @deprecated Use the constructor without the species index. To be removed
//! after Cantera 2.2.
SpeciesThermoInterpType(size_t n, doublereal tlow,
doublereal thigh, doublereal pref);
SpeciesThermoInterpType(double tlow, double thigh, double pref);
SpeciesThermoInterpType(const SpeciesThermoInterpType& b);
@ -198,17 +193,6 @@ public:
//! Returns an integer representing the type of parameterization
virtual int reportType() const = 0;
//! Returns an integer representing the species index
//! @deprecated
virtual size_t speciesIndex() const {
return m_index;
}
//! @deprecated
virtual void setIndex(size_t index) {
m_index = index;
}
//! Number of terms in the temperature polynomial for this parameterization
virtual size_t temperaturePolySize() const { return 1; }
@ -316,8 +300,6 @@ protected:
doublereal m_highT;
//! Reference state pressure
doublereal m_Pref;
//! species index @deprecated
size_t m_index;
};
//! Class for the thermodynamic manager for an individual species' reference
@ -339,22 +321,6 @@ public:
//! Constructor
STITbyPDSS();
//! Main Constructor
/*!
* @param speciesIndex species index for this object. Note, this must
* agree with what was internally set before.
*
* @param vpssmgr_ptr Pointer to the Variable pressure standard state
* manager that owns the PDSS object that will handle calls for this
* object
*
* @param PDSS_ptr Pointer to the PDSS object that handles calls for
* this object
* @deprecated Use the constructor which does not require the species
* index. To be removed after Cantera 2.2.
*/
STITbyPDSS(size_t speciesIndex, VPSSMgr* vpssmgr_ptr, PDSS* PDSS_ptr);
//! Main Constructor
/*!
* @param vpssmgr_ptr Pointer to the Variable pressure standard state

224
include/cantera/thermo/SpeciesThermoMgr.h
View file

@ -1,224 +0,0 @@
/**
* @file SpeciesThermoMgr.h
* This file contains descriptions of templated subclasses of
* the virtual base class, SpeciesThermo, which includes SpeciesThermoDuo
* (see \ref mgrsrefcalc and class
* \link Cantera::SpeciesThermoDuo SpeciesThermoDuo\endlink)
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_SPECIESTHERMO_MGR_H
#define CT_SPECIESTHERMO_MGR_H
#include "cantera/base/ctexceptions.h"
#include "cantera/base/stringUtils.h"
#include "SpeciesThermo.h"
#include "cantera/base/utilities.h"
namespace Cantera
{
//! Unknown species thermo manager string error
/*!
* @ingroup mgrsrefcalc
*/
class UnknownSpeciesThermo : public CanteraError
{
public:
//! constructor
/*!
* @param proc name of the procecdure
* @param type unknown type
*/
UnknownSpeciesThermo(const std::string& proc, int type) :
CanteraError(proc, "Specified species parameterization type (" + int2str(type)
+ ") does not match any known type.") {}
//! Alternate constructor
/*!
* @param proc name of the procecdure
* @param stype String name for the unknown type
*/
UnknownSpeciesThermo(const std::string& proc, const std::string& stype) :
CanteraError(proc, "Specified species parameterization type (" + stype
+ ") does not match any known type.") {}
};
/**
* This species thermo manager requires that all species have one
* of two parameterizations.
*
* Note this seems to be a slow way to do things, and it may be on its way out.
*
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo instead.
* @ingroup mgrsrefcalc
*/
template<class T1, class T2>
class SpeciesThermoDuo : public SpeciesThermo
{
public:
//! Constructor
SpeciesThermoDuo() {
warn_deprecated("class SpeciesThermoDuo", "To be removed after "
"Cantera 2.2. Use GeneralSpeciesThermo instead.");
};
//! copy constructor
/*!
* @param right Object to be copied
*/
SpeciesThermoDuo(const SpeciesThermoDuo& right) {
*this = right;
}
//! Assignment operator
/*!
* @param right Object to be copied
*/
SpeciesThermoDuo& operator=(const SpeciesThermoDuo& right);
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const;
virtual void install(const std::string& name, size_t sp, int type,
const doublereal* c,
doublereal minTemp, doublereal maxTemp,
doublereal refPressure);
virtual void install_STIT(size_t index,
shared_ptr<SpeciesThermoInterpType> stit_ptr) {
throw CanteraError("install_STIT", "not implemented");
}
virtual void update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const;
virtual doublereal minTemp(size_t k = npos) const {
return std::max(m_thermo1.minTemp(),m_thermo2.minTemp());
}
virtual doublereal maxTemp(size_t k = npos) const {
return std::min(m_thermo1.maxTemp(), m_thermo2.maxTemp());
}
virtual doublereal refPressure(size_t k = npos) const {
return m_p0;
}
virtual int reportType(size_t k) const;
virtual void reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp,
doublereal& maxTemp,
doublereal& refPressure) const;
virtual doublereal reportOneHf298(const size_t k) const {
throw CanteraError("reportHF298", "unimplemented");
}
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New) {
throw CanteraError("reportHF298", "unimplemented");
}
private:
//! Thermo Type 1
T1 m_thermo1;
//! Thermo Type 2
T2 m_thermo2;
//! Reference pressure
doublereal m_p0;
//! map from species to type
std::map<size_t, int> speciesToType;
};
// ------------------------- cpp part of file -------------------------------------
// Definitions for the SpeciesThermoDuo<T1,T2> templated class
template<class T1, class T2>
SpeciesThermoDuo<T1, T2> &
SpeciesThermoDuo<T1, T2>::operator=(const SpeciesThermoDuo& right)
{
if (&right == this) {
return *this;
}
SpeciesThermo::operator=(right);
m_thermo1 = right.m_thermo1;
m_thermo2 = right.m_thermo2;
m_p0 = right.m_p0;
speciesToType = right.speciesToType;
return *this;
}
template<class T1, class T2>
SpeciesThermo*
SpeciesThermoDuo<T1, T2>::duplMyselfAsSpeciesThermo() const
{
return new SpeciesThermoDuo<T1,T2>(*this);
}
template<class T1, class T2>
void
SpeciesThermoDuo<T1, T2>::install(const std::string& name, size_t sp, int type,
const doublereal* c,
doublereal minTemp_,
doublereal maxTemp_,
doublereal refPressure_)
{
m_p0 = refPressure_;
if (type == m_thermo1.ID) {
m_thermo1.install(name, sp, type, c, minTemp_, maxTemp_,
refPressure_);
speciesToType[sp] = m_thermo1.ID;
} else if (type == m_thermo2.ID) {
m_thermo2.install(name, sp, type, c, minTemp_, maxTemp_,
refPressure_);
speciesToType[sp] = m_thermo2.ID;
} else {
throw UnknownSpeciesThermo("SpeciesThermoDuo:install",type);
}
markInstalled(sp);
}
template<class T1, class T2>
void
SpeciesThermoDuo<T1, T2>::update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const
{
m_thermo1.update(t, cp_R, h_RT, s_R);
m_thermo2.update(t, cp_R, h_RT, s_R);
}
template<class T1, class T2>
int
SpeciesThermoDuo<T1, T2>::reportType(size_t k) const
{
return getValue(speciesToType, k, -1);
}
template<class T1, class T2>
void
SpeciesThermoDuo<T1, T2>::reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp_,
doublereal& maxTemp_,
doublereal& refPressure_) const
{
int ctype = reportType(index);
if (ctype == m_thermo1.ID) {
m_thermo1.reportParams(index, type, c, minTemp_, maxTemp_,
refPressure_);
} else if (ctype == m_thermo2.ID) {
m_thermo2.reportParams(index, type, c, minTemp_, maxTemp_,
refPressure_);
} else {
throw CanteraError("SpeciesThermoDuo", "mismatched SpeciesThermoInterpType");
}
}
}
#endif

1
include/cantera/thermo/StatMech.h
View file

@ -14,7 +14,6 @@
#include "cantera/base/global.h"
#include "SpeciesThermoInterpType.h"
#include "SpeciesThermoMgr.h"
namespace Cantera
{

54
include/cantera/thermo/StoichSubstanceSSTP.h
View file

@ -477,60 +477,6 @@ public:
virtual void setParametersFromXML(const XML_Node& eosdata);
};
//! Class %electrodeElectron represents an electron in a
//! metal using the Standard hydrogen reference electrode
/*!
* The class is based on the electron have a chemical potential
* equal to one-half of the entropy of the H2 gas at 1 bar.
*
* @deprecated Deprecated in favor of class MetalSHEelectrons. To be removed
* after Cantera 2.2.
*/
class electrodeElectron : public StoichSubstanceSSTP
{
public:
//! Default constructor for the electrodeElectron class
electrodeElectron();
//! Construct and initialize a electrodeElectron ThermoPhase object
//! directly from an ASCII input file
/*!
* @param infile name of the input file
* @param id name of the phase id in the file.
* If this is blank, the first phase in the file is used.
*/
electrodeElectron(const std::string& infile, std::string id = "");
//! Construct and initialize a electrodeElectron ThermoPhase object
//! directly from an XML database
/*!
* @param phaseRef XML node pointing to a electrodeElectron description
* @param id Id of the phase.
*/
electrodeElectron(XML_Node& phaseRef, const std::string& id = "");
//! Copy constructor
/*!
* @param right Object to be copied
*/
electrodeElectron(const electrodeElectron& right);
//! Assignment operator
/*!
* @param right Object to be copied
*/
electrodeElectron& operator=(const electrodeElectron& right);
//! Destructor
virtual ~electrodeElectron() {}
void setParametersFromXML(const XML_Node& eosdata);
virtual void initThermoXML(XML_Node& phaseNode, const std::string& id);
void setParameters(int n, doublereal* const c);
};
}
#endif

61
include/cantera/thermo/ThermoFactory.h
View file

@ -18,9 +18,6 @@
namespace Cantera
{
class SpeciesThermoFactory;
class VPSSMgr;
/*!
* @addtogroup thermoprops
*
@ -225,66 +222,14 @@ ThermoPhase* newPhase(const std::string& infile, std::string id="");
* @param spfactory species Thermo factory pointer, if
* available. If not available, one will be
* created.
* @deprecated the 'spfactory' argument is unused and will be removed after
* Cantera 2.2.
* @ingroup thermoprops
*
* @deprecated: The return value of this function is always 'true'. After
* Cantera 2.2, this function will return 'void'.
*/
bool importPhase(XML_Node& phase, ThermoPhase* th, SpeciesThermoFactory* spfactory = 0);
void importPhase(XML_Node& phase, ThermoPhase* th);
//! Add the elements given in an XML_Node tree to the specified phase
void installElements(Phase& th, const XML_Node& phaseNode);
//! Install a species into a ThermoPhase object, which defines
//! the phase thermodynamics and speciation.
/*!
* This routine first gathers the information from the Species XML
* tree and calls addUniqueSpecies() to add it to the
* ThermoPhase object, p.
* This information consists of:
* ecomp[] = element composition of species.
* chgr = electric charge of species
* name = string name of species
* sz = size of the species
* (option double used a lot in thermo)
*
* Then, the routine processes the "thermo" XML element and
* calls underlying utility routines to read the XML elements
* containing the thermodynamic information for the reference
* state of the species. Failures or lack of information trigger
* an "UnknownSpeciesThermoModel" exception being thrown.
*
* @param k Species Index in the phase
* @param s XML_Node containing the species data for this species.
* @param p Reference to the ThermoPhase object.
* @param spthermo_ptr Reference to the SpeciesThermo object, where
* the standard state thermo properties for this
* species will be installed.
* @param rule Parameter that handles what to do with species
* who have elements that aren't declared.
* Check that all elements in the species
* exist in 'p'. If rule != 0, quietly skip
* this species if some elements are undeclared;
* otherwise, throw an exception
* @param phaseNode_ptr Pointer to the XML_Node for this phase
* (defaults to 0)
* @param vpss_ptr pointer to the Manager that calculates standard
* state thermo properties
* @param factory Pointer to the SpeciesThermoFactory .
* (defaults to 0)
* @deprecated Use newSpecies and addSpecies. For VPStandardStateTP phases, call
* createInstallPDSS as well. To be removed after Cantera 2.2.
* @return
* Returns true if everything is ok, false otherwise.
*/
bool installSpecies(size_t k, const XML_Node& s, thermo_t& p,
SpeciesThermo* spthermo_ptr, int rule,
XML_Node* phaseNode_ptr = 0,
VPSSMgr* vpss_ptr = 0,
SpeciesThermoFactory* factory = 0);
//! Search an XML tree for species data.
/*!
* This utility routine will search the XML tree for the species
@ -295,8 +240,6 @@ bool installSpecies(size_t k, const XML_Node& s, thermo_t& p,
* @param kname String containing the name of the species.
* @param phaseSpeciesData Pointer to the XML speciesData element
* containing the species data for that phase.
*
*
*/
const XML_Node* speciesXML_Node(const std::string& kname,
const XML_Node* phaseSpeciesData);
@ -306,5 +249,3 @@ const XML_Node* speciesXML_Node(const std::string& kname,
}
#endif

1
include/cantera/transport.h
View file

@ -13,7 +13,6 @@
#include "transport/DustyGasTransport.h"
#include "transport/MultiTransport.h"
#include "transport/MixTransport.h"
#include "transport/PecosTransport.h"
#include "transport/LiquidTransport.h"
#include "transport/HighPressureGasTransport.h"
#endif

16
include/cantera/transport/DustyGasTransport.h
View file

@ -93,22 +93,6 @@ public:
return cDustyGasTransport;
}
//! Set the Parameters in the model
/*!
* @param type Type of the parameter to set
* 0 - porosity
* 1 - tortuosity
* 2 - mean pore radius
* 3 - mean particle radius
* 4 - permeability
* @param k Unused int
* @param p pointer to double for the input list of parameters
* @deprecated Use the individual methods setPorosity(),
* setTortuosity(), setMeanPoreRadius(), setMeanParticleDiameter(),
* and setPermeability()
*/
virtual void setParameters(const int type, const int k, const doublereal* const p);
//! Return the Multicomponent diffusion coefficients. Units: [m^2/s].
/*!
* Returns the array of multicomponent diffusion coefficients.

314
include/cantera/transport/PecosTransport.h
View file

@ -1,314 +0,0 @@
/**
* @file PecosTransport.h
* Header file defining class PecosTransport
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_PECOSTRAN_H
#define CT_PECOSTRAN_H
#include "TransportBase.h"
#include "cantera/numerics/DenseMatrix.h"
namespace Cantera
{
class GasTransportParams;
/**
* Class PecosTransport implements mixture-averaged transport
* properties for ideal gas mixtures.
* @deprecated Incomplete stub class, to be removed after Cantera 2.2.
*/
class PecosTransport : public Transport
{
public:
virtual int model() const {
return cPecosTransport;
}
//! Viscosity of the mixture
/*!
* The viscosity is computed using the Wilke mixture rule.
* \f[
* \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}.
* \f]
* Here \f$ \mu_k \f$ is the viscosity of pure species \e k,
* and
* \f[
* \Phi_{k,j} = \frac{\left[1
* + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_k}}\right)}\right]^2}
* {\sqrt{8}\sqrt{1 + M_k/M_j}}
* \f]
* @see updateViscosity_T();
*/
virtual doublereal viscosity();
virtual void getSpeciesViscosities(doublereal* const visc) {
update_T();
updateViscosity_T();
copy(m_visc.begin(), m_visc.end(), visc);
}
//! Return the thermal diffusion coefficients
/*!
* For this approximation, these are all zero.
*/
virtual void getThermalDiffCoeffs(doublereal* const dt);
//! Returns the mixture thermal conductivity
/*!
* This is computed using the lumped model,
* \f[
* k = k^{tr} + k^{ve}
* \f]
* where,
* \f[
* k^{tr}= 5/2 \mu_s C_{v,s}^{trans} + \mu_s C_{v,s}^{rot}
* \f]
* and,
* \f[
* k^{ve}= \mu_s C_{v,s}^{vib} + \mu_s C_{v,s}^{elec}
* \f]
*
* The thermal conductivity is computed using the Wilke mixture rule.
* \f[
* k = \sum_s \frac{k_s X_s}{\sum_j \Phi_{s,j} X_j}.
* \f]
* Here \f$ k_s \f$ is the conductivity of pure species \e s,
* and
* \f[
* \Phi_{s,j} = \frac{\left[1
* + \sqrt{\left(\frac{\mu_k}{\mu_j}\sqrt{\frac{M_j}{M_s}}\right)}\right]^2}
* {\sqrt{8}\sqrt{1 + M_s/M_j}}
* \f]
* @see updateCond_T();
* @todo Reconcile these these formulas with the implementation
*/
virtual doublereal thermalConductivity();
//! binary diffusion coefficients
/*!
* Using Ramshaw's self-consistent Effective Binary Diffusion
* (1990, J. Non-Equilib. Thermo)
*/
virtual void getBinaryDiffCoeffs(const size_t ld, doublereal* const d);
//! Mixture-averaged diffusion coefficients [m^2/s].
/*!
* For the single species case or the pure fluid case the routine returns
* the self-diffusion coefficient. This is need to avoid a NaN result.
*/
virtual void getMixDiffCoeffs(doublereal* const d);
//! Returns the mixture-averaged diffusion coefficients [m^2/s].
//! These are the coefficients for calculating the molar diffusive fluxes
//! from the species mole fraction gradients, computed according to
//! Eq. 12.176 in "Chemically Reacting Flow":
//!
//! \f[ D_{km}^* = \frac{1-X_k}{\sum_{j \ne k}^K X_j/\mathcal{D}_{kj}} \f]
//!
//! @param[out] d vector of mixture-averaged diffusion coefficients for
//! each species, length m_nsp.
void getMixDiffCoeffsMole(doublereal* const d);
//! Returns the mixture-averaged diffusion coefficients [m^2/s].
//! These are the coefficients for calculating the diffusive mass fluxes
//! from the species mass fraction gradients, computed according to
//! Eq. 12.178 in "Chemically Reacting Flow":
//!
//! \f[ \frac{1}{D_{km}} = \sum_{j \ne k}^K \frac{X_j}{\mathcal{D}_{kj}} +
//! \frac{X_k}{1-Y_k} \sum_{j \ne k}^K \frac{Y_j}{\mathcal{D}_{kj}} \f]
//!
//! @param[out] d vector of mixture-averaged diffusion coefficients for
//! each species, length m_nsp.
void getMixDiffCoeffsMass(doublereal* const d);
virtual void getMobilities(doublereal* const mobil);
virtual void update_T();
/**
* This is called the first time any transport property is requested from
* Mixture after the concentrations have changed.
*/
virtual void update_C();
//! Get the species diffusive mass fluxes wrt to the mass averaged
//! velocity, given the gradients in mole fraction and temperature
/*!
* The diffusive mass flux of species \e k is computed from
* \f[
* \vec{j}_k = -n M_k D_k \nabla X_k + \frac{\rho_k}{\rho} \sum_r n M_r D_r \nabla X_r
* \f]
* This neglects pressure, forced and thermal diffusion.
* Units for the returned fluxes are kg m-2 s-1.
*
* @param ndim Number of dimensions in the flux expressions
* @param grad_T Gradient of the temperature
* (length = ndim)
* @param ldx Leading dimension of the grad_X array
* (usually equal to m_nsp but not always)
* @param grad_X Gradients of the mole fraction
* Flat vector with the m_nsp in the inner loop.
* length = ldx * ndim
* @param ldf Leading dimension of the fluxes array
* (usually equal to m_nsp but not always)
* @param fluxes Output of the diffusive mass fluxes
* Flat vector with the m_nsp in the inner loop.
* length = ldx * ndim
*/
virtual void getSpeciesFluxes(size_t ndim,
const doublereal* const grad_T,
size_t ldx,
const doublereal* const grad_X,
size_t ldf, doublereal* const fluxes);
//! Initialize the transport object
/*!
* Here we change all of the internal dimensions to be sufficient.
* We get the object ready to do property evaluations.
*
* @param tr Transport parameters for all of the species in the phase.
*/
virtual bool initGas(GasTransportParams& tr);
/**
* Reads the transport table specified (currently defaults to internal file)
*
* Reads the user-specified transport table, appending new species
* data and/or replacing default species data.
*/
void read_blottner_transport_table();
friend class TransportFactory;
protected:
PecosTransport();
private:
//! Calculate the pressure from the ideal gas law
doublereal pressure_ig() const {
return (m_thermo->molarDensity() * GasConstant *
m_thermo->temperature());
}
// mixture attributes
int m_nsp;
vector_fp m_mw;
// polynomial fits
std::vector<vector_fp> m_visccoeffs;
std::vector<vector_fp> m_condcoeffs;
std::vector<vector_fp> m_diffcoeffs;
vector_fp m_polytempvec;
// blottner fits
//int species = 20;
double a[500], b[500], c[500];
// property values
DenseMatrix m_bdiff;
vector_fp m_visc;
vector_fp m_sqvisc;
vector_fp m_cond;
vector_fp m_molefracs;
std::vector<std::vector<int> > m_poly;
std::vector<vector_fp> m_astar_poly;
std::vector<vector_fp> m_bstar_poly;
std::vector<vector_fp> m_cstar_poly;
std::vector<vector_fp> m_om22_poly;
DenseMatrix m_astar;
DenseMatrix m_bstar;
DenseMatrix m_cstar;
DenseMatrix m_om22;
DenseMatrix m_phi; // viscosity weighting functions
DenseMatrix m_wratjk, m_wratkj1;
vector_fp m_zrot;
vector_fp m_crot;
vector_fp m_cinternal;
vector_fp m_eps;
vector_fp m_alpha;
vector_fp m_dipoleDiag;
doublereal m_temp, m_logt, m_kbt, m_t14, m_t32;
doublereal m_sqrt_kbt, m_sqrt_t;
vector_fp m_sqrt_eps_k;
DenseMatrix m_log_eps_k;
vector_fp m_frot_298;
vector_fp m_rotrelax;
doublereal m_lambda;
doublereal m_viscmix;
// work space
vector_fp m_spwork;
void updateThermal_T();
/**
* Update the temperature-dependent viscosity terms. Updates the array of
* pure species viscosities, and the weighting functions in the viscosity
* mixture rule. The flag m_visc_ok is set to true.
*/
void updateViscosity_T();
/**
* Update the temperature-dependent parts of the mixture-averaged
* thermal conductivity.
*
* Calculated as,
* \f[
* k= \mu_s (5/2 * C_{v,s}^{trans} + C_{v,s}^{rot} + C_{v,s}^{vib}
* \f]
*/
void updateCond_T();
/**
* Update the pure-species viscosities. (Pa-s) = (kg/m/sec)
*
* Using Blottner fit for viscosity. Defines kinematic viscosity
* of the form
* \f[
* \mu_s\left(T\right) = 0.10 \exp\left(A_s\left(\log T\right)^2 + B_s\log T + C_s\right)
* \f]
* where \f$ A_s \f$, \f$ B_s \f$, and \f$ C_s \f$ are constants.
*/
void updateSpeciesViscosities();
/**
* Update the binary diffusion coefficients. These are evaluated
* from the polynomial fits at unit pressure (1 Pa).
*/
void updateDiff_T();
void correctBinDiffCoeffs();
bool m_viscmix_ok;
bool m_viscwt_ok;
bool m_spvisc_ok;
bool m_diffmix_ok;
bool m_bindiff_ok;
bool m_abc_ok;
bool m_spcond_ok;
bool m_condmix_ok;
int m_mode;
DenseMatrix m_epsilon;
DenseMatrix m_diam;
DenseMatrix incl;
bool m_debug;
// specific heats
vector_fp cv_rot;
vector_fp cp_R;
vector_fp cv_int;
};
}
#endif

1
include/cantera/transport/TransportBase.h
View file

@ -52,7 +52,6 @@ const int cAqueousTransport = 750;
const int cSimpleTransport = 770;
const int cRadiativeTransport = 800;
const int cWaterTransport = 721;
const int cPecosTransport = 900;
//! \endcond
//! The diffusion fluxes must be referenced to a particular reference

16
include/cantera/transport/TransportFactory.h
View file

@ -107,22 +107,6 @@ public:
virtual Transport*
newTransport(thermo_t* thermo, int log_level=0);
//! Initialize an existing transport manager
/*!
* This routine sets up an existing gas-phase transport manager. It
* calculates the collision integrals and calls the initGas() function to
* populate the species-dependent data structure.
*
* @param tr Pointer to the Transport manager
* @param thermo Pointer to the ThermoPhase object
* @param mode Chemkin compatible mode or not. This alters the specification of the
* collision integrals. defaults to no.
* @param log_level Defaults to zero, no logging
* @deprecated To be removed after Cantera 2.2. This initialization is now
* handled directly by GasTransport::init.
*/
virtual void initTransport(Transport* tr, thermo_t* thermo, int mode=0, int log_level=0);
//! Initialize an existing transport manager for liquid phase
/*!
* This routine sets up an existing liquid-phase transport manager. It is

194
include/cantera/transport/TransportParams.h
View file

@ -54,200 +54,6 @@ public:
int log_level;
};
//! This structure holds transport model parameters relevant to transport in ideal
//! gases with a kinetic theory of gases derived transport model.
/*!
* This structure is used by TransportFactory object.
* @deprecated Unused. Mostly merged into class GasTransport. This class will be
* removed after Cantera 2.2.
*/
class GasTransportParams : public TransportParams
{
public:
GasTransportParams();
// polynomial fits
//! temperature-fit of the viscosity
/*!
* The outer loop the number of species, nsp
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> visccoeffs;
//! temperature-fits of the heat conduction
/*!
* The outer loop the number of species, nsp
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> condcoeffs;
//! temperature-fits of the diffusivity
/*!
* The outer loop the number of species, nsp
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> diffcoeffs;
//! This is vector of vectors containing the integer lookup value for the (i,j) interaction
/*!
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<std::vector<int> > poly;
//! This is vector of vectors containing the astar fit.
/*!
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> omega22_poly;
//! This is vector of vectors containing the astar fit.
/*!
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> astar_poly;
//! This is vector of vectors containing the astar fit.
/*!
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> bstar_poly;
//! This is vector of vectors containing the astar fit.
/*!
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*
* The inner loop is over degree + 1, which is the polynomial order of the collision integral fit.
*/
std::vector<vector_fp> cstar_poly;
//! Rotational relaxation number for the species in the current phase
/*!
* length is the number of species in the phase
* units are dimensionless
*/
vector_fp zrot;
//! Dimensionless rotational heat capacity of the species in the current phase
/*!
* These values are 0, 1 and 1.5 for single-molecule, linear, and nonlinear species respectively
* length is the number of species in the phase
* units are dimensionless (Cr / R)
*/
vector_fp crot;
//! Vector of booleans indicating whether a species is a polar molecule
/*!
* Length is nsp
*/
std::vector<bool> polar;
//! Polarizability of each species in the phase
/*!
* Length = nsp
* Units = m^3
*/
vector_fp alpha;
//! This is vector containing the values of delta(i,j) that are used in the collision integral fits.
/*!
* This is used in astar_poly, bstar_poly, cstar_poly, and omega22_poly.
* The outer loop is over a flat (i,j) index that is parameterized on the tr.delta(i,j) value.
* Unique values of delta get their own spot in the array. The values of delta are stored in
* the fitlist vector.
*/
vector_fp fitlist;
//! Lennard-Jones well-depth of the species in the current phase
/*!
* length is the number of species in the phase
* Units are Joules (Note this is not Joules/kmol) (note, no kmol -> this is a per molecule amount)
*/
vector_fp eps;
//! Lennard-Jones diameter of the species in the current phase
/*!
* length is the number of species in the phase
* units are in meters.
*/
vector_fp sigma;
//! This is the reduced mass of the interaction between species i and j
/*!
* tr.reducedMass(i,j) = tr.mw[i] * tr.mw[j] / (Avogadro * (tr.mw[i] + tr.mw[j]));
*
* Units are kg (note, no kmol -> this is a per molecule amount)
*
* Length nsp * nsp. This is a symmetric matrix
*/
DenseMatrix reducedMass;
//! hard-sphere diameter for (i,j) collision
/*!
* diam(i,j) = 0.5*(tr.sigma[i] + tr.sigma[j]);
* Units are m (note, no kmol -> this is a per molecule amount)
*
* Length nsp * nsp. This is a symmetric matrix.
*/
DenseMatrix diam;
//! The effective well depth for (i,j) collisions
/*!
* epsilon(i,j) = sqrt(tr.eps[i]*tr.eps[j]);
* Units are Joules (note, no kmol -> this is a per molecule amount)
*
* Length nsp * nsp. This is a symmetric matrix.
*/
DenseMatrix epsilon;
//! The effective dipole moment for (i,j) collisions
/*!
* dipoleMoment has units of Debye. A Debye is 3.335e-30 C-m
*
* tr.dipole(i,i) = 1.e-21 / lightSpeed * dipoleMoment;
* tr.dipole(i,j) = sqrt(tr.dipole(i,i)*tr.dipole(j,j));
* (note, no kmol -> this is a per molecule amount)
*
* Length nsp * nsp. This is a symmetric matrix.
*/
DenseMatrix dipole;
//! Matrix containing the reduced dipole moment of the interaction between two species
/*!
* This is the reduced dipole moment of the interaction between two species
* 0.5 * tr.dipole(i,j)^2 / (4 * Pi * epsilon_0 * epsilon(i,j) * d^3);
*
* Length nsp * nsp .This is a symmetric matrix
*/
DenseMatrix delta;
//! Pitzer acentric factor
/*!
* Length is the number of species in the phase.
* Unitless
*/
vector_fp w_ac;
};
} // End of namespace Cantera
#endif //CT_TRANSPORTPARAMS_H

7
include/cantera/zeroD/ReactorNet.h
View file

@ -117,13 +117,6 @@ public:
//! Add the reactor *r* to this reactor network.
void addReactor(Reactor& r);
//! Add the reactor *r* to this reactor network.
/**
* @deprecated To be removed after Cantera 2.2. Use addReactor(Reactor&)
* instead.
*/
void addReactor(Reactor* r, bool iown = false);
//! Return a reference to the *n*-th reactor in this network. The reactor
//! indices are determined by the order in which the reactors were added
//! to the reactor network.

