From 341b1377669899174386790476f9f381d5214d66 Mon Sep 17 00:00:00 2001 From: Ray Speth Date: Mon, 25 May 2015 17:59:20 -0400 Subject: [PATCH] [Doc] Capitalize proper nouns and acronyms --- SConstruct | 3 +- include/cantera/base/ctexceptions.h | 2 +- include/cantera/base/ctml.h | 6 +- include/cantera/base/global.h | 16 ++-- include/cantera/base/xml.h | 28 +++---- include/cantera/equil/ChemEquil.h | 10 +-- include/cantera/equil/vcs_MultiPhaseEquil.h | 2 +- include/cantera/equil/vcs_VolPhase.h | 12 +-- include/cantera/equil/vcs_solve.h | 4 +- include/cantera/kinetics/ElectrodeKinetics.h | 2 +- include/cantera/kinetics/ImplicitSurfChem.h | 2 +- include/cantera/kinetics/InterfaceKinetics.h | 14 ++-- include/cantera/kinetics/Kinetics.h | 6 +- include/cantera/kinetics/KineticsFactory.h | 4 +- include/cantera/kinetics/StoichManager.h | 4 +- include/cantera/kinetics/importKinetics.h | 10 +-- include/cantera/kinetics/solveSP.h | 4 +- include/cantera/numerics/BEulerInt.h | 18 ++--- include/cantera/numerics/BandMatrix.h | 8 +- include/cantera/numerics/CVodesIntegrator.h | 2 +- include/cantera/numerics/DenseMatrix.h | 6 +- include/cantera/numerics/GeneralMatrix.h | 8 +- include/cantera/numerics/IDA_Solver.h | 20 ++--- include/cantera/numerics/NonlinearSolver.h | 80 +++++++++---------- include/cantera/numerics/ResidJacEval.h | 18 ++--- include/cantera/numerics/solveProb.h | 10 +-- include/cantera/oneD/MultiJac.h | 4 +- include/cantera/thermo/ConstDensityThermo.h | 6 +- include/cantera/thermo/DebyeHuckel.h | 2 +- include/cantera/thermo/FixedChemPotSSTP.h | 6 +- include/cantera/thermo/GibbsExcessVPSSTP.h | 4 +- include/cantera/thermo/HMWSoln.h | 10 +-- include/cantera/thermo/IdealGasPhase.h | 10 +-- include/cantera/thermo/IdealMolalSoln.h | 2 +- include/cantera/thermo/IdealSolidSolnPhase.h | 16 ++-- .../cantera/thermo/IonsFromNeutralVPSSTP.h | 6 +- include/cantera/thermo/LatticePhase.h | 12 +-- include/cantera/thermo/LatticeSolidPhase.h | 8 +- include/cantera/thermo/MargulesVPSSTP.h | 34 ++++---- .../cantera/thermo/MaskellSolidSolnPhase.h | 2 +- include/cantera/thermo/MetalSHEelectrons.h | 6 +- include/cantera/thermo/MineralEQ3.h | 4 +- .../cantera/thermo/MixedSolventElectrolyte.h | 34 ++++---- include/cantera/thermo/MixtureFugacityTP.h | 4 +- include/cantera/thermo/MolarityIonicVPSSTP.h | 4 +- include/cantera/thermo/NasaPoly2.h | 2 +- include/cantera/thermo/PDSS.h | 6 +- include/cantera/thermo/PDSS_ConstVol.h | 2 +- include/cantera/thermo/PDSS_HKFT.h | 4 +- include/cantera/thermo/PDSS_IdealGas.h | 2 +- include/cantera/thermo/PDSS_IonsFromNeutral.h | 2 +- include/cantera/thermo/PDSS_SSVol.h | 2 +- include/cantera/thermo/PDSS_Water.h | 2 +- include/cantera/thermo/Phase.h | 4 +- .../cantera/thermo/PhaseCombo_Interaction.h | 36 ++++----- include/cantera/thermo/PseudoBinaryVPSSTP.h | 4 +- include/cantera/thermo/PureFluidPhase.h | 4 +- include/cantera/thermo/RedlichKisterVPSSTP.h | 16 ++-- include/cantera/thermo/SingleSpeciesTP.h | 2 +- include/cantera/thermo/SpeciesThermo.h | 10 +-- include/cantera/thermo/SpeciesThermoFactory.h | 2 +- .../cantera/thermo/SpeciesThermoInterpType.h | 8 +- include/cantera/thermo/StoichSubstance.h | 10 +-- include/cantera/thermo/StoichSubstanceSSTP.h | 4 +- include/cantera/thermo/SurfPhase.h | 6 +- include/cantera/thermo/ThermoFactory.h | 6 +- include/cantera/thermo/ThermoPhase.h | 12 +-- include/cantera/thermo/VPSSMgr.h | 6 +- include/cantera/thermo/VPStandardStateTP.h | 2 +- include/cantera/thermo/WaterPropsIAPWSphi.h | 2 +- include/cantera/thermo/WaterSSTP.h | 10 +-- include/cantera/transport/AqueousTransport.h | 6 +- include/cantera/transport/LTPspecies.h | 2 +- .../cantera/transport/LiquidTranInteraction.h | 4 +- include/cantera/transport/LiquidTransport.h | 14 ++-- include/cantera/transport/SimpleTransport.h | 2 +- include/cantera/transport/TransportBase.h | 4 +- include/cantera/transport/TransportParams.h | 2 +- interfaces/cython/cantera/ctml_writer.py | 2 +- interfaces/cython/cantera/mixture.pyx | 2 +- interfaces/cython/cantera/thermo.pyx | 2 +- platform/posix/SConscript | 2 +- src/base/application.h | 2 +- src/base/ctml.cpp | 2 +- src/equil/BasisOptimize.cpp | 2 +- src/equil/ChemEquil.cpp | 6 +- src/equil/vcs_MultiPhaseEquil.cpp | 4 +- src/equil/vcs_TP.cpp | 2 +- src/equil/vcs_VolPhase.cpp | 2 +- src/equil/vcs_phaseStability.cpp | 2 +- src/equil/vcs_solve_TP.cpp | 4 +- src/kinetics/KineticsFactory.cpp | 2 +- src/kinetics/importKinetics.cpp | 14 ++-- src/kinetics/solveSP.cpp | 6 +- src/numerics/BEulerInt.cpp | 16 ++-- src/numerics/CVodeInt.cpp | 6 +- src/numerics/CVodeInt.h | 6 +- src/numerics/CVodesIntegrator.cpp | 4 +- src/numerics/NonlinearSolver.cpp | 60 +++++++------- src/numerics/solveProb.cpp | 8 +- src/thermo/DebyeHuckel.cpp | 4 +- src/thermo/Elements.cpp | 2 +- src/thermo/GibbsExcessVPSSTP.cpp | 2 +- src/thermo/HMWSoln.cpp | 2 +- src/thermo/IdealMolalSoln.cpp | 2 +- src/thermo/IonsFromNeutralVPSSTP.cpp | 2 +- src/thermo/MargulesVPSSTP.cpp | 2 +- src/thermo/MixedSolventElectrolyte.cpp | 2 +- src/thermo/MixtureFugacityTP.cpp | 2 +- src/thermo/MolarityIonicVPSSTP.cpp | 4 +- src/thermo/NasaThermo.h | 2 +- src/thermo/PseudoBinaryVPSSTP.cpp | 4 +- src/thermo/RedlichKisterVPSSTP.cpp | 2 +- src/thermo/ThermoFactory.cpp | 4 +- src/thermo/VPSSMgrFactory.cpp | 4 +- src/transport/LTPspecies.cpp | 2 +- src/transport/TransportParams.cpp | 2 +- .../VCSnonideal/NaCl_equil/HMW_NaCl.xml | 6 +- .../HMW_dupl_test/HMW_NaCl_sp1977_alt.xml | 6 +- .../HMW_graph_CpvT/HMW_NaCl_sp1977_alt.xml | 6 +- .../cathermo/HMW_graph_GvI/HMW_NaCl.xml | 4 +- .../HMW_graph_GvT/HMW_NaCl_sp1977_alt.xml | 6 +- .../cathermo/HMW_graph_GvT/HMW_graph_GvT.cpp | 2 +- .../HMW_graph_HvT/HMW_NaCl_sp1977_alt.xml | 6 +- .../HMW_graph_VvT/HMW_NaCl_sp1977_alt.xml | 6 +- .../surfSolverTest/surfaceSolver.cpp | 8 +- .../surfSolverTest/surfaceSolver2.cpp | 10 +-- 127 files changed, 466 insertions(+), 467 deletions(-) diff --git a/SConstruct b/SConstruct index 00fd2ec24..53e39864b 100644 --- a/SConstruct +++ b/SConstruct @@ -1384,8 +1384,7 @@ if env['use_sundials'] == 'y': else: env['sundials_libs'] = [] -# Add lapack and blas to the link line -# If there is a special blas and lapack add that in +# Add LAPACK and BLAS to the link line if env['blas_lapack_libs']: linkLibs.extend(env['blas_lapack_libs']) linkSharedLibs.extend(env['blas_lapack_libs']) diff --git a/include/cantera/base/ctexceptions.h b/include/cantera/base/ctexceptions.h index 83ae80e2f..b64ce0453 100644 --- a/include/cantera/base/ctexceptions.h +++ b/include/cantera/base/ctexceptions.h @@ -58,7 +58,7 @@ namespace Cantera //! Enum containing Cantera's behavior for situations where overflow or underflow of real variables //! may occur. /*! - * Note this frequently occurs when taking exponentials of delta gibbs energies of reactions + * Note this frequently occurs when taking exponentials of delta Gibbs energies of reactions * or when taking the exponentials of logs of activity coefficients. */ enum CT_RealNumber_Range_Behavior { diff --git a/include/cantera/base/ctml.h b/include/cantera/base/ctml.h index 4cba4450e..ff410b7db 100644 --- a/include/cantera/base/ctml.h +++ b/include/cantera/base/ctml.h @@ -727,7 +727,7 @@ void getNamedStringValue(const Cantera::XML_Node& node, const std::string& nameS std::string& typeString); //! This function reads a child node with the name, nameString, and returns -//! its xml value as the return string +//! its XML value as the return string /*! * If the child XML_node named "name" doesn't exist, the empty string is returned. * @@ -783,7 +783,7 @@ void ct2ctml(const char* file, const int debug = 0); //! Get a string with the ctml representation of a cti file. /*! * @param file Path to the input file in CTI format - * @return String containing the xml representation of the input file + * @return String containing the XML representation of the input file * * @ingroup inputfiles */ @@ -792,7 +792,7 @@ std::string ct2ctml_string(const std::string& file); //! Get a string with the ctml representation of a cti input string. /*! * @param cti String containing the cti representation - * @return String containing the xml representation of the input + * @return String containing the XML representation of the input * * @ingroup inputfiles */ diff --git a/include/cantera/base/global.h b/include/cantera/base/global.h index 43c31fc83..332184745 100644 --- a/include/cantera/base/global.h +++ b/include/cantera/base/global.h @@ -85,7 +85,7 @@ void popError(); * Additional directories may be added by calling function addDirectory. * * There are two different types of input files within %Cantera: - * - ctml: This is an xml file laid out in such a way that %Cantera can + * - ctml: This is an XML file laid out in such a way that %Cantera can * interpret the contents. This is the essential input file within * Cantera, and contains all elements that are involved with simulation, * error propagation, data support, and versioning. @@ -224,15 +224,15 @@ void close_XML_File(const std::string& file); * * @param file_ID This is a concatenation of two strings separated * by the "#" character. The string before the - * pound character is the file name of an xml + * pound character is the file name of an XML * file to carry out the search. The string after * the # character is the ID attribute - * of the xml element to search for. + * of the XML element to search for. * The string is interpreted as a file string if * no # character is in the string. * * @param root If the file string is empty, searches for the - * xml element with matching ID attribute are + * XML element with matching ID attribute are * carried out from this XML node. * * @return @@ -249,21 +249,21 @@ XML_Node* get_XML_Node(const std::string& file_ID, XML_Node* root); * XML element name and the ID attribute of the XML element. * An exact match of both is usually required. However, the * ID attribute may be set to "", in which case the first - * xml element with the correct element name will be returned. + * XML element with the correct element name will be returned. * * @param nameTarget This is the XML element name to look for. * * @param file_ID This is a concatenation of two strings separated * by the "#" character. The string before the - * pound character is the file name of an xml + * pound character is the file name of an XML * file to carry out the search. The string after * the # character is the ID attribute - * of the xml element to search for. + * of the XML element to search for. * The string is interpreted as a file string if * no # character is in the string. * * @param root If the file string is empty, searches for the - * xml element with matching ID attribute are + * XML element with matching ID attribute are * carried out from this XML node. * * @return diff --git a/include/cantera/base/xml.h b/include/cantera/base/xml.h index 1361ac6fa..c18733df9 100644 --- a/include/cantera/base/xml.h +++ b/include/cantera/base/xml.h @@ -156,7 +156,7 @@ public: */ XML_Node& addChild(const std::string& sname); - //! Add a child node to the current xml node, and at the + //! Add a child node to the current XML node, and at the //! same time add a value to the child /*! * Resulting XML string: @@ -169,7 +169,7 @@ public: */ XML_Node& addChild(const std::string& name, const std::string& value); - //! Add a child node to the current xml node, and at the + //! Add a child node to the current XML node, and at the //! same time add a formatted value to the child /*! * This version supplies a formatting string (printf format) @@ -419,7 +419,7 @@ public: //! Return an unchangeable reference to the vector of children of the current node /*! * Each of the individual XML_Node child pointers, however, - * is to a changeable xml node object. + * is to a changeable XML node object. * */ const std::vector& children() const; @@ -434,7 +434,7 @@ public: //! Boolean function indicating whether a comment bool isComment() const; - //! Require that the current xml node have an attribute named by the first + //! Require that the current XML node have an attribute named by the first //! argument, a, and that this attribute have the the string value listed //! in the second argument, v. /*! @@ -446,13 +446,13 @@ public: void _require(const std::string& a, const std::string& v) const; //! This routine carries out a recursive search for an XML node based - //! on both the xml element name and the attribute ID. + //! on both the XML element name and the attribute ID. /*! * If exact matches are found for both fields, the pointer * to the matching XML Node is returned. * * The ID attribute may be defaulted by