18
interfaces/cython/cantera/ctml_writer.py
View file

@ -994,8 +994,7 @@ class Arrhenius(rate_expression):
A = 0.0,
b = 0.0,
E = 0.0,
coverage = [],
n = None):
coverage = []):
"""
:param A:
The pre-exponential coefficient. Required input. If entered without
@ -1011,22 +1010,7 @@ class Arrhenius(rate_expression):
parameters. For multiple coverage dependencies, a list of lists
containing the individual sets of coverage parameters. Only used for
surface and edge reactions.
:param n:
The temperature exponent. Dimensionless. Default: 0.0. Deprecated usage
provided for compatibility.
"""
if n is not None and b != 0.0:
raise CTI_Error("n and b cannot both be specified for the "
"temperature exponent. Specify one or the other.")
elif n is not None and b == 0.0:
b = n
_printerr(
"Warning: Usage of n to specify the temperature exponent is "
"deprecated and will be removed in a future version. Use b "
"to specify the temperature exponent by keyword. Please check "
"your cti file for places where the temperature exponent of "
"the reaction rate is set by n = XXX and change them to "
"b = XXX.")
self._c = [A, b, E]

18
src/base/ct2ctml.cpp
View file

@ -274,22 +274,4 @@ void ck2cti(const std::string& in_file, const std::string& thermo_file,
}
}
void get_CTML_Tree(XML_Node* rootPtr, const std::string& file, const int debug)
{
warn_deprecated("get_CTML_Tree", "To be removed after Cantera 2.2. "
"Use get_XML_File instead.");
XML_Node* src = get_XML_File(file);
src->copy(rootPtr);
}
XML_Node getCtmlTree(const std::string& file)
{
warn_deprecated("getCtmlTree", "To be removed after Cantera 2.2. "
"Use get_XML_File instead.");
XML_Node root;
XML_Node* src = get_XML_File(file);
src->copy(&root);
return root;
}
}

19
src/base/xml.cpp
View file

@ -471,13 +471,6 @@ std::string XML_Node::value() const
return m_value;
}
std::string XML_Node::operator()() const
{
warn_deprecated("XML_Node::operator()",
"To be removed after Cantera 2.2. Use XML_Node::value().");
return m_value;
}
doublereal XML_Node::fp_value() const
{
return fpValueCheck(m_value);
@ -912,18 +905,6 @@ void XML_Node::unlock()
}
}
void XML_Node::getChildren(const std::string& nm,
std::vector<XML_Node*>& children_) const
{
warn_deprecated("XML_Node::getChildren", "To be removed after Cantera 2.2."
"Use overload that returns the vector of XML_Node pointers.");
for (size_t i = 0; i < nChildren(); i++) {
if (child(i).name() == nm) {
children_.push_back(&child(i));
}
}
}
std::vector<XML_Node*> XML_Node::getChildren(const std::string& nm) const
{
std::vector<XML_Node*> children_;

9
src/equil/BasisOptimize.cpp
View file

@ -419,10 +419,10 @@ static void print_stringTrunc(const char* str, int space, int alignment)
}
}
size_t ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
MultiPhase* mphase,
std::vector<size_t>& orderVectorSpecies,
std::vector<size_t>& orderVectorElements)
void ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
MultiPhase* mphase,
std::vector<size_t>& orderVectorSpecies,
std::vector<size_t>& orderVectorElements)
{
size_t j, k, l, i, jl, ml, jr, ielem, jj, kk=0;
@ -627,7 +627,6 @@ size_t ElemRearrange(size_t nComponents, const vector_fp& elementAbundances,
* jr is counted from 0, via the C convention.
*/
} while (jr < (nComponents-1));
return nComponents;
}
}

124
src/equil/equilibrate.cpp
View file

@ -1,124 +0,0 @@
/**
* @file equilibrate.cpp Driver routines for the chemical equilibrium solvers.
*/
#include "cantera/equil/ChemEquil.h"
#include "cantera/equil/vcs_MultiPhaseEquil.h"
namespace Cantera
{
doublereal equilibrate(MultiPhase& s, const char* XY,
doublereal tol, int maxsteps, int maxiter,
int loglevel)
{
warn_deprecated("equilibrate(MultiPhase&, ...)",
"Use MultiPhase::equilibrate instead. To be removed after Cantera 2.2.");
s.init();
int ixy = _equilflag(XY);
if (ixy == TP || ixy == HP || ixy == SP || ixy == TV) {
try {
double err = s.equilibrate(ixy, tol, maxsteps, maxiter, loglevel);
return err;
} catch (CanteraError& err) {
err.save();
throw err;
}
} else {
throw CanteraError("equilibrate","unsupported option");
return -1.0;
}
return 0.0;
}
int equilibrate(thermo_t& s, const char* XY, int solver,
doublereal rtol, int maxsteps, int maxiter, int loglevel)
{
warn_deprecated("equilibrate(ThermoPhase&, ...)",
"Use ThermoPhase::equilibrate instead. To be removed after Cantera 2.2.");
bool redo = true;
int retn = -1;
int nAttempts = 0;
int retnSub = 0;
while (redo) {
if (solver >= 2) {
int printLvlSub = loglevel;
int estimateEquil = 0;
try {
MultiPhase m;
m.addPhase(&s, 1.0);
m.init();
nAttempts++;
vcs_equilibrate(m, XY, estimateEquil, printLvlSub, solver,
rtol, maxsteps, maxiter, loglevel-1);
redo = false;
retn = nAttempts;
} catch (CanteraError& err) {
err.save();
if (nAttempts < 2) {
solver = -1;
} else {
throw err;
}
}
} else if (solver == 1) {
try {
MultiPhase m;
m.addPhase(&s, 1.0);
m.init();
nAttempts++;
equilibrate(m, XY, rtol, maxsteps, maxiter, loglevel-1);
redo = false;
retn = nAttempts;
} catch (CanteraError& err) {
err.save();
if (nAttempts < 2) {
solver = -1;
} else {
throw err;
}
}
} else { // solver <= 0
/*
* Call the element potential solver
*/
try {
ChemEquil e;
e.options.maxIterations = maxsteps;
e.options.relTolerance = rtol;
nAttempts++;
bool useThermoPhaseElementPotentials = true;
retnSub = e.equilibrate(s, XY, useThermoPhaseElementPotentials,
loglevel-1);
if (retnSub < 0) {
if (nAttempts < 2) {
solver = 1;
} else {
throw CanteraError("equilibrate",
"Both equilibrium solvers failed");
}
}
retn = nAttempts;
s.setElementPotentials(e.elementPotentials());
redo = false;
}
catch (CanteraError& err) {
err.save();
// If ChemEquil fails, try the MultiPhase solver
if (solver < 0) {
solver = 1;
} else {
redo = false;
throw err;
}
}
}
} // while (redo)
/*
* We are here only for a success
*/
return retn;
}
}

188
src/equil/vcs_equilibrate.cpp
View file

@ -1,188 +0,0 @@
/**
* @file vcs_equilibrate.cpp
* Driver routines for equilibrium solvers
*/
/*
* Copyright (2006) Sandia Corporation. Under the terms of
* Contract DE-AC04-94AL85000 with Sandia Corporation, the
* U.S. Government retains certain rights in this software.
*/
#include "cantera/equil/vcs_MultiPhaseEquil.h"
#include "cantera/equil/equil.h"
#include "cantera/base/stringUtils.h"
#include "cantera/equil/ChemEquil.h"
using namespace std;
namespace Cantera
{
int vcs_equilibrate(thermo_t& s, const char* XY,
int estimateEquil, int printLvl,
int solver,
doublereal rtol, int maxsteps, int maxiter,
int loglevel)
{
warn_deprecated("vcs_equilibrate", "Use ThermoPhase::equilibrate instead. "
"To be removed after Cantera 2.2.");
MultiPhase* m = 0;
int retn = 1;
if (solver == 2) {
m = new MultiPhase;
try {
/*
* Set the kmoles of the phase to 1.0, arbitrarily.
* It actually doesn't matter.
*/
m->addPhase(&s, 1.0);
m->init();
retn = vcs_equilibrate(*m, XY, estimateEquil, printLvl, solver,
rtol, maxsteps, maxiter, loglevel);
delete m;
} catch (CanteraError& err) {
err.save();
delete m;
throw err;
}
} else if (solver == 1) {
m = new MultiPhase;
try {
m->addPhase(&s, 1.0);
m->init();
(void) equilibrate(*m, XY, rtol, maxsteps, maxiter, loglevel-1);
delete m;
retn = 1;
} catch (CanteraError& err) {
err.save();
delete m;
throw err;
}
} else if (solver == 0) {
ChemEquil* e = new ChemEquil;
try {
e->options.maxIterations = maxsteps;
e->options.relTolerance = rtol;
bool useThermoPhaseElementPotentials = false;
if (estimateEquil == 0) {
useThermoPhaseElementPotentials = true;
}
int retnSub = e->equilibrate(s, XY,
useThermoPhaseElementPotentials, loglevel-1);
if (retnSub < 0) {
delete e;
throw CanteraError("equilibrate",
"ChemEquil equilibrium solver failed");
}
retn = 1;
s.setElementPotentials(e->elementPotentials());
delete e;
} catch (CanteraError& err) {
err.save();
delete e;
throw err;
}
} else {
throw CanteraError("vcs_equilibrate",
"unknown solver");
}
/*
* We are here only for a success
*/
return retn;
}
int vcs_equilibrate(MultiPhase& s, const char* XY,
int estimateEquil, int printLvl, int solver,
doublereal tol, int maxsteps, int maxiter,
int loglevel)
{
int ixy = _equilflag(XY);
int retn = vcs_equilibrate_1(s, ixy, estimateEquil, printLvl, solver,
tol, maxsteps, maxiter, loglevel);
return retn;
}
int vcs_equilibrate_1(MultiPhase& s, int ixy,
int estimateEquil, int printLvl, int solver,
doublereal tol, int maxsteps, int maxiter, int loglevel)
{
warn_deprecated("vcs_equilibrate_1", "Use MultiPhase::equilibrate instead. "
"To be removed after Cantera 2.2.");
static int counter = 0;
int retn = 1;
int printLvlSub = std::max(0, printLvl-1);
s.init();
if (solver == 2) {
try {
vcs_MultiPhaseEquil* eqsolve = new vcs_MultiPhaseEquil(&s, printLvlSub);
int err = eqsolve->equilibrate(ixy, estimateEquil, printLvlSub, tol, maxsteps, loglevel);
if (err != 0) {
retn = -1;
}
// hard code a csv output file.
if (printLvl > 0) {
string reportFile = "vcs_equilibrate_res.csv";
if (counter > 0) {
reportFile = "vcs_equilibrate_res_" + int2str(counter) + ".csv";
}
eqsolve->reportCSV(reportFile);
counter++;
}
delete eqsolve;
} catch (CanteraError& e) {
e.save();
retn = -1;
throw e;
}
} else if (solver == 1) {
if (ixy == TP || ixy == HP || ixy == SP || ixy == TV) {
try {
s.equilibrate(ixy, tol, maxsteps, maxiter, loglevel);
return 0;
} catch (CanteraError& e) {
e.save();
throw e;
}
} else {
throw CanteraError("equilibrate","unsupported option");
}
} else {
throw CanteraError("vcs_equilibrate_1", "unknown solver");
}
return retn;
}
int vcs_determine_PhaseStability(MultiPhase& s, int iphase,
double& funcStab, int printLvl, int loglevel)
{
int iStab = 0;
static int counter = 0;
int printLvlSub = std::max(0, printLvl-1);
s.init();
try {
vcs_MultiPhaseEquil* eqsolve = new vcs_MultiPhaseEquil(&s, printLvlSub);
iStab = eqsolve->determine_PhaseStability(iphase, funcStab, printLvlSub, loglevel);
// hard code a csv output file.
if (printLvl > 0) {
string reportFile = "vcs_phaseStability.csv";
if (counter > 0) {
reportFile = "vcs_phaseStability_" + int2str(counter) + ".csv";
}
eqsolve->reportCSV(reportFile);
counter++;
}
delete eqsolve;
} catch (CanteraError& e) {
throw e;
}
return iStab;
}
}

9
src/kinetics/AqueousKinetics.cpp
View file

@ -148,15 +148,6 @@ void AqueousKinetics::getFwdRateConstants(doublereal* kfwd)
}
}
void AqueousKinetics::addReaction(ReactionData& r)
{
if (r.reactionType == ELEMENTARY_RXN) {
addElementaryReaction(r);
}
BulkKinetics::addReaction(r);
}
bool AqueousKinetics::addReaction(shared_ptr<Reaction> r)
{
bool added = BulkKinetics::addReaction(r);

18
src/kinetics/BulkKinetics.cpp
View file

@ -115,19 +115,6 @@ void BulkKinetics::getRevRateConstants(doublereal* krev, bool doIrreversible)
}
}
void BulkKinetics::addReaction(ReactionData& r)
{
Kinetics::addReaction(r);
m_dn.push_back(accumulate(r.pstoich.begin(), r.pstoich.end(), 0.0) -
accumulate(r.rstoich.begin(), r.rstoich.end(), 0.0));
if (r.reversible) {
m_revindex.push_back(nReactions());
} else {
m_irrev.push_back(nReactions());
}
}
bool BulkKinetics::addReaction(shared_ptr<Reaction> r)
{
bool added = Kinetics::addReaction(r);
@ -156,11 +143,6 @@ bool BulkKinetics::addReaction(shared_ptr<Reaction> r)
return true;
}
void BulkKinetics::addElementaryReaction(ReactionData& r)
{
m_rates.install(nReactions(), r);
}
void BulkKinetics::addElementaryReaction(ElementaryReaction& r)
{
m_rates.install(nReactions()-1, r.rate);

49
src/kinetics/ElectrodeKinetics.cpp
View file

@ -484,55 +484,6 @@ void ElectrodeKinetics::updateROP()
}
//==================================================================================================================
//
// This version of takes the electrons out of the reaction rate expression
// (note: with proper specification of the phase, this shouldn't make a numerical difference (power of 1).
// But it certainly is a complication and unneeded work)
// (TODO: probably can take stoichiometric solids out of the reaction order expression as well.
// They all contribute powers of 1 as well)
//
void ElectrodeKinetics::determineFwdOrdersBV(ReactionData& rdata, std::vector<doublereal>& fwdFullorders)
{
//
// Start out with the full ROP orders vector.
// This vector will have the BV exchange current density orders in it.
//
fwdFullorders = rdata.forwardFullOrder_;
//
// forward and reverse beta values
//
double betaf = rdata.beta;
//double betar = 1.0 - betaf;
//
// Loop over the reactants doing away the BV terms.
// This should leave the reactant terms only, even if they are non-mass action.
//
for (size_t j = 0; j < rdata.reactants.size(); j++) {
size_t kkin = rdata.reactants[j];
double oo = rdata.rstoich[j];
if (kkin != kElectronIndex_) {
fwdFullorders[kkin] += betaf * oo;
if (abs(fwdFullorders[kkin]) < 0.00001) {
fwdFullorders[kkin] = 0.0;
}
} else {
fwdFullorders[kkin] = 0.0;
}
}
for (size_t j = 0; j < rdata.products.size(); j++) {
size_t kkin = rdata.products[j];
double oo = rdata.pstoich[j];
if (kkin != kElectronIndex_) {
fwdFullorders[kkin] -= betaf * oo;
if (abs(fwdFullorders[kkin]) < 0.00001) {
fwdFullorders[kkin] = 0.0;
}
} else {
fwdFullorders[kkin] = 0.0;
}
}
}
//==================================================================================================================
//
// When the BV form is used we still need to go backwards to calculate the forward rate of progress.
// This routine does that
//

71
src/kinetics/GasKinetics.cpp
View file

@ -240,33 +240,6 @@ void GasKinetics::getFwdRateConstants(doublereal* kfwd)
}
}
void GasKinetics::addReaction(ReactionData& r)
{
switch (r.reactionType) {
case ELEMENTARY_RXN:
addElementaryReaction(r);
break;
case THREE_BODY_RXN:
addThreeBodyReaction(r);
break;
case FALLOFF_RXN:
case CHEMACT_RXN:
addFalloffReaction(r);
break;
case PLOG_RXN:
addPlogReaction(r);
break;
case CHEBYSHEV_RXN:
addChebyshevReaction(r);
break;
default:
throw CanteraError("GasKinetics::addReaction", "Invalid reaction type specified");
}
// operations common to all reaction types
BulkKinetics::addReaction(r);
}
bool GasKinetics::addReaction(shared_ptr<Reaction> r)
{
// operations common to all reaction types
@ -299,50 +272,6 @@ bool GasKinetics::addReaction(shared_ptr<Reaction> r)
return true;
}
void GasKinetics::addFalloffReaction(ReactionData& r)
{
// install high and low rate coeff calculators
// and add constant terms to high and low rate coeff value vectors
m_falloff_high_rates.install(m_nfall, r);
m_rfn_high.push_back(r.rateCoeffParameters[0]);
std::swap(r.rateCoeffParameters, r.auxRateCoeffParameters);
m_falloff_low_rates.install(m_nfall, r);
m_rfn_low.push_back(r.rateCoeffParameters[0]);
// add this reaction number to the list of falloff reactions
m_fallindx.push_back(nReactions());
m_rfallindx[nReactions()] = m_nfall;
// install the enhanced third-body concentration calculator for this
// reaction
m_falloff_concm.install(m_nfall, r.thirdBodyEfficiencies,
r.default_3b_eff);
// install the falloff function calculator for this reaction
m_falloffn.install(m_nfall, r.falloffType, r.reactionType,
r.falloffParameters);
// increment the falloff reaction counter
++m_nfall;
}
void GasKinetics::addThreeBodyReaction(ReactionData& r)
{
m_rates.install(nReactions(), r);
m_3b_concm.install(nReactions(), r.thirdBodyEfficiencies,
r.default_3b_eff);
}
void GasKinetics::addPlogReaction(ReactionData& r)
{
m_plog_rates.install(nReactions(), r);
}
void GasKinetics::addChebyshevReaction(ReactionData& r)
{
m_cheb_rates.install(nReactions(), r);
}
void GasKinetics::addFalloffReaction(FalloffReaction& r)
{
// install high and low rate coeff calculators

151
src/kinetics/InterfaceKinetics.cpp
View file

@ -6,7 +6,6 @@
#include "cantera/kinetics/InterfaceKinetics.h"
#include "cantera/kinetics/EdgeKinetics.h"
#include "cantera/kinetics/ReactionData.h"
#include "cantera/kinetics/RateCoeffMgr.h"
#include "cantera/kinetics/ImplicitSurfChem.h"
#include "cantera/thermo/SurfPhase.h"
@ -764,123 +763,6 @@ void InterfaceKinetics::getDeltaSSEntropy(doublereal* deltaS)
getReactionDelta(DATA_PTR(m_grt), deltaS);
}
void InterfaceKinetics::addReaction(ReactionData& r)
{
int reactionType = r.reactionType;
// Install rate coeff calculator
if (r.cov.size() > 3) {
m_has_coverage_dependence = true;
}
for (size_t m = 0; m < r.cov.size(); m++) {
r.rateCoeffParameters.push_back(r.cov[m]);
}
/*
* Temporarily change the reaction rate coefficient type to surface arrhenius.
* This is what is expected. We'll handle exchange current types below by hand.
*/
int reactionRateCoeffType_orig = r.rateCoeffType;
if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) {
r.rateCoeffType = SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE;
}
if (r.rateCoeffType == ARRHENIUS_REACTION_RATECOEFF_TYPE) {
r.rateCoeffType = SURF_ARRHENIUS_REACTION_RATECOEFF_TYPE;
}
/*
* Install the reaction rate into the vector of reactions handled by this class
*/
m_rates.install(m_ii, r);
/*
* Change the reaction rate coefficient type back to its original value
*/
r.rateCoeffType = reactionRateCoeffType_orig;
// Store activation energy
m_E.push_back(r.rateCoeffParameters[2]);
if (r.beta > 0.0) {
m_has_electrochem_rxns = true;
m_beta.push_back(r.beta);
m_ctrxn.push_back(m_ii);
if (r.rateCoeffType == EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE) {
m_has_exchange_current_density_formulation = true;
m_ctrxn_ecdf.push_back(1);
} else {
m_ctrxn_ecdf.push_back(0);
}
m_ctrxn_resistivity_.push_back(r.filmResistivity);
if (reactionType == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN ||
reactionType == BUTLERVOLMER_RXN ||
reactionType == SURFACEAFFINITY_RXN ||
reactionType == GLOBAL_RXN) {
// Specify alternative forms of the electrochemical reaction
if (r.reactionType == BUTLERVOLMER_RXN) {
m_ctrxn_BVform.push_back(1);
} else if (r.reactionType == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN) {
m_ctrxn_BVform.push_back(2);
} else {
// set the default to be the normal forward / reverse calculation method
m_ctrxn_BVform.push_back(0);
}
if (r.forwardFullOrder_.size() > 0) {
RxnOrders* ro = new RxnOrders();
ro->fill(r.forwardFullOrder_);
m_ctrxn_ROPOrdersList_.push_back(ro);
m_ctrxn_FwdOrdersList_.push_back(0);
// Fill in the Fwd Orders dependence here for B-V reactions
if (r.reactionType == BUTLERVOLMER_NOACTIVITYCOEFFS_RXN ||
r.reactionType == BUTLERVOLMER_RXN) {
vector_fp fwdFullorders(m_kk, 0.0);
determineFwdOrdersBV(r, fwdFullorders);
RxnOrders* ro = new RxnOrders();
ro->fill(fwdFullorders);
m_ctrxn_FwdOrdersList_[m_ii] = ro;
}
} else {
m_ctrxn_ROPOrdersList_.push_back(0);
m_ctrxn_FwdOrdersList_.push_back(0);
}
} else {
m_ctrxn_BVform.push_back(0);
m_ctrxn_ROPOrdersList_.push_back(0);
m_ctrxn_FwdOrdersList_.push_back(0);
if (r.filmResistivity > 0.0) {
throw CanteraError("InterfaceKinetics::addReaction()",
"film resistivity set for elementary reaction");
}
}
}
if (r.reversible) {
m_revindex.push_back(nReactions());
m_nrev++;
} else {
m_irrev.push_back(nReactions());
m_nirrev++;
}
Kinetics::addReaction(r);
m_rxnPhaseIsReactant.push_back(std::vector<bool>(nPhases(), false));
m_rxnPhaseIsProduct.push_back(std::vector<bool>(nPhases(), false));
size_t i = m_ii - 1;
for (size_t ik = 0; ik < r.reactants.size(); ik++) {
size_t k = r.reactants[ik];
size_t p = speciesPhaseIndex(k);
m_rxnPhaseIsReactant[i][p] = true;
}
for (size_t ik = 0; ik < r.products.size(); ik++) {
size_t k = r.products[ik];
size_t p = speciesPhaseIndex(k);
m_rxnPhaseIsProduct[i][p] = true;
}
}
bool InterfaceKinetics::addReaction(shared_ptr<Reaction> r_base)
{
size_t i = nReactions();
@ -1259,39 +1141,6 @@ void InterfaceKinetics::setPhaseStability(const size_t iphase, const int isStabl
}
}
void InterfaceKinetics::determineFwdOrdersBV(ReactionData& rdata, std::vector<doublereal>& fwdFullorders)
{
// Start out with the full ROP orders vector.
// This vector will have the BV exchange current density orders in it.
fwdFullorders = rdata.forwardFullOrder_;
// forward and reverse beta values
double betaf = rdata.beta;
// Loop over the reactants doing away with the BV terms.
// This should leave the reactant terms only, even if they are non-mass action.
for (size_t j = 0; j < rdata.reactants.size(); j++) {
size_t kkin = rdata.reactants[j];
double oo = rdata.rstoich[j];
fwdFullorders[kkin] += betaf * oo;
// just to make sure roundoff doesn't leave a term that should be zero (haven't checked this out yet)
if (abs(fwdFullorders[kkin]) < 0.00001) {
fwdFullorders[kkin] = 0.0;
}
}
// Loop over the products doing away with the BV terms.
// This should leave the reactant terms only, even if they are non-mass action.
for (size_t j = 0; j < rdata.products.size(); j++) {
size_t kkin = rdata.products[j];
double oo = rdata.pstoich[j];
fwdFullorders[kkin] -= betaf * oo;
if (abs(fwdFullorders[kkin]) < 0.00001) {
fwdFullorders[kkin] = 0.0;
}
}
}
void InterfaceKinetics::determineFwdOrdersBV(ElectrochemicalReaction& r, std::vector<doublereal>& fwdFullOrders)
{
// Start out with the full ROP orders vector.

100
src/kinetics/Kinetics.cpp
View file

@ -8,7 +8,6 @@
// Copyright 2001-2004 California Institute of Technology
#include "cantera/kinetics/Kinetics.h"
#include "cantera/kinetics/ReactionData.h"
#include "cantera/kinetics/Reaction.h"
#include "cantera/base/stringUtils.h"
@ -554,105 +553,6 @@ void Kinetics::finalize()
}
}
void Kinetics::addReaction(ReactionData& r) {
// vectors rk and pk are lists of species numbers, with repeated entries
// for species with stoichiometric coefficients > 1. This allows the
// reaction to be defined with unity reaction order for each reactant, and
// so the faster method 'multiply' can be used to compute the rate of
// progress instead of 'power'.
std::vector<size_t> rk;
for (size_t n = 0; n < r.reactants.size(); n++) {
double nsFlt = r.rstoich[n];
size_t ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
if (r.rstoich[n] != 0.0) {
m_rrxn[r.reactants[n]][m_ii] += r.rstoich[n];
}
for (size_t m = 0; m < ns; m++) {
rk.push_back(r.reactants[n]);
}
}
m_reactants.push_back(rk);
std::vector<size_t> pk;
for (size_t n = 0; n < r.products.size(); n++) {
double nsFlt = r.pstoich[n];
size_t ns = (size_t) nsFlt;
if ((double) ns != nsFlt) {
ns = std::max<size_t>(ns, 1);
}
if (r.pstoich[n] != 0.0) {
m_prxn[r.products[n]][m_ii] += r.pstoich[n];
}
for (size_t m = 0; m < ns; m++) {
pk.push_back(r.products[n]);
}
}
m_products.push_back(pk);
std::vector<size_t> extReactants = r.reactants;
vector_fp extRStoich = r.rstoich;
vector_fp extROrder = r.rorder;
// If the reaction order involves non-reactant species, add extra terms to
// the reactants with zero stoichiometry so that the stoichiometry manager
// can be used to compute the global forward reaction rate.
if (r.forwardFullOrder_.size() > 0) {
size_t nsp = r.forwardFullOrder_.size();
// Set up a signal vector to indicate whether the species has been added
// into the input vectors for the stoich manager
vector_int kHandled(nsp, 0);
// Loop over the reactants which are also nonzero stoichioemtric entries
// making sure the forwardFullOrder_ entries take precedence over rorder
// entries
for (size_t kk = 0; kk < r.reactants.size(); kk++) {
size_t k = r.reactants[kk];
double oo = r.rorder[kk];
double of = r.forwardFullOrder_[k];
if (of != oo) {
extROrder[kk] = of;
}
kHandled[k] = 1;
}
for (size_t k = 0; k < nsp; k++) {
double of = r.forwardFullOrder_[k];
if (of != 0.0) {
if (kHandled[k] == 0) {
// Add extra entries to reactant inputs. Set their reactant
// stoichiometric entries to zero.
extReactants.push_back(k);
extROrder.push_back(of);
extRStoich.push_back(0.0);
}
}
}
}
size_t irxn = nReactions();
m_reactantStoich.add(irxn, extReactants, extROrder, extRStoich);
if (r.reversible) {
m_revProductStoich.add(irxn, r.products, r.porder, r.pstoich);
} else {
m_irrevProductStoich.add(irxn, r.products, r.porder, r.pstoich);
}
installGroups(nReactions(), r.rgroups, r.pgroups);
incrementRxnCount();
m_rxneqn.push_back(r.equation);
m_reactantStrings.push_back(r.reactantString);
m_productStrings.push_back(r.productString);
m_rxntype.push_back(r.reactionType);
m_rfn.push_back(0.0);
m_rkcn.push_back(0.0);
m_ropf.push_back(0.0);
m_ropr.push_back(0.0);
m_ropnet.push_back(0.0);
}
bool Kinetics::addReaction(shared_ptr<Reaction> r)
{
r->validate();

336
src/kinetics/ReactionStoichMgr.cpp
View file

@ -1,336 +0,0 @@
//------------------------------------------------
///
/// @file ReactionStoichMgr.cpp
///
///
//------------------------------------------------
#include "cantera/kinetics/ReactionStoichMgr.h"
#include "cantera/base/ctexceptions.h"
#include "cantera/kinetics/ReactionData.h"
#include "cantera/kinetics/Reaction.h"
#include <fstream>
using namespace std;
namespace Cantera
{
ReactionStoichMgr::ReactionStoichMgr()
{
warn_deprecated("class ReactionStoichMgr",
"To be removed after Cantera 2.2.");
m_dummy.resize(10,1.0);
}
ReactionStoichMgr::ReactionStoichMgr(const ReactionStoichMgr& right) :
m_reactants(right.m_reactants),
m_revproducts(right.m_revproducts),
m_irrevproducts(right.m_irrevproducts),
m_dummy(right.m_dummy)
{
}
ReactionStoichMgr& ReactionStoichMgr::operator=(const ReactionStoichMgr& right)
{
if (this != &right) {
m_reactants = right.m_reactants;
m_revproducts = right.m_revproducts;
m_irrevproducts = right.m_irrevproducts;
m_dummy = right.m_dummy;
}
return *this;
}
void ReactionStoichMgr::add(size_t rxn, const std::vector<size_t>& reactants,
const std::vector<size_t>& products,
bool reversible)
{
m_reactants.add(rxn, reactants);
if (reversible) {
m_revproducts.add(rxn, products);
} else {
m_irrevproducts.add(rxn, products);
}
}
// Add the reaction into the stoichiometric manager
void ReactionStoichMgr::add(size_t rxn, const ReactionData& r)
{
size_t k;
std::vector<size_t> rk;
doublereal frac;
doublereal oo, os, of;
bool doGlobal = false;
std::vector<size_t> extReactants = r.reactants;
vector_fp extRStoich = r.rstoich;
vector_fp extROrder = r.rorder;
//
// If we have a complete global reaction then we need to do something more complete
// than the previous treatment. Basically we will use the reactant manager to calculate the
// global forward reaction rate of progress.
//
if (r.forwardFullOrder_.size() > 0) {
//
// Trigger a treatment where the order of the reaction and the stoichiometry
// are treated as different.
//
doGlobal = true;
size_t nsp = r.forwardFullOrder_.size();
//
// Set up a signal vector to indicate whether the species has been added into
// the input vectors for the stoich manager
//
vector_int kHandled(nsp, 0);
//
// Loop over the reactants which are also nonzero stoichioemtric entries
// making sure the forwardFullOrder_ entries take precedence over rorder entries
//
for (size_t kk = 0; kk < r.reactants.size(); kk++) {
k = r.reactants[kk];
os = r.rstoich[kk];
oo = r.rorder[kk];
of = r.forwardFullOrder_[k];
if (of != oo) {
extROrder[kk] = of;
}
kHandled[k] = 1;
}
for (k = 0; k < nsp; k++) {
of = r.forwardFullOrder_[k];
if (of != 0.0) {
if (kHandled[k] == 0) {
//
// Add extra entries to reactant inputs. Set their reactant stoichiometric entries to zero.
//
extReactants.push_back(k);
extROrder.push_back(of);
extRStoich.push_back(0.0);
}
}
}
}
bool isfrac = false;
for (size_t n = 0; n < r.reactants.size(); n++) {
size_t ns = size_t(r.rstoich[n]);
frac = r.rstoich[n] - 1.0*int(r.rstoich[n]);
if (frac != 0.0) {
isfrac = true;
}
for (size_t m = 0; m < ns; m++) {
rk.push_back(r.reactants[n]);
}
}
//
// If the reaction is non-mass action add it in in a general way
// Reactants get extra terms for the forward reaction rate of progress
// that may have zero stoichiometries.
//
if (doGlobal) {
m_reactants.add(rxn, extReactants, extROrder, extRStoich);
} else {
//
// this is confusing. The only issue should be whether rorder is different than rstoich!
//
if (isfrac || r.global || rk.size() > 3) {
m_reactants.add(rxn, r.reactants, r.rorder, r.rstoich);
} else {
m_reactants.add(rxn, rk);
}
}
std::vector<size_t> pk;
isfrac = false;
for (size_t n = 0; n < r.products.size(); n++) {
size_t ns = size_t(r.pstoich[n]);
frac = r.pstoich[n] - 1.0*int(r.pstoich[n]);
if (frac != 0.0) {
isfrac = true;
}
for (size_t m = 0; m < ns; m++) {
pk.push_back(r.products[n]);
}
}
if (r.reversible) {
//
// this is confusing. The only issue should be whether porder is different than pstoich!
//
if (pk.size() > 3 || r.isReversibleWithFrac) {
m_revproducts.add(rxn, r.products, r.porder, r.pstoich);
} else {
m_revproducts.add(rxn, pk);
}
} else {
//
// this is confusing. The only issue should be whether porder is different than pstoich!
//
if (isfrac || pk.size() > 3) {
m_irrevproducts.add(rxn, r.products, r.porder, r.pstoich);
} else {
m_irrevproducts.add(rxn, pk);
}
}
}
void ReactionStoichMgr::getCreationRates(size_t nsp, const doublereal* ropf,
const doublereal* ropr, doublereal* c)
{
// zero out the output array
fill(c, c + nsp, 0.0);
// the forward direction creates product species
m_revproducts.incrementSpecies(ropf, c);
m_irrevproducts.incrementSpecies(ropf, c);
// the reverse direction creates reactant species
m_reactants.incrementSpecies(ropr, c);
}
void ReactionStoichMgr::getDestructionRates(size_t nsp, const doublereal* ropf,
const doublereal* ropr,
doublereal* d)
{
fill(d, d + nsp, 0.0);
// the reverse direction destroys products in reversible reactions
m_revproducts.incrementSpecies(ropr, d);
// the forward direction destroys reactants
m_reactants.incrementSpecies(ropf, d);
}
void ReactionStoichMgr::getNetProductionRates(size_t nsp,
const doublereal* ropnet,
doublereal* w)
{
fill(w, w + nsp, 0.0);
// products are created for positive net rate of progress
m_revproducts.incrementSpecies(ropnet, w);
m_irrevproducts.incrementSpecies(ropnet, w);
// reactants are destroyed for positive net rate of progress
m_reactants.decrementSpecies(ropnet, w);
}
void ReactionStoichMgr::getReactionDelta(size_t nr, const doublereal* g,
doublereal* dg)
{
fill(dg, dg + nr, 0.0);
// products add
m_revproducts.incrementReactions(g, dg);
m_irrevproducts.incrementReactions(g, dg);
// reactants subtract
m_reactants.decrementReactions(g, dg);
}
void ReactionStoichMgr::getRevReactionDelta(size_t nr, const doublereal* g,
doublereal* dg)
{
fill(dg, dg + nr, 0.0);
m_revproducts.incrementReactions(g, dg);
m_reactants.decrementReactions(g, dg);
}
void ReactionStoichMgr::multiplyReactants(const doublereal* c, doublereal* r)
{
m_reactants.multiply(c, r);
}
void ReactionStoichMgr::multiplyRevProducts(const doublereal* c, doublereal* r)
{
m_revproducts.multiply(c, r);
}
void ReactionStoichMgr::write(const string& filename)
{
ofstream f(filename.c_str());
f << "namespace mech {" << endl;
writeCreationRates(f);
writeDestructionRates(f);
writeNetProductionRates(f);
writeMultiplyReactants(f);
writeMultiplyRevProducts(f);
f << "} // namespace mech" << endl;
f.close();
}
void ReactionStoichMgr::writeCreationRates(ostream& f)
{
f << " void getCreationRates(const doublereal* rf, const doublereal* rb," << endl;
f << " doublereal* c) {" << endl;
map<size_t, string> out;
m_revproducts.writeIncrementSpecies("rf",out);
m_irrevproducts.writeIncrementSpecies("rf",out);
m_reactants.writeIncrementSpecies("rb",out);
map<size_t, string>::iterator b;
for (b = out.begin(); b != out.end(); ++b) {
string rhs = wrapString(b->second);
rhs[1] = '=';
f << " c[" << b->first << "] " << rhs << ";" << endl;
}
f << " }" << endl << endl << endl;
}
void ReactionStoichMgr::writeDestructionRates(ostream& f)
{
f << " void getDestructionRates(const doublereal* rf, const doublereal* rb," << endl;
f << " doublereal* d) {" << endl;
map<size_t, string> out;
m_revproducts.writeIncrementSpecies("rb",out);
m_reactants.writeIncrementSpecies("rf",out);
map<size_t, string>::iterator b;
for (b = out.begin(); b != out.end(); ++b) {
string rhs = wrapString(b->second);
rhs[1] = '=';
f << " d[" << b->first << "] " << rhs << ";" << endl;
}
f << " }" << endl << endl << endl;
}
void ReactionStoichMgr::writeNetProductionRates(ostream& f)
{
f << " void getNetProductionRates(const doublereal* r, doublereal* w) {" << endl;
map<size_t, string> out;
m_revproducts.writeIncrementSpecies("r",out);
m_irrevproducts.writeIncrementSpecies("r",out);
m_reactants.writeDecrementSpecies("r",out);
map<size_t, string>::iterator b;
for (b = out.begin(); b != out.end(); ++b) {
string rhs = wrapString(b->second);
rhs[1] = '=';
f << " w[" << b->first << "] " << rhs << ";" << endl;
}
f << " }" << endl << endl << endl;
}
void ReactionStoichMgr::writeMultiplyReactants(ostream& f)
{
f << " void multiplyReactants(const doublereal* c, doublereal* r) {" << endl;
map<size_t, string> out;
m_reactants.writeMultiply("c",out);
map<size_t, string>::iterator b;
for (b = out.begin(); b != out.end(); ++b) {
string rhs = b->second;
f << " r[" << b->first << "] *= " << rhs << ";" << endl;
}
f << " }" << endl << endl << endl;
}
void ReactionStoichMgr::writeMultiplyRevProducts(ostream& f)
{
f << " void multiplyRevProducts(const doublereal* c, doublereal* r) {" << endl;
map<size_t, string> out;
m_revproducts.writeMultiply("c",out);
map<size_t, string>::iterator b;
for (b = out.begin(); b != out.end(); ++b) {
string rhs = b->second;
f << " r[" << b->first << "] *= " << rhs << ";" << endl;
}
f << " }" << endl << endl << endl;
}
}

131
src/kinetics/RxnRates.cpp
View file

@ -13,18 +13,6 @@ Arrhenius::Arrhenius()
{
}
Arrhenius::Arrhenius(const ReactionData& rdata)
: m_b(rdata.rateCoeffParameters[1])
, m_E(rdata.rateCoeffParameters[2])
, m_A(rdata.rateCoeffParameters[0])
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = std::log(m_A);
}
}
Arrhenius::Arrhenius(doublereal A, doublereal b, doublereal E)
: m_b(b)
, m_E(E)
@ -63,31 +51,6 @@ SurfaceArrhenius::SurfaceArrhenius(double A, double b, double Ta)
{
}
SurfaceArrhenius::SurfaceArrhenius(const ReactionData& rdata)
: m_b(rdata.rateCoeffParameters[1])
, m_E(rdata.rateCoeffParameters[2])
, m_A(rdata.rateCoeffParameters[0])
, m_acov(0.0)
, m_ecov(0.0)
, m_mcov(0.0)
, m_ncov(0)
, m_nmcov(0)
{
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = std::log(m_A);
}
const vector_fp& data = rdata.rateCoeffParameters;
if (data.size() >= 7) {
for (size_t n = 3; n < data.size()-3; n += 4) {
addCoverageDependence(size_t(data[n]), data[n+1],
data[n+2], data[n+3]);
}
}
}
void SurfaceArrhenius::addCoverageDependence(size_t k, doublereal a,
doublereal m, doublereal e) {
m_ncov++;
@ -101,80 +64,6 @@ void SurfaceArrhenius::addCoverageDependence(size_t k, doublereal a,
}
}
ExchangeCurrent::ExchangeCurrent()
: m_logA(-1.0E300)
, m_b(0.0)
, m_E(0.0)
, m_A(0.0)
{
warn_deprecated("class ExchangeCurrent", "Duplicate of class Arrhenius."
" To be removed after Cantera 2.2.");
}
ExchangeCurrent::ExchangeCurrent(const ReactionData& rdata)
: m_b(rdata.rateCoeffParameters[1])
, m_E(rdata.rateCoeffParameters[2])
, m_A(rdata.rateCoeffParameters[0])
{
warn_deprecated("class ExchangeCurrent", "Duplicate of class Arrhenius."
" To be removed after Cantera 2.2.");
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = std::log(m_A);
}
}
ExchangeCurrent::ExchangeCurrent(doublereal A, doublereal b, doublereal E)
: m_b(b)
, m_E(E)
, m_A(A)
{
warn_deprecated("class ExchangeCurrent", "Duplicate of class Arrhenius."
" To be removed after Cantera 2.2.");
if (m_A <= 0.0) {
m_logA = -1.0E300;
} else {
m_logA = std::log(m_A);
}
}
Plog::Plog(const ReactionData& rdata)
: logP_(-1000)
, logP1_(1000)
, logP2_(-1000)
, rDeltaP_(-1.0)
{
typedef std::multimap<double, vector_fp>::const_iterator iter_t;
size_t j = 0;
// Insert intermediate pressures
rates_.reserve(rdata.plogParameters.size());
for (iter_t iter = rdata.plogParameters.begin();
iter != rdata.plogParameters.end();
iter++) {
double logp = std::log(iter->first);
if (pressures_.empty() || pressures_.rbegin()->first != logp) {
// starting a new group
pressures_[logp] = std::make_pair(j, j+1);
} else {
// another rate expression at the same pressure
pressures_[logp].second = j+1;
}
j++;
rates_.push_back(Arrhenius(iter->second[0], iter->second[1],
iter->second[2]));
}
// Duplicate the first and last groups to handle P < P_0 and P > P_N
pressures_.insert(std::make_pair(-1000.0, pressures_.begin()->second));
pressures_.insert(std::make_pair(1000.0, pressures_.rbegin()->second));
if (rdata.validate) {
validate(rdata.equation);
}
}
Plog::Plog(const std::multimap<double, Arrhenius>& rates)
: logP_(-1000)
@ -244,26 +133,6 @@ std::vector<std::pair<double, Arrhenius> > Plog::rates() const
return R;
}
ChebyshevRate::ChebyshevRate(const ReactionData& rdata)
: Tmin_(rdata.chebTmin)
, Tmax_(rdata.chebTmax)
, Pmin_(rdata.chebPmin)
, Pmax_(rdata.chebPmax)
, nP_(rdata.chebDegreeP)
, nT_(rdata.chebDegreeT)
, chebCoeffs_(rdata.chebCoeffs)
, dotProd_(rdata.chebDegreeT)
{
double logPmin = std::log10(rdata.chebPmin);
double logPmax = std::log10(rdata.chebPmax);
double TminInv = 1.0 / rdata.chebTmin;
double TmaxInv = 1.0 / rdata.chebTmax;
TrNum_ = - TminInv - TmaxInv;
TrDen_ = 1.0 / (TmaxInv - TminInv);
PrNum_ = - logPmin - logPmax;
PrDen_ = 1.0 / (logPmax - logPmin);
}
ChebyshevRate::ChebyshevRate(double Tmin, double Tmax, double Pmin, double Pmax,
const Array2D& coeffs)

526
src/kinetics/importKinetics.cpp
View file

@ -13,7 +13,6 @@
#include "cantera/kinetics/importKinetics.h"
#include "cantera/thermo/ThermoFactory.h"
#include "cantera/kinetics/ReactionData.h"
#include "cantera/kinetics/Reaction.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/ctml.h"
@ -32,531 +31,6 @@ ReactionRules::ReactionRules() :
{
}
void checkRxnElementBalance(Kinetics& kin,
const ReactionData& rdata, doublereal errorTolerance)
{
warn_deprecated("checkRxnElementBalance", "Now handled by "
"Kinetics::checkReactionBalance. To be removed after Cantera 2.2.");
doublereal kstoich;
map<string, double> bal, balr, balp;
bal.clear();
balp.clear();
balr.clear();
size_t np = rdata.products.size();
// iterate over the products
for (size_t index = 0; index < np; index++) {
size_t kp = rdata.products[index]; // index of the product in 'kin'
size_t n = kin.speciesPhaseIndex(kp); // phase this product belongs to
size_t klocal = kp - kin.kineticsSpeciesIndex(0,n); // index within this phase
kstoich = rdata.pstoich[index]; // product stoichiometric coeff
const ThermoPhase& ph = kin.speciesPhase(kp);
for (size_t m = 0; m < ph.nElements(); m++) {
bal[ph.elementName(m)] += kstoich*ph.nAtoms(klocal,m);
balp[ph.elementName(m)] += kstoich*ph.nAtoms(klocal,m);
}
}
for (size_t index = 0; index < rdata.reactants.size(); index++) {
size_t kr = rdata.reactants[index];
size_t n = kin.speciesPhaseIndex(kr);
size_t klocal = kr - kin.kineticsSpeciesIndex(0,n);
kstoich = rdata.rstoich[index];
const ThermoPhase& ph = kin.speciesPhase(kr);
for (size_t m = 0; m < ph.nElements(); m++) {
bal[ph.elementName(m)] -= kstoich*ph.nAtoms(klocal,m);
balr[ph.elementName(m)] += kstoich*ph.nAtoms(klocal,m);
}
}
map<string, double>::iterator b = bal.begin();
string msg = "\n\tElement Reactants Products";
bool ok = true;
doublereal err, elemsum;
for (; b != bal.end(); ++b) {
elemsum = fabs(balr[b->first]) + fabs(balp[b->first]);
if (elemsum > 0.0) {
err = fabs(b->second/elemsum);
if (err > errorTolerance) {
ok = false;
msg += "\n\t"+b->first+" "+ fp2str(balr[b->first])
+" "+ fp2str(balp[b->first]);
}
}
}
if (!ok) {
msg = "The following reaction is unbalanced:\n\t"
+ rdata.equation + "\n" + msg + "\n";
throw CanteraError("checkRxnElementBalance",msg);
}
}
bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp,
std::string default_phase, std::vector<size_t>& spnum,
vector_fp& stoich, vector_fp& order,
const ReactionRules& rules)
{
warn_deprecated("getReagents", "Now handled through newReaction() and its "
"support functions. To be removed after Cantera 2.2.");
string rptype;
/*
* The id of reactants and products are kept in child elements
* of reaction, named "reactants" and "products". We search
* the XML tree for these children based on the value of rp,
* and store the XML element pointer here.
*/
if (rp == 1) {
rptype = "reactants";
} else {
rptype = "products";
}
const XML_Node& rg = rxn.child(rptype);
/*
* The species and stoichiometric coefficient for the species
* are stored as a colon separated pair. Get all of these
* pairs in the reactions/products object.
*/
std::vector<string> key, val;
getPairs(rg, key, val);
/*
* Loop over each of the pairs and process them
*/
doublereal ord, stch;
string ph, spName;
map<string, size_t> speciesMap;
for (size_t n = 0; n < key.size(); n++) {
spName = key[n]; // sp is the string name for species
ph = "";
/*
* Search for the species in the kinetics object using the
* member function kineticsSpeciesIndex(). We will search
* for the species in all phases defined in the kinetics operator.
*/
size_t isp = kin.kineticsSpeciesIndex(spName);
if (isp == npos) {
if (rules.skipUndeclaredSpecies) {
return false;
} else {
throw CanteraError("getReagents",
"Undeclared reactant or product species " + spName);
return false;
}
}
/*
* For each reagent, we store the the species number, isp
* the stoichiometric coefficient, val[n], and the order
* species in the reaction rate expression. We assume mass
* action kinetics here, but will modify this below for
* specified species.
*/
spnum.push_back(isp);
stch = fpValue(val[n]);
stoich.push_back(stch);
ord = doublereal(stch);
order.push_back(ord);
/*
* Needed to process reaction orders below.
*/
speciesMap[spName] = order.size();
}
/*
* Check to see if reaction orders have been specified.
*/
if (rp == 1 && rxn.hasChild("order")) {
std::vector<XML_Node*> ord = rxn.getChildren("order");
doublereal forder;
for (size_t nn = 0; nn < ord.size(); nn++) {
const XML_Node& oo = *ord[nn];
string sp = oo["species"];
size_t loc = speciesMap[sp];
if (loc == 0)
throw CanteraError("getReagents",
"reaction order specified for non-reactant: "
+sp);
forder = oo.fp_value();
if (forder < 0.0) {
throw CanteraError("getReagents",
"reaction order must be non-negative");
}
// replace the stoichiometric coefficient
// stored above in 'order' with the specified
// reaction order
order[loc-1] = forder;
}
}
return true;
}
/**
* getArrhenius() parses the XML element called Arrhenius.
* The Arrhenius expression is
* \f[ k = A T^(b) exp (-E_a / RT). \f]
* @deprecated to be removed after Cantera 2.2.
*/
static void getArrhenius(const XML_Node& node, int& labeled,
doublereal& A, doublereal& b, doublereal& E)
{
if (node["name"] == "k0") {
labeled = -1;
} else if (node["name"] == "kHigh") {
labeled = 1;
} else {
labeled = 0;
}
/*
* We parse the children for the A, b, and E components.
*/
A = getFloat(node, "A", "toSI");
b = getFloat(node, "b");
E = getFloat(node, "E", "actEnergy");
E /= GasConstant;
}
/**
* getStick() processes the XML element called Stick that specifies
* the sticking coefficient reaction. This routine will
* translate the sticking coefficient value into a "normal"
* rate constant for the surface reaction.
*
* Output
* -----------
* Output is the normal Arrhenius expressions for a surface
* reaction rate constant.
*
* A - units such that rate of rxn has kmol/m^2/s when
* A is multiplied by activity concentrations of
* reactants in the normal manner.
* n - unitless
* E - Units 1/Kelvin
* @deprecated to be removed after Cantera 2.2.
*/
static void getStick(const XML_Node& node, Kinetics& kin,
ReactionData& r, doublereal& A, doublereal& b, doublereal& E)
{
size_t nr = r.reactants.size();
size_t k, klocal, not_surf = 0;
size_t np = 0;
doublereal f = 1.0;
doublereal order;
/*
* species is the name of the special reactant whose surface
* flux rate will be calculated.
* isp = species # in the local phase
* ispKinetics = species # in the kinetics object
* ispPhaseIndex = phase # of the special species
*/
string spname = node["species"];
ThermoPhase& th = kin.speciesPhase(spname);
size_t isp = th.speciesIndex(spname);
size_t ispKinetics = kin.kineticsSpeciesIndex(spname);
size_t ispPhaseIndex = kin.speciesPhaseIndex(ispKinetics);
doublereal ispMW = th.molecularWeights()[isp];
doublereal sc;
// loop over the reactants
for (size_t n = 0; n < nr; n++) {
k = r.reactants[n];
order = r.rorder[n]; // stoich coeff
// get the phase species k belongs to
np = kin.speciesPhaseIndex(k);
const ThermoPhase& p = kin.thermo(np);
// get the local index of species k in this phase
klocal = p.speciesIndex(kin.kineticsSpeciesName(k));
// if it is a surface species, divide f by the standard
// concentration for this species, in order to convert
// from concentration units used in the law of mass action
// to coverages used in the sticking probability expression
if (p.eosType() == cSurf || p.eosType() == cEdge) {
sc = p.standardConcentration(klocal);
f /= pow(sc, order);
}
// Otherwise:
else {
// We only allow one species to be in the phase containing the
// special sticking coefficient species.
if (ispPhaseIndex == np) {
not_surf++;
}
// Other bulk phase species on the other side of ther interface are
// treated like surface species.
else {
sc = p.standardConcentration(klocal);
f /= pow(sc, order);
}
}
}
if (not_surf != 1) {
throw CanteraError("getStick",
"reaction probabilities can only be used in "
"reactions with exactly 1 gas/liquid species.");
}
doublereal cbar = sqrt(8.0*GasConstant/(Pi*ispMW));
A = 0.25 * getFloat(node, "A", "toSI") * cbar * f;
b = getFloat(node, "b") + 0.5;
E = getFloat(node, "E", "actEnergy");
E /= GasConstant;
}
//! Read the XML data concerning the coverage dependence of an interfacial reaction
/*!
* @param node XML node with name reaction containing the reaction information
* @param surfphase Surface phase
* @param rdata Reaction data for the reaction.
*
* Example:
* @verbatim
<coverage species="CH3*">
<a> 1.0E-5 </a>
<m> 0.0 </m>
<actEnergy> 0.0 </actEnergy>
</coverage>
@endverbatim
* @deprecated to be removed after Cantera 2.2.
*/
static void getCoverageDependence(const XML_Node& node,
thermo_t& surfphase, ReactionData& rdata)
{
vector<XML_Node*> cov = node.getChildren("coverage");
size_t k, nc = cov.size();
doublereal e;
string spname;
if (nc > 0) {
for (size_t n = 0; n < nc; n++) {
const XML_Node& cnode = *cov[n];
spname = cnode["species"];
k = surfphase.speciesIndex(spname);
rdata.cov.push_back(doublereal(k));
rdata.cov.push_back(getFloat(cnode, "a"));
rdata.cov.push_back(getFloat(cnode, "m"));
e = getFloat(cnode, "e", "actEnergy");
rdata.cov.push_back(e/GasConstant);
}
}
}
//! Get falloff parameters for a reaction.
/*!
* This routine reads the falloff XML node and extracts parameters into a
* vector of doubles
*
* @verbatim
<falloff type="Troe"> 0.5 73.2 5000. 9999. </falloff>
@endverbatim
* @deprecated to be removed after Cantera 2.2.
*/
static void getFalloff(const XML_Node& f, ReactionData& rdata)
{
string type = f["type"];
vector<string> p;
getStringArray(f,p);
vector_fp c;
size_t np = p.size();
for (size_t n = 0; n < np; n++) {
c.push_back(fpValue(p[n]));
}
if (type == "Troe") {
if (np == 3 || np == 4) {
rdata.falloffType = TROE_FALLOFF;
} else {
throw CanteraError("getFalloff()", "Troe parameterization is specified by number of parameters, "
+ int2str(np) + ", is not equal to 3 or 4");
}
} else if (type == "SRI") {
if (np == 3 || np == 5) {
rdata.falloffType = SRI_FALLOFF;
} else {
throw CanteraError("getFalloff()", "SRI parameterization is specified by number of parameters, "
+ int2str(np) + ", is not equal to 3 or 5");
}
}
rdata.falloffParameters = c;
}
/**
* Get the enhanced collision efficiencies. It is assumed that the
* reaction mechanism is homogeneous, so that all species belong
* to phase(0) of 'kin'.
* @deprecated to be removed after Cantera 2.2.
*/
static void getEfficiencies(const XML_Node& eff, Kinetics& kin,
ReactionData& rdata, const ReactionRules& rules)
{
// set the default collision efficiency
rdata.default_3b_eff = fpValue(eff["default"]);
vector<string> key, val;
getPairs(eff, key, val);
string nm;
string phse = kin.thermo(0).id();
for (size_t n = 0; n < key.size(); n++) {
nm = key[n];
size_t k = kin.kineticsSpeciesIndex(nm, phse);
if (k != npos) {
rdata.thirdBodyEfficiencies[k] = fpValue(val[n]);
} else if (!rules.skipUndeclaredThirdBodies) {
throw CanteraError("getEfficiencies", "Encountered third-body "
"efficiency for undefined species \"" + nm + "\"\n"
"while adding reaction " + int2str(rdata.number+1) + ".");
}
}
}
void getRateCoefficient(const XML_Node& kf, Kinetics& kin,
ReactionData& rdata, const ReactionRules& rules)
{
warn_deprecated("getRateCoefficent", "Now handled through newReaction() "
"and its support functions. To be removed after Cantera 2.2.");
if (rdata.reactionType == PLOG_RXN) {
rdata.rateCoeffType = PLOG_REACTION_RATECOEFF_TYPE;
for (size_t m = 0; m < kf.nChildren(); m++) {
const XML_Node& node = kf.child(m);
double p = getFloat(node, "P", "toSI");
vector_fp& rate = rdata.plogParameters.insert(
std::make_pair(p, vector_fp()))->second;
rate.resize(3);
rate[0] = getFloat(node, "A", "toSI");
rate[1] = getFloat(node, "b");
rate[2] = getFloat(node, "E", "actEnergy") / GasConstant;
}
} else if (rdata.reactionType == CHEBYSHEV_RXN) {
rdata.rateCoeffType = CHEBYSHEV_REACTION_RATECOEFF_TYPE;
rdata.chebTmin = getFloat(kf, "Tmin", "toSI");
rdata.chebTmax = getFloat(kf, "Tmax", "toSI");
rdata.chebPmin = getFloat(kf, "Pmin", "toSI");
rdata.chebPmax = getFloat(kf, "Pmax", "toSI");
const XML_Node& coeffs = kf.child("floatArray");
rdata.chebDegreeP = atoi(coeffs["degreeP"].c_str());
rdata.chebDegreeT = atoi(coeffs["degreeT"].c_str());
getFloatArray(kf, rdata.chebCoeffs, false);
} else {
string type = kf.attrib("type");
if (type == "") {
type = "Arrhenius";
rdata.rateCoeffType = ARRHENIUS_REACTION_RATECOEFF_TYPE;
}
if (type == "ExchangeCurrentDensity") {
rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
} else if (type == "Arrhenius") {
} else {
throw CanteraError("getRateCoefficient", "Unknown type: " + type);
}
vector_fp c_alt(3,0.0), c_base(3,0.0);
for (size_t m = 0; m < kf.nChildren(); m++) {
const XML_Node& c = kf.child(m);
string nm = c.name();
int labeled=0;
if (nm == "Arrhenius") {
vector_fp coeff(3);
if (c["type"] == "stick") {
getStick(c, kin, rdata, coeff[0], coeff[1], coeff[2]);
c_base = coeff;
} else {
getArrhenius(c, labeled, coeff[0], coeff[1], coeff[2]);
if (labeled == 0 || rdata.reactionType == THREE_BODY_RXN
|| rdata.reactionType == ELEMENTARY_RXN) {
c_base = coeff;
} else {
c_alt = coeff;
}
}
if (rdata.reactionType == SURFACE_RXN || rdata.reactionType == EDGE_RXN) {
getCoverageDependence(c,
kin.thermo(kin.surfacePhaseIndex()), rdata);
}
if (coeff[0] < 0.0 && !rules.allowNegativeA) {
throw CanteraError("getRateCoefficient",
"negative A coefficient for reaction "+int2str(rdata.number));
}
} else if (nm == "Arrhenius_ExchangeCurrentDensity") {
vector_fp coeff(3);
getArrhenius(c, labeled, coeff[0], coeff[1], coeff[2]);
c_base = coeff;
rdata.rateCoeffType = EXCHANGE_CURRENT_REACTION_RATECOEFF_TYPE;
} else if (nm == "falloff") {
getFalloff(c, rdata);
} else if (nm == "efficiencies") {
getEfficiencies(c, kin, rdata, rules);
} else if (nm == "electrochem") {
rdata.beta = fpValue(c["beta"]);
}
}
/*
* Store the coefficients in the ReactionData object for return
* from this function.
*/
if (rdata.reactionType == FALLOFF_RXN) {
rdata.rateCoeffParameters = c_base;
rdata.auxRateCoeffParameters = c_alt;
} else if (rdata.reactionType == CHEMACT_RXN) {
rdata.rateCoeffParameters = c_alt;
rdata.auxRateCoeffParameters = c_base;
} else {
rdata.rateCoeffParameters = c_base;
}
}
}
doublereal isDuplicateReaction(std::map<int, doublereal>& r1,
std::map<int, doublereal>& r2)
{
warn_deprecated("isDuplicateReaction", "Now handled by "
"Kinetics::checkDuplicateStoich. To be removed after Cantera 2.2.");
map<int, doublereal>::const_iterator b = r1.begin(), e = r1.end();
int k1 = b->first;
// check for duplicate written in the same direction
doublereal ratio = 0.0;
if (r1[k1] && r2[k1]) {
ratio = r2[k1]/r1[k1];
++b;
bool different = false;
for (; b != e; ++b) {
k1 = b->first;
if (!r1[k1] || !r2[k1] || fabs(r2[k1]/r1[k1] - ratio) > 1.e-8) {
different = true;
break;
}
}
if (!different) {
return ratio;
}
}
// check for duplicate written in the reverse direction
b = r1.begin();
k1 = b->first;
if (r1[k1] == 0.0 || r2[-k1] == 0.0) {
return 0.0;
}
ratio = r2[-k1]/r1[k1];
++b;
for (; b != e; ++b) {
k1 = b->first;
if (!r1[k1] || !r2[-k1] || fabs(r2[-k1]/r1[k1] - ratio) > 1.e-8) {
return 0.0;
}
}
return ratio;
}
bool installReactionArrays(const XML_Node& p, Kinetics& kin,
std::string default_phase, bool check_for_duplicates)

31
src/thermo/ConstCpPoly.cpp
View file

@ -19,18 +19,6 @@ ConstCpPoly::ConstCpPoly()
{
}
ConstCpPoly::ConstCpPoly(size_t n, doublereal tlow, doublereal thigh,
doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref)
{
m_t0 = coeffs[0];
m_h0_R = coeffs[1] / GasConstant;
m_s0_R = coeffs[2] / GasConstant;
m_cp0_R = coeffs[3] / GasConstant;
m_logt0 = log(m_t0);
}
ConstCpPoly::ConstCpPoly(double tlow, double thigh, double pref,
const double* coeffs) :
SpeciesThermoInterpType(tlow, thigh, pref)
@ -56,9 +44,9 @@ void ConstCpPoly::updateProperties(const doublereal* tt,
double t = *tt;
doublereal logt = log(t);
doublereal rt = 1.0/t;
cp_R[m_index] = m_cp0_R;
h_RT[m_index] = rt*(m_h0_R + (t - m_t0) * m_cp0_R);
s_R[m_index] = m_s0_R + m_cp0_R * (logt - m_logt0);
*cp_R = m_cp0_R;
*h_RT = rt*(m_h0_R + (t - m_t0) * m_cp0_R);
*s_R = m_s0_R + m_cp0_R * (logt - m_logt0);
}
void ConstCpPoly::updatePropertiesTemp(const doublereal temp,
@ -68,9 +56,9 @@ void ConstCpPoly::updatePropertiesTemp(const doublereal temp,
{
doublereal logt = log(temp);
doublereal rt = 1.0/temp;
cp_R[m_index] = m_cp0_R;
h_RT[m_index] = rt*(m_h0_R + (temp - m_t0) * m_cp0_R);
s_R[m_index] = m_s0_R + m_cp0_R * (logt - m_logt0);
*cp_R = m_cp0_R;
*h_RT = rt*(m_h0_R + (temp - m_t0) * m_cp0_R);
*s_R = m_s0_R + m_cp0_R * (logt - m_logt0);
}
void ConstCpPoly::reportParameters(size_t& n, int& type,
@ -78,7 +66,7 @@ void ConstCpPoly::reportParameters(size_t& n, int& type,
doublereal& pref,
doublereal* const coeffs) const
{
n = m_index;
n = 0;
type = CONSTANT_CP;
tlow = m_lowT;
thigh = m_highT;
@ -103,16 +91,13 @@ doublereal ConstCpPoly::reportHf298(doublereal* const h298) const
double temp = 298.15;
doublereal h = GasConstant * (m_h0_R + (temp - m_t0) * m_cp0_R);
if (h298) {
h298[m_index] = h;
*h298 = h;
}
return h;
}
void ConstCpPoly::modifyOneHf298(const size_t k, const doublereal Hf298New)
{
if (k != m_index) {
return;
}
doublereal hnow = reportHf298();
doublereal delH = Hf298New - hnow;
m_h0_R += delH / GasConstant;

438
src/thermo/Elements.cpp
View file

@ -135,39 +135,6 @@ static struct awData aWTable[] = {
};
// Static function to look up an atomic weight
/*
* This static function looks up the argument string in the
* database above and returns the associated molecular weight.
* The data are from the periodic table.
*
* Note: The idea behind this function is to provide a unified
* source for the element atomic weights. This helps to
* ensure that mass is conserved.
*
* @param s String, Only the first 3 characters are significant
*
* @return
* Return value contains the atomic weight of the element
* If a match for the string is not found, a value of -1.0 is
* returned.
*
* @exception CanteraError
* If a match is not found, a CanteraError is thrown as well
*/
doublereal Elements::LookupWtElements(const std::string& ename)
{
int num = sizeof(aWTable) / sizeof(struct awData);
string s3 = ename.substr(0,3);
for (int i = 0; i < num; i++) {
if (s3 == aWTable[i].name) {
return aWTable[i].atomicWeight;
}
}
throw CanteraError("LookupWtElements", "element not found");
return -1.0;
}
doublereal LookupWtElements(const std::string& ename)
{
int num = sizeof(aWTable) / sizeof(struct awData);
@ -181,409 +148,4 @@ doublereal LookupWtElements(const std::string& ename)
return -1.0;
}
//! Exception class to indicate a fixed set of elements.
/*!
* This class is used to warn the user when the number of elements
* are changed after at least one species is defined.
*/
class ElementsFrozen : public CanteraError
{
public:
//! Constructor for class
/*!
* @param func Function where the error occurred.
*/
ElementsFrozen(string func)
: CanteraError(func,
"elements cannot be added after species.") {}
};
/*
* Elements Class Constructor
* We initialize all internal variables to zero here.
*/
Elements::Elements() :
m_mm(0),
m_elementsFrozen(false),
m_elem_type(0),
numSubscribers(0)
{
warn_deprecated("class Elements",
"Functionality is now part of class Phase. "
"To be removed after Cantera 2.2.");
}
/*
* Elements Class Destructor
* If the number of subscribers is not zero, through an error.
* A logic problem has occurred.
*
* @exception CanteraError
*/
Elements::~Elements()
{
if (numSubscribers != 0) {
throw CanteraError("~Elements", "numSubscribers not zero");
}
}
Elements::Elements(const Elements& right) :
m_mm(0),
m_elementsFrozen(false),
numSubscribers(0)
{
*this = right;
}
Elements& Elements::operator=(const Elements& right)
{
if (&right == this) {
return *this;
}
m_mm = right.m_mm;
m_elementsFrozen = right.m_elementsFrozen;
m_atomicWeights = right.m_atomicWeights;
m_atomicNumbers = right.m_atomicNumbers;
m_elementNames = right.m_elementNames;
m_entropy298 = right.m_entropy298;
m_elem_type = right.m_elem_type;
numSubscribers = 0;
return *this;
}
/*
* freezeElements():
*
* Set the freeze flag. This is a prerequesite to other
* activivities, i.e., this is done before species are defined.
*/
void Elements::freezeElements()
{
m_elementsFrozen = true;
}
/*
* elementIndex():
*
* Index of element named \c name. The index is an integer
* assigned to each element in the order it was added,
* beginning with 0 for the first element. If \c name is not
* the name of an element in the set, then the value -1 is
* returned.
*
*/
int Elements::elementIndex(const std::string& name) const
{
for (int i = 0; i < m_mm; i++) {
if (m_elementNames[i] == name) {
return i;
}
}
return -1;
}
/*
*
* Name of the element with index \c m. @param m Element
* index. If m < 0 or m >= nElements() an exception is thrown.
*/
string Elements::elementName(int m) const
{
if (m < 0 || m >= nElements()) {
throw CanteraError("Elements::elementName()", "out of bounds: " + int2str(m) + " " + int2str(nElements()));
}
return m_elementNames[m];
}
doublereal Elements::entropyElement298(int m) const
{
AssertThrowMsg(m_entropy298[m] != ENTROPY298_UNKNOWN,
"Elements::entropy298",
"Entropy at 298 K of element is unknown");
AssertTrace(m >= 0 && m < m_mm);
return m_entropy298[m];
}
//====================================================================================================================
//! Return the element constraint type
/*!
* Possible types include:
*
* CT_ELEM_TYPE_TURNEDOFF -1
* CT_ELEM_TYPE_ABSPOS 0
* CT_ELEM_TYPE_ELECTRONCHARGE 1
* CT_ELEM_TYPE_CHARGENEUTRALITY 2
* CT_ELEM_TYPE_LATTICERATIO 3
* CT_ELEM_TYPE_KINETICFROZEN 4
* CT_ELEM_TYPE_SURFACECONSTRAINT 5
* CT_ELEM_TYPE_OTHERCONSTRAINT 6
*
* The default is CT_ELEM_TYPE_ABSPOS
*/
int Elements::elementType(int m) const
{
return m_elem_type[m];
}
//====================================================================================================================
// Change the element type of the mth constraint
/*
* Reassigns an element type
*
* @param m Element index
* @param elem_type New elem type to be assigned
*
* @return Returns the old element type
*/
int Elements::changeElementType(int m, int elem_type)
{
int old = m_elem_type[m];
m_elem_type[m] = elem_type;
return old;
}
//====================================================================================================================
/*
*
* Add an element to the current set of elements in the current object.
* @param symbol symbol string
* @param weight atomic weight in kg/kmol.
*
* The default weight is a special value, which will cause the
* routine to look up the actual weight via a string lookup.
*
* There are two interfaces to this routine. The XML interface
* looks up the required parameters for the regular interface
* and then calls the base routine.
*/
void Elements::addElement(const std::string& symbol, doublereal weight)
{
if (weight == -12345.0) {
weight = LookupWtElements(symbol);
if (weight < 0.0) {
throw ElementsFrozen("addElement");
}
}
if (m_elementsFrozen) {
throw ElementsFrozen("addElement");
return;
}
m_atomicWeights.push_back(weight);
m_elementNames.push_back(symbol);
if (symbol == "E") {
m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE);
} else {
m_elem_type.push_back(CT_ELEM_TYPE_ABSPOS);
}
m_mm++;
}
//===========================================================================================================
void Elements::addElement(const XML_Node& e)
{
doublereal weight = fpValue(e["atomicWt"]);
string symbol = e["name"];
addElement(symbol, weight);
}
//===========================================================================================================
/*
* addUniqueElement():
*
* Add a unique element to the set. This routine will not allow
* duplicate elements to be input.
*
* @param symbol symbol string
* @param weight atomic weight in kg/kmol.
*
*
* The default weight is a special value, which will cause the
* routine to look up the actual weight via a string lookup.
*/
void Elements::addUniqueElement(const std::string& symbol, doublereal weight,
int atomicNumber_, doublereal entropy298,
int elem_type)
{
if (weight == -12345.0) {
weight = LookupWtElements(symbol);
if (weight < 0.0) {
throw ElementsFrozen("addElement");
}
}
/*
* First decide if this element has been previously added
* by conducting a string search. If it unique, add it to
* the list.
*/
int ifound = 0;
int i = 0;
for (vector<string>::const_iterator it = m_elementNames.begin();
it < m_elementNames.end(); ++it, ++i) {
if (*it == symbol) {
ifound = 1;
break;
}
}
if (!ifound) {
if (m_elementsFrozen) {
throw ElementsFrozen("addElement");
return;
}
m_atomicWeights.push_back(weight);
m_elementNames.push_back(symbol);
m_atomicNumbers.push_back(atomicNumber_);
m_entropy298.push_back(entropy298);
if (symbol == "E") {
m_elem_type.push_back(CT_ELEM_TYPE_ELECTRONCHARGE);
} else {
m_elem_type.push_back(elem_type);
}
m_mm++;
} else {
if (m_atomicWeights[i] != weight) {
throw CanteraError("AddUniqueElement",
"Duplicate Elements (" + symbol + ") have different weights");
}
}
}
/*
* @todo call addUniqueElement(symbol, weight) instead of
* addElement.
*/
void Elements::addUniqueElement(const XML_Node& e)
{
doublereal weight = 0.0;
if (e.hasAttrib("atomicWt")) {
weight = fpValue(stripws(e["atomicWt"]));
}
int anum = 0;
if (e.hasAttrib("atomicNumber")) {
anum = atoi(stripws(e["atomicNumber"]).c_str());
}
string symbol = e["name"];
doublereal entropy298 = ENTROPY298_UNKNOWN;
if (e.hasChild("entropy298")) {
XML_Node& e298Node = e.child("entropy298");
if (e298Node.hasAttrib("value")) {
entropy298 = fpValueCheck(stripws(e298Node["value"]));
}
}
if (weight != 0.0) {
addUniqueElement(symbol, weight, anum, entropy298);
} else {
addUniqueElement(symbol);
}
}
// True if freezeElements has been called.
bool Elements::elementsFrozen() const
{
return m_elementsFrozen;
}
/*
* clear()
*
* Remove all elements from the structure.
*/
void Elements::clear()
{
m_mm = 0;
m_atomicWeights.resize(0);
m_elementNames.resize(0);
m_entropy298.resize(0);
m_elem_type.resize(0);
m_elementsFrozen = false;
}
/*
* ready():
*
* True if the elements have been frozen
*/
bool Elements::ready() const
{
return m_elementsFrozen;
}
void Elements::addElementsFromXML(const XML_Node& phase)
{
// get the declared element names
if (! phase.hasChild("elementArray")) {
throw CanteraError("Elements::addElementsFromXML",
"phase XML node doesn't have \"elementArray\" XML Node");
}
XML_Node& elements = phase.child("elementArray");
vector<string> enames;
getStringArray(elements, enames);
// // element database defaults to elements.xml
string element_database = "elements.xml";
if (elements.hasAttrib("datasrc")) {
element_database = elements["datasrc"];
}
XML_Node* doc = get_XML_File(element_database);
XML_Node* dbe = &doc->child("elementData");
XML_Node& root = phase.root();
XML_Node* local_db = 0;
if (root.hasChild("elementData")) {
local_db = &root.child("elementData");
}
int nel = static_cast<int>(enames.size());
int i;
string enm;
XML_Node* e = 0;
for (i = 0; i < nel; i++) {
e = 0;
if (local_db) {
e = local_db->findByAttr("name",enames[i]);
}
if (!e) {
e = dbe->findByAttr("name",enames[i]);
}
if (e) {
addUniqueElement(*e);
} else {
throw CanteraError("addElementsFromXML","no data for element "
+enames[i]);
}
}
}
/*
* subscribe(), unsubscribe(), and reportSubscriptions():
*
* Handles setting and reporting the number of subscriptions to this
* object.
*/
void Elements::subscribe()
{
++numSubscribers;
}
int Elements::unsubscribe()
{
--numSubscribers;
return numSubscribers;
}
int Elements::reportSubscriptions() const
{
return numSubscribers;
}
/********************* GLOBAL STATIC SECTION **************************/
/*
* We keep track of a vector of pointers to element objects.
* Initially there are no Elements objects. Whenever one is created,
* the pointer to that object is added onto this list.
*/
vector<Elements*> Elements::Global_Elements_List;
/***********************************************************************/
}

30
src/thermo/GeneralSpeciesThermo.cpp
View file

@ -8,6 +8,9 @@
#include "cantera/thermo/GeneralSpeciesThermo.h"
#include "cantera/thermo/SpeciesThermoFactory.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/utilities.h"
#include "cantera/base/ctexceptions.h"
namespace Cantera
{
@ -76,31 +79,6 @@ GeneralSpeciesThermo::duplMyselfAsSpeciesThermo() const
return new GeneralSpeciesThermo(*this);
}
void GeneralSpeciesThermo::install(const std::string& name,
size_t index,
int type,
const doublereal* c,
doublereal minTemp_,
doublereal maxTemp_,
doublereal refPressure_)
{
warn_deprecated("GeneralSpeciesThermo::install",
"Use newSpeciesThermoInterpType and "
"GeneralSpeciesThermo::install_STIT instead");
if (minTemp_ <= 0.0) {
throw CanteraError("GeneralSpeciesThermo::install",
"T_min must be positive");
}
/*
* Create the necessary object
*/
shared_ptr<SpeciesThermoInterpType> sp(newSpeciesThermoInterpType(type,
minTemp_, maxTemp_, refPressure_, c));
sp->validate(name);
install_STIT(index, sp);
}
void GeneralSpeciesThermo::install_STIT(size_t index,
shared_ptr<SpeciesThermoInterpType> stit_ptr)
{
@ -126,7 +104,7 @@ void GeneralSpeciesThermo::install_STIT(size_t index,
void GeneralSpeciesThermo::installPDSShandler(size_t k, PDSS* PDSS_ptr,
VPSSMgr* vpssmgr_ptr)
{
shared_ptr<SpeciesThermoInterpType> stit_ptr(new STITbyPDSS(k, vpssmgr_ptr, PDSS_ptr));
shared_ptr<SpeciesThermoInterpType> stit_ptr(new STITbyPDSS(vpssmgr_ptr, PDSS_ptr));
install_STIT(k, stit_ptr);
}

1
src/thermo/LatticeSolidPhase.cpp
View file

@ -11,6 +11,7 @@
#include "cantera/thermo/SpeciesThermoFactory.h"
#include "cantera/thermo/GeneralSpeciesThermo.h"
#include "cantera/base/ctml.h"
#include "cantera/base/stringUtils.h"
#include "cantera/base/utilities.h"
using namespace std;

18
src/thermo/Mu0Poly.cpp
View file

@ -19,16 +19,6 @@ Mu0Poly::Mu0Poly() : m_numIntervals(0),
{
}
Mu0Poly::Mu0Poly(size_t n, doublereal tlow, doublereal thigh,
doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_numIntervals(0),
m_H298(0.0)
{
processCoeffs(coeffs);
}
Mu0Poly::Mu0Poly(double tlow, double thigh, double pref, const double* coeffs) :
SpeciesThermoInterpType(tlow, thigh, pref),
m_numIntervals(0),
@ -57,9 +47,9 @@ void Mu0Poly::updateProperties(const doublereal* tt, doublereal* cp_R,
}
double T1 = m_t0_int[j];
double cp_Rj = m_cp0_R_int[j];
cp_R[m_index] = cp_Rj;
h_RT[m_index] = (m_h0_R_int[j] + (T - T1) * cp_Rj)/T;
s_R[m_index] = m_s0_R_int[j] + cp_Rj * (log(T/T1));
*cp_R = cp_Rj;
*h_RT = (m_h0_R_int[j] + (T - T1) * cp_Rj)/T;
*s_R = m_s0_R_int[j] + cp_Rj * (log(T/T1));
}
void Mu0Poly::updatePropertiesTemp(const doublereal T,
@ -75,7 +65,7 @@ void Mu0Poly::reportParameters(size_t& n, int& type,
doublereal& pref,
doublereal* const coeffs) const
{
n = m_index;
n = 0;
type = MU0_INTERP;
tlow = m_lowT;
thigh = m_highT;

19
src/thermo/Nasa9Poly1.cpp
View file

@ -21,14 +21,6 @@ Nasa9Poly1::Nasa9Poly1()
m_Pref = 1.0e5;
}
Nasa9Poly1::Nasa9Poly1(size_t n, doublereal tlow, doublereal thigh,
doublereal pref,
const doublereal* coeffs) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
m_coeff(coeffs, coeffs + 9)
{
}
Nasa9Poly1::Nasa9Poly1(double tlow, double thigh, double pref,
const double* coeffs) :
SpeciesThermoInterpType(tlow, thigh, pref),
@ -77,11 +69,10 @@ void Nasa9Poly1::updateProperties(const doublereal* tt,
doublereal sdivR = -0.5*ct0 - ct1 + tt[6]*ct2 + ct3 + 0.5*ct4
+ 1.0/3.0*ct5 + 0.25*ct6 + m_coeff[8];
// return the computed properties in the location in the output
// arrays for this species
cp_R[m_index] = cpdivR;
h_RT[m_index] = hdivRT;
s_R[m_index] = sdivR;
// return the computed properties for this species
*cp_R = cpdivR;
*h_RT = hdivRT;
*s_R = sdivR;
}
void Nasa9Poly1::updatePropertiesTemp(const doublereal temp,
@ -98,7 +89,7 @@ void Nasa9Poly1::reportParameters(size_t& n, int& type,
doublereal& pref,
doublereal* const coeffs) const
{
n = m_index;
n = 0;
type = NASA9;
tlow = m_lowT;
thigh = m_highT;

14
src/thermo/Nasa9PolyMultiTempRegion.cpp
View file

@ -37,13 +37,8 @@ Nasa9PolyMultiTempRegion::Nasa9PolyMultiTempRegion(vector<Nasa9Poly1*>& regionPt
m_lowT = m_regionPts[0]->minTemp();
m_highT = m_regionPts[m_numTempRegions-1]->maxTemp();
m_Pref = m_regionPts[0]->refPressure();
m_index = m_regionPts[0]->speciesIndex();
for (size_t i = 0; i < m_numTempRegions; i++) {
m_lowerTempBounds[i] = m_regionPts[i]->minTemp();
if (m_regionPts[i]->speciesIndex() != m_index) {
throw CanteraError("Nasa9PolyMultiTempRegion::Nasa9PolyMultiTempRegion",
"m_index inconsistency");
}
if (fabs(m_regionPts[i]->refPressure() - m_Pref) > 0.0001) {
throw CanteraError("Nasa9PolyMultiTempRegion::Nasa9PolyMultiTempRegion",
"refPressure inconsistency");
@ -113,13 +108,6 @@ int Nasa9PolyMultiTempRegion::reportType() const
return NASA9MULTITEMP;
}
void Nasa9PolyMultiTempRegion::setIndex(size_t index) {
SpeciesThermoInterpType::setIndex(index);
for (size_t i = 0; i < m_numTempRegions; i++) {
m_regionPts[i]->setIndex(index);
}
}
void Nasa9PolyMultiTempRegion::updateTemperaturePoly(double T, double* T_poly) const
{
T_poly[0] = T;
@ -168,7 +156,7 @@ void Nasa9PolyMultiTempRegion::reportParameters(size_t& n, int& type,
doublereal& pref,
doublereal* const coeffs) const
{
n = m_index;
n = 0;
type = NASA9MULTITEMP;
tlow = m_lowT;
thigh = m_highT;

7
src/thermo/NasaPoly2.cpp
View file

@ -6,13 +6,10 @@ namespace Cantera {
void NasaPoly2::validate(const std::string& name)
{
size_t offset = mnp_low.speciesIndex();
double cp_low, h_low, s_low;
double cp_high, h_high, s_high;
mnp_low.updatePropertiesTemp(m_midT, &cp_low - offset,
&h_low - offset, &s_low - offset);
mnp_high.updatePropertiesTemp(m_midT, &cp_high - offset,
&h_high - offset, &s_high - offset);
mnp_low.updatePropertiesTemp(m_midT, &cp_low, &h_low, &s_low);
mnp_high.updatePropertiesTemp(m_midT, &cp_high, &h_high, &s_high);
double delta = cp_low - cp_high;
if (fabs(delta/(fabs(cp_low)+1.0E-4)) > 0.001) {

473
src/thermo/NasaThermo.cpp
View file

@ -1,473 +0,0 @@
/*!
* @file NasaThermo.cpp Implementation of class Cantera::NasaThermo
*/
#include "NasaThermo.h"
#include "cantera/numerics/DenseMatrix.h"
#include "cantera/numerics/ctlapack.h"
namespace Cantera
{
NasaThermo::NasaThermo() :
ID(NASA),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_ngroups(0)
{
warn_deprecated("class NasaThermo", "To be removed after "
"Cantera 2.2. Use GeneralSpeciesThermo instead.");
m_t.resize(6);
}
NasaThermo::NasaThermo(const NasaThermo& right) :
ID(NASA),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_ngroups(0) {
*this = right;
}
NasaThermo& NasaThermo::operator=(const NasaThermo& right)
{
/*
* Check for self assignment.
*/
if (this == &right) {
return *this;
}
SpeciesThermo::operator=(right);
m_high = right.m_high;
m_low = right.m_low;
m_index = right.m_index;
m_tmid = right.m_tmid;
m_tlow_max = right.m_tlow_max;
m_thigh_min = right.m_thigh_min;
m_tlow = right.m_tlow;
m_thigh = right.m_thigh;
m_p0 = right.m_p0;
m_ngroups = right.m_ngroups;
m_t = right.m_t;
m_group_map = right.m_group_map;
m_posInGroup_map = right.m_posInGroup_map;
m_name = right.m_name;
return *this;
}
void NasaThermo::install(const std::string& name, size_t index, int type,
const doublereal* c,
doublereal min_temp, doublereal max_temp,
doublereal ref_pressure)
{
if (type != NASA) {
throw CanteraError("NasaThermo::install",
"Incompatible thermo parameterization: Got " +
int2str(type) + " but " + int2str(NASA) +
" was expected.");
}
m_name[index] = name;
int imid = int(c[0]); // midpoint temp converted to integer
int igrp = m_index[imid]; // has this value been seen before?
if (igrp == 0) { // if not, prepare new group
std::vector<NasaPoly1> v;
m_high.push_back(v);
m_low.push_back(v);
m_tmid.push_back(c[0]);
m_index[imid] = igrp = static_cast<int>(m_high.size());
m_ngroups++;
}
m_group_map[index] = igrp;
m_posInGroup_map[index] = (int) m_low[igrp-1].size();
doublereal tlow = min_temp;
doublereal tmid = c[0];
doublereal thigh = max_temp;
vector_fp chigh(c+8, c+15);
vector_fp clow(c+1, c+8);
checkContinuity(name, tmid, &clow[0], &chigh[0]);
m_high[igrp-1].push_back(NasaPoly1(index, tmid, thigh,
ref_pressure, &chigh[0]));
m_low[igrp-1].push_back(NasaPoly1(index, tlow, tmid,
ref_pressure, &clow[0]));
m_tlow_max = std::max(tlow, m_tlow_max);
m_thigh_min = std::min(thigh, m_thigh_min);
if (m_tlow.size() < index + 1) {
m_tlow.resize(index + 1, tlow);
m_thigh.resize(index + 1, thigh);
}
m_tlow[index] = tlow;
m_thigh[index] = thigh;
if (m_p0 < 0.0) {
m_p0 = ref_pressure;
} else if (fabs(m_p0 - ref_pressure) > 0.1) {
std::string logmsg = " ERROR NasaThermo: New Species, " + name + ", has a different reference pressure, "
+ fp2str(ref_pressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n";
writelog(logmsg);
logmsg = " This is now a fatal error\n";
writelog(logmsg);
throw CanteraError("install()", "species have different reference pressures");
}
m_p0 = ref_pressure;
markInstalled(index);
}
void NasaThermo::update_one(size_t k, doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const
{
m_t[0] = t;
m_t[1] = t*t;
m_t[2] = m_t[1]*t;
m_t[3] = m_t[2]*t;
m_t[4] = 1.0/t;
m_t[5] = log(t);
size_t grp = getValue(m_group_map, k);
size_t pos = getValue(m_posInGroup_map, k);
const std::vector<NasaPoly1> &mlg = m_low[grp-1];
const NasaPoly1* nlow = &(mlg[pos]);
doublereal tmid = nlow->maxTemp();
if (t < tmid) {
nlow->updateProperties(&m_t[0], cp_R, h_RT, s_R);
} else {
const std::vector<NasaPoly1> &mhg = m_high[grp-1];
const NasaPoly1* nhigh = &(mhg[pos]);
nhigh->updateProperties(&m_t[0], cp_R, h_RT, s_R);
}
}
void NasaThermo::update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const
{
// load functions of temperature into m_t vector
m_t[0] = t;
m_t[1] = t*t;
m_t[2] = m_t[1]*t;
m_t[3] = m_t[2]*t;
m_t[4] = 1.0/t;
m_t[5] = log(t);
// iterate over the groups
std::vector<NasaPoly1>::const_iterator _begin, _end;
for (int i = 0; i != m_ngroups; i++) {
if (t > m_tmid[i]) {
_begin = m_high[i].begin();
_end = m_high[i].end();
} else {
_begin = m_low[i].begin();
_end = m_low[i].end();
}
for (; _begin != _end; ++_begin) {
_begin->updateProperties(&m_t[0], cp_R, h_RT, s_R);
}
}
}
void NasaThermo::reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp,
doublereal& maxTemp,
doublereal& refPressure) const
{
type = reportType(index);
if (type == NASA) {
size_t grp = getValue(m_group_map, index);
size_t pos = getValue(m_posInGroup_map, index);
const std::vector<NasaPoly1> &mlg = m_low[grp-1];
const std::vector<NasaPoly1> &mhg = m_high[grp-1];
const NasaPoly1* lowPoly = &(mlg[pos]);
const NasaPoly1* highPoly = &(mhg[pos]);
int itype = NASA;
doublereal tmid = lowPoly->maxTemp();
c[0] = tmid;
size_t n;
double ttemp;
lowPoly->reportParameters(n, itype, minTemp, ttemp, refPressure,
c + 1);
if (n != index) {
throw CanteraError("NasaThermo::reportParams", "Index mismatch");
}
if (itype != NASA1) {
throw CanteraError("NasaThermo::reportParams",
"Thermo type mismatch for low-T polynomial");
}
highPoly->reportParameters(n, itype, ttemp, maxTemp, refPressure,
c + 8);
if (n != index) {
throw CanteraError("NasaThermo::reportParams", "Index mismatch");
}
if (itype != NASA1) {
throw CanteraError("NasaThermo::reportParams",
"Thermo type mismatch for high-T polynomial");
}
} else {
throw CanteraError("NasaThermo::reportParams", "Thermo type mismatch");
}
}
doublereal NasaThermo::reportOneHf298(const size_t k) const
{
size_t grp = getValue(m_group_map, k);
size_t pos = getValue(m_posInGroup_map, k);
const std::vector<NasaPoly1> &mlg = m_low[grp-1];
const NasaPoly1* nlow = &(mlg[pos]);
doublereal tmid = nlow->maxTemp();
if (298.15 <= tmid) {
return nlow->reportHf298(0);
} else {
const std::vector<NasaPoly1> &mhg = m_high[grp-1];
const NasaPoly1* nhigh = &(mhg[pos]);
return nhigh->reportHf298(0);
}
}
void NasaThermo::modifyOneHf298(const size_t k, const doublereal Hf298New)
{
size_t grp = getValue(m_group_map, k);
size_t pos = getValue(m_posInGroup_map, k);
std::vector<NasaPoly1> &mlg = m_low[grp-1];
NasaPoly1* nlow = &(mlg[pos]);
std::vector<NasaPoly1> &mhg = m_high[grp-1];
NasaPoly1* nhigh = &(mhg[pos]);
doublereal tmid = nlow->maxTemp();
double hnow = reportOneHf298(k);
double delH = Hf298New - hnow;
if (298.15 <= tmid) {
nlow->modifyOneHf298(k, Hf298New);
double h = nhigh->reportHf298(0);
double hnew = h + delH;
nhigh->modifyOneHf298(k, hnew);
} else {
nhigh->modifyOneHf298(k, Hf298New);
double h = nlow->reportHf298(0);
double hnew = h + delH;
nlow->modifyOneHf298(k, hnew);
}
}
doublereal NasaThermo::cp_R(double t, const doublereal* c)
{
return poly4(t, c+2);
}
doublereal NasaThermo::enthalpy_RT(double t, const doublereal* c) {
return c[2] + 0.5*c[3]*t + 1.0/3.0*c[4]*t*t
+ 0.25*c[5]*t*t*t + 0.2*c[6]*t*t*t*t
+ c[0]/t;
}
doublereal NasaThermo::entropy_R(double t, const doublereal* c) {
return c[2]*log(t) + c[3]*t + 0.5*c[4]*t*t
+ 1.0/3.0*c[5]*t*t*t + 0.25*c[6]*t*t*t*t
+ c[1];
}
doublereal NasaThermo::checkContinuity(const std::string& name, double tmid,
doublereal* clow, doublereal* chigh)
{
// heat capacity
doublereal cplow = cp_R(tmid, clow);
doublereal cphigh = cp_R(tmid, chigh);
doublereal delta = cplow - cphigh;
doublereal maxError = std::abs(delta);
if (fabs(delta/(fabs(cplow)+1.0E-4)) > 0.001) {
writelog("\n\n**** WARNING ****\nFor species "+name+
", discontinuity in cp/R detected at Tmid = "
+fp2str(tmid)+"\n");
writelog("\tValue computed using low-temperature polynomial: "
+fp2str(cplow)+".\n");
writelog("\tValue computed using high-temperature polynomial: "
+fp2str(cphigh)+".\n");
}
// enthalpy
doublereal hrtlow = enthalpy_RT(tmid, clow);
doublereal hrthigh = enthalpy_RT(tmid, chigh);
delta = hrtlow - hrthigh;
maxError = std::max(std::abs(delta), maxError);
if (fabs(delta/(fabs(hrtlow)+cplow*tmid)) > 0.001) {
writelog("\n\n**** WARNING ****\nFor species "+name+
", discontinuity in h/RT detected at Tmid = "
+fp2str(tmid)+"\n");
writelog("\tValue computed using low-temperature polynomial: "
+fp2str(hrtlow)+".\n");
writelog("\tValue computed using high-temperature polynomial: "
+fp2str(hrthigh)+".\n");
}
// entropy
doublereal srlow = entropy_R(tmid, clow);
doublereal srhigh = entropy_R(tmid, chigh);
delta = srlow - srhigh;
maxError = std::max(std::abs(delta), maxError);
if (fabs(delta/(fabs(srlow)+cplow)) > 0.001) {
writelog("\n\n**** WARNING ****\nFor species "+name+
", discontinuity in s/R detected at Tmid = "
+fp2str(tmid)+"\n");
writelog("\tValue computed using low-temperature polynomial: "
+fp2str(srlow)+".\n");
writelog("\tValue computed using high-temperature polynomial: "
+fp2str(srhigh)+".\n");
}
return maxError;
}
void NasaThermo::fixDiscontinuities(doublereal Tlow, doublereal Tmid,
doublereal Thigh, doublereal* clow,
doublereal* chigh)
{
// The thermodynamic parameters can be written in terms nondimensionalized
// coefficients A[i] and the nondimensional temperature t = T/Tmid as:
//
// C_low(t) = A[0] + A[i] * t**i
// H_low(t) = A[0] + A[i] / (i+1) * t**i + A[5] / t
// S_low(t) = A[0]*ln(t) + A[i] / i * t**i + A[6]
//
// where the implicit sum is over the range 1 <= i <= 4 and the
// nondimensional coefficients are related to the dimensional coefficients
// a[i] by:
//
// A[0] = a[0]
// A[i] = Tmid**i * a[i], 1 <= i <= 4
// A[5] = a[5] / Tmid
// A[6] = a[6] + a[0] * ln(Tmid)
//
// and corresponding relationships hold for the high-temperature
// polynomial coefficients B[i]. This nondimensionalization is necessary
// in order for the resulting matrix to be well-conditioned.
//
// The requirement that C_low(1) = C_high(1) is satisfied by:
//
// B[0] = A[0] + (A[i] - B[i])
// C_high(t) = A[0] + (A[i] + B[i] * t**i - 1)
//
// The requirement that H_low(1) = H_high(1) is satisfied by:
//
// B[5] = A[5] + (i / (i+1) * (B[i] - A[i]))
// H_high(t) = A[0] + A[5] / t + (1 - i / (i+1) / t) * A[i] +
// (t**i / (i+1) - 1 + i / (i+1) / t) * B[i]
//
// The requirement that S_low(1) = S_high(1) is satisfied by:
//
// B[6] = A[6] + (A[i] - B[i]) / i
// S_high(t) = A[0] * ln(t) + A[6] + (ln(t) + 1 / i) * A[i] +
// (-ln(t) + t**i / i - 1 / i) * B[i]
// Formulate a linear least squares problem for the nondimensionalized
// coefficients. In the system of equations M*x = b:
// - each row of M consists of the factors in one of the above equations
// for C_low, H_high, etc. evaluated at some temperature between Tlow
// and Thigh
// - x is a vector of the 11 independent coefficients (A[0] through A[6]
// and B[1] through B[4])
// - B is a vector of the corresponding value of C, H, or S computed using
// the original polynomial.
const size_t nTemps = 12;
const size_t nCols = 11; // number of independent coefficients
const size_t nRows = 3*nTemps; // Evaluate C, H, and S at each temperature
DenseMatrix M(nRows, nCols, 0.0);
vector_fp b(nRows);
doublereal sqrtDeltaT = sqrt(Thigh) - sqrt(Tlow);
vector_fp tpow(5);
for (size_t j = 0; j < nTemps; j++) {
double T = pow(sqrt(Tlow) + sqrtDeltaT * j / (nTemps - 1.0), 2);
double t = T / Tmid; // non-dimensionalized temperature
double logt = std::log(t);
size_t n = 3 * j; // row index
for (int i = 1; i <= 4; i++) {
tpow[i] = pow(t, i);
}
// row n: Cp/R
// row n+1: H/RT
// row n+2: S/R
// columns 0 through 6 are for the low-T coefficients
// columns 7 through 10 are for the independent high-T coefficients
M(n, 0) = 1.0;
M(n+1,0) = 1.0;
M(n+2,0) = logt;
M(n+1,5) = 1.0 / t;
M(n+2,6) = 1.0;
if (t <= 1.0) {
for (int i = 1; i <= 4; i++) {
M(n,i) = tpow[i];
M(n+1,i) = tpow[i] / (i+1);
M(n+2,i) = tpow[i] / i;
}
b[n] = cp_R(T, clow);
b[n+1] = enthalpy_RT(T, clow);
b[n+2] = entropy_R(T, clow);
} else {
for (int i = 1; i <= 4; i++) {
M(n,i) = 1.0;
M(n,i+6) = tpow[i] - 1.0;
M(n+1,i) = 1 - i / ((i + 1.0) * t);
M(n+1,i+6) = -1 + tpow[i] / (i+1) + i / ((i+1) * t);
M(n+2,i) = logt + 1.0 / i;
M(n+2,i+6) = -logt + (tpow[i] - 1.0) / i;
}
b[n] = cp_R(T, chigh);
b[n+1] = enthalpy_RT(T, chigh);
b[n+2] = entropy_R(T, chigh);
}
}
// Solve the least squares problem
vector_fp sigma(nRows);
size_t rank;
int info;
vector_fp work(1);
int lwork = -1;
// First get the desired size of the work array
ct_dgelss(nRows, nCols, 1, &M(0,0), nRows, &b[0], nRows,
&sigma[0], -1, rank, &work[0], lwork, info);
work.resize(static_cast<size_t>(work[0]));
lwork = static_cast<int>(work[0]);
ct_dgelss(nRows, nCols, 1, &M(0,0), nRows, &b[0], nRows,
&sigma[0], -1, rank, &work[0], lwork, info);
AssertTrace(info == 0);
AssertTrace(rank == nCols);
AssertTrace(sigma[0] / sigma[10] < 1e20); // condition number
// Compute the full set of nondimensionalized coefficients
// (dgelss returns the solution of M*x = b in b).
// Note that clow and chigh store the coefficients in the order:
// clow = [a[5], a[6], a[0], a[1], a[2], a[3], a[4]]
clow[2] = chigh[2] = b[0];
clow[0] = chigh[0] = b[5];
clow[1] = chigh[1] = b[6];
for (int i = 1; i <= 4; i++) {
clow[2+i] = b[i];
chigh[2+i] = b[6+i];
chigh[2] += clow[2+i] - chigh[2+i];
chigh[0] += i / (i + 1.0) * (chigh[2+i] - clow[2+i]);
chigh[1] += (clow[2+i] - chigh[2+i]) / i;
}
// redimensionalize
for (int i = 1; i <= 4; i++) {
clow[2+i] /= pow(Tmid, i);
chigh[2+i] /= pow(Tmid, i);
}
clow[0] *= Tmid;
chigh[0] *= Tmid;
clow[1] -= clow[2] * std::log(Tmid);
chigh[1] -= chigh[2] * std::log(Tmid);
}
}

293
src/thermo/NasaThermo.h
View file

@ -1,293 +0,0 @@
/**
* @file NasaThermo.h
* Header for the 2 regime 7 coefficient NASA thermodynamic
* polynomials for multiple species in a phase, derived from the
* \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref mgrsrefcalc and
* \link Cantera::NasaThermo NasaThermo\endlink).
*/
// Copyright 2003 California Institute of Technology
#ifndef CT_NASATHERMO_H
#define CT_NASATHERMO_H
#include "cantera/thermo/SpeciesThermoMgr.h"
#include "cantera/thermo/NasaPoly1.h"
namespace Cantera
{
/**
* A species thermodynamic property manager for the NASA
* polynomial parameterization with two temperature ranges.
*
* This class is designed to efficiently evaluate the properties
* of a large number of species with the NASA parameterization.
*
* The original NASA polynomial parameterization expressed the
* heat capacity as a fourth-order polynomial in temperature, with
* separate coefficients for each of two temperature ranges. (The
* newer NASA format adds coefficients for 1/T and 1/T^2, and
* allows multiple temperature ranges.) This class is designed for
* use with the original parameterization, which is used, for
* example, by the Chemkin software package.
*
* In many cases, the midpoint temperature is the same for many
* species. To take advantage of this, class NasaThermo groups
* species with a common midpoint temperature, so that checking
* which range the desired temperature is in need be done only
* once for each group.
*
* @note There is a special CTML element for entering the
* coefficients of this parameterization.
* @see importCTML
*
* @ingroup mgrsrefcalc
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo instead.
*/
class NasaThermo : public SpeciesThermo
{
public:
NasaThermo();
NasaThermo(const NasaThermo& right);
NasaThermo& operator=(const NasaThermo& right);
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const {
NasaThermo* nt = new NasaThermo(*this);
return (SpeciesThermo*) nt;
}
//! install a new species thermodynamic property
//! parameterization for one species.
/*!
* @param name Name of the species
* @param index The 'update' method will update the property values for
* this species at position i index in the property
* arrays.
* @param type int flag specifying the type of parameterization to be
* installed.
* @param c vector of coefficients for the parameterization.
* - c[0] midpoint temperature
* - c[1] - c[7] coefficients for low T range
* - c[8] - c[14] coefficients for high T range
* @param min_temp minimum temperature for which this parameterization
* is valid.
* @param max_temp maximum temperature for which this parameterization
* is valid.
* @param ref_pressure standard-state pressure for this parameterization.
* @see speciesThermoTypes.h
*/
virtual void install(const std::string& name, size_t index, int type,
const doublereal* c,
doublereal min_temp, doublereal max_temp,
doublereal ref_pressure);
virtual void install_STIT(size_t index, shared_ptr<SpeciesThermoInterpType> stit_ptr) {
throw CanteraError("install_STIT", "not implemented");
}
//! Like update(), but only updates the single species k.
/*!
* @param k species index
* @param t Temperature (Kelvin)
* @param cp_R Vector of Dimensionless heat capacities. (length m_kk).
* @param h_RT Vector of Dimensionless enthalpies. (length m_kk).
* @param s_R Vector of Dimensionless entropies. (length m_kk).
*/
virtual void update_one(size_t k, doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const;
virtual void update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const;
virtual doublereal minTemp(size_t k=npos) const {
if (k == npos) {
return m_tlow_max;
} else {
return m_tlow[k];
}
}
virtual doublereal maxTemp(size_t k=npos) const {
if (k == npos) {
return m_thigh_min;
} else {
return m_thigh[k];
}
}
virtual doublereal refPressure(size_t k=npos) const {
return m_p0;
}
virtual int reportType(size_t index) const {
return NASA;
}
/*!
* This utility function reports back the type of
* parameterization and all of the parameters for the
* species, index.
*
* @param index Species index
* @param type Integer type of the standard type
* @param c Vector of coefficients used to set the
* parameters for the standard state.
* For the NASA object, there are 15 coefficients.
* @param minTemp output - Minimum temperature
* @param maxTemp output - Maximum temperature
* @param refPressure output - reference pressure (Pa).
*/
virtual void reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp,
doublereal& maxTemp,
doublereal& refPressure) const;
virtual doublereal reportOneHf298(const size_t k) const;
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New);
//! Initialized to the type of parameterization
/*!
* Note, this value is used in some template functions
*/
const int ID;
protected:
//! Vector of vector of NasaPoly1's for the high temp region.
/*!
* This is the high temp region representation.
* The first Length is equal to the number of groups.
* The second vector is equal to the number of species
* in that particular group.
*/
std::vector<std::vector<NasaPoly1> > m_high;
//! Vector of vector of NasaPoly1's for the low temp region.
/*!
* This is the low temp region representation.
* The first Length is equal to the number of groups.
* The second vector is equal to the number of species
* in that particular group.
*/
std::vector<std::vector<NasaPoly1> > m_low;
//! Map between the midpoint temperature, as an int, to the group number
/*!
* Length is equal to the number of groups. Only used in the setup.
*/
std::map<int, int> m_index;
//! Vector of log temperature limits
/*!
* Length is equal to the number of groups.
*/
vector_fp m_tmid;
//! Maximum value of the low temperature limit
doublereal m_tlow_max;
//! Minimum value of the high temperature limit
doublereal m_thigh_min;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of species
*/
vector_fp m_tlow;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of species
*/
vector_fp m_thigh;
//! Reference pressure (Pa)
/*!
* all species must have the same reference pressure.
*/
doublereal m_p0;
//! number of groups
int m_ngroups;
//! Vector of temperature polynomials
mutable vector_fp m_t;
/*!
* This map takes as its index, the species index in the phase.
* It returns the group index, where the temperature polynomials
* for that species are stored. group indices start at 1,
* so a decrement is always performed to access vectors.
*/
std::map<size_t, size_t> m_group_map;
/*!
* This map takes as its index, the species index in the phase.
* It returns the position index within the group, where the
* temperature polynomials for that species are stored.
*/
std::map<size_t, size_t> m_posInGroup_map;
//! Species name as a function of the species index
std::map<size_t, std::string> m_name;
protected:
//! Compute the nondimensional heat capacity using the given NASA polynomial
/*!
* @param t temperature
* @param c coefficient array
*/
doublereal cp_R(double t, const doublereal* c);
//! Compute the nondimensional enthalpy using the given NASA polynomial
/*!
* @param t temperature
* @param c coefficient array
*/
doublereal enthalpy_RT(double t, const doublereal* c);
//! Compute the nondimensional entropy using the given NASA polynomial
/*!
* @param t temperature
* @param c coefficient array
*/
doublereal entropy_R(double t, const doublereal* c);
//! Adjust polynomials to be continuous at the midpoint temperature.
/*!
* Check to see if the provided coefficients are nearly continuous. Adjust
* the values to get more precise continuity to avoid convergence
* issues with algorithms that expect these quantities to be continuous.
*
* @param name string name of species
* @param tmid Mid temperature, between the two temperature regions
* @param clow coefficients for lower temperature region
* @param chigh coefficients for higher temperature region
*/
double checkContinuity(const std::string& name, double tmid,
doublereal* clow, doublereal* chigh);
//! Adjust polynomials to be continuous at the midpoint temperature.
/*!
* We seek a set of coefficients for the low- and high-temperature
* polynomials which are continuous in Cp, H, and S at the midpoint while
* minimizing the difference between the values in Cp, H, and S over the
* entire valid temperature range. To do this, we formulate a linear
* least-squares problem to be solved for 11 of the 14 coefficients, with
* the remaining 3 coefficients eliminated in the process of satisfying
* the continuity constraints.
*
* @param Tlow Minimum temperature at which the low-T polynomial is valid
* @param Tmid Mid temperature, between the two temperature regions
* @param Thigh Maximum temperature at which the high-T polynomial is valid
* @param clow coefficients for lower temperature region
* @param chigh coefficients for higher temperature region
*/
void fixDiscontinuities(doublereal Tlow, doublereal Tmid, doublereal Thigh,
doublereal* clow, doublereal* chigh);
};
}
#endif

133
src/thermo/Phase.cpp
View file

@ -531,18 +531,6 @@ const vector_fp& Phase::molecularWeights() const
return m_molwts;
}
void Phase::getMoleFractionsByName(compositionMap& x) const
{
warn_deprecated("void Phase::getMoleFractionsByName(compositionMap&)",
"To be removed after Cantera 2.2. Use"
" 'compositionMap getMoleFractionsByName(double threshold)'"
" instead");
x.clear();
for (size_t k = 0; k < m_kk; k++) {
x[speciesName(k)] = Phase::moleFraction(k);
}
}
compositionMap Phase::getMoleFractionsByName(double threshold) const
{
compositionMap comp;
@ -778,79 +766,6 @@ size_t Phase::addElement(const std::string& symbol, doublereal weight,
return m_mm-1;
}
void Phase::addElement(const XML_Node& e)
{
warn_deprecated("Phase::addElement(XML_Node&)",
"To be removed after Cantera 2.2.");
doublereal weight = 0.0;
if (e.hasAttrib("atomicWt")) {
weight = fpValue(stripws(e["atomicWt"]));
}
int anum = 0;
if (e.hasAttrib("atomicNumber")) {
anum = atoi(stripws(e["atomicNumber"]).c_str());
}
string symbol = e["name"];
doublereal entropy298 = ENTROPY298_UNKNOWN;
if (e.hasChild("entropy298")) {
XML_Node& e298Node = e.child("entropy298");
if (e298Node.hasAttrib("value")) {
entropy298 = fpValueCheck(stripws(e298Node["value"]));
}
}
if (weight != 0.0) {
addElement(symbol, weight, anum, entropy298);
} else {
addElement(symbol);
}
}
void Phase::addUniqueElement(const std::string& symbol, doublereal weight,
int atomic_number, doublereal entropy298,
int elem_type)
{
warn_deprecated("Phase::addUniqueElement",
"Equivalent to Phase::addElement. "
"To be removed after Cantera 2.2.");
addElement(symbol, weight, atomic_number, entropy298, elem_type);
}
void Phase::addUniqueElement(const XML_Node& e)
{
warn_deprecated("Phase::addUniqueElement",
"To be removed after Cantera 2.2.");
addElement(e);
}
void Phase::addElementsFromXML(const XML_Node& phase)
{
warn_deprecated("Phase::addElementsFromXML",
"Use 'addElements' function. "
"To be removed after Cantera 2.2.");
installElements(*this, phase);
}
void Phase::freezeElements()
{
warn_deprecated("Phase::freezeElements", "To be removed after Cantera 2.2.");
}
bool Phase::elementsFrozen()
{
warn_deprecated("Phase::elementsFrozen", "To be removed after Cantera 2.2.");
return false;
}
size_t Phase::addUniqueElementAfterFreeze(const std::string& symbol,
doublereal weight, int atomicNumber,
doublereal entropy298, int elem_type)
{
warn_deprecated("Phase::addUniqueElementAfterFreeze",
"Equivalent to Phase::addElement. "
"To be removed after Cantera 2.2");
return addElement(symbol, weight, atomicNumber, entropy298, elem_type);
}
bool Phase::addSpecies(shared_ptr<Species> spec) {
m_species[spec->name] = spec;
vector_fp comp(nElements());
@ -937,54 +852,6 @@ bool Phase::addSpecies(shared_ptr<Species> spec) {
return true;
}
void Phase::addSpecies(const std::string& name_, const doublereal* comp,
doublereal charge_, doublereal size_)
{
warn_deprecated("Phase::addSpecies(string, double*, double, double)",
"Use AddSpecies(shared_ptr<Species> spec) instead. To be removed "
"after Cantera 2.2.");
compositionMap cmap;
for (size_t i = 0; i < nElements(); i++) {
if (comp[i]) {
cmap[elementName(i)] = comp[i];
}
}
shared_ptr<Species> sp(new Species(name_, cmap, charge_, size_));
Phase::addSpecies(sp);
}
void Phase::addUniqueSpecies(const std::string& name_, const doublereal* comp,
doublereal charge_, doublereal size_)
{
warn_deprecated("Phase::addUniqueSpecies",
"Use AddSpecies(shared_ptr<Species> spec) instead. To be removed "
"after Cantera 2.2.");
for (size_t k = 0; k < m_kk; k++) {
if (m_speciesNames[k] == name_) {
// We have found a match. Do some compatibility checks.
for (size_t i = 0; i < m_mm; i++) {
if (comp[i] != m_speciesComp[k * m_mm + i]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"compositions: " + name_);
}
}
if (charge_ != m_speciesCharge[k]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"charges: " + name_);
}
if (size_ != m_speciesSize[k]) {
throw CanteraError("addUniqueSpecies",
"Duplicate species have different "
"sizes: " + name_);
}
return;
}
}
addSpecies(name_, comp, charge_, size_);
}
shared_ptr<Species> Phase::species(const std::string& name) const
{
return getValue(m_species, name);

451
src/thermo/ShomateThermo.h
View file

@ -1,451 +0,0 @@
/**
* @file ShomateThermo.h
* Header for the 2 regions Shomate polynomial
* for multiple species in a phase, derived from the
* \link Cantera::SpeciesThermo SpeciesThermo\endlink base class (see \ref mgrsrefcalc and
* \link Cantera::ShomateThermo ShomateThermo\endlink).
*/
// Copyright 2001 California Institute of Technology
#ifndef CT_SHOMATETHERMO_H
#define CT_SHOMATETHERMO_H
#include "cantera/thermo/SpeciesThermoMgr.h"
#include "cantera/thermo/ShomatePoly.h"
#include "cantera/base/global.h"
#include "cantera/base/utilities.h"
namespace Cantera
{
//! A species thermodynamic property manager for the Shomate polynomial parameterization.
/*!
* This is the parameterization used
* in the NIST Chemistry WebBook (http://webbook.nist.gov/chemistry)
* The parameterization assumes there are two temperature regions
* each with its own Shomate polynomial representation, for each
* species in the phase.
*
* \f[
* \tilde{c}_p^0(T) = A + B t + C t^2 + D t^3 + \frac{E}{t^2}
* \f]
* \f[
* \tilde{h}^0(T) = A t + \frac{B t^2}{2} + \frac{C t^3}{3}
+ \frac{D t^4}{4} - \frac{E}{t} + F.
* \f]
* \f[
* \tilde{s}^0(T) = A\ln t + B t + \frac{C t^2}{2}
+ \frac{D t^3}{3} - \frac{E}{2t^2} + G.
* \f]
*
* In the above expressions, the thermodynamic polynomials are expressed
* in dimensional units, but the temperature,\f$ t \f$, is divided by 1000. The
* following dimensions are assumed in the above expressions:
*
* - \f$ \tilde{c}_p^0(T)\f$ = Heat Capacity (J/gmol*K)
* - \f$ \tilde{h}^0(T) \f$ = standard Enthalpy (kJ/gmol)
* - \f$ \tilde{s}^0(T) \f$= standard Entropy (J/gmol*K)
* - \f$ t \f$= temperature (K) / 1000.
*
* Note, the polynomial data (i.e., A, ... , G) is entered in dimensional form.
*
* This is in contrast to the NASA database polynomials which are entered in
* nondimensional form (i.e., NASA parameterizes C_p/R, while Shomate
* parameterizes C_p assuming units of J/gmol*K - and kJ/gmol*K for H).
* Note, also that the H - H_298.15 equation has units of kJ/gmol, because of
* the implicit integration of (t = T 1000), which provides a
* multiplier of 1000 to the Enthalpy equation.
*
* @deprecated To be removed after Cantera 2.2. Use GeneralSpeciesThermo instead.
* @ingroup mgrsrefcalc
*/
class ShomateThermo : public SpeciesThermo
{
public:
//! Initialized to the type of parameterization
/*!
* Note, this value is used in some template functions
*/
const int ID;
//! constructor
ShomateThermo() :
ID(SHOMATE),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_ngroups(0) {
warn_deprecated("class ShomateThermo", "To be removed after "
"Cantera 2.2. Use GeneralSpeciesThermo instead.");
m_t.resize(7);
}
//! Copy Constructor
/*!
* @param right Object to be copied
*/
ShomateThermo(const ShomateThermo& right) :
ID(SHOMATE),
m_tlow_max(0.0),
m_thigh_min(1.e30),
m_p0(-1.0),
m_ngroups(0) {
*this = right;
}
//! Assignment Operator
/*!
* @param right Object to be copied
*/
ShomateThermo& operator=(const ShomateThermo& right) {
if (&right == this) {
return *this;
}
SpeciesThermo::operator=(right);
m_high = right.m_high;
m_low = right.m_low;
m_index = right.m_index;
m_tmid = right.m_tmid;
m_tlow_max = right.m_tlow_max;
m_thigh_min = right.m_thigh_min;
m_tlow = right.m_tlow;
m_thigh = right.m_thigh;
m_p0 = right.m_p0;
m_ngroups = right.m_ngroups;
m_t = right.m_t;
m_group_map = right.m_group_map;
m_posInGroup_map = right.m_posInGroup_map;
return *this;
}
virtual SpeciesThermo* duplMyselfAsSpeciesThermo() const {
return new ShomateThermo(*this);
}
//! Install a new species thermodynamic property
//! parameterization for one species using Shomate polynomials
/*!
* Two temperature regions are assumed.
*
* @param name Name of the species
* @param index Species index
* @param type int flag specifying the type of parameterization to be
* installed.
* @param c Vector of coefficients for the parameterization.
* There are 15 coefficients for the 2-zone Shomate polynomial.
* The first coefficient is the value of Tmid. The next 7
* coefficients are the low temperature range Shomate coefficients.
* The last 7 are the high temperature range Shomate coefficients.
*
* @param minTemp minimum temperature for which this parameterization
* is valid.
* @param maxTemp maximum temperature for which this parameterization
* is valid.
* @param refPressure standard-state pressure for this
* parameterization.
*
* @see ShomatePoly
* @see ShomatePoly2
*/
virtual void install(const std::string& name, size_t index, int type,
const doublereal* c,
doublereal minTemp, doublereal maxTemp,
doublereal refPressure) {
if (type != SHOMATE) {
throw CanteraError("ShomateThermo::install",
"Incompatible thermo parameterization: Got " +
int2str(type) + " but " + int2str(SHOMATE) +
" was expected.");
}
int imid = int(c[0]); // midpoint temp converted to integer
int igrp = m_index[imid]; // has this value been seen before?
if (igrp == 0) { // if not, prepare new group
std::vector<ShomatePoly> v;
m_high.push_back(v);
m_low.push_back(v);
m_tmid.push_back(c[0]);
m_index[imid] = igrp = static_cast<int>(m_high.size());
m_ngroups++;
}
m_group_map[index] = igrp;
m_posInGroup_map[index] = (int) m_low[igrp-1].size();
doublereal tlow = minTemp;
doublereal tmid = c[0];
doublereal thigh = maxTemp;
const doublereal* clow = c + 1;
const doublereal* chigh = c + 8;
m_high[igrp-1].push_back(ShomatePoly(index, tmid, thigh,
refPressure, chigh));
m_low[igrp-1].push_back(ShomatePoly(index, tlow, tmid,
refPressure, clow));
m_tlow_max = std::max(m_tlow_max, tlow);
m_thigh_min = std::min(m_thigh_min, thigh);
if (m_tlow.size() < index + 1) {
m_tlow.resize(index + 1, tlow);
m_thigh.resize(index + 1, thigh);
}
m_tlow[index] = tlow;
m_thigh[index] = thigh;
if (m_p0 < 0.0) {
m_p0 = refPressure;
} else if (fabs(m_p0 - refPressure) > 0.1) {
std::string logmsg = " ERROR ShomateThermo: New Species, " + name
+ ", has a different reference pressure, "
+ fp2str(refPressure) + ", than existing reference pressure, " + fp2str(m_p0) + "\n";
writelog(logmsg);
logmsg = " This is now a fatal error\n";
writelog(logmsg);
throw CanteraError("install()", "Species have different reference pressures");
}
m_p0 = refPressure;
markInstalled(index);
}
virtual void install_STIT(size_t index,
shared_ptr<SpeciesThermoInterpType> stit_ptr) {
throw CanteraError("install_STIT", "not implemented");
}
//! Like update(), but only updates the single species k.
/*!
* @param k species index
* @param t Temperature (Kelvin)
* @param cp_R Vector of Dimensionless heat capacities. (length m_kk).
* @param h_RT Vector of Dimensionless enthalpies. (length m_kk).
* @param s_R Vector of Dimensionless entropies. (length m_kk).
*/
virtual void update_one(size_t k, doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const {
doublereal tt = 1.e-3*t;
m_t[0] = tt;
m_t[1] = tt*tt;
m_t[2] = m_t[1]*tt;
m_t[3] = 1.0/m_t[1];
m_t[4] = log(tt);
m_t[5] = 1.0/GasConstant;
m_t[6] = 1.0/(GasConstant * t);
size_t grp = getValue(m_group_map, k);
size_t pos = getValue(m_posInGroup_map, k);
const std::vector<ShomatePoly> &mlg = m_low[grp-1];
const ShomatePoly* nlow = &(mlg[pos]);
if (t < nlow->maxTemp()) {
nlow->updateProperties(&m_t[0], cp_R, h_RT, s_R);
} else {
const std::vector<ShomatePoly> &mhg = m_high[grp-1];
const ShomatePoly* nhigh = &(mhg[pos]);
nhigh->updateProperties(&m_t[0], cp_R, h_RT, s_R);
}
}
virtual void update(doublereal t, doublereal* cp_R,
doublereal* h_RT, doublereal* s_R) const {
doublereal tt = 1.e-3*t;
m_t[0] = tt;
m_t[1] = tt*tt;
m_t[2] = m_t[1]*tt;
m_t[3] = 1.0/m_t[1];
m_t[4] = log(tt);
m_t[5] = 1.0/GasConstant;
m_t[6] = 1.0/(GasConstant * t);
std::vector<ShomatePoly>::const_iterator _begin, _end;
for (int i = 0; i != m_ngroups; i++) {
if (t > m_tmid[i]) {
_begin = m_high[i].begin();
_end = m_high[i].end();
} else {
_begin = m_low[i].begin();
_end = m_low[i].end();
}
for (; _begin != _end; ++_begin) {
_begin->updateProperties(&m_t[0], cp_R, h_RT, s_R);
}
}
}
virtual doublereal minTemp(size_t k=npos) const {
if (k == npos) {
return m_tlow_max;
} else {
return m_tlow[k];
}
}
virtual doublereal maxTemp(size_t k=npos) const {
if (k == npos) {
return m_thigh_min;
} else {
return m_thigh[k];
}
}
virtual doublereal refPressure(size_t k=npos) const {
return m_p0;
}
virtual int reportType(size_t index) const {
return SHOMATE;
}
virtual void reportParams(size_t index, int& type,
doublereal* const c,
doublereal& minTemp,
doublereal& maxTemp,
doublereal& refPressure) const {
type = reportType(index);
if (type == SHOMATE) {
size_t grp = getValue(m_group_map, index);
size_t pos = getValue(m_posInGroup_map, index);
int itype = SHOMATE;
const std::vector<ShomatePoly> &mlg = m_low[grp-1];
const std::vector<ShomatePoly> &mhg = m_high[grp-1];
const ShomatePoly* lowPoly = &(mlg[pos]);
const ShomatePoly* highPoly = &(mhg[pos]);
doublereal tmid = lowPoly->maxTemp();
c[0] = tmid;
size_t n;
double ttemp;
lowPoly->reportParameters(n, itype, minTemp, ttemp, refPressure,
c + 1);
if (n != index) {
throw CanteraError("ShomateThermo::reportParams",
"Index mismatch in low-T polynomial");
}
if (itype != SHOMATE && itype != SHOMATE1) {
throw CanteraError("ShomateThermo::reportParams",
"Thermo type mismatch in low-T polynomial");
}
highPoly->reportParameters(n, itype, ttemp, maxTemp,
refPressure, c + 8);
if (n != index) {
throw CanteraError("ShomateThermo::reportParams",
"Index mismatch in high-T polynomial");
}
if (itype != SHOMATE && itype != SHOMATE1) {
throw CanteraError("ShomateThermo::reportParams",
"Thermo type mismatch in high-T polynomial");
}
} else {
throw CanteraError("ShomateThermo::reportParams", "Thermo type mismatch");
}
}
virtual doublereal reportOneHf298(const size_t k) const {
size_t grp = getValue(m_group_map, k);
size_t pos = getValue(m_posInGroup_map, k);
const ShomatePoly& nlow = m_low[grp-1][pos];
if (nlow.maxTemp() > 298.15) {
return nlow.reportHf298();
} else {
const ShomatePoly& nhigh = m_high[grp-1][pos];
return nhigh.reportHf298();
}
}
virtual void modifyOneHf298(const size_t k, const doublereal Hf298New) {
size_t grp = m_group_map[k];
size_t pos = m_posInGroup_map[k];
ShomatePoly& nlow = m_low[grp-1][pos];
ShomatePoly& nhigh = m_high[grp-1][pos];
double hnow = reportOneHf298(k);
double delH = Hf298New - hnow;
if (nlow.maxTemp() > 298.15) {
nlow.modifyOneHf298(k, Hf298New);
double h = nhigh.reportHf298(0);
double hnew = h + delH;
nhigh.modifyOneHf298(k, hnew);
} else {
nhigh.modifyOneHf298(k, Hf298New);
double h = nlow.reportHf298(0);
double hnew = h + delH;
nlow.modifyOneHf298(k, hnew);
}
}
protected:
//! Vector of vector of NasaPoly1's for the high temp region.
/*!
* This is the high temp region representation. The first Length is equal
* to the number of groups. The second vector is equal to the number of
* species in that particular group.
*/
std::vector<std::vector<ShomatePoly> > m_high;
//! Vector of vector of NasaPoly1's for the low temp region.
/*!
* This is the low temp region representation. The first Length is equal
* to the number of groups. The second vector is equal to the number of
* species in that particular group.
*/
std::vector<std::vector<ShomatePoly> > m_low;
//! Map between the midpoint temperature, as an int, to the group number
/*!
* Length is equal to the number of groups. Only used in the setup.
*/
std::map<int, int> m_index;
//! Vector of log temperature limits
/*!
* Length is equal to the number of groups.
*/
vector_fp m_tmid;
//! Maximum value of the low temperature limit
doublereal m_tlow_max;
//! Minimum value of the high temperature limit
doublereal m_thigh_min;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of species
*/
vector_fp m_tlow;
//! Vector of low temperature limits (species index)
/*!
* Length is equal to number of species
*/
vector_fp m_thigh;
//! Reference pressure (Pa)
/*!
* all species must have the same reference pressure.
*/
doublereal m_p0;
//! number of groups
int m_ngroups;
//! Vector of temperature polynomials
mutable vector_fp m_t;
/*!
* This map takes as its index, the species index in the phase.
* It returns the group index, where the temperature polynomials
* for that species are stored. group indices start at 1,
* so a decrement is always performed to access vectors.
*/
std::map<size_t, size_t> m_group_map;
/*!
* This map takes as its index, the species index in the phase.
* It returns the position index within the group, where the
* temperature polynomials for that species are stored.
*/
std::map<size_t, size_t> m_posInGroup_map;
};
}
#endif

231
src/thermo/SpeciesThermoFactory.cpp
View file

@ -1,187 +1,32 @@
/**
* @file SpeciesThermoFactory.cpp
* Definitions for factory to build instances of classes that manage the
* standard-state thermodynamic properties of a set of species
* (see \ref spthermo and class \link Cantera::SpeciesThermoFactory SpeciesThermoFactory\endlink);
* Definitions for factory functions to build instances of classes that
* manage the standard-state thermodynamic properties of a set of species
* (see \ref spthermo);
*/
// Copyright 2001 California Institute of Technology
#include "cantera/thermo/SpeciesThermoFactory.h"
#include "cantera/thermo/SpeciesThermo.h"
#include "NasaThermo.h"
#include "ShomateThermo.h"
#include "cantera/thermo/SimpleThermo.h"
#include "cantera/thermo/GeneralSpeciesThermo.h"
#include "cantera/thermo/Mu0Poly.h"
#include "cantera/thermo/Nasa9PolyMultiTempRegion.h"
#include "cantera/thermo/Nasa9Poly1.h"
#include "cantera/thermo/StatMech.h"
#include "cantera/thermo/NasaPoly2.h"
#include "cantera/thermo/ShomatePoly.h"
#include "cantera/thermo/ConstCpPoly.h"
#include "cantera/thermo/AdsorbateThermo.h"
#include "cantera/thermo/SpeciesThermoMgr.h"
#include "cantera/thermo/speciesThermoTypes.h"
#include "cantera/thermo/VPSSMgr.h"
#include "cantera/thermo/VPStandardStateTP.h"
#include "cantera/base/ctml.h"
#include "cantera/base/stringUtils.h"
using namespace std;
namespace Cantera
{
SpeciesThermoFactory* SpeciesThermoFactory::s_factory = 0;
mutex_t SpeciesThermoFactory::species_thermo_mutex;
//! Examine the types of species thermo parameterizations,
//! and return a flag indicating the type of reference state thermo manager
//! that will be needed in order to evaluate them all.
/*!
*
* @param spDataNodeList This vector contains a list
* of species XML nodes that will be in the phase
* @param has_nasa Return int that indicates whether the phase has a NASA polynomial form for one of its species
* @param has_shomate Return int that indicates whether the phase has a SHOMATE polynomial form for one of its species
* @param has_simple Return int that indicates whether the phase has a SIMPLE polynomial form for one of its species
* @param has_other Return int that indicates whether the phase has a form for one of its species that is not one of the ones listed above.
*
* @todo Make sure that spDadta_node is species Data XML node by checking its name is speciesData
* @deprecated
*/
static void getSpeciesThermoTypes(std::vector<XML_Node*> & spDataNodeList,
int& has_nasa, int& has_shomate, int& has_simple,
int& has_other)
{
for (size_t n = 0; n < spDataNodeList.size(); n++) {
XML_Node* spNode = spDataNodeList[n];
if (spNode->hasChild("standardState")) {
string mname = spNode->child("standardState")["model"];
if (mname == "water" || mname == "waterIAPWS") {
has_other = 1;
continue;
}
}
if (spNode->hasChild("thermo")) {
const XML_Node& th = spNode->child("thermo");
if (th.hasChild("NASA")) {
has_nasa = 1;
} else if (th.hasChild("Shomate")) {
has_shomate = 1;
} else if (th.hasChild("MinEQ3")) {
has_shomate = 1;
} else if (th.hasChild("const_cp")) {
has_simple = 1;
} else if (th.hasChild("poly")) {
if (th.child("poly")["order"] == "1") {
has_simple = 1;
} else throw CanteraError("newSpeciesThermo",
"poly with order > 1 not yet supported");
} else if (th.hasChild("Mu0")) {
has_other = 1;
} else if (th.hasChild("NASA9")) {
has_other = 1;
} else if (th.hasChild("NASA9MULTITEMP")) {
has_other = 1;
} else if (th.hasChild("adsorbate")) {
has_other = 1;
} else {
has_other = 1;
}
} else {
throw CanteraError("getSpeciesThermoTypes:",
spNode->attrib("name") + " is missing the thermo XML node");
}
}
}
SpeciesThermoFactory* SpeciesThermoFactory::factory()
{
warn_deprecated("class SpeciesThermoFactory",
"To be removed after Cantera 2.2.");
ScopedLock lock(species_thermo_mutex);
if (!s_factory) {
s_factory = new SpeciesThermoFactory;
}
return s_factory;
}
void SpeciesThermoFactory::deleteFactory()
{
ScopedLock lock(species_thermo_mutex);
delete s_factory;
s_factory = 0;
}
SpeciesThermo* SpeciesThermoFactory::newSpeciesThermo(std::vector<XML_Node*> & spDataNodeList) const
{
warn_deprecated("SpeciesThermoFactory::newSpeciesThermo",
"To be removed after Cantera 2.2. Use class GeneralSpeciesThermo directly.");
int inasa = 0, ishomate = 0, isimple = 0, iother = 0;
try {
getSpeciesThermoTypes(spDataNodeList, inasa, ishomate, isimple, iother);
} catch (UnknownSpeciesThermoModel) {
iother = 1;
popError();
}
if (iother) {
return new GeneralSpeciesThermo();
}
return newSpeciesThermo(NASA*inasa
+ SHOMATE*ishomate + SIMPLE*isimple);
}
SpeciesThermo* SpeciesThermoFactory::newSpeciesThermo(int type) const
{
warn_deprecated("SpeciesThermoFactory::newSpeciesThermo",
"To be removed after Cantera 2.2. Use class GeneralSpeciesThermo directly.");
switch (type) {
case NASA:
return new NasaThermo;
case SHOMATE:
return new ShomateThermo;
case SIMPLE:
return new SimpleThermo;
case NASA + SHOMATE:
return new SpeciesThermoDuo<NasaThermo, ShomateThermo>;
case NASA + SIMPLE:
return new SpeciesThermoDuo<NasaThermo, SimpleThermo>;
case SHOMATE + SIMPLE:
return new SpeciesThermoDuo<ShomateThermo, SimpleThermo>;
default:
throw UnknownSpeciesThermo("SpeciesThermoFactory::newSpeciesThermo",
type);
return 0;
}
}
SpeciesThermo* SpeciesThermoFactory::newSpeciesThermoManager(const std::string& stype) const
{
warn_deprecated("SpeciesThermoFactory::newSpeciesThermo",
"To be removed after Cantera 2.2. Use class GeneralSpeciesThermo directly.");
std::string ltype = lowercase(stype);
if (ltype == "nasa") {
return new NasaThermo;
} else if (ltype == "shomate") {
return new ShomateThermo;
} else if (ltype == "simple" || ltype == "constant_cp") {
return new SimpleThermo;
} else if (ltype == "nasa_shomate_duo") {
return new SpeciesThermoDuo<NasaThermo, ShomateThermo>;
} else if (ltype == "nasa_simple_duo") {
return new SpeciesThermoDuo<NasaThermo, SimpleThermo>;
} else if (ltype == "shomate_simple_duo") {
return new SpeciesThermoDuo<ShomateThermo, SimpleThermo>;
} else if (ltype == "general") {
return new GeneralSpeciesThermo();
} else if (ltype == "") {
return (SpeciesThermo*) 0;
} else {
throw UnknownSpeciesThermo("SpeciesThermoFactory::newSpeciesThermoManager",
stype);
}
return (SpeciesThermo*) 0;
}
SpeciesThermoInterpType* newSpeciesThermoInterpType(int type, double tlow,
double thigh, double pref, const double* coeffs)
@ -561,37 +406,7 @@ static SpeciesThermoInterpType* newAdsorbateThermoFromXML(const XML_Node& f)
coeffs[0] = static_cast<double>(freqs.size());
coeffs[1] = getFloat(f, "binding_energy", "toSI");
copy(freqs.begin(), freqs.end(), coeffs.begin() + 2);
return new Adsorbate(0, tmin, tmax, pref, &coeffs[0]);
}
void SpeciesThermoFactory::installThermoForSpecies
(size_t k, const XML_Node& speciesNode, ThermoPhase* th_ptr,
SpeciesThermo& spthermo, const XML_Node* phaseNode_ptr) const
{
shared_ptr<SpeciesThermoInterpType> stit(
newSpeciesThermoInterpType(speciesNode.child("thermo")));
stit->validate(speciesNode["name"]);
spthermo.install_STIT(k, stit);
}
void SpeciesThermoFactory::installVPThermoForSpecies(size_t k,
const XML_Node& speciesNode,
VPStandardStateTP* vp_ptr,
VPSSMgr* vpssmgr_ptr,
SpeciesThermo* spthermo_ptr,
const XML_Node* phaseNode_ptr) const
{
warn_deprecated("SpeciesThermoFactory::installVPThermoForSpecies",
"Call VPStandardStateTP::createInstallPDSS directly.");
// Call the VPStandardStateTP object to install the pressure dependent species
// standard state into the object.
//
// We don't need to pass spthermo_ptr down, because it's already installed
// into vp_ptr.
//
// We don't need to pass vpssmgr_ptr down, because it's already installed
// into vp_ptr.
vp_ptr->createInstallPDSS(k, speciesNode, phaseNode_ptr);
return new Adsorbate(tmin, tmax, pref, &coeffs[0]);
}
SpeciesThermoInterpType* newSpeciesThermoInterpType(const XML_Node& thermo)
@ -626,7 +441,7 @@ SpeciesThermoInterpType* newSpeciesThermoInterpType(const XML_Node& thermo)
std::string model = lowercase(thermo["model"]);
if (model == "mineraleq3") {
if (thermoType != "mineq3") {
throw CanteraError("SpeciesThermoFactory::installThermoForSpecies",
throw CanteraError("newSpeciesThermoInterpType",
"confused: expected MinEQ3");
}
return newShomateForMineralEQ3(*tp[0]);
@ -655,36 +470,4 @@ SpeciesThermoInterpType* newSpeciesThermoInterpType(const XML_Node& thermo)
}
}
SpeciesThermo* newSpeciesThermoMgr(int type, SpeciesThermoFactory* f)
{
warn_deprecated("newSpeciesThermoMgr", "To be removed after Cantera 2.2. "
"Use class GeneralSpeciesThermo directly.");
if (f == 0) {
f = SpeciesThermoFactory::factory();
}
return f->newSpeciesThermo(type);
}
SpeciesThermo* newSpeciesThermoMgr(const std::string& stype,
SpeciesThermoFactory* f)
{
warn_deprecated("newSpeciesThermoMgr", "To be removed after Cantera 2.2. "
"Use class GeneralSpeciesThermo directly.");
if (f == 0) {
f = SpeciesThermoFactory::factory();
}
return f->newSpeciesThermoManager(stype);
}
SpeciesThermo* newSpeciesThermoMgr(std::vector<XML_Node*> spData_nodes,
SpeciesThermoFactory* f)
{
warn_deprecated("newSpeciesThermoMgr", "To be removed after Cantera 2.2. "
"Use class GeneralSpeciesThermo directly.");
if (f == 0) {
f = SpeciesThermoFactory::factory();
}
return f->newSpeciesThermo(spData_nodes);
}
}

48
src/thermo/SpeciesThermoInterpType.cpp
View file

@ -14,40 +14,23 @@ namespace Cantera
SpeciesThermoInterpType::SpeciesThermoInterpType() :
m_lowT(0.0),
m_highT(0.0),
m_Pref(0.0),
m_index(0)
m_Pref(0.0)
{
}
SpeciesThermoInterpType::SpeciesThermoInterpType(size_t n, doublereal tlow,
doublereal thigh,
doublereal pref) :
m_lowT(tlow),
m_highT(thigh),
m_Pref(pref),
m_index(n)
{
warn_deprecated("Constructor SpeciesThermoInterpType(size_t n, ...)",
"Use the constructor which does not take a species index."
" Applies to all classes derived from SpeciesThermoInterpType."
" To be removed after Cantera 2.2.");
}
SpeciesThermoInterpType::SpeciesThermoInterpType(double tlow,
double thigh,
double pref) :
m_lowT(tlow),
m_highT(thigh),
m_Pref(pref),
m_index(0)
m_Pref(pref)
{
}
SpeciesThermoInterpType::SpeciesThermoInterpType(const SpeciesThermoInterpType &b) :
m_lowT(b.m_lowT),
m_highT(b.m_highT),
m_Pref(b.m_Pref),
m_index(b.m_index)
m_Pref(b.m_Pref)
{
}
@ -75,15 +58,6 @@ void SpeciesThermoInterpType::modifyOneHf298(const size_t k,
STITbyPDSS::STITbyPDSS()
{
m_index = npos;
}
STITbyPDSS::STITbyPDSS(size_t k, VPSSMgr* vpssmgr_ptr, PDSS* PDSS_ptr) :
SpeciesThermoInterpType(),
m_vpssmgr_ptr(vpssmgr_ptr),
m_PDSS_ptr(PDSS_ptr)
{
m_index = k;
}
STITbyPDSS::STITbyPDSS(VPSSMgr* vpssmgr_ptr, PDSS* PDSS_ptr) :
@ -109,8 +83,6 @@ STITbyPDSS::duplMyselfAsSpeciesThermoInterpType() const
void STITbyPDSS::initAllPtrs(size_t speciesIndex, VPSSMgr* vpssmgr_ptr,
PDSS* PDSS_ptr)
{
AssertThrow(speciesIndex == m_index,
"STITbyPDSS::initAllPtrs internal confusion");
m_vpssmgr_ptr = vpssmgr_ptr;
m_PDSS_ptr = PDSS_ptr;
}
@ -149,11 +121,9 @@ void STITbyPDSS::updatePropertiesTemp(const doublereal temp,
doublereal* s_R) const
{
m_PDSS_ptr->setTemperature(temp);
AssertThrowMsg(m_index != npos, "STITbyPDSS::updatePropertiesTemp",
"object was probably not installed correctly");
h_RT[m_index] = m_PDSS_ptr->enthalpy_RT_ref();
cp_R[m_index] = m_PDSS_ptr->cp_R_ref();
s_R[m_index] = m_PDSS_ptr->entropy_R_ref();
*h_RT = m_PDSS_ptr->enthalpy_RT_ref();
*cp_R = m_PDSS_ptr->cp_R_ref();
*s_R = m_PDSS_ptr->entropy_R_ref();
}
void STITbyPDSS::reportParameters(size_t& index, int& type,
@ -161,10 +131,10 @@ void STITbyPDSS::reportParameters(size_t& index, int& type,
doublereal& refPressure,
doublereal* const coeffs) const
{
index = m_index;
index = 0;
type = PDSS_TYPE;
minTemp = m_vpssmgr_ptr->minTemp(m_index);
maxTemp = m_vpssmgr_ptr->maxTemp(m_index);
minTemp = m_vpssmgr_ptr->minTemp();
maxTemp = m_vpssmgr_ptr->maxTemp();
refPressure = m_PDSS_ptr->refPressure();
}

11
src/thermo/StatMech.cpp
View file

@ -6,6 +6,7 @@
// Copyright 2007 Sandia National Laboratories
#include "cantera/thermo/StatMech.h"
#include "cantera/base/ctexceptions.h"
#include <iostream>
namespace Cantera
@ -18,7 +19,7 @@ StatMech::StatMech(int n, doublereal tlow, doublereal thigh,
doublereal pref,
const doublereal* coeffs,
const std::string& my_name) :
SpeciesThermoInterpType(n, tlow, thigh, pref),
SpeciesThermoInterpType(tlow, thigh, pref),
sp_name(my_name)
{
// should error on zero -- cannot take ln(0)
@ -591,9 +592,9 @@ void StatMech::updateProperties(const doublereal* tt,
// return the computed properties in the location in the output
// arrays for this species
cp_R[m_index] = cpdivR;
h_RT[m_index] = hdivRT;
s_R [m_index] = sdivR;
*cp_R = cpdivR;
*h_RT = hdivRT;
*s_R = sdivR;
}
void StatMech::updatePropertiesTemp(const doublereal temp,
@ -612,7 +613,7 @@ void StatMech::reportParameters(size_t& n, int& type,
{
species* s;
n = m_index;
n = 0;
type = STAT;
tlow = m_lowT;
thigh = m_highT;

79
src/thermo/StoichSubstanceSSTP.cpp
View file

@ -255,83 +255,4 @@ void StoichSubstanceSSTP::setParametersFromXML(const XML_Node& eosdata)
setDensity(getFloat(eosdata, "density", "toSI"));
}
// ------ Methods of class electrodeElectron ------
electrodeElectron::electrodeElectron():
StoichSubstanceSSTP()
{
warn_deprecated("Class electrodeElectron",
"To be removed after Cantera 2.2.");
}
electrodeElectron::electrodeElectron(const std::string& infile, std::string id_) :
StoichSubstanceSSTP()
{
XML_Node* root = get_XML_File(infile);
if (id_ == "-") {
id_ = "";
}
XML_Node* xphase = get_XML_NameID("phase", std::string("#")+id_, root);
if (!xphase) {
throw CanteraError("electrodeElectron::electrodeElectron",
"Couldn't find phase name in file:" + id_);
}
// Check the model name to ensure we have compatibility
if (xphase->child("thermo")["model"] != "electrodeElectron") {
throw CanteraError("electrodeElectron::electrodeElectron",
"thermo model attribute must be electrodeElectron");
}
importPhase(*xphase, this);
}
electrodeElectron::electrodeElectron(XML_Node& xmlphase, const std::string& id_) :
StoichSubstanceSSTP()
{
if (id_ != "" && id_ != xmlphase["id"]) {
throw CanteraError("electrodeElectron::electrodeElectron",
"id's don't match");
}
if (xmlphase.child("thermo")["model"] != "electrodeElectron") {
throw CanteraError("electrodeElectron::electrodeElectron",
"thermo model attribute must be electrodeElectron");
}
importPhase(xmlphase, this);
}
electrodeElectron::electrodeElectron(const electrodeElectron& right) :
StoichSubstanceSSTP()
{
*this = right;
}
electrodeElectron&
electrodeElectron::operator=(const electrodeElectron& right)
{
if (&right != this) {
StoichSubstanceSSTP::operator=(right);
}
return *this;
}
void electrodeElectron::setParametersFromXML(const XML_Node& eosdata)
{
if (eosdata["model"] != "electrodeElectron") {
throw CanteraError("electrodeElectron::setParametersFromXML",
"thermo model attribute must be electrodeElectron");
}
}
void electrodeElectron::initThermoXML(XML_Node& phaseNode, const std::string& id_)
{
doublereal rho = 10.0;
setDensity(rho);
SingleSpeciesTP::initThermoXML(phaseNode, id_);
}
void electrodeElectron::setParameters(int n, doublereal* const c)
{
doublereal rho = 10.0;
setDensity(rho);
}
}

22
src/thermo/ThermoFactory.cpp
View file

@ -313,8 +313,7 @@ static void formSpeciesXMLNodeList(std::vector<XML_Node*> &spDataNodeList,
}
}
bool importPhase(XML_Node& phase, ThermoPhase* th,
SpeciesThermoFactory* spfactory)
void importPhase(XML_Node& phase, ThermoPhase* th)
{
// Check the the supplied XML node in fact represents a phase.
if (phase.name() != "phase") {
@ -490,8 +489,6 @@ bool importPhase(XML_Node& phase, ThermoPhase* th,
// that requires the XML phase object
std::string id = "";
th->initThermoXML(phase, id);
return true;
}
void installElements(Phase& th, const XML_Node& phaseNode)
@ -559,23 +556,6 @@ void installElements(Phase& th, const XML_Node& phaseNode)
}
}
bool installSpecies(size_t k, const XML_Node& s, thermo_t& th,
SpeciesThermo* spthermo_ptr, int rule,
XML_Node* phaseNode_ptr,
VPSSMgr* vpss_ptr,
SpeciesThermoFactory* factory)
{
warn_deprecated("installSpecies", "Use newSpecies and addSpecies. For"
" VPStandardStateTP phases, call createInstallPDSS as well."
" To be removed after Cantera 2.2.");
th.addSpecies(newSpecies(s));
VPStandardStateTP* vp_ptr = dynamic_cast<VPStandardStateTP*>(&th);
if (vp_ptr) {
vp_ptr->createInstallPDSS(k, s, phaseNode_ptr);
}
return true;
}
const XML_Node* speciesXML_Node(const std::string& kname,
const XML_Node* phaseSpeciesData)
{

2
src/thermo/VPSSMgr_IdealGas.cpp
View file

@ -15,8 +15,8 @@
#include "cantera/thermo/VPSSMgr_IdealGas.h"
#include "cantera/base/ctml.h"
#include "cantera/thermo/SpeciesThermoFactory.h"
#include "cantera/thermo/SpeciesThermo.h"
#include "cantera/thermo/PDSS_IdealGas.h"
#include "cantera/thermo/SpeciesThermoInterpType.h"
using namespace std;

1
src/thermo/VPSSMgr_Water_HKFT.cpp
View file

@ -20,6 +20,7 @@
#include "cantera/thermo/VPStandardStateTP.h"
#include "cantera/thermo/GeneralSpeciesThermo.h"
#include "cantera/base/xml.h"
#include "cantera/base/stringUtils.h"
using namespace std;

24
src/transport/DustyGasTransport.cpp
View file

@ -96,30 +96,6 @@ void DustyGasTransport::setThermo(thermo_t& thermo)
m_gastran->setThermo(thermo);
}
void DustyGasTransport::setParameters(const int type, const int k, const doublereal* const p)
{
warn_deprecated("DustyGasTransport::setParameters", "To be removed after Cantera 2.2");
switch (type) {
case 0:
setPorosity(p[0]);
break;
case 1:
setTortuosity(p[0]);
break;
case 2:
setMeanPoreRadius(p[0]);
break;
case 3:
setMeanParticleDiameter(p[0]);
break;
case 4:
setPermeability(p[0]);
break;
default:
throw CanteraError("DustyGasTransport::init", "unknown parameter");
}
}
void DustyGasTransport::initialize(ThermoPhase* phase, Transport* gastr)
{

547
src/transport/PecosTransport.cpp
View file

@ -1,547 +0,0 @@
/**
* @file PecosTransport.cpp
* Mixture-averaged transport properties.
*/
#include "cantera/transport/PecosTransport.h"
#include "cantera/transport/TransportParams.h"
#include "cantera/base/stringUtils.h"
#include "cantera/thermo/IdealGasPhase.h"
#include <sstream>
using namespace std;
namespace Cantera
{
PecosTransport::PecosTransport() :
m_nsp(0),
m_temp(-1.0),
m_logt(0.0)
{
warn_deprecated("class PecosTransport", "To be removed after Cantera 2.2");
}
bool PecosTransport::initGas(GasTransportParams& tr)
{
// constant substance attributes
m_thermo = tr.thermo;
m_nsp = static_cast<int>(m_thermo->nSpecies());
// make a local copy of the molecular weights
m_mw.resize(m_nsp);
copy(m_thermo->molecularWeights().begin(),
m_thermo->molecularWeights().end(), m_mw.begin());
// copy polynomials and parameters into local storage
m_poly = tr.poly;
m_visccoeffs = tr.visccoeffs;
m_condcoeffs = tr.condcoeffs;
m_diffcoeffs = tr.diffcoeffs;
m_zrot = tr.zrot;
m_crot = tr.crot;
m_epsilon = tr.epsilon;
m_mode = tr.mode_;
m_diam = tr.diam;
m_eps = tr.eps;
m_alpha = tr.alpha;
m_dipoleDiag.resize(m_nsp);
for (int i = 0; i < m_nsp; i++) {
m_dipoleDiag[i] = tr.dipole(i,i);
}
m_phi.resize(m_nsp, m_nsp, 0.0);
m_wratjk.resize(m_nsp, m_nsp, 0.0);
m_wratkj1.resize(m_nsp, m_nsp, 0.0);
int j, k;
for (j = 0; j < m_nsp; j++)
for (k = j; k < m_nsp; k++) {
m_wratjk(j,k) = sqrt(m_mw[j]/m_mw[k]);
m_wratjk(k,j) = sqrt(m_wratjk(j,k));
m_wratkj1(j,k) = sqrt(1.0 + m_mw[k]/m_mw[j]);
}
m_polytempvec.resize(5);
m_visc.resize(m_nsp);
m_sqvisc.resize(m_nsp);
m_cond.resize(m_nsp);
m_bdiff.resize(m_nsp, m_nsp);
m_molefracs.resize(m_nsp);
m_spwork.resize(m_nsp);
// set flags all false
m_viscmix_ok = false;
m_viscwt_ok = false;
m_spvisc_ok = false;
m_spcond_ok = false;
m_condmix_ok = false;
m_spcond_ok = false;
m_diffmix_ok = false;
m_abc_ok = false;
// read blottner fit parameters (A,B,C)
read_blottner_transport_table();
// set specific heats
cv_rot.resize(m_nsp);
cp_R.resize(m_nsp);
cv_int.resize(m_nsp);
for (k = 0; k < m_nsp; k++) {
cv_rot[k] = tr.crot[k];
cp_R[k] = ((IdealGasPhase*)tr.thermo)->cp_R_ref()[k];
cv_int[k] = cp_R[k] - 2.5 - cv_rot[k];
}
return true;
}
doublereal PecosTransport::viscosity()
{
update_T();
update_C();
if (m_viscmix_ok) {
return m_viscmix;
}
doublereal vismix = 0.0;
int k;
// update m_visc and m_phi if necessary
if (!m_viscwt_ok) {
updateViscosity_T();
}
multiply(m_phi, DATA_PTR(m_molefracs), DATA_PTR(m_spwork));
for (k = 0; k < m_nsp; k++) {
vismix += m_molefracs[k] * m_visc[k]/m_spwork[k]; //denom;
}
m_viscmix = vismix;
return vismix;
}
void PecosTransport::getBinaryDiffCoeffs(const size_t ld, doublereal* const d)
{
int i,j;
update_T();
// if necessary, evaluate the binary diffusion coefficents
if (!m_bindiff_ok) {
updateDiff_T();
}
doublereal rp = 1.0/pressure_ig();
for (i = 0; i < m_nsp; i++)
for (j = 0; j < m_nsp; j++) {
d[ld*j + i] = rp * m_bdiff(i,j);
}
}
void PecosTransport::getMobilities(doublereal* const mobil)
{
int k;
getMixDiffCoeffs(DATA_PTR(m_spwork));
doublereal c1 = ElectronCharge / (Boltzmann * m_temp);
for (k = 0; k < m_nsp; k++) {
mobil[k] = c1 * m_spwork[k] * m_thermo->charge(k);
}
}
doublereal PecosTransport::thermalConductivity()
{
int k;
doublereal lambda = 0.0;
update_T();
update_C();
// update m_cond and m_phi if necessary
if (!m_spcond_ok) {
updateCond_T();
}
if (!m_condmix_ok) {
multiply(m_phi, DATA_PTR(m_molefracs), DATA_PTR(m_spwork));
for (k = 0; k < m_nsp; k++) {
lambda += m_molefracs[k] * m_cond[k]/m_spwork[k]; //denom;
}
}
m_lambda = lambda;
return m_lambda;
}
void PecosTransport::getThermalDiffCoeffs(doublereal* const dt)
{
int k;
for (k = 0; k < m_nsp; k++) {
dt[k] = 0.0;
}
}
void PecosTransport::getSpeciesFluxes(size_t ndim,
const doublereal* const grad_T,
size_t ldx, const doublereal* const grad_X,
size_t ldf, doublereal* const fluxes)
{
size_t n = 0;
int k;
update_T();
update_C();
getMixDiffCoeffs(DATA_PTR(m_spwork));
const vector_fp& mw = m_thermo->molecularWeights();
const doublereal* y = m_thermo->massFractions();
doublereal rhon = m_thermo->molarDensity();
vector_fp sum(ndim,0.0);
doublereal correction=0.0;
// grab 2nd (summation) term -- still need to multiply by mass fraction (\rho_s / \rho)
for (k = 0; k < m_nsp; k++) {
correction += rhon * mw[k] * m_spwork[k] * grad_X[n*ldx + k];
}
for (n = 0; n < ndim; n++) {
for (k = 0; k < m_nsp; k++) {
fluxes[n*ldf + k] = -rhon * mw[k] * m_spwork[k] * grad_X[n*ldx + k] + y[k]*correction;
sum[n] += fluxes[n*ldf + k];
}
}
// add correction flux to enforce sum to zero
for (n = 0; n < ndim; n++) {
for (k = 0; k < m_nsp; k++) {
fluxes[n*ldf + k] -= y[k]*sum[n];
}
}
}
void PecosTransport::getMixDiffCoeffs(doublereal* const d)
{
update_T();
update_C();
// update the binary diffusion coefficients if necessary
if (!m_bindiff_ok) {
updateDiff_T();
}
int k, j;
doublereal mmw = m_thermo->meanMolecularWeight();
doublereal sumxw = 0.0, sum2;
doublereal p = pressure_ig();
if (m_nsp == 1) {
d[0] = m_bdiff(0,0) / p;
} else {
for (k = 0; k < m_nsp; k++) {
sumxw += m_molefracs[k] * m_mw[k];
}
for (k = 0; k < m_nsp; k++) {
sum2 = 0.0;
for (j = 0; j < m_nsp; j++) {
if (j != k) {
sum2 += m_molefracs[j] / m_bdiff(j,k);
}
}
if (sum2 <= 0.0) {
d[k] = m_bdiff(k,k) / p;
} else {
d[k] = (sumxw - m_molefracs[k] * m_mw[k])/(p * mmw * sum2);
}
}
}
}
void PecosTransport::getMixDiffCoeffsMole(doublereal* const d)
{
update_T();
update_C();
// update the binary diffusion coefficients if necessary
if (!m_bindiff_ok) {
updateDiff_T();
}
doublereal p = m_thermo->pressure();
if (m_nsp == 1) {
d[0] = m_bdiff(0,0) / p;
} else {
for (int k = 0; k < m_nsp; k++) {
double sum2 = 0.0;
for (int j = 0; j < m_nsp; j++) {
if (j != k) {
sum2 += m_molefracs[j] / m_bdiff(j,k);
}
}
if (sum2 <= 0.0) {
d[k] = m_bdiff(k,k) / p;
} else {
d[k] = (1 - m_molefracs[k]) / (p * sum2);
}
}
}
}
void PecosTransport::getMixDiffCoeffsMass(doublereal* const d)
{
update_T();
update_C();
// update the binary diffusion coefficients if necessary
if (!m_bindiff_ok) {
updateDiff_T();
}
doublereal mmw = m_thermo->meanMolecularWeight();
doublereal p = m_thermo->pressure();
if (m_nsp == 1) {
d[0] = m_bdiff(0,0) / p;
} else {
for (int k=0; k<m_nsp; k++) {
double sum1 = 0.0;
double sum2 = 0.0;
for (int i=0; i<m_nsp; i++) {
if (i==k) {
continue;
}
sum1 += m_molefracs[i] / m_bdiff(k,i);
sum2 += m_molefracs[i] * m_mw[i] / m_bdiff(k,i);
}
sum1 *= p;
sum2 *= p * m_molefracs[k] / (mmw - m_mw[k]*m_molefracs[k]);
d[k] = 1.0 / (sum1 + sum2);
}
}
}
/**
* @internal This is called whenever a transport property is
* requested from ThermoSubstance if the temperature has changed
* since the last call to update_T.
*/
void PecosTransport::update_T()
{
doublereal t = m_thermo->temperature();
if (t == m_temp) {
return;
}
if (t <= 0.0) {
throw CanteraError("PecosTransport::update_T",
"negative temperature "+fp2str(t));
}
m_temp = t;
m_logt = log(m_temp);
m_kbt = Boltzmann * m_temp;
m_sqrt_t = sqrt(m_temp);
m_t14 = sqrt(m_sqrt_t);
m_t32 = m_temp * m_sqrt_t;
m_sqrt_kbt = sqrt(Boltzmann*m_temp);
// compute powers of log(T)
m_polytempvec[0] = 1.0;
m_polytempvec[1] = m_logt;
m_polytempvec[2] = m_logt*m_logt;
m_polytempvec[3] = m_logt*m_logt*m_logt;
m_polytempvec[4] = m_logt*m_logt*m_logt*m_logt;
// temperature has changed, so polynomial fits will need to be redone.
m_viscmix_ok = false;
m_spvisc_ok = false;
m_viscwt_ok = false;
m_spcond_ok = false;
m_diffmix_ok = false;
m_bindiff_ok = false;
m_abc_ok = false;
m_condmix_ok = false;
}
void PecosTransport::update_C()
{
// signal that concentration-dependent quantities will need to
// be recomputed before use, and update the local mole
// fractions.
m_viscmix_ok = false;
m_diffmix_ok = false;
m_condmix_ok = false;
m_thermo->getMoleFractions(DATA_PTR(m_molefracs));
// add an offset to avoid a pure species condition
int k;
for (k = 0; k < m_nsp; k++) {
m_molefracs[k] = std::max(Tiny, m_molefracs[k]);
}
}
void PecosTransport::updateCond_T()
{
int k;
doublereal fivehalves = 5/2;
for (k = 0; k < m_nsp; k++) {
// need to add cv_elec in the future
m_cond[k] = m_visc[k] * (fivehalves * cv_int[k] + cv_rot[k] + m_thermo->cv_vib(k,m_temp));
}
m_spcond_ok = true;
m_condmix_ok = false;
}
void PecosTransport::updateDiff_T()
{
// evaluate binary diffusion coefficients at unit pressure
int i,j;
int ic = 0;
if (m_mode == CK_Mode) {
for (i = 0; i < m_nsp; i++) {
for (j = i; j < m_nsp; j++) {
m_bdiff(i,j) = exp(dot4(m_polytempvec, m_diffcoeffs[ic]));
m_bdiff(j,i) = m_bdiff(i,j);
ic++;
}
}
} else {
for (i = 0; i < m_nsp; i++) {
for (j = i; j < m_nsp; j++) {
m_bdiff(i,j) = m_temp * m_sqrt_t*dot5(m_polytempvec,
m_diffcoeffs[ic]);
m_bdiff(j,i) = m_bdiff(i,j);
ic++;
}
}
}
m_bindiff_ok = true;
m_diffmix_ok = false;
}
void PecosTransport::updateSpeciesViscosities()
{
int k;
// iterate over species, update pure-species viscosity
for (k = 0; k < m_nsp; k++) {
m_visc[k] = 0.10*std::exp(a[k]*(m_logt*m_logt) + b[k]*m_logt + c[k]);
m_sqvisc[k] = sqrt(m_visc[k]);
}
// time to update mixing
m_spvisc_ok = true;
}
void PecosTransport::read_blottner_transport_table()
{
// from: AIAA-1997-2474 and Sandia Report SC-RR-70-754
//
// # Air -- Identical to N2 fit
// # N -- Sandia Report SC-RR-70-754
// # N2 -- Sandia Report SC-RR-70-754
// # CPN2 -- Identical to N2 fit
// # NO -- Sandia Report SC-RR-70-754
// # O -- Sandia Report SC-RR-70-754
// # O2 -- Sandia Report SC-RR-70-754
// # C -- AIAA-1997-2474
// # C2 -- AIAA-1997-2474
// # C3 -- AIAA-1997-2474
// # C2H -- wild-ass guess: identical to HCN fit
// # CN -- AIAA-1997-2474
// # CO -- AIAA-1997-2474
// # CO2 -- AIAA-1997-2474
// # HCN -- AIAA-1997-2474
// # H -- AIAA-1997-2474
// # H2 -- AIAA-1997-2474
// # e -- Sandia Report SC-RR-70-754
istringstream blot
("Air 2.68142000000e-02 3.17783800000e-01 -1.13155513000e+01\n"
"CPAir 2.68142000000e-02 3.17783800000e-01 -1.13155513000e+01\n"
"N 1.15572000000e-02 6.03167900000e-01 -1.24327495000e+01\n"
"N2 2.68142000000e-02 3.17783800000e-01 -1.13155513000e+01\n"
"CPN2 2.68142000000e-02 3.17783800000e-01 -1.13155513000e+01\n"
"NO 4.36378000000e-02 -3.35511000000e-02 -9.57674300000e+00\n"
"O 2.03144000000e-02 4.29440400000e-01 -1.16031403000e+01\n"
"O2 4.49290000000e-02 -8.26158000000e-02 -9.20194750000e+00\n"
"C -8.3285e-3 0.7703240 -12.7378000\n"
"C2 -8.4311e-3 0.7876060 -13.0268000\n"
"C3 -8.4312e-3 0.7876090 -12.8240000\n"
"C2H -2.4241e-2 1.0946550 -14.5835500\n"
"CN -8.3811e-3 0.7860330 -12.9406000\n"
"CO -0.019527394 1.013295 -13.97873\n"
"CO2 -0.019527387 1.047818 -14.32212\n"
"HCN -2.4241e-2 1.0946550 -14.5835500\n"
"H -8.3912e-3 0.7743270 -13.6653000\n"
"H2 -8.3346e-3 0.7815380 -13.5351000\n"
"e 0.00000000000e+00 0.00000000000e+00 -1.16031403000e+01\n");
string line;
string name;
string ss1,ss2,ss3,ss4,sss;
int k;
int i = 0;
while (std::getline(blot, line)) {
istringstream ss(line);
std::getline(ss, ss1, ' ');
std::getline(ss, ss2, ' ');
std::getline(ss, ss3, ' ');
std::getline(ss, ss4, ' ');
name = ss1;
// now put coefficients in correct species
for (k = 0; k < m_nsp; k++) {
string sss = m_thermo->speciesName(k);
// this is the right species index
if (sss.compare(ss1) == 0) {
a[k] = fpValue(ss2);
b[k] = fpValue(ss3);
c[k] = fpValue(ss4);
// index
i++;
} else { // default to air
a[k] = 0.026;
b[k] = 0.3;
c[k] = -11.3;
}
} // done with for loop
}
}
void PecosTransport::updateViscosity_T()
{
doublereal vratiokj, wratiojk, factor1;
if (!m_spvisc_ok) {
updateSpeciesViscosities();
}
// see Eq. (9-5.15) of Reid, Prausnitz, and Poling
int j, k;
for (j = 0; j < m_nsp; j++) {
for (k = j; k < m_nsp; k++) {
vratiokj = m_visc[k]/m_visc[j];
wratiojk = m_mw[j]/m_mw[k];
// Note that m_wratjk(k,j) holds the square root of
// m_wratjk(j,k)!
factor1 = 1.0 + (m_sqvisc[k]/m_sqvisc[j]) * m_wratjk(k,j);
m_phi(k,j) = factor1*factor1 /
(sqrt(8.0) * m_wratkj1(j,k));
m_phi(j,k) = m_phi(k,j)/(vratiokj * wratiojk);
}
}
m_viscwt_ok = true;
}
}

11
src/transport/TransportFactory.cpp
View file

@ -6,7 +6,6 @@
// known transport models
#include "cantera/transport/MultiTransport.h"
#include "cantera/transport/PecosTransport.h"
#include "cantera/transport/MixTransport.h"
#include "cantera/transport/SolidTransport.h"
#include "cantera/transport/DustyGasTransport.h"
@ -59,7 +58,6 @@ TransportFactory::TransportFactory()
m_models["Simple"] = cSimpleTransport;
m_models["User"] = cUserTransport;
m_models["HighP"] = cHighP;
m_models["Pecos"] = cPecosTransport;
m_models["None"] = None;
for (map<string, int>::iterator iter = m_models.begin();
iter != m_models.end();
@ -277,15 +275,6 @@ Transport* TransportFactory::newTransport(thermo_t* phase, int log_level)
return newTransport(transportModel, phase,log_level);
}
void TransportFactory::initTransport(Transport* tr, thermo_t* thermo,
int mode, int log_level)
{
warn_deprecated("TransportFactory::initTransport",
"To be removed after Cantera 2.2. This initialization is "
"now handled directly by GasTransport::init");
tr->init(thermo);
}
void TransportFactory::setupLiquidTransport(thermo_t* thermo, int log_level,
LiquidTransportParams& trParam)
{

27
src/transport/TransportParams.cpp
View file

@ -24,31 +24,4 @@ TransportParams::TransportParams() :
{
}
GasTransportParams::GasTransportParams() :
TransportParams(),
visccoeffs(0),
condcoeffs(0),
diffcoeffs(0),
poly(0),
omega22_poly(0),
astar_poly(0),
bstar_poly(0),
cstar_poly(0),
zrot(0),
crot(0),
polar(0),
alpha(0),
fitlist(0),
eps(0),
sigma(0),
reducedMass(0, 0),
diam(0, 0),
epsilon(0, 0),
dipole(0, 0),
delta(0, 0)
{
warn_deprecated("class GasTransportParams",
"To be removed after Cantera 2.2.");
}
} // End of namespace Cantera

19
src/zeroD/ReactorNet.cpp
View file

@ -138,25 +138,6 @@ double ReactorNet::step(doublereal time)
return m_time;
}
void ReactorNet::addReactor(Reactor* r, bool iown)
{
warn_deprecated("ReactorNet::addReactor(Reactor*)",
"To be removed after Cantera 2.2. Use 'addReactor(Reactor&) instead'.");
if (iown) {
warn_deprecated("ReactorNet::addReactor",
"Ownership of Reactors by ReactorNet is deprecated.");
}
r->setNetwork(this);
if (r->type() >= ReactorType) {
m_reactors.push_back(r);
m_iown.push_back(iown);
writelog("Adding reactor "+r->name()+"\n", m_verbose);
} else {
writelog("Not adding reactor "+r->name()+
", since type = "+int2str(r->type())+"\n", m_verbose);
}
}
void ReactorNet::addReactor(Reactor& r)
{
r.setNetwork(this);

1
test/thermo/MaskellSolidSolnPhase_Test.cpp
View file

@ -1,6 +1,5 @@
#include "gtest/gtest.h"
#include "cantera/thermo/MaskellSolidSolnPhase.h"
#include "cantera/thermo/SimpleThermo.h"
#include "cantera/thermo/VPSSMgr_General.h"
#include "cantera/thermo/ThermoFactory.h"
#include <iostream>

2
test/thermo/nasapoly.cpp
View file

@ -36,7 +36,6 @@ protected:
EXPECT_EQ(poly.minTemp(), q.minTemp());
EXPECT_EQ(poly.maxTemp(), q.maxTemp());
EXPECT_EQ(poly.refPressure(), q.refPressure());
EXPECT_EQ(poly.speciesIndex(), q.speciesIndex());
double cp_R1, h_RT1, s_R1;
double cp_R2, h_RT2, s_R2;
@ -57,7 +56,6 @@ TEST_F(NasaPoly1Test, Initialization)
EXPECT_EQ(poly.minTemp(), 200.0);
EXPECT_EQ(poly.maxTemp(), 1000.0);
EXPECT_EQ(poly.refPressure(), 101325.0);
EXPECT_EQ(poly.speciesIndex(), (size_t) 0);
}
TEST_F(NasaPoly1Test, Copy)

2
test/thermo/thermoParameterizations.cpp
View file

@ -1,11 +1,11 @@
#include "gtest/gtest.h"
#include "cantera/thermo/speciesThermoTypes.h"
#include "cantera/thermo/SimpleThermo.h"
#include "cantera/thermo/IdealGasPhase.h"
#include "cantera/thermo/ConstCpPoly.h"
#include "cantera/thermo/GeneralSpeciesThermo.h"
#include "cantera/thermo/NasaPoly2.h"
#include "cantera/thermo/ShomatePoly.h"
#include "cantera/base/stringUtils.h"
#include "thermo_data.h"
using namespace Cantera;

252
test_problems/PecosTransport/PecosTransport.cpp
View file

@ -1,252 +0,0 @@
/**
* @file mixGasTransport.cpp
* test problem for mixture transport
*/
// Example
//
// Test case for mixture transport in a gas
// The basic idea is to set up a gradient of some kind.
// Then the resulting transport coefficients out.
// Essentially all of the interface routines should be
// exercised and the results dumped out.
//
// A blessed solution test will make sure that the actual
// solution doesn't change as a function of time or
// further development.
// perhaps, later, an analytical solution could be added
#include "cantera/transport.h"
#include "cantera/IdealGasMix.h"
#include "cantera/transport/TransportFactory.h"
#include <cstdio>
using namespace std;
using namespace Cantera;
void printDbl(double val)
{
if (fabs(val) < 5.0E-17) {
cout << " nil";
} else {
cout << val;
}
}
int main(int argc, char** argv)
{
size_t k;
string infile = "diamond.xml";
try {
IdealGasMix g("gri30.xml", "gri30_mix");
size_t nsp = g.nSpecies();
double pres = 1.0E5;
vector_fp Xset(nsp, 0.0);
Xset[0] = 0.269205 ;
Xset[1] = 0.000107082;
Xset[2] = 1.36377e-09 ;
Xset[3] = 4.35475e-10;
Xset[4] = 4.34036e-06 ;
Xset[5] = 0.192249;
Xset[6] = 3.59356e-13;
Xset[7] = 2.78061e-12 ;
Xset[8] = 4.7406e-18 ;
Xset[9] = 4.12955e-17 ;
Xset[10] = 2.58549e-14 ;
Xset[11] = 8.96502e-16 ;
Xset[12] = 6.09056e-11 ;
Xset[13] = 7.56752e-09 ;
Xset[14] = 0.192253;
Xset[15] = 0.0385036;
Xset[16] = 1.49596e-08 ;
Xset[17] = 2.22378e-08 ;
Xset[18] = 1.43096e-13 ;
Xset[19] = 1.45312e-15 ;
Xset[20] = 1.96948e-12 ;
Xset[21] = 8.41937e-19;
Xset[22] = 3.18852e-13 ;
Xset[23] = 7.93625e-18 ;
Xset[24] = 3.20653e-15 ;
Xset[25] = 1.15149e-19 ;
Xset[26] = 1.61189e-18 ;
Xset[27] = 1.4719e-15 ;
Xset[28] = 5.24728e-13 ;
Xset[29] = 6.90582e-17 ;
Xset[30] = 6.37248e-12 ;
Xset[31] =5.93728e-11 ;
Xset[32] = 2.71219e-09 ;
Xset[33] = 2.66645e-06 ;
Xset[34] = 6.57142e-11 ;
Xset[35] = 9.52453e-08 ;
Xset[36] = 1.26006e-14;
Xset[37] = 3.49802e-12;
Xset[38] = 1.19232e-11 ;
Xset[39] = 7.17782e-13 ;
Xset[40] = 1.85347e-07 ;
Xset[41] = 8.25325e-14 ;
Xset[42] = 5.00914e-20 ;
Xset[43] = 1.54407e-16 ;
Xset[44] =3.07176e-11 ;
Xset[45] =4.93198e-08 ;
Xset[46] =4.84792e-12 ;
Xset[47] = 0.307675 ;
Xset[48] =0;
Xset[49] =6.21649e-29;
Xset[50] = 8.42393e-28 ;
Xset[51] = 6.77865e-18;
Xset[52] = 2.19225e-16;
double T1 = 1500.;
double sum = 0.0;
for (k = 0; k < nsp; k++) {
sum += Xset[k];
}
for (k = 0; k < nsp; k++) {
Xset[k] /= sum;
}
vector_fp X2set(nsp, 0.0);
X2set[0] = 0.25 ;
X2set[5] = 0.17;
X2set[14] = 0.15;
X2set[15] = 0.05;
X2set[47] = 0.38 ;
double T2 = 1200.;
double dist = 0.1;
vector_fp X3set(nsp, 0.0);
X3set[0] = 0.27 ;
X3set[5] = 0.15;
X3set[14] = 0.18;
X3set[15] = 0.06;
X3set[47] = 0.36 ;
double T3 = 1400.;
vector_fp grad_T(3, 0.0);
Array2D grad_X(nsp, 2, 0.0);
for (k = 0; k < nsp; k++) {
grad_X(k,0) = (X2set[k] - Xset[k])/dist;
grad_X(k,1) = (X3set[k] - Xset[k])/dist;
}
grad_T[0] = (T2 - T1) / dist;
grad_T[1] = (T3 - T1) / dist;
int log_level = 0;
Transport* tran = newTransportMgr("Pecos", &g, log_level=0);
PecosTransport* tranMix = dynamic_cast<PecosTransport*>(tran);
g.setState_TPX(1500.0, pres, DATA_PTR(Xset));
vector_fp mixDiffs(nsp, 0.0);
tranMix->getMixDiffCoeffsMass(DATA_PTR(mixDiffs));
printf(" Dump of the mixture Diffusivities:\n");
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" %15s %13.5g\n", sss.c_str(), mixDiffs[k]);
}
vector_fp specVisc(nsp, 0.0);
tranMix->getSpeciesViscosities(DATA_PTR(specVisc));
printf(" Dump of the species viscosities:\n");
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" %15s %13.5g\n", sss.c_str(), specVisc[k]);
}
vector_fp thermDiff(nsp, 0.0);
tranMix->getThermalDiffCoeffs(DATA_PTR(thermDiff));
printf(" Dump of the Thermal Diffusivities :\n");
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" %15s %13.5g\n", sss.c_str(), thermDiff[k]);
}
printf("Viscoscity and thermal Cond vs. T\n");
for (k = 0; k < 10; k++) {
T1 = 400. + 100. * k;
g.setState_TPX(T1, pres, DATA_PTR(Xset));
double visc = tran->viscosity();
double cond = tran->thermalConductivity();
printf(" %13g %13.5g %13.5g\n", T1, visc, cond);
}
g.setState_TPX(T1, pres, DATA_PTR(Xset));
Array2D Bdiff(nsp, nsp, 0.0);
printf("Binary Diffusion Coefficients H2 vs species\n");
tranMix->getBinaryDiffCoeffs(nsp, Bdiff.ptrColumn(0));
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" H2 - %15s %13.5g %13.5g\n", sss.c_str(), Bdiff(0,k), Bdiff(k,0));
}
vector_fp specMob(nsp, 0.0);
tranMix->getMobilities(DATA_PTR(specMob));
printf(" Dump of the species mobilities:\n");
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" %15s %13.5g\n", sss.c_str(), specMob[k]);
}
Array2D fluxes(nsp, 2, 0.0);
tranMix->getSpeciesFluxes(2, DATA_PTR(grad_T), nsp,
grad_X.ptrColumn(0), nsp, fluxes.ptrColumn(0));
printf(" Dump of the species fluxes:\n");
double sum1 = 0.0;
double sum2 = 0.0;
double max1 = 0.0;
double max2 = 0.0;
for (k = 0; k < nsp; k++) {
string sss = g.speciesName(k);
printf(" %15s %13.5g %13.5g\n", sss.c_str(), fluxes(k,0), fluxes(k,1));
sum1 += fluxes(k,0);
if (fabs(fluxes(k,0)) > max1) {
max1 = fabs(fluxes(k,0));
}
sum2 += fluxes(k,1);
if (fabs(fluxes(k,1)) > max2) {
max2 = fabs(fluxes(k,0));
}
}
// Make sure roundoff error doesn't interfere with the printout.
// these should be zero.
if (fabs(sum1) * 1.0E14 > max1) {
printf("sum in x direction = %13.5g\n", sum1);
} else {
printf("sum in x direction = 0\n");
}
if (fabs(sum2) * 1.0E14 > max2) {
printf("sum in y direction = %13.5g\n", sum1);
} else {
printf("sum in y direction = 0\n");
}
std::cout << "Sum of Diffusive Mass Fluxes: " << sum1 << std::endl;
std::cout << "Sum of Diffusive Mass Fluxes: " << sum2 << std::endl;
} catch (CanteraError) {
showErrors(cout);
}
return 0;
}
/***********************************************************/

176
test_problems/PecosTransport/output_blessed.txt
View file

@ -1,176 +0,0 @@
Dump of the mixture Diffusivities:
H2 0.001204
H 0.0022584
O 0.00064032
O2 0.00042264
OH 0.00062946
H2O 0.00051533
HO2 0.00042019
H2O2 0.00041763
C 0.00059188
CH 0.00068026
CH2 0.0004608
CH2(S) 0.0004608
CH3 0.00045156
CH4 0.00044985
CO 0.0004216
CO2 0.00034577
HCO 0.00036192
CH2O 0.00035926
CH2OH 0.00035027
CH3O 0.00035027
CH3OH 0.00035149
C2H 0.0003524
C2H2 0.00034919
C2H3 0.00034618
C2H4 0.00034633
C2H5 0.00031771
C2H6 0.00031538
HCCO 0.00053082
CH2CO 0.00030634
HCCOH 0.00030634
N 0.00056491
NH 0.00067404
NH2 0.00066041
NH3 0.00050222
NNH 0.00040495
NO 0.00041226
NO2 0.00037026
N2O 0.00033509
HNO 0.00041903
CN 0.00040648
HCN 0.00035852
H2CN 0.00035559
HCNN 0.00053081
HCNO 0.00033642
HOCN 0.00033642
HNCO 0.00033642
NCO 0.00033783
N2 0.00043046
AR 0.00041248
C3H7 0.00024676
C3H8 0.00024577
CH2CHO 0.00030507
CH3CHO 0.00030384
Dump of the species viscosities:
H2 4.4588e-05
H 4.4588e-05
O 4.4588e-05
O2 4.4588e-05
OH 4.4588e-05
H2O 4.4588e-05
HO2 4.4588e-05
H2O2 4.4588e-05
C 4.4588e-05
CH 4.4588e-05
CH2 4.4588e-05
CH2(S) 4.4588e-05
CH3 4.4588e-05
CH4 4.4588e-05
CO 4.4588e-05
CO2 4.4588e-05
HCO 4.4588e-05
CH2O 4.4588e-05
CH2OH 4.4588e-05
CH3O 4.4588e-05
CH3OH 4.4588e-05
C2H 4.4588e-05
C2H2 4.4588e-05
C2H3 4.4588e-05
C2H4 4.4588e-05
C2H5 4.4588e-05
C2H6 4.4588e-05
HCCO 4.4588e-05
CH2CO 4.4588e-05
HCCOH 4.4588e-05
N 4.4588e-05
NH 4.4588e-05
NH2 4.4588e-05
NH3 4.4588e-05
NNH 4.4588e-05
NO 4.4588e-05
NO2 4.4588e-05
N2O 4.4588e-05
HNO 4.4588e-05
CN 4.4588e-05
HCN 4.4588e-05
H2CN 4.4588e-05
HCNN 4.4588e-05
HCNO 4.4588e-05
HOCN 4.4588e-05
HNCO 4.4588e-05
NCO 4.4588e-05
N2 4.4588e-05
AR 4.4588e-05
C3H7 4.4588e-05
C3H8 4.4588e-05
CH2CHO 4.4588e-05
CH3CHO 4.4588e-05
Dump of the Thermal Diffusivities :
H2 0
H 0
O 0
O2 0
OH 0
H2O 0
HO2 0
H2O2 0
C 0
CH 0
CH2 0
CH2(S) 0
CH3 0
CH4 0
CO 0
CO2 0
HCO 0
CH2O 0
CH2OH 0
CH3O 0
CH3OH 0
C2H 0
C2H2 0
C2H3 0
C2H4 0
C2H5 0
C2H6 0
HCCO 0
CH2CO 0
HCCOH 0
N 0
NH 0
NH2 0
NH3 0
NNH 0
NO 0
NO2 0
N2O 0
HNO 0
CN 0
HCN 0
H2CN 0
HCNN 0
HCNO 0
HOCN 0
HNCO 0
NCO 0
N2 0
AR 0
C3H7 0
C3H8 0
CH2CHO 0
CH3CHO 0
Viscoscity and thermal Cond vs. T
************************************************
Cantera Error!
************************************************
Procedure: Error in IdealGasPhase.cpp
Error: cv_vib only supported for StatMech!.

36
test_problems/PecosTransport/runtest
View file

@ -1,36 +0,0 @@
#!/bin/sh
#
#
temp_success="1"
/bin/rm -f output.txt outputa.txt
tname="PecosTransport"
#################################################################
#
#################################################################
CANTERA_DATA=${CANTERA_DATA:=../../data/inputs}; export CANTERA_DATA
CANTERA_BIN=${CANTERA_BIN:=../../bin}
./PecosTransport > output.txt
retnStat=$?
if [ $retnStat != "0" ]
then
temp_success="0"
echo "$tname ($tname test) returned with bad status, $retnStat, check output"
exit 1
fi
../../bin/exp3to2.sh output.txt > outputa.txt
diff -w outputa.txt output_blessed.txt > diff_test.out
retnStat=$?
if [ $retnStat = "0" ]
then
echo "successful diff comparison on $tname test"
exit 0
else
echo "unsuccessful diff comparison on $tname test"
echo "FAILED" > csvCode.txt
temp_success="0"
exit 1
fi

1
test_problems/statmech_transport/output_blessed.txt
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here

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test_problems/statmech_transport/statmech_transport.cpp
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/**
* @file statmech
* test problem for statistical mechanics in cantera
*/
// Example
//
// Test case for the statistical mechanics in cantera
//
#include "cantera/transport.h"
#include "cantera/IdealGasMix.h"
#include "cantera/equil/equil.h"
using namespace std;
using namespace Cantera;
int main(int argc, char** argv)
{
try {
int k;
IdealGasMix g("test_stat_trans.xml", "example");
int nsp = g.nSpecies();
double pres = 1.0E5;
vector_fp Xset(nsp, 0.0);
Xset[0] = 0.5 ;
Xset[1] = 0.5;
g.setState_TPX(1500.0, pres, DATA_PTR(Xset));
equilibrate(g, "TP", -1);
// init pecos transport
int log_level = 0;
Transport* tran = newTransportMgr("Pecos", &g, log_level=0);
PecosTransport* tranMix = dynamic_cast<PecosTransport*>(tran);
cout << "here" << std::endl;
vector_fp cp_R(nsp, 0.0);
g.getCp_R(DATA_PTR(cp_R));
//for(int i=0;i<nsp;i++)
//{
// std::cout.precision(10);
// std::cout << cp_R[i] << std::endl;
// }
// error check-- exactly 2.5 for atoms
if (cp_R[0] != 2.5) {
std::cout << "Error for monotomic Species!\n";
return 1;
}
// error check: analytical result is more complicated for
// molecules. One species should suffice, lets try NO2, with
// three vibrational modes:
/// theta[0]: 1.07900e3
/// theta[1]: 1.90000e3
/// theta[2]: 2.32700e3
// at T = 1500
//
// This is precisely: 6.655804161 (e.g. 5/2 + 2 + 3.1558..)
//
double theta[3];
theta[0] = 1.07900e3;
theta[1] = 1.90000e3;
theta[2] = 2.32700e3;
double T;
T = 1500.0;
double denom;
double ctr = 0.0;
double GasConstant = 1.0;
for (int i = 0; i < 3; i++) {
denom = exp(2*theta[i]/T) - 2* exp(theta[i]/T) + 1;
ctr += GasConstant * theta[i] * (theta[i] * exp(theta[i]/T)/(T*T))/ (denom);
//std::cout << "survey says: " << ctr << " and denom is: " << denom << std::endl;
}
//std::cout << "survey says: " << ctr << " and denom is: " << denom << std::endl;
double sol = ctr + 5/2 + 2;
double tol = 1e-9;
if (abs(cp_R[3] - sol) >= tol) {
double diff = cp_R[3]-sol;
std::cout << "Error for Species NO2!\n";
std::cout << "Diff was: " << diff << "\n";
return 1;
}
} catch (CanteraError) {
showErrors(cout);
return 1;
}
// Mark it zero!
return 0;
}

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test_problems/statmech_transport/test_stat_trans.xml
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<?xml version="1.0"?>
<ctml>
<validate reactions="yes" species="yes"/>
<!-- phase H -->
<phase dim="3" id="example">
<elementArray datasrc="elements.xml">
O H C N Na
</elementArray>
<speciesArray datasrc="#species_test"> H O N NO2</speciesArray>
<thermo model="IdealGas">
<density units="g/cm3">2.165</density>
</thermo>
<kinetics model="none"/>
<transport model="Pecos"/>
</phase>
<!-- species definitions -->
<speciesData id="species_test">
<!-- species H -->
<species name="H">
<atomArray> H:1 </atomArray>
<thermo>
<StatMech P0="100000.0" Tmax="3000.0" Tmin="1.0">
</StatMech>
</thermo>
<density units="g/cm3">2.165</density>
<transport model="Pecos">
<string title="geometry">atom</string>
<LJ_welldepth units="K">80.000</LJ_welldepth>
<LJ_diameter units="A">2.750</LJ_diameter>
<dipoleMoment units="Debye">0.000</dipoleMoment>
<polarizability units="A3">0.000</polarizability>
<rotRelax>0.000</rotRelax>
</transport>
</species>
<!-- species O -->
<species name="O">
<atomArray>O:1</atomArray>
<thermo>
<StatMech P0="100000.0" Tmax="3000.0" Tmin="1.0">
</StatMech>
</thermo>
<density units="g/cm3">2.165</density>
<transport model="Pecos">
<string title="geometry">atom</string>
<LJ_welldepth units="K">80.000</LJ_welldepth>
<LJ_diameter units="A">2.750</LJ_diameter>
<dipoleMoment units="Debye">0.000</dipoleMoment>
<polarizability units="A3">0.000</polarizability>
<rotRelax>0.000</rotRelax>
</transport>
</species>
<!-- species N -->
<species name="N">
<atomArray>N:1</atomArray>
<thermo>
<StatMech P0="100000.0" Tmax="3000.0" Tmin="1.0">
</StatMech>
</thermo>
<density units="g/cm3">2.165</density>
<transport model="Pecos">
<string title="geometry">atom</string>
<LJ_welldepth units="K">80.000</LJ_welldepth>
<LJ_diameter units="A">2.750</LJ_diameter>
<dipoleMoment units="Debye">0.000</dipoleMoment>
<polarizability units="A3">0.000</polarizability>
<rotRelax>0.000</rotRelax>
</transport>
</species>
<!-- species NO2 -->
<species name="NO2">
<atomArray>O:2 N:1</atomArray>
<thermo>
<StatMech P0="100000.0" Tmax="3000.0" Tmin="1.0">
</StatMech>
<StatMech P0="100000.0" Tmax="3000.0" Tmin="1.0">
</StatMech>
</thermo>
<density units="g/cm3">2.165</density>
<transport model="Pecos">
<string title="geometry">atom</string>
<LJ_welldepth units="K">80.000</LJ_welldepth>
<LJ_diameter units="A">2.750</LJ_diameter>
<dipoleMoment units="Debye">0.000</dipoleMoment>
<polarizability units="A3">0.000</polarizability>
<rotRelax>0.000</rotRelax>
</transport>
</species>
</speciesData>
</ctml>