setting it to "". In this case the - * pointer to the first xml element matching the name only is returned. + * pointer to the first XML element matching the name only is returned. * * @param nameTarget Name of the XML Node that is being searched for * @param idTarget "id" attribute of the XML Node that the routine @@ -468,14 +468,14 @@ public: const std::string& idTarget) const; //! This routine carries out a search for an XML node based - //! on both the xml element name and the attribute ID and an integer index. + //! on both the XML element name and the attribute ID and an integer index. /*! * If exact matches are found for all fields, the pointer * to the matching XML Node is returned. The search is only carried out on * the current element and the child elements of the current element. * * The "id" attribute may be defaulted by setting it to "". - * In this case the pointer to the first xml element matching the name + * In this case the pointer to the first XML element matching the name * only is returned. * * @param nameTarget Name of the XML Node that is being searched for @@ -490,13 +490,13 @@ public: const std::string& idTarget, const int index) const; //! This routine carries out a recursive search for an XML node based - //! on the xml element attribute, "id" + //! on the XML element attribute, "id" /*! * If exact match is found, the pointer * to the matching XML Node is returned. If not, 0 is returned. * * The ID attribute may be defaulted by setting it to "". - * In this case the pointer to the first xml element matching the name + * In this case the pointer to the first XML element matching the name * only is returned. * * @param id "id" attribute of the XML Node that the routine @@ -588,7 +588,7 @@ public: */ XML_Node& child(const std::string& loc) const; - //! Write the header to the xml file to the specified ostream + //! Write the header to the XML file to the specified ostream /*! * @param s ostream to write the output to */ @@ -664,7 +664,7 @@ private: /*! * This is the main recursive routine. It doesn't put a final endl * on. This is fixed up in the public method. A method to only write out a limited - * amount of the xml tree has been added. + * amount of the XML tree has been added. * * @param s ostream to write to * @param level Indentation level to work from @@ -685,10 +685,10 @@ protected: */ std::string m_name; - //! Value of the xml node + //! Value of the XML node /*! * This is the string contents of the XML node. For - * example. The xml node named eps: + * example. The XML node named eps: * * * valueString diff --git a/include/cantera/equil/ChemEquil.h b/include/cantera/equil/ChemEquil.h index d9a834d81..95d78b967 100644 --- a/include/cantera/equil/ChemEquil.h +++ b/include/cantera/equil/ChemEquil.h @@ -132,7 +132,7 @@ public: * @param loglevel Specify amount of debug logging (0 to disable) * @return Successful returns are indicated by a return value of 0. * Unsuccessful returns are indicated by a return value of -1 for lack - * of convergence or -3 for a singular jacobian. + * of convergence or -3 for a singular Jacobian. */ int equilibrate(thermo_t& s, const char* XY, vector_fp& elMoles, bool useThermoPhaseElementPotentials = false, int loglevel = 0); @@ -195,7 +195,7 @@ protected: * * We have found that the previous estimate may not be good enough to * avoid drastic numerical issues associated with the use of a numerically - * generated jacobian used in the main algorithm. + * generated Jacobian used in the main algorithm. * * The Brinkley algorithm, here, assumes a constant T, P system and uses a * linearized analytical Jacobian that turns out to be very stable even @@ -211,14 +211,14 @@ protected: * * Nonideal phases are handled in principle. This is done by calculating * the activity coefficients and adding them into the formula in the - * correct position. However, these are treated as a rhs contribution + * correct position. However, these are treated as a RHS contribution * only. Therefore, convergence might be a problem. This has not been * tested. Also molality based unit systems aren't handled. * * On return, int return value contains the success code: * - 0 - successful * - 1 - unsuccessful, max num iterations exceeded - * - -3 - unsuccessful, singular jacobian + * - -3 - unsuccessful, singular Jacobian * * NOTE: update for activity coefficients. */ @@ -325,7 +325,7 @@ protected: vector_fp m_mu_RT; /** - * Dimensionless values of the gibbs free energy for the + * Dimensionless values of the Gibbs free energy for the * standard state of each species, at the temperature and * pressure of the solution (the star standard state). */ diff --git a/include/cantera/equil/vcs_MultiPhaseEquil.h b/include/cantera/equil/vcs_MultiPhaseEquil.h index 5db3d65fb..246dc197d 100644 --- a/include/cantera/equil/vcs_MultiPhaseEquil.h +++ b/include/cantera/equil/vcs_MultiPhaseEquil.h @@ -171,7 +171,7 @@ namespace VCSnonideal * @param mphase MultiPhase object that is the source for all of the information * @param vprob VCS_PROB problem definition that gets all of the information * - * Note, both objects share the underlying Thermophase objects. So, neither + * Note, both objects share the underlying ThermoPhase objects. So, neither * can be const objects. */ int vcs_Cantera_to_vprob(Cantera::MultiPhase* mphase, diff --git a/include/cantera/equil/vcs_VolPhase.h b/include/cantera/equil/vcs_VolPhase.h index 9b9ddd6d3..97eeb1d29 100644 --- a/include/cantera/equil/vcs_VolPhase.h +++ b/include/cantera/equil/vcs_VolPhase.h @@ -211,7 +211,7 @@ public: * The results are held internally within the object. * * @param kspec Species number (within the phase) - * @return Gstar[kspec] returns the gibbs free energy for the + * @return Gstar[kspec] returns the Gibbs free energy for the * standard state of the kth species. */ double GStar_calc_one(size_t kspec) const; @@ -220,7 +220,7 @@ public: //! of a species, return a value for one species /*! * @param kspec species index - * @return return value of the gibbs free energy + * @return return value of the Gibbs free energy */ double G0_calc_one(size_t kspec) const; @@ -274,12 +274,12 @@ public: */ void setState_T(const double temperature_Kelvin); - // Downloads the ln ActCoeff jacobian into the VCS version of the - // ln ActCoeff jacobian. + // Downloads the ln ActCoeff Jacobian into the VCS version of the + // ln ActCoeff Jacobian. /* * This is essentially a scatter operation. * - * @param LnAcJac_VCS jacobian parameter + * @param LnAcJac_VCS Jacobian parameter * The Jacobians are actually d( lnActCoeff) / d (MolNumber); * dLnActCoeffdMolNumber(k,j) * @@ -486,7 +486,7 @@ public: * Also decide whether we need a new charge neutrality element in the * phase to enforce a charge neutrality constraint. * - * @param tPhase Pointer to the thermophase object + * @param tPhase Pointer to the ThermoPhase object */ size_t transferElementsFM(const Cantera::ThermoPhase* const tPhase); diff --git a/include/cantera/equil/vcs_solve.h b/include/cantera/equil/vcs_solve.h index 782e10b8e..7f8323504 100644 --- a/include/cantera/equil/vcs_solve.h +++ b/include/cantera/equil/vcs_solve.h @@ -666,7 +666,7 @@ public: * The actual problem statement is assumed to be in the structure * already. This is a wrapper around the solve_TP() function. In this * wrapper, we nondimensionalize the system we calculate the standard - * state gibbs free energies of the species, and we decide whether to we + * state Gibbs free energies of the species, and we decide whether to we * need to use the initial guess algorithm. * * @param ipr = 1 -> Print results to standard output; @@ -1305,7 +1305,7 @@ private: double vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete, char* ANOTE=0) const; - //! This routine optimizes the minimization of the total gibbs free energy + //! This routine optimizes the minimization of the total Gibbs free energy //! by making sure the slope of the following functional stays negative: /*! * The slope of the following functional is equivalent to the slope diff --git a/include/cantera/kinetics/ElectrodeKinetics.h b/include/cantera/kinetics/ElectrodeKinetics.h index 5d41bd8c0..6734d604f 100644 --- a/include/cantera/kinetics/ElectrodeKinetics.h +++ b/include/cantera/kinetics/ElectrodeKinetics.h @@ -37,7 +37,7 @@ public: * @param thermo The optional parameter may be used to initialize * the object with one ThermoPhase object. * HKM Note -> Since the interface kinetics - * object will probably require multiple thermophase + * object will probably require multiple ThermoPhase * objects, this is probably not a good idea * to have this parameter. */ diff --git a/include/cantera/kinetics/ImplicitSurfChem.h b/include/cantera/kinetics/ImplicitSurfChem.h index 6a6c6425c..db58ea599 100644 --- a/include/cantera/kinetics/ImplicitSurfChem.h +++ b/include/cantera/kinetics/ImplicitSurfChem.h @@ -245,7 +245,7 @@ protected: size_t m_numTotalSpecies; std::vector pLocVec; - //! Pointer to the cvode integrator + //! Pointer to the CVODE integrator Integrator* m_integ; doublereal m_atol, m_rtol; // tolerances doublereal m_maxstep; //!< max step size diff --git a/include/cantera/kinetics/InterfaceKinetics.h b/include/cantera/kinetics/InterfaceKinetics.h index ffc5c736e..e46e5086d 100644 --- a/include/cantera/kinetics/InterfaceKinetics.h +++ b/include/cantera/kinetics/InterfaceKinetics.h @@ -93,7 +93,7 @@ public: * @param thermo The optional parameter may be used to initialize * the object with one ThermoPhase object. * HKM Note -> Since the interface kinetics - * object will probably require multiple thermophase + * object will probably require multiple ThermoPhase * objects, this is probably not a good idea * to have this parameter. */ @@ -135,7 +135,7 @@ public: */ void updateExchangeCurrentQuantities(); - //! Return the vector of values for the reaction gibbs free energy change. + //! Return the vector of values for the reaction Gibbs free energy change. /*! * (virtual from Kinetics.h) * These values depend upon the concentration of the solution. @@ -330,7 +330,7 @@ public: * kmoles/m2/s. * * For a reaction rate constant that was given in units of kmol/m2/sec when the - * reaction type is a butler-volmer form, convert it to exchange current density + * reaction type is a Butler-Volmer form, convert it to exchange current density * form (amps/m2). * * @param kfwd Vector of forward reaction rate constants, given in either @@ -553,7 +553,7 @@ protected: */ std::vector m_ctrxn; - //! Vector of Reactions which follow the butler volmer methodology for specifying the + //! Vector of Reactions which follow the Butler-Volmer methodology for specifying the //! exchange current density first. Then, the other forms are specified based on this form. /*! * Length is equal to the number of reactions with charge transfer coefficients, m_ctrxn[] @@ -605,14 +605,14 @@ protected: */ vector_fp m_StandardConc; - //! Vector of delta G^0, the standard state gibbs free energies for each reaction + //! Vector of delta G^0, the standard state Gibbs free energies for each reaction /*! * Length is the number of reactions * units are Joule kmol-1 */ vector_fp m_deltaG0; - //! Vector of deltaG[] of reaction, the delta gibbs free energies for each reaction + //! Vector of deltaG[] of reaction, the delta Gibbs free energies for each reaction /*! * Length is the number of reactions * units are Joule kmol-1 @@ -661,7 +661,7 @@ protected: //! Boolean flag indicating whether any reaction in the mechanism //! is described by an exchange current density expression /*! - * If this is true, the standard state gibbs free energy of the reaction + * If this is true, the standard state Gibbs free energy of the reaction * and the product of the reactant standard concentrations must be * precalculated in order to calculate the rate constant. */ diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h index 5992579e1..df617150b 100644 --- a/include/cantera/kinetics/Kinetics.h +++ b/include/cantera/kinetics/Kinetics.h @@ -474,7 +474,7 @@ public: */ virtual void getRevReactionDelta(const doublereal* g, doublereal* dg); - //! Return the vector of values for the reaction gibbs free energy change. + //! Return the vector of values for the reaction Gibbs free energy change. /*! * (virtual from Kinetics.h) * These values depend upon the concentration of the solution. @@ -527,7 +527,7 @@ public: /** * Return the vector of values for the reaction standard state - * gibbs free energy change. These values don't depend upon + * Gibbs free energy change. These values don't depend upon * the concentration of the solution. * * units = J kmol-1 @@ -1063,7 +1063,7 @@ protected: std::vector m_start; /** - * Mapping of the phase id, i.e., the id attribute in the xml + * Mapping of the phase id, i.e., the id attribute in the XML * phase element to the position of the phase within the * kinetics object. Positions start with the value of 1. The * member function, phaseIndex() decrements by one before diff --git a/include/cantera/kinetics/KineticsFactory.h b/include/cantera/kinetics/KineticsFactory.h index 1541c90f9..516b6263d 100644 --- a/include/cantera/kinetics/KineticsFactory.h +++ b/include/cantera/kinetics/KineticsFactory.h @@ -51,8 +51,8 @@ public: * progress of the reactions and for calculating the source terms for * species. * - * @param phase An XML_Node that contains the xml data describing the - * phase. Of particular note to this routine is the child xml + * @param phase An XML_Node that contains the XML data describing the + * phase. Of particular note to this routine is the child XML * element called "kinetics". The element has one attribute * called "model", with a string value. The value of this * string is used to decide which kinetics manager is used to diff --git a/include/cantera/kinetics/StoichManager.h b/include/cantera/kinetics/StoichManager.h index 98318c2eb..bd9cb0850 100644 --- a/include/cantera/kinetics/StoichManager.h +++ b/include/cantera/kinetics/StoichManager.h @@ -110,8 +110,8 @@ namespace Cantera * * The functions incrementReaction() and decrementReaction() are used to find * the standard state equilibrium constant for a reaction. Here, output[] is a - * vector of length number of reactions, usually the standard gibbs free - * energies of reaction, while input, usually the standard state gibbs free + * vector of length number of reactions, usually the standard Gibbs free + * energies of reaction, while input, usually the standard state Gibbs free * energies of species, is a vector of length number of species. * * Note the stoichiometric coefficient for a species in a reaction is handled diff --git a/include/cantera/kinetics/importKinetics.h b/include/cantera/kinetics/importKinetics.h index 9b709ba7b..40cd36932 100644 --- a/include/cantera/kinetics/importKinetics.h +++ b/include/cantera/kinetics/importKinetics.h @@ -69,7 +69,7 @@ void checkRxnElementBalance(Kinetics& kin, * 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] 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 @@ -94,7 +94,7 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp, std::string default //! Read the rate coefficient data from the XML file. /*! - * Extract the rate coefficient for a reaction from the xml node, kf. + * 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. @@ -116,9 +116,9 @@ void getRateCoefficient(const XML_Node& kf, Kinetics& kin, ReactionData& rdata, //! Install information about reactions into the kinetics object, kin. /*! - * At this point, parent usually refers to the phase xml element. + * At this point, parent usually refers to the phase XML element. * One of the children of this element is reactionArray, - * the element which determines where in the xml file to + * the element which determines where in the XML file to * look up the reaction rate data. * * @param p parent XML phase element @@ -148,7 +148,7 @@ bool installReactionArrays(const XML_Node& p, Kinetics& kin, * argument. The vector of ThermoPhase objects should consist of pointers to * phases I, A, and B. * - * @param phase This is an xml node containing a description of the owning + * @param phase This is an XML node containing a description of the owning * phase for the kinetics object. Within the phase is a XML * element called reactionArray containing the location of the * description of the reactions that make up the kinetics object. diff --git a/include/cantera/kinetics/solveSP.h b/include/cantera/kinetics/solveSP.h index 496731d1f..6d6b717d4 100644 --- a/include/cantera/kinetics/solveSP.h +++ b/include/cantera/kinetics/solveSP.h @@ -31,7 +31,7 @@ const int SFLUX_INITIALIZE = 1; const int SFLUX_RESIDUAL = 2; //! Calculation of the surface problem is due to the need for a numerical -//! jacobian for the gas-problem. The solution is expected to be very close to +//! Jacobian for the gas-problem. The solution is expected to be very close to //! the initial guess, and accuracy is needed because solution variables have //! been perturbed from nominal values to create Jacobian entries. const int SFLUX_JACOBIAN = 3; @@ -303,7 +303,7 @@ private: * @param resid output Vector of residuals, length = m_neq * @param CSolnSP Vector of species concentrations, unknowns in the * problem, length = m_neq. These are tweaked in order - * to derive the columns of the jacobian. + * to derive the columns of the Jacobian. * @param CSolnSPOld Old Vector of species concentrations, unknowns in the * problem, length = m_neq * @param do_time Calculate a time dependent residual diff --git a/include/cantera/numerics/BEulerInt.h b/include/cantera/numerics/BEulerInt.h index 4dc8cd3e4..d9573cdc3 100644 --- a/include/cantera/numerics/BEulerInt.h +++ b/include/cantera/numerics/BEulerInt.h @@ -57,7 +57,7 @@ class BEulerInt : public Integrator { public: /*! - * Constructor. Default settings: dense jacobian, no user-supplied + * Constructor. Default settings: dense Jacobian, no user-supplied * Jacobian function, Newton iteration. */ BEulerInt(); @@ -118,7 +118,7 @@ public: * @param printSolnFirstSteps The solution is printed out the first * "printSolnFirstSteps" steps. After these steps the * other parameters determine the printing. default = 0 - * @param dumpJacobians Dump jacobians to disk. + * @param dumpJacobians Dump Jacobians to disk. */ virtual void setPrintSolnOptions(int printSolnStepInterval, int printSolnNumberToTout, @@ -155,7 +155,7 @@ public: * residual at the current time step. * @param J = Jacobian matrix to be filled in * @param f = Right hand side. This routine returns the current - * value of the rhs (output), so that it does + * value of the RHS (output), so that it does * not have to be computed again. */ void beuler_jac(GeneralMatrix& J, double* const f, @@ -307,7 +307,7 @@ protected: * @param CJ Inverse of the time step * @param time_curr Current value of the time * @param jac Jacobian - * @param num_newt_its number of newton iterations + * @param num_newt_its number of Newton iterations * @param num_linear_solves number of linear solves * @param num_backtracks number of backtracs * @param loglevel Log level @@ -351,8 +351,8 @@ protected: * couldn't possibly be representative if the * variable is changed by a lot. (true for * nonlinear systems, false for linear systems) - * Maximum increase in variable in any one newton iteration: factor of 2 - * Maximum decrease in variable in any one newton iteration: factor of 5 + * Maximum increase in variable in any one Newton iteration: factor of 2 + * Maximum decrease in variable in any one Newton iteration: factor of 5 * * @param y Current value of the solution * @param step0 Current raw step change in y[] @@ -416,7 +416,7 @@ protected: bool m_colScaling; /** * m_matrixConditioning is a boolean. If true, then the - * Jacobian and every rhs is multiplied by the inverse + * Jacobian and every RHS is multiplied by the inverse * of a matrix that is suppose to reduce the condition * number of the matrix. This is done before row scaling. */ @@ -532,7 +532,7 @@ protected: vector_fp m_rowScales; vector_fp m_colScales; - //! Pointer to the jacobian representing the time dependent problem + //! Pointer to the Jacobian representing the time dependent problem GeneralMatrix* tdjac_ptr; /** @@ -558,7 +558,7 @@ protected: */ int m_nJacEval; - //! Number of total newton iterations + //! Number of total Newton iterations int m_numTotalNewtIts; //! Total number of linear iterations diff --git a/include/cantera/numerics/BandMatrix.h b/include/cantera/numerics/BandMatrix.h index 5c77ac14f..dfdad36cc 100644 --- a/include/cantera/numerics/BandMatrix.h +++ b/include/cantera/numerics/BandMatrix.h @@ -170,7 +170,7 @@ public: //! Solve the matrix problem Ax = b /*! - * @param b INPUT rhs of the problem + * @param b INPUT RHS of the problem * @param x OUTPUT solution to the problem * * @return Return a success flag @@ -181,7 +181,7 @@ public: //! Solve the matrix problem Ax = b /*! - * @param b INPUT rhs of the problem + * @param b INPUT RHS of the problem * OUTPUT solution to the problem * @param nrhs Number of right hand sides to solve * @param ldb Leading dimension of `b`. Default is nColumns() @@ -278,7 +278,7 @@ public: */ virtual void copyData(const GeneralMatrix& y); - //! Check to see if we have any zero rows in the jacobian + //! Check to see if we have any zero rows in the Jacobian /*! * This utility routine checks to see if any rows are zero. * The smallest row is returned along with the largest coefficient in that row @@ -289,7 +289,7 @@ public: */ virtual size_t checkRows(doublereal& valueSmall) const; - //! Check to see if we have any zero columns in the jacobian + //! Check to see if we have any zero columns in the Jacobian /*! * This utility routine checks to see if any columns are zero. * The smallest column is returned along with the largest coefficient in that column diff --git a/include/cantera/numerics/CVodesIntegrator.h b/include/cantera/numerics/CVodesIntegrator.h index d36c06af0..02c10297f 100644 --- a/include/cantera/numerics/CVodesIntegrator.h +++ b/include/cantera/numerics/CVodesIntegrator.h @@ -37,7 +37,7 @@ class CVodesIntegrator : public Integrator { public: /** - * Constructor. Default settings: dense jacobian, no user-supplied + * Constructor. Default settings: dense Jacobian, no user-supplied * Jacobian function, Newton iteration. */ CVodesIntegrator(); diff --git a/include/cantera/numerics/DenseMatrix.h b/include/cantera/numerics/DenseMatrix.h index 8f4eae6af..3ab35e8fc 100644 --- a/include/cantera/numerics/DenseMatrix.h +++ b/include/cantera/numerics/DenseMatrix.h @@ -110,7 +110,7 @@ public: //! Return a const vector of const pointers to the columns /*! - * Note, the jacobian can not be altered by this routine, and + * Note, the Jacobian can not be altered by this routine, and * therefore the member function is const. * * @return returns a vector of pointers to the top of the columns @@ -196,7 +196,7 @@ public: * The system is then solved using the LAPACK routine dgetrs * * @param A Dense matrix to be factored - * @param b rhs(s) to be solved. + * @param b RHS(s) to be solved. * @param nrhs Number of right hand sides to solve * @param ldb Leading dimension of b, if nrhs > 1 */ @@ -205,7 +205,7 @@ int solve(DenseMatrix& A, double* b, size_t nrhs=1, size_t ldb=0); //! Solve Ax = b for multiple right-hand-side vectors. /*! * @param A Dense matrix to be factored - * @param b Dense matrix of rhs's. Each column is a rhs + * @param b Dense matrix of RHS's. Each column is a RHS */ int solve(DenseMatrix& A, DenseMatrix& b); diff --git a/include/cantera/numerics/GeneralMatrix.h b/include/cantera/numerics/GeneralMatrix.h index 2b1173f03..82f6ed1a6 100644 --- a/include/cantera/numerics/GeneralMatrix.h +++ b/include/cantera/numerics/GeneralMatrix.h @@ -76,7 +76,7 @@ public: /*! * we set m_factored to 2 to indicate the matrix is now QR factored * - * @return Returns the info variable from lapack + * @return Returns the info variable from LAPACK */ virtual int factorQR() { throw NotImplementedError("GeneralMatrix::factorQR"); @@ -136,7 +136,7 @@ public: //! Solves the Ax = b system returning x in the b spot. /*! - * @param b Vector for the rhs of the equation system + * @param b Vector for the RHS of the equation system * @param nrhs Number of right-hand sides to solve, default 1 * @param ldb Leading dimension of the right-hand side array. * Defaults to nRows() @@ -204,7 +204,7 @@ public: */ virtual doublereal* const* colPts() = 0; - //! Check to see if we have any zero rows in the jacobian + //! Check to see if we have any zero rows in the Jacobian /*! * This utility routine checks to see if any rows are zero. * The smallest row is returned along with the largest coefficient in that row @@ -215,7 +215,7 @@ public: */ virtual size_t checkRows(doublereal& valueSmall) const = 0; - //! Check to see if we have any zero columns in the jacobian + //! Check to see if we have any zero columns in the Jacobian /*! * This utility routine checks to see if any columns are zero. * The smallest column is returned along with the largest coefficient in that column diff --git a/include/cantera/numerics/IDA_Solver.h b/include/cantera/numerics/IDA_Solver.h index 3fe11ff8a..1df09e001 100644 --- a/include/cantera/numerics/IDA_Solver.h +++ b/include/cantera/numerics/IDA_Solver.h @@ -14,7 +14,7 @@ #include "sundials/sundials_nvector.h" -// These constants are defined internally in the ida package, ida.c +// These constants are defined internally in the IDA package, ida.c #define IDA_NN 0 #define IDA_SS 1 #define IDA_SV 2 @@ -43,7 +43,7 @@ public: //! Constructor. /*! - * Default settings: dense jacobian, no user-supplied Jacobian function, Newton iteration. + * Default settings: dense Jacobian, no user-supplied Jacobian function, Newton iteration. * * @param f Function that will supply the time dependent residual to be solved */ @@ -95,13 +95,13 @@ public: virtual double getCurrentStepFromIDA(); - //! Set the form of the jacobian + //! Set the form of the Jacobian /*! * - * @param formJac Form of the jacobian + * @param formJac Form of the Jacobian * - * 0 numerical jacobian - * 1 analytical jacobian given by the evalJacobianDP() function + * 0 numerical Jacobian + * 1 analytical Jacobian given by the evalJacobianDP() function */ virtual void setJacobianType(int formJac); @@ -261,12 +261,12 @@ protected: //! maximum time step order of the method int m_maxord; - //! Form of the jacobian + //! Form of the Jacobian /*! - * 0 numerical jacobian created by ida - * 1 analytical jacobian. Must have populated the evalJacobianDP() + * 0 numerical Jacobian created by IDA + * 1 analytical Jacobian. Must have populated the evalJacobianDP() * function in the ResidJacEval class. - * 2 numerical jacobian formed by the ResidJacEval class (unimplemented) + * 2 numerical Jacobian formed by the ResidJacEval class (unimplemented) */ int m_formJac; diff --git a/include/cantera/numerics/NonlinearSolver.h b/include/cantera/numerics/NonlinearSolver.h index 462b3f2f3..b2a8551b4 100644 --- a/include/cantera/numerics/NonlinearSolver.h +++ b/include/cantera/numerics/NonlinearSolver.h @@ -53,9 +53,9 @@ namespace Cantera #define NSOLN_RETN_FAIL_STEPTOOSMALL -1 //! The nonlinear problem didn't solve the problem #define NSOLN_RETN_FAIL_DAMPSTEP -2 -//! The nonlinear problem's jacobian is singular +//! The nonlinear problem's Jacobian is singular #define NSOLN_RETN_MATRIXINVERSIONERROR -3 -//! The nonlinear problem's jacobian formation produced an error +//! The nonlinear problem's Jacobian formation produced an error #define NSOLN_RETN_JACOBIANFORMATIONERROR -4 //! The nonlinear problem's base residual produced an error #define NSOLN_RETN_RESIDUALFORMATIONERROR -5 @@ -66,9 +66,9 @@ namespace Cantera //@{ /// @name Constant which determines the type of the Jacobian -//! The jacobian will be calculated from a numerical method +//! The Jacobian will be calculated from a numerical method #define NSOLN_JAC_NUM 1 -//! The jacobian is calculated from an analytical function +//! The Jacobian is calculated from an analytical function #define NSOLN_JAC_ANAL 2 //@} @@ -128,7 +128,7 @@ class NonlinearSolver public: //! Default constructor /*! - * @param func Residual and jacobian evaluator function object + * @param func Residual and Jacobian evaluator function object */ NonlinearSolver(ResidJacEval* func); @@ -216,9 +216,9 @@ public: * current values of the solution vector, m_y_n, and the solution time * derivative, m_ydot_n. The Jacobian is not recomputed. * - * A factored jacobian is reused, if available. If a factored jacobian - * is not available, then the jacobian is factored. Before factoring, - * the jacobian is row and column-scaled. Column scaling is not + * A factored Jacobian is reused, if available. If a factored Jacobian + * is not available, then the Jacobian is factored. Before factoring, + * the Jacobian is row and column-scaled. Column scaling is not * recomputed. The row scales are recomputed here, after column * scaling has been implemented. * @@ -228,14 +228,14 @@ public: * @param delta_y return value of the raw change in y * @param jac Jacobian * - * @return Returns the result code from lapack. A zero means success. + * @return Returns the result code from LAPACK. A zero means success. * Anything else indicates a failure. */ int doNewtonSolve(const doublereal time_curr, const doublereal* const y_curr, const doublereal* const ydot_curr, doublereal* const delta_y, GeneralMatrix& jac); - //! Compute the newton step, either by direct newton's or by solving a + //! Compute the Newton step, either by direct Newton's or by solving a //! close problem that is represented by a Hessian /*! * This is algorith A.6.5.1 in Dennis / Schnabel @@ -247,9 +247,9 @@ public: * solution vector, m_y_n, and the solution time derivative, m_ydot_n. * The Jacobian is not recomputed. * - * A factored jacobian is reused, if available. If a factored jacobian - * is not available, then the jacobian is factored. Before factoring, - * the jacobian is row and column-scaled. Column scaling is not + * A factored Jacobian is reused, if available. If a factored Jacobian + * is not available, then the Jacobian is factored. Before factoring, + * the Jacobian is row and column-scaled. Column scaling is not * recomputed. The row scales are recomputed here, after column * scaling has been implemented. * @@ -262,7 +262,7 @@ public: * --------------- * internal m_resid Stored residual is used as input * - * @return Returns the result code from lapack. A zero means success. Anything + * @return Returns the result code from LAPACK. A zero means success. Anything * else indicates a failure. */ int doAffineNewtonSolve(const doublereal* const y_curr, const doublereal* const ydot_curr, @@ -349,9 +349,9 @@ public: * couldn't possibly be representative if the * variable is changed by a lot. (true for * nonlinear systems, false for linear systems) - * Maximum increase in variable in any one newton iteration: + * Maximum increase in variable in any one Newton iteration: * factor of 2 - * Maximum decrease in variable in any one newton iteration: + * Maximum decrease in variable in any one Newton iteration: * factor of 5 * * @param y Current solution value of the old step @@ -386,18 +386,18 @@ public: */ void calc_ydot(const int order, const doublereal* const y_curr, doublereal* const ydot_curr) const; - //! Function called to evaluate the jacobian matrix and the current + //! Function called to evaluate the Jacobian matrix and the current //! residual vector at the current time step /*! * @param J Jacobian matrix to be filled in * @param f Right hand side. This routine returns the current - * value of the rhs (output), so that it does + * value of the RHS (output), so that it does * not have to be computed again. * @param time_curr Current time * @param CJ inverse of the value of deltaT * @param y value of the solution vector * @param ydot value of the time derivative of the solution vector - * @param num_newt_its Number of newton iterations + * @param num_newt_its Number of Newton iterations * * @return Returns a flag to indicate that operation is successful. * 1 Means a successful operation @@ -429,12 +429,12 @@ public: doublereal* const ydot_current); //! Return the factor by which the undamped Newton step 'step0' - //! must be multiplied in order to keep the update within the bounds of an accurate jacobian. + //! must be multiplied in order to keep the update within the bounds of an accurate Jacobian. /*! * The idea behind these is that the Jacobian couldn't possibly be representative, if the * variable is changed by a lot. (true for nonlinear systems, false for linear systems) - * Maximum increase in variable in any one newton iteration: factor of 1.5 - * Maximum decrease in variable in any one newton iteration: factor of 2 + * Maximum increase in variable in any one Newton iteration: factor of 1.5 + * Maximum decrease in variable in any one Newton iteration: factor of 2 * * @param y Initial value of the solution vector * @param step0 initial proposed step size @@ -501,8 +501,8 @@ public: * converged value of the solution derivative. * @param CJ Inverse of the value of deltaT * @param time_curr Current value of the time - * @param jac Matrix that will be used to store the jacobian - * @param num_newt_its Number of newton iterations taken + * @param jac Matrix that will be used to store the Jacobian + * @param num_newt_its Number of Newton iterations taken * @param num_linear_solves Number of linear solves taken * @param num_backtracks Number of backtracking steps taken * @param loglevelInput Input log level determines the amount of printing. @@ -679,9 +679,9 @@ public: */ void setResidualTols(double residRtol, double* residAtol, int residNormHandling = 2); - //! Set the value of the maximum # of newton iterations + //! Set the value of the maximum # of Newton iterations /*! - * @param maxNewtIts Maximum number of newton iterations + * @param maxNewtIts Maximum number of Newton iterations */ void setMaxNewtIts(const int maxNewtIts); @@ -716,7 +716,7 @@ public: * * The theoretical linearized residual decline * The actual residual decline in the steepest descent direction determined by numerical differencing - * The actual residual decline in the newton direction determined by numerical differencing + * The actual residual decline in the Newton direction determined by numerical differencing * * This routine doesn't need to be called for the solution of the nonlinear problem. * @@ -785,7 +785,7 @@ public: * @param ydot_n_1 INPUT First trial value of the derivative of the solution vector * @param stepNorm_1 OUTPUT Norm of the vector step_1 * @param stepNorm_2 OUTPUT Estimated norm of the vector step_2 - * @param jac INPUT jacobian + * @param jac INPUT Jacobian * @param num_backtracks OUTPUT number of backtracks taken in the current damping step * * @return 1 Successful step was taken. The predicted residual norm is less than one @@ -840,7 +840,7 @@ public: * @param alpha Relative distance along the particular curve. * * @return Returns the expected value of the residual at that point according to the quadratic model. - * The residual at the newton point will always be zero. + * The residual at the Newton point will always be zero. */ doublereal expectedResidLeg(int leg, doublereal alpha) const; @@ -891,7 +891,7 @@ public: */ private: - //! Pointer to the residual and jacobian evaluator for the + //! Pointer to the residual and Jacobian evaluator for the //! function /*! * See ResidJacEval.h for an evaluator. @@ -944,13 +944,13 @@ private: //! Weights for normalizing the values of the residuals /*! * These are computed if row scaling, m_rowScaling, is turned on. They are calculated currently as the - * sum of the absolute values of the rows of the jacobian. + * sum of the absolute values of the rows of the Jacobian. */ std::vector m_rowScales; //! Weights for normalizing the values of the residuals /*! - * They are calculated as the sum of the absolute values of the jacobian + * They are calculated as the sum of the absolute values of the Jacobian * multiplied by the solution weight function. * This is carried out in scaleMatrix(). */ @@ -989,7 +989,7 @@ private: //! Norm of the solution update created by the iteration in its raw, undamped form, using the solution norm doublereal m_normDeltaSoln_Newton; - //! Norm of the distance to the cauchy point using the solution norm + //! Norm of the distance to the Cauchy point using the solution norm doublereal m_normDeltaSoln_CP; //! Norm of the residual for a trial calculation which may or may not be used @@ -1044,15 +1044,15 @@ private: //! Number of local linear solves done during the current iteration int m_numLocalLinearSolves; - //! Total number of newton iterations + //! Total number of Newton iterations int m_numTotalNewtIts; public: - //! Minimum number of newton iterations to use + //! Minimum number of Newton iterations to use int m_min_newt_its; private: - //! Maximum number of newton iterations + //! Maximum number of Newton iterations int maxNewtIts_; //! Jacobian formation method @@ -1123,9 +1123,9 @@ private: //! Scale factor for turning residual norms into solution norms doublereal m_ScaleSolnNormToResNorm; - //! Copy of the jacobian that doesn't get overwritten when the inverse is determined + //! Copy of the Jacobian that doesn't get overwritten when the inverse is determined /*! - * The jacobian stored here is the raw matrix, before any row or column scaling is carried out + * The Jacobian stored here is the raw matrix, before any row or column scaling is carried out */ Cantera::GeneralMatrix* jacCopyPtr_; @@ -1139,7 +1139,7 @@ private: //! Steepest descent direction. This is also the distance to the Cauchy Point std::vector deltaX_CP_; - //! Newton Step - This is the newton step determined from the straight Jacobian + //! Newton Step - This is the Newton step determined from the straight Jacobian /* * Newton step for the current step only */ @@ -1246,7 +1246,7 @@ private: //! Expected DResid_dS for the Newton path - output variable doublereal ResidDecreaseNewtExp_; - //! Actual DResid_dS for the newton path - output variable + //! Actual DResid_dS for the Newton path - output variable doublereal ResidDecreaseNewt_; /******************************************************************************************* diff --git a/include/cantera/numerics/ResidJacEval.h b/include/cantera/numerics/ResidJacEval.h index 19d10ef54..19b01f7a5 100644 --- a/include/cantera/numerics/ResidJacEval.h +++ b/include/cantera/numerics/ResidJacEval.h @@ -86,7 +86,7 @@ public: * @param resid Value of the residual that is computed (output) * @param evalType Type of the residual being computed (defaults to Base_ResidEval) * @param id_x Index of the variable that is being numerically differenced to find - * the jacobian (defaults to -1, which indicates that no variable is being + * the Jacobian (defaults to -1, which indicates that no variable is being * differenced or that the residual doesn't take this issue into account) * @param delta_x Value of the delta used in the numerical differencing * @@ -186,7 +186,7 @@ public: * @param t Time (input) * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) - * @param delta_y Value of the delta to be used in calculating the numerical jacobian + * @param delta_y Value of the delta to be used in calculating the numerical Jacobian * @param solnWeights Value of the solution weights that are used in determining convergence (default = 0) * * @return Returns a flag to indicate that operation is successful. @@ -245,7 +245,7 @@ public: //! Multiply the matrix by another matrix that leads to better conditioning /*! - * Provide a left sided matrix that will multiply the current jacobian, after scaling + * Provide a left sided matrix that will multiply the current Jacobian, after scaling * and lead to a better conditioned system. * This routine is called just before the matrix is factored. * @@ -255,9 +255,9 @@ public: * New problem: * M (J delta_x) = - M Resid * - * @param matrix Pointer to the current jacobian (if zero, it's already been factored) + * @param matrix Pointer to the current Jacobian (if zero, it's already been factored) * @param nrows offsets for the matrix - * @param rhs residual vector. This also needs to be lhs multiplied by M + * @param rhs residual vector. This also needs to be LHS multiplied by M * * @return Returns a flag to indicate that operation is successful. * 1 Means a successful operation @@ -266,13 +266,13 @@ public: virtual int matrixConditioning(doublereal* const matrix, const int nrows, doublereal* const rhs); - //! Calculate an analytical jacobian and the residual at the current time and values. + //! Calculate an analytical Jacobian and the residual at the current time and values. /*! * Only called if the jacFormation method is set to analytical * * @param t Time (input) * @param delta_t The current value of the time step (input) - * @param cj Coefficient of yprime used in the evaluation of the jacobian + * @param cj Coefficient of yprime used in the evaluation of the Jacobian * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) * @param J Reference to the SquareMatrix object to be calculated (output) @@ -286,13 +286,13 @@ public: const doublereal* const y, const doublereal* const ydot, GeneralMatrix& J, doublereal* const resid); - //! Calculate an analytical jacobian and the residual at the current time and values. + //! Calculate an analytical Jacobian and the residual at the current time and values. /*! * Only called if the jacFormation method is set to analytical * * @param t Time (input) * @param delta_t The current value of the time step (input) - * @param cj Coefficient of yprime used in the evaluation of the jacobian + * @param cj Coefficient of yprime used in the evaluation of the Jacobian * @param y Solution vector (input, do not modify) * @param ydot Rate of change of solution vector. (input, do not modify) * @param jacobianColPts Pointer to the vector of pts to columns of the SquareMatrix diff --git a/include/cantera/numerics/solveProb.h b/include/cantera/numerics/solveProb.h index edbb442a6..4047bf19a 100644 --- a/include/cantera/numerics/solveProb.h +++ b/include/cantera/numerics/solveProb.h @@ -39,7 +39,7 @@ * algorithm to determine when to shut off * time-stepping. * 3: SOLVEPROB_JACOBIAN = Calculation of the surface problem is due to the - * need for a numerical jacobian for the gas-problem. + * need for a numerical Jacobian for the gas-problem. * The solution is expected to be very close to the * initial guess, and accuracy is needed. * 4: SOLVEPROB_TRANSIENT = The transient calculation is performed here for an @@ -97,11 +97,11 @@ namespace Cantera * time-stepping. * * 3: SOLVEPROB_JACOBIAN = Calculation of the surface problem is due to the - * need for a numerical jacobian for the gas-problem. + * need for a numerical Jacobian for the gas-problem. * The solution is expected to be very close to the * initial guess, and extra accuracy is needed because * solution variables have been delta'd from - * nominal values to create jacobian entries. + * nominal values to create Jacobian entries. * * 4: SOLVEPROB_TRANSIENT = The transient calculation is performed here for an * amount of time specified by "time_scale". It is @@ -309,7 +309,7 @@ private: * @param resid output Vector of residuals, length = m_neq * @param CSolnSP Vector of species concentrations, unknowns in the * problem, length = m_neq. These are tweaked in order - * to derive the columns of the jacobian. + * to derive the columns of the Jacobian. * @param CSolnSPOld Old Vector of species concentrations, unknowns in the * problem, length = m_neq * @param do_time Calculate a time dependent residual @@ -416,7 +416,7 @@ private: */ vector_fp m_resid; - //! Vector of pointers to the top of the columns of the jacobians + //! Vector of pointers to the top of the columns of the Jacobians /*! * The "dim" by "dim" computed Jacobian matrix for the * local Newton's method. diff --git a/include/cantera/oneD/MultiJac.h b/include/cantera/oneD/MultiJac.h index 5f485fd27..78baf0777 100644 --- a/include/cantera/oneD/MultiJac.h +++ b/include/cantera/oneD/MultiJac.h @@ -70,10 +70,10 @@ public: void incrementDiagonal(int j, doublereal d); protected: - //! Residual evaluator for this jacobian + //! Residual evaluator for this Jacobian /*! * This is a pointer to the residual evaluator. This object isn't owned - * by this jacobian object. + * by this Jacobian object. */ OneDim* m_resid; diff --git a/include/cantera/thermo/ConstDensityThermo.h b/include/cantera/thermo/ConstDensityThermo.h index c0a1872c5..c11604b00 100644 --- a/include/cantera/thermo/ConstDensityThermo.h +++ b/include/cantera/thermo/ConstDensityThermo.h @@ -148,7 +148,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const { @@ -181,7 +181,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const { @@ -312,7 +312,7 @@ protected: //! Temporary storage for dimensionless reference state heat capacities mutable vector_fp m_cp0_R; - //! Temporary storage for dimensionless reference state gibbs energies + //! Temporary storage for dimensionless reference state Gibbs energies mutable vector_fp m_g0_RT; //! Temporary storage for dimensionless reference state entropies diff --git a/include/cantera/thermo/DebyeHuckel.h b/include/cantera/thermo/DebyeHuckel.h index edffaa547..f4fe0ba9c 100644 --- a/include/cantera/thermo/DebyeHuckel.h +++ b/include/cantera/thermo/DebyeHuckel.h @@ -96,7 +96,7 @@ class PDSS_Water; * \f] * * The standard state heat capacity and entropy are independent - * of pressure. The standard state gibbs free energy is obtained + * of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * The vector Phase::m_speciesSize[] is used to hold the diff --git a/include/cantera/thermo/FixedChemPotSSTP.h b/include/cantera/thermo/FixedChemPotSSTP.h index 6e0c5e144..a24576054 100644 --- a/include/cantera/thermo/FixedChemPotSSTP.h +++ b/include/cantera/thermo/FixedChemPotSSTP.h @@ -69,7 +69,7 @@ namespace Cantera * Instantiation of the Class * * This phase may be instantiated by calling the default ThermoFactory routine - * for %Cantera. This new FixedChemPotSSTP object must then have a standalone xml file + * for %Cantera. This new FixedChemPotSSTP object must then have a standalone XML file * description an example of which is given below. * * It may also be created by the following code snippets. The code @@ -392,7 +392,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -474,7 +474,7 @@ public: /*! * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * diff --git a/include/cantera/thermo/GibbsExcessVPSSTP.h b/include/cantera/thermo/GibbsExcessVPSSTP.h index 024ec1b8c..587c34a8b 100644 --- a/include/cantera/thermo/GibbsExcessVPSSTP.h +++ b/include/cantera/thermo/GibbsExcessVPSSTP.h @@ -1,7 +1,7 @@ /** * @file GibbsExcessVPSSTP.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::GibbsExcessVPSSTP GibbsExcessVPSSTP\endlink). * @@ -124,7 +124,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ diff --git a/include/cantera/thermo/HMWSoln.h b/include/cantera/thermo/HMWSoln.h index e38d1d79d..d1e0258e6 100644 --- a/include/cantera/thermo/HMWSoln.h +++ b/include/cantera/thermo/HMWSoln.h @@ -143,7 +143,7 @@ class WaterProps; * * * The solute standard state heat capacity and entropy are independent - * of pressure. The solute standard state gibbs free energy is obtained + * of pressure. The solute standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * The vector Phase::m_speciesSize[] is used to hold the @@ -297,8 +297,8 @@ class WaterProps; * *

Specification of the Excess Gibbs Free Energy

* - * Pitzer's formulation may best be represented as a specification of the excess gibbs - * free energy, \f$ G^{ex} \f$, defined as the deviation of the total gibbs free energy from + * Pitzer's formulation may best be represented as a specification of the excess Gibbs + * free energy, \f$ G^{ex} \f$, defined as the deviation of the total Gibbs free energy from * that of an ideal molal solution. * \f[ * G = G^{id} + G^{ex} @@ -577,7 +577,7 @@ class WaterProps; * below the critical temperature of water. * They found a temperature functional form for fitting the 3 following * coefficients that describe the Pitzer parameterization for a single salt - * to be adequate to describe how the excess gibbs free energy values for + * to be adequate to describe how the excess Gibbs free energy values for * the binary salt changes with respect to temperature. * The following functional form * was used to fit the temperature dependence of the Pitzer Coefficients @@ -1308,7 +1308,7 @@ public: * about the species, including their reference state thermodynamic * polynomials. We then freeze the state of the species. * - * Then, we read the species molar volumes from the xml tree to finish the + * Then, we read the species molar volumes from the XML tree to finish the * initialization. * * @param phaseNode This object must be the phase node of a complete XML tree diff --git a/include/cantera/thermo/IdealGasPhase.h b/include/cantera/thermo/IdealGasPhase.h index 9ce7d2ef0..6aec2b327 100644 --- a/include/cantera/thermo/IdealGasPhase.h +++ b/include/cantera/thermo/IdealGasPhase.h @@ -70,7 +70,7 @@ namespace Cantera * \f[ * S^o_k(T,P) = S^{ref}_k(T) - R \ln(\frac{P}{P_{ref}}) * \f] - * The standard state gibbs free energy is obtained from the enthalpy and entropy + * The standard state Gibbs free energy is obtained from the enthalpy and entropy * functions: * * \f[ @@ -690,7 +690,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -699,7 +699,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const; @@ -754,7 +754,7 @@ public: virtual void getGibbs_RT_ref(doublereal* grt) const; //! Returns the vector of the - //! gibbs function of the reference state at the current temperature + //! Gibbs function of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! * units = J/kmol @@ -899,7 +899,7 @@ protected: //! Temporary storage for dimensionless reference state heat capacities mutable vector_fp m_cp0_R; - //! Temporary storage for dimensionless reference state gibbs energies + //! Temporary storage for dimensionless reference state Gibbs energies mutable vector_fp m_g0_RT; //! Temporary storage for dimensionless reference state entropies diff --git a/include/cantera/thermo/IdealMolalSoln.h b/include/cantera/thermo/IdealMolalSoln.h index c32032eec..f77366b9c 100644 --- a/include/cantera/thermo/IdealMolalSoln.h +++ b/include/cantera/thermo/IdealMolalSoln.h @@ -188,7 +188,7 @@ public: //! Molar Gibbs function for the solution: Units J/kmol. /*! - * Returns the gibbs free energy of the solution per mole of the solution. + * Returns the Gibbs free energy of the solution per mole of the solution. * * \f[ * \bar{g}(T, P, X_k) = \sum_k X_k \mu_k(T) diff --git a/include/cantera/thermo/IdealSolidSolnPhase.h b/include/cantera/thermo/IdealSolidSolnPhase.h index cd0d2e9fa..32a0aac33 100644 --- a/include/cantera/thermo/IdealSolidSolnPhase.h +++ b/include/cantera/thermo/IdealSolidSolnPhase.h @@ -55,7 +55,7 @@ public: * Constructor for IdealSolidSolnPhase. * The generalized concentrations can have three different forms * depending on the value of the member attribute #m_formGC, which - * is supplied in the constructor or read from the xml data file. + * is supplied in the constructor or read from the XML data file. * * @param formCG This parameter initializes the #m_formGC variable. */ @@ -67,7 +67,7 @@ public: * This constructor will also fully initialize the object. * The generalized concentrations can have three different forms * depending on the value of the member attribute #m_formGC, which - * is supplied in the constructor or read from the xml data file. + * is supplied in the constructor or read from the XML data file. * * @param infile File name for the XML datafile containing information * for this phase @@ -146,15 +146,15 @@ public: virtual doublereal entropy_mole() const; /** - * Molar gibbs free energy of the solution. Units: J/kmol. + * Molar Gibbs free energy of the solution. Units: J/kmol. * For an ideal, constant partial molar volume solution mixture with * pure species phases which exhibit zero volume expansivity: * \f[ * \hat g(T, P) = \sum_k X_k \hat g^0_k(T,P) + \hat R T \sum_k X_k log(X_k) * \f] - * The reference-state pure-species gibbs free energies + * The reference-state pure-species Gibbs free energies * \f$ \hat g^0_k(T) \f$ are computed by the species thermodynamic - * property manager, while the standard state gibbs free energies + * property manager, while the standard state Gibbs free energies * \f$ \hat g^0_k(T,P) \f$ are computed by the member function, gibbs_RT(). * @see SpeciesThermo */ @@ -603,7 +603,7 @@ public: void getEntropy_R(doublereal* sr) const; /** - * Get the nondimensional gibbs function for the species + * Get the nondimensional Gibbs function for the species * standard states at the current T and P of the solution. * * \f[ @@ -615,7 +615,7 @@ public: * * @param grt Vector of length m_kk, which on return sr[k] * will contain the nondimensional - * standard state gibbs function for species k. + * standard state Gibbs function for species k. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -697,7 +697,7 @@ public: /** * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * diff --git a/include/cantera/thermo/IonsFromNeutralVPSSTP.h b/include/cantera/thermo/IonsFromNeutralVPSSTP.h index d754aa04e..5cf5d9fc2 100644 --- a/include/cantera/thermo/IonsFromNeutralVPSSTP.h +++ b/include/cantera/thermo/IonsFromNeutralVPSSTP.h @@ -44,7 +44,7 @@ enum IonSolnType_enumType { * for the same phase expressed in terms of combinations of the * ionic species that represent neutral molecules. It's expected * that the neutral molecules will be represented in terms of - * an excess gibbs free energy approximation that is a derivative + * an excess Gibbs free energy approximation that is a derivative * of the GbbsExcessVPSSTP object. All of the e Excess Gibbs free * energy formulations in this area employ * symmetrical formulations. @@ -156,7 +156,7 @@ public: /// the phase and setting its parameters from a specification in an /// input file. - //! Initialization of an IonsFromNeutralVPSSTP phase using an xml file + //! Initialization of an IonsFromNeutralVPSSTP phase using an XML file /*! * This routine is a precursor to initThermo(XML_Node*) * routine, which does most of the work. @@ -179,7 +179,7 @@ public: * reference state thermodynamic polynomials. We then freeze * the state of the species. * - * Then, we read the species molar volumes from the xml + * Then, we read the species molar volumes from the XML * tree to finish the initialization. * * @param phaseNode This object must be the phase node of a complete XML tree diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h index e83aadeae..2e031e97f 100644 --- a/include/cantera/thermo/LatticePhase.h +++ b/include/cantera/thermo/LatticePhase.h @@ -57,7 +57,7 @@ namespace Cantera * \f] * * The standard state heat capacity, internal energy, and entropy are independent - * of pressure. The standard state gibbs free energy is obtained + * of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * The standard state molar volume is independent of temperature, pressure, @@ -595,7 +595,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const; @@ -647,14 +647,14 @@ public: //! Get the nondimensional Gibbs functions for the species //! standard states at the current T and P of the solution. /*! - * The standard gibbs free energies are obtained from the enthalpy + * The standard Gibbs free energies are obtained from the enthalpy * and entropy formulation. * * \f[ * g^o_k(T,P) = h^{o}_k(T,P) - T s^{o}_k(T,P) * \f] * - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -719,7 +719,7 @@ public: */ virtual void getGibbs_RT_ref(doublereal* grt) const; - //! Returns the vector of the gibbs function of the reference state at the current temperature + //! Returns the vector of the Gibbs function of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! * units = J/kmol @@ -858,7 +858,7 @@ protected: //! Temporary storage for the reference state heat capacities mutable vector_fp m_cp0_R; - //! Temporary storage for the reference state gibbs energies + //! Temporary storage for the reference state Gibbs energies mutable vector_fp m_g0_RT; //! Temporary storage for the reference state entropies at the current temperature diff --git a/include/cantera/thermo/LatticeSolidPhase.h b/include/cantera/thermo/LatticeSolidPhase.h index de56ca883..5283eed29 100644 --- a/include/cantera/thermo/LatticeSolidPhase.h +++ b/include/cantera/thermo/LatticeSolidPhase.h @@ -226,7 +226,7 @@ public: //! Return the Molar Gibbs energy. Units: J/kmol. /*! - * The molar gibbs free energy is determined by the following formula, where \f$ \theta_n \f$ is the + * The molar Gibbs free energy is determined by the following formula, where \f$ \theta_n \f$ is the * lattice stoichiometric coefficient of the nth lattice * * \f[ @@ -545,7 +545,7 @@ public: /*! * This function fills in its one entry in hrt[] by calling * the underlying species thermo function for the - * dimensionless gibbs free energy, calculated from the + * dimensionless Gibbs free energy, calculated from the * dimensionless enthalpy and entropy. * * @param grt Vector of dimensionless Gibbs free energies of the reference state @@ -553,13 +553,13 @@ public: */ virtual void getGibbs_RT_ref(doublereal* grt) const; - //! Returns the vector of the gibbs function of the reference state at the current + //! Returns the vector of the Gibbs function of the reference state at the current //! temperatureof the solution and the reference pressure for the species. /*! * units = J/kmol * * This function fills in its one entry in g[] by calling the underlying species thermo - * functions for the gibbs free energy, calculated from enthalpy and the + * functions for the Gibbs free energy, calculated from enthalpy and the * entropy, and the multiplying by RT. * * @param g Vector of Gibbs free energies of the reference state. diff --git a/include/cantera/thermo/MargulesVPSSTP.h b/include/cantera/thermo/MargulesVPSSTP.h index c1af68104..522e983ca 100644 --- a/include/cantera/thermo/MargulesVPSSTP.h +++ b/include/cantera/thermo/MargulesVPSSTP.h @@ -1,7 +1,7 @@ /** * @file MargulesVPSSTP.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). * @@ -29,13 +29,13 @@ namespace Cantera */ //! MargulesVPSSTP is a derived class of GibbsExcessVPSSTP that employs -//! the Margules approximation for the excess gibbs free energy +//! the Margules approximation for the excess Gibbs free energy /*! * * MargulesVPSSTP derives from class GibbsExcessVPSSTP which is derived * from VPStandardStateTP, * and overloads the virtual methods defined there with ones that - * use expressions appropriate for the Margules Excess gibbs free energy + * use expressions appropriate for the Margules Excess Gibbs free energy * approximation. * * The independent unknowns are pressure, temperature, and mass fraction. @@ -270,7 +270,7 @@ public: MargulesVPSSTP(); //! Construct and initialize a MargulesVPSSTP ThermoPhase object - //! directly from an xml input file + //! directly from an XML input file /*! * Working constructors * @@ -321,7 +321,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ @@ -668,51 +668,51 @@ protected: size_t numBinaryInteractions_; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_d_ij; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_d_ij; //! vector of species indices representing species A in the interaction diff --git a/include/cantera/thermo/MaskellSolidSolnPhase.h b/include/cantera/thermo/MaskellSolidSolnPhase.h index dbc2770ab..10ccaebb3 100644 --- a/include/cantera/thermo/MaskellSolidSolnPhase.h +++ b/include/cantera/thermo/MaskellSolidSolnPhase.h @@ -227,7 +227,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const; diff --git a/include/cantera/thermo/MetalSHEelectrons.h b/include/cantera/thermo/MetalSHEelectrons.h index b5cce4518..0b342864c 100644 --- a/include/cantera/thermo/MetalSHEelectrons.h +++ b/include/cantera/thermo/MetalSHEelectrons.h @@ -51,7 +51,7 @@ namespace Cantera * S^o_k(T,P) = S^{ref}_k(T) - R \ln(\frac{P}{P_{ref}}) * \f] * - * The standard state gibbs free energy is obtained from the enthalpy and entropy + * The standard state Gibbs free energy is obtained from the enthalpy and entropy * functions: * * \f[ @@ -115,7 +115,7 @@ namespace Cantera * ThermoPhase *eMetal = newPhase("MetalSHEelectrons.xml", "MetalSHEelectrons"); * @endcode * - * Additionally, this phase may be created without including an xml file with + * Additionally, this phase may be created without including an XML file with * the special command, where the default file is embedded into this object. * * @code @@ -389,7 +389,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; diff --git a/include/cantera/thermo/MineralEQ3.h b/include/cantera/thermo/MineralEQ3.h index e0cca09ca..c45ecf534 100644 --- a/include/cantera/thermo/MineralEQ3.h +++ b/include/cantera/thermo/MineralEQ3.h @@ -61,7 +61,7 @@ namespace Cantera * \f] * * The standard state heat capacity and entropy are independent - * of pressure. The standard state gibbs free energy is obtained + * of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * Specification of Solution Thermodynamic Properties @@ -305,7 +305,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; diff --git a/include/cantera/thermo/MixedSolventElectrolyte.h b/include/cantera/thermo/MixedSolventElectrolyte.h index 0b3d19b4a..26247d996 100644 --- a/include/cantera/thermo/MixedSolventElectrolyte.h +++ b/include/cantera/thermo/MixedSolventElectrolyte.h @@ -1,7 +1,7 @@ /** * @file MixedSolventElectrolyte.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). * @@ -29,13 +29,13 @@ namespace Cantera */ //! MixedSolventElectrolyte is a derived class of GibbsExcessVPSSTP that employs -//! the DH and local Marguless approximations for the excess gibbs free energy +//! the DH and local Marguless approximations for the excess Gibbs free energy /*! * * MixedSolventElectrolyte derives from class GibbsExcessVPSSTP which is derived * from VPStandardStateTP, * and overloads the virtual methods defined there with ones that - * use expressions appropriate for the Margules Excess gibbs free energy + * use expressions appropriate for the Margules Excess Gibbs free energy * approximation. * * The independent unknowns are pressure, temperature, and mass fraction. @@ -271,7 +271,7 @@ public: MixedSolventElectrolyte(); //! Construct and initialize a MixedSolventElectrolyte ThermoPhase object - //! directly from an xml input file + //! directly from an XML input file /*! * @param inputFile Name of the input file containing the phase XML data * to set up the object @@ -313,7 +313,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ @@ -659,51 +659,51 @@ protected: size_t numBinaryInteractions_; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_d_ij; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_d_ij; //! vector of species indices representing species A in the interaction diff --git a/include/cantera/thermo/MixtureFugacityTP.h b/include/cantera/thermo/MixtureFugacityTP.h index 5996bc039..ba1acc499 100644 --- a/include/cantera/thermo/MixtureFugacityTP.h +++ b/include/cantera/thermo/MixtureFugacityTP.h @@ -496,7 +496,7 @@ protected: public: /*! * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * @@ -830,7 +830,7 @@ protected: //! Temporary storage for dimensionless reference state heat capacities mutable vector_fp m_cp0_R; - //! Temporary storage for dimensionless reference state gibbs energies + //! Temporary storage for dimensionless reference state Gibbs energies mutable vector_fp m_g0_RT; //! Temporary storage for dimensionless reference state entropies diff --git a/include/cantera/thermo/MolarityIonicVPSSTP.h b/include/cantera/thermo/MolarityIonicVPSSTP.h index a095a29ab..9654bde57 100644 --- a/include/cantera/thermo/MolarityIonicVPSSTP.h +++ b/include/cantera/thermo/MolarityIonicVPSSTP.h @@ -1,7 +1,7 @@ /** * @file MolarityIonicVPSSTP.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::MolarityIonicVPSSTP MolarityIonicVPSSTP\endlink). * @@ -103,7 +103,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ diff --git a/include/cantera/thermo/NasaPoly2.h b/include/cantera/thermo/NasaPoly2.h index 02a341fbe..dff9b39e6 100644 --- a/include/cantera/thermo/NasaPoly2.h +++ b/include/cantera/thermo/NasaPoly2.h @@ -5,7 +5,7 @@ * on the NASA temperature polynomial form applied to two temperature regions * (see \ref spthermo and class \link Cantera::NasaPoly2 NasaPoly2\endlink). * - * Two zoned Nasa polynomial parameterization + * Two zoned NASA polynomial parameterization */ // Copyright 2001 California Institute of Technology diff --git a/include/cantera/thermo/PDSS.h b/include/cantera/thermo/PDSS.h index f8a38aaff..77c5733a4 100644 --- a/include/cantera/thermo/PDSS.h +++ b/include/cantera/thermo/PDSS.h @@ -339,7 +339,7 @@ public: //! the current pressure and the reference pressure, p0 virtual doublereal entropyDelp_mole() const; - //! Get the difference in the standard state gibbs free energy + //! Get the difference in the standard state Gibbs free energy //! between the current pressure and the reference pressure, p0. virtual doublereal gibbsDelp_mole() const; @@ -366,9 +366,9 @@ public: return m_maxTemp; } - //! Return the molar gibbs free energy divided by RT at reference pressure + //! Return the molar Gibbs free energy divided by RT at reference pressure /*! - * @return The reference state gibbs free energy at the current + * @return The reference state Gibbs free energy at the current * temperature, divided by RT. */ virtual doublereal gibbs_RT_ref() const; diff --git a/include/cantera/thermo/PDSS_ConstVol.h b/include/cantera/thermo/PDSS_ConstVol.h index 565cc624b..a0b0b7c16 100644 --- a/include/cantera/thermo/PDSS_ConstVol.h +++ b/include/cantera/thermo/PDSS_ConstVol.h @@ -139,7 +139,7 @@ public: void constructPDSSFile(VPStandardStateTP* vptp_ptr, size_t spindex, const std::string& inputFile, const std::string& id); - //! Initialization of a PDSS object using an xml tree + //! Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the object. * diff --git a/include/cantera/thermo/PDSS_HKFT.h b/include/cantera/thermo/PDSS_HKFT.h index 5bceb4595..14a557fe8 100644 --- a/include/cantera/thermo/PDSS_HKFT.h +++ b/include/cantera/thermo/PDSS_HKFT.h @@ -160,7 +160,7 @@ public: void constructPDSSFile(VPStandardStateTP* vptp_ptr, size_t spindex, const std::string& inputFile, const std::string& id); - //! Initialization of a PDSS object using an xml tree + //! Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the object. * @@ -218,7 +218,7 @@ public: //@} private: - //! Main routine that actually calculates the gibbs free energy difference + //! Main routine that actually calculates the Gibbs free energy difference //! between the reference state at Tr, Pr and T,P /*! * This is eEqn. 59 in Johnson et al. (1992). diff --git a/include/cantera/thermo/PDSS_IdealGas.h b/include/cantera/thermo/PDSS_IdealGas.h index a070e5cc6..0ed637fc8 100644 --- a/include/cantera/thermo/PDSS_IdealGas.h +++ b/include/cantera/thermo/PDSS_IdealGas.h @@ -138,7 +138,7 @@ public: void constructPDSSFile(VPStandardStateTP* vptp_ptr, size_t spindex, const std::string& inputFile, const std::string& id); - //!Initialization of a PDSS object using an xml tree + //!Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the object. * diff --git a/include/cantera/thermo/PDSS_IonsFromNeutral.h b/include/cantera/thermo/PDSS_IonsFromNeutral.h index e0bfdaf31..0f70fd459 100644 --- a/include/cantera/thermo/PDSS_IonsFromNeutral.h +++ b/include/cantera/thermo/PDSS_IonsFromNeutral.h @@ -153,7 +153,7 @@ public: void constructPDSSFile(VPStandardStateTP* vptp_ptr, size_t spindex, const std::string& inputFile, const std::string& id); - //! Initialization of a PDSS object using an xml tree + //! Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the object. * diff --git a/include/cantera/thermo/PDSS_SSVol.h b/include/cantera/thermo/PDSS_SSVol.h index 7364785c1..4def807da 100644 --- a/include/cantera/thermo/PDSS_SSVol.h +++ b/include/cantera/thermo/PDSS_SSVol.h @@ -279,7 +279,7 @@ private: void constructPDSSFile(VPStandardStateTP* vptp_ptr, size_t spindex, const std::string& inputFile, const std::string& id); - //! Initialization of a PDSS object using an xml tree + //! Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the object. * diff --git a/include/cantera/thermo/PDSS_Water.h b/include/cantera/thermo/PDSS_Water.h index 7efbba1a4..629e17865 100644 --- a/include/cantera/thermo/PDSS_Water.h +++ b/include/cantera/thermo/PDSS_Water.h @@ -245,7 +245,7 @@ public: void constructPDSSFile(VPStandardStateTP* vptp_ptr, int spindex, const std::string& inputFile, const std::string& id); - //!Initialization of a PDSS object using an xml tree + //!Initialization of a PDSS object using an XML tree /*! * This routine is a driver for the initialization of the * object. diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h index 7e6d0ac19..d8cb64b93 100644 --- a/include/cantera/thermo/Phase.h +++ b/include/cantera/thermo/Phase.h @@ -81,10 +81,10 @@ namespace Cantera * * Specify that the input mole, mass, and volume fraction vectors must sum to one on entry to the set state routines. * Non-conforming mole/mass fraction vectors are not thermodynamically consistent. - * Moreover, unless we do this, the calculation of jacobians will be altered whenever the treatment of non-conforming mole + * Moreover, unless we do this, the calculation of Jacobians will be altered whenever the treatment of non-conforming mole * fractions is changed. Add setState functions corresponding to specifying mole numbers, which is actually what * is being done (well one of the options, there are many) when non-conforming mole fractions are input. - * Note, we realize that most numerical jacobian and some analytical jacobians use non-conforming calculations. + * Note, we realize that most numerical Jacobian and some analytical Jacobians use non-conforming calculations. * These can easily be changed to the set mole number setState functions. * * @ingroup phases diff --git a/include/cantera/thermo/PhaseCombo_Interaction.h b/include/cantera/thermo/PhaseCombo_Interaction.h index e4573aafa..a0c0d8c35 100644 --- a/include/cantera/thermo/PhaseCombo_Interaction.h +++ b/include/cantera/thermo/PhaseCombo_Interaction.h @@ -1,7 +1,7 @@ /** * @file PhaseCombo_Interaction.h * Header for intermediate ThermoPhase object for phases which - * employ the Margules gibbs free energy formulation and eliminates the ideal mixing term. + * employ the Margules Gibbs free energy formulation and eliminates the ideal mixing term. * (see \ref thermoprops * and class \link Cantera::PhaseCombo_Interaction PhaseCombo_Interaction\endlink). */ @@ -25,12 +25,12 @@ namespace Cantera */ //! PhaseCombo_Interaction is a derived class of GibbsExcessVPSSTP that employs -//! the Margules approximation for the excess gibbs free energy while eliminating +//! the Margules approximation for the excess Gibbs free energy while eliminating //! the entropy of mixing term. /*! * PhaseCombo_Interaction derives from class GibbsExcessVPSSTP which is derived from VPStandardStateTP, * and overloads the virtual methods defined there with ones that - * use expressions appropriate for the Margules Excess gibbs free energy approximation. + * use expressions appropriate for the Margules Excess Gibbs free energy approximation. * The reader should refer to the MargulesVPSSTP class for information on that class. * This class in addition adds a term to the activity coefficient that eliminates the * ideal solution mixing term within the chemical potential. This is a very radical thing @@ -78,7 +78,7 @@ namespace Cantera * Each of the interactions are binary interactions involving two of the species in the phase, denoted, Ai * and Bi. * This is the generalization of the Margules formulation for a phase - * that has more than 2 species. The second term in the excess gibbs free energy is a negation of the + * that has more than 2 species. The second term in the excess Gibbs free energy is a negation of the * ideal solution's mixing term. * * \f[ @@ -345,7 +345,7 @@ public: PhaseCombo_Interaction(); //! Construct and initialize a PhaseCombo_Interaction ThermoPhase object - //! directly from an xml input file + //! directly from an XML input file /*! * @param inputFile Name of the input file containing the phase XML data * to set up the object @@ -386,7 +386,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ @@ -744,51 +744,51 @@ protected: size_t numBinaryInteractions_; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_HE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_SE_d_ij; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_b_ij; //! Enthalpy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_c_ij; //! Enthalpy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VHE_d_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_b_ij; //! Entropy term for the ternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_c_ij; //! Entropy term for the quaternary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable vector_fp m_VSE_d_ij; //! vector of species indices representing species A in the interaction diff --git a/include/cantera/thermo/PseudoBinaryVPSSTP.h b/include/cantera/thermo/PseudoBinaryVPSSTP.h index ebafbc384..631c64e0f 100644 --- a/include/cantera/thermo/PseudoBinaryVPSSTP.h +++ b/include/cantera/thermo/PseudoBinaryVPSSTP.h @@ -1,7 +1,7 @@ /** * @file PseudoBinaryVPSSTP.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::PseudoBinaryVPSSTP PseudoBinaryVPSSTP\endlink). * @@ -92,7 +92,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ diff --git a/include/cantera/thermo/PureFluidPhase.h b/include/cantera/thermo/PureFluidPhase.h index 7a3590836..638ee60a6 100644 --- a/include/cantera/thermo/PureFluidPhase.h +++ b/include/cantera/thermo/PureFluidPhase.h @@ -269,7 +269,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -299,7 +299,7 @@ public: */ virtual void getGibbs_RT_ref(doublereal* grt) const; - //! Returns the vector of the gibbs function of the reference state at the current temperature + //! Returns the vector of the Gibbs function of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! * units = J/kmol diff --git a/include/cantera/thermo/RedlichKisterVPSSTP.h b/include/cantera/thermo/RedlichKisterVPSSTP.h index e5a2db136..521b009c3 100644 --- a/include/cantera/thermo/RedlichKisterVPSSTP.h +++ b/include/cantera/thermo/RedlichKisterVPSSTP.h @@ -1,7 +1,7 @@ /** * @file RedlichKisterVPSSTP.h * Header for intermediate ThermoPhase object for phases which - * employ gibbs excess free energy based formulations + * employ Gibbs excess free energy based formulations * (see \ref thermoprops * and class \link Cantera::RedlichKisterVPSSTP RedlichKisterVPSSTP\endlink). * @@ -30,11 +30,11 @@ namespace Cantera */ //! RedlichKisterVPSSTP is a derived class of GibbsExcessVPSSTP that employs -//! the Redlich-Kister approximation for the excess gibbs free energy +//! the Redlich-Kister approximation for the excess Gibbs free energy /*! * RedlichKisterVPSSTP derives from class GibbsExcessVPSSTP which is derived * from VPStandardStateTP, and overloads the virtual methods defined there with ones that - * use expressions appropriate for the Redlich Kister Excess gibbs free energy approximation. + * use expressions appropriate for the Redlich Kister Excess Gibbs free energy approximation. * * The independent unknowns are pressure, temperature, and mass fraction. * @@ -86,7 +86,7 @@ namespace Cantera * G^E_{i} = n X_{Ai} X_{Bi} \sum_m \left( A^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) * \f] * - * and where we can break down the gibbs free energy contributions into enthalpy and entropy contributions + * and where we can break down the Gibbs free energy contributions into enthalpy and entropy contributions * * \f[ * H^E_i = n X_{Ai} X_{Bi} \sum_m \left( H^{i}_m {\left( X_{Ai} - X_{Bi} \right)}^m \right) @@ -267,7 +267,7 @@ public: RedlichKisterVPSSTP(); //! Construct and initialize a RedlichKisterVPSSTP ThermoPhase object - //! directly from an xml input file + //! directly from an XML input file /*! * * @param inputFile Name of the input file containing the phase XML data @@ -309,7 +309,7 @@ public: //! Duplication routine for objects which inherit from ThermoPhase. /*! - * This virtual routine can be used to duplicate thermophase objects + * This virtual routine can be used to duplicate ThermoPhase objects * inherited from ThermoPhase even if the application only has * a pointer to ThermoPhase to work with. */ @@ -664,11 +664,11 @@ protected: std::vector m_N_ij; //! Enthalpy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable std::vector< vector_fp> m_HE_m_ij; //! Entropy term for the binary mole fraction interaction of the - //! excess gibbs free energy expression + //! excess Gibbs free energy expression mutable std::vector< vector_fp> m_SE_m_ij; //! form of the RedlichKister interaction expression diff --git a/include/cantera/thermo/SingleSpeciesTP.h b/include/cantera/thermo/SingleSpeciesTP.h index d7f84c441..edee5fe0f 100644 --- a/include/cantera/thermo/SingleSpeciesTP.h +++ b/include/cantera/thermo/SingleSpeciesTP.h @@ -348,7 +348,7 @@ public: /*! * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * diff --git a/include/cantera/thermo/SpeciesThermo.h b/include/cantera/thermo/SpeciesThermo.h index a2bdffc6e..0cd0d1bcf 100644 --- a/include/cantera/thermo/SpeciesThermo.h +++ b/include/cantera/thermo/SpeciesThermo.h @@ -87,7 +87,7 @@ class SpeciesThermoInterpType; * * - NasaThermo in file NasaThermo.h * - This is a two zone model, with each zone consisting of a 7 - * coefficient Nasa Polynomial format. + * 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. @@ -106,10 +106,10 @@ class SpeciesThermoInterpType; * * - NasaPoly1 in file NasaPoly1.h * - This is a one zone model, consisting of a 7 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * - NasaPoly2 in file NasaPoly2.h * - This is a two zone model, with each zone consisting of a 7 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * - ShomatePoly in file ShomatePoly.h * - This is a one zone model, consisting of a 7 * coefficient Shomate Polynomial format. @@ -124,10 +124,10 @@ class SpeciesThermoInterpType; * the heat capacity is treated as a constant. * - Nasa9Poly1 in file Nasa9Poly1.h * - This is a one zone model, consisting of the 9 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * - Nasa9PolyMultiTempRegion in file Nasa9PolyMultiTempRegion.h * - This is a multiple zone model, consisting of the 9 - * coefficient Nasa Polynomial format in each zone. + * 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 diff --git a/include/cantera/thermo/SpeciesThermoFactory.h b/include/cantera/thermo/SpeciesThermoFactory.h index 57abe14e1..2755cdd42 100644 --- a/include/cantera/thermo/SpeciesThermoFactory.h +++ b/include/cantera/thermo/SpeciesThermoFactory.h @@ -152,7 +152,7 @@ public: * 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. + * 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 diff --git a/include/cantera/thermo/SpeciesThermoInterpType.h b/include/cantera/thermo/SpeciesThermoInterpType.h index ddb566115..2ce78ddcd 100644 --- a/include/cantera/thermo/SpeciesThermoInterpType.h +++ b/include/cantera/thermo/SpeciesThermoInterpType.h @@ -77,11 +77,11 @@ class VPSSMgr; * * - NasaPoly1 in file NasaPoly1.h * - This is a one zone model, consisting of a 7 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * . * - NasaPoly2 in file NasaPoly2.h * - This is a two zone model, with each zone consisting of a 7 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * . * - ShomatePoly in file ShomatePoly.h * - This is a one zone model, consisting of a 7 @@ -101,11 +101,11 @@ class VPSSMgr; * . * - Nasa9Poly1 in file Nasa9Poly1.h * - This is a one zone model, consisting of the 9 - * coefficient Nasa Polynomial format. + * coefficient NASA Polynomial format. * . * - Nasa9PolyMultiTempRegion in file Nasa9PolyMultiTempRegion.h * - This is a multiple zone model, consisting of the 9 - * coefficient Nasa Polynomial format in each zone. + * coefficient NASA Polynomial format in each zone. * . * - STITbyPDSS in file SpeciesThermoInterpType.h * - This is an object that calculates reference state thermodynamic diff --git a/include/cantera/thermo/StoichSubstance.h b/include/cantera/thermo/StoichSubstance.h index fece38d42..fa529c4b4 100644 --- a/include/cantera/thermo/StoichSubstance.h +++ b/include/cantera/thermo/StoichSubstance.h @@ -198,7 +198,7 @@ public: /** * For a stoichiometric substance, there is only one species. - * This method returns the molar gibbs function in the + * This method returns the molar Gibbs function in the * first element of array \c mu. */ virtual void getChemPotentials(doublereal* mu) const; @@ -272,7 +272,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const; @@ -312,20 +312,20 @@ public: * * This function fills in its one entry in hrt[] by calling * the underlying species thermo function for the - * dimensionless gibbs free energy, calculated from the + * dimensionless Gibbs free energy, calculated from the * dimensionless enthalpy and entropy. */ virtual void getGibbs_RT_ref(doublereal* grt) const; /** * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * * This function fills in its one entry in g[] by calling * the underlying species thermo functions for the - * gibbs free energy, calculated from enthalpy and the + * Gibbs free energy, calculated from enthalpy and the * entropy, and the multiplying by RT. */ virtual void getGibbs_ref(doublereal* g) const; diff --git a/include/cantera/thermo/StoichSubstanceSSTP.h b/include/cantera/thermo/StoichSubstanceSSTP.h index 362746b39..0906b9342 100644 --- a/include/cantera/thermo/StoichSubstanceSSTP.h +++ b/include/cantera/thermo/StoichSubstanceSSTP.h @@ -60,7 +60,7 @@ namespace Cantera * \f] * * The standard state heat capacity and entropy are independent - * of pressure. The standard state gibbs free energy is obtained + * of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * Specification of Solution Thermodynamic Properties @@ -368,7 +368,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; diff --git a/include/cantera/thermo/SurfPhase.h b/include/cantera/thermo/SurfPhase.h index 7239a8fde..6b4b36cd0 100644 --- a/include/cantera/thermo/SurfPhase.h +++ b/include/cantera/thermo/SurfPhase.h @@ -46,7 +46,7 @@ namespace Cantera * \f] * * Also, the standard state chemical potentials, entropy, and heat capacities - * are independent of pressure. The standard state gibbs free energy is obtained + * are independent of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * * Specification of Solution Thermodynamic Properties @@ -420,7 +420,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const; @@ -582,7 +582,7 @@ protected: //! Temporary storage for the reference state heat capacities mutable vector_fp m_cp0; - //! Temporary storage for the reference state gibbs energies + //! Temporary storage for the reference state Gibbs energies mutable vector_fp m_mu0; //! Temporary work array diff --git a/include/cantera/thermo/ThermoFactory.h b/include/cantera/thermo/ThermoFactory.h index adedf6c57..18463a112 100644 --- a/include/cantera/thermo/ThermoFactory.h +++ b/include/cantera/thermo/ThermoFactory.h @@ -133,7 +133,7 @@ std::string eosTypeString(int ieos, int length = 100); //! tree. /*! * This routine first looks up the identity of the model for the solution - * thermodynamics in the model attribute of the thermo child of the xml phase + * thermodynamics in the model attribute of the thermo child of the XML phase * node. Then, it does a string lookup using Cantera's internal ThermoPhase * Factory routines on the model to figure out what ThermoPhase derived class * should be assigned. It creates a new instance of that class, and then calls @@ -163,7 +163,7 @@ ThermoPhase* newPhase(XML_Node& phase); */ ThermoPhase* newPhase(const std::string& infile, std::string id=""); -//! Import a phase information into an empty thermophase object +//! Import a phase information into an empty ThermoPhase object /*! * Here we read an XML description of the thermodynamic information * for a phase. At the end of this routine, the phase should @@ -218,7 +218,7 @@ ThermoPhase* newPhase(const std::string& infile, std::string id=""); * the species in the phase. * @param th Pointer to the ThermoPhase object which will * handle the thermodynamics for this phase. - * We initialize part of the Thermophase object + * We initialize part of the ThermoPhase object * here, especially for those objects which are * part of the Cantera Kernel. * diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h index 8d9e71feb..55bdd0d0a 100644 --- a/include/cantera/thermo/ThermoPhase.h +++ b/include/cantera/thermo/ThermoPhase.h @@ -80,9 +80,9 @@ const int cSS_CONVENTION_SLAVE = 2; * dimensionless. * * K_p is the calculation of the equilibrium constant from the - * reference state gibbs free energy values. It is by definition + * reference state Gibbs free energy values. It is by definition * dimensionless. The pressure dependence is handled entirely - * on the rhs of the equilibrium expression. + * on the RHS of the equilibrium expression. * * K_c is the equilibrium constant calculated from the * activity concentrations. The dimensions depend on the number @@ -694,7 +694,7 @@ public: //! Get the nondimensional Gibbs functions for the species //! in their standard states at the current T and P of the solution. /*! - * @param grt Output vector of nondimensional standard state gibbs free energies + * @param grt Output vector of nondimensional standard state Gibbs free energies * Length: m_kk. */ virtual void getGibbs_RT(doublereal* grt) const { @@ -705,7 +705,7 @@ public: //! state of the species at the current T and P of the solution /*! * Units are Joules/kmol - * @param gpure Output vector of standard state gibbs free energies + * @param gpure Output vector of standard state Gibbs free energies * Length: m_kk. */ virtual void getPureGibbs(doublereal* gpure) const { @@ -802,7 +802,7 @@ public: } //! Returns the vector of the - //! gibbs function of the reference state at the current temperature + //! Gibbs function of the reference state at the current temperature //! of the solution and the reference pressure for the species. /*! * units = J/kmol @@ -1648,7 +1648,7 @@ protected: * Occasionally, the need arises to find a safe mole fraction vector to initialize * the object to. This contains such a vector. * The algorithm will pick up the mole fraction vector that is applied from - * the state xml file in the input file + * the state XML file in the input file */ std::vector xMol_Ref; diff --git a/include/cantera/thermo/VPSSMgr.h b/include/cantera/thermo/VPSSMgr.h index 9960b4ea1..57f68ee99 100644 --- a/include/cantera/thermo/VPSSMgr.h +++ b/include/cantera/thermo/VPSSMgr.h @@ -406,7 +406,7 @@ public: } /*! - * Returns the vector of the gibbs function of the reference state at the + * Returns the vector of the Gibbs function of the reference state at the * current temperature of the solution and the reference pressure for the * species. units = J/kmol * @@ -822,7 +822,7 @@ protected: */ mutable vector_fp mPDSS_cp0_R; - //! species reference gibbs free energies - used by individual PDSS objects + //! species reference Gibbs free energies - used by individual PDSS objects /** * Vector containing the species reference Gibbs functions * at T = m_tlast and P = p_ref. @@ -857,7 +857,7 @@ protected: */ mutable vector_fp mPDSS_cpss_R; - //! species standard state gibbs free energies - used by individual PDSS objects + //! species standard state Gibbs free energies - used by individual PDSS objects /** * Vector containing the species standard state Gibbs functions * at T = m_tlast and P = p_ref. diff --git a/include/cantera/thermo/VPStandardStateTP.h b/include/cantera/thermo/VPStandardStateTP.h index c5b0d4bce..2c5555ac5 100644 --- a/include/cantera/thermo/VPStandardStateTP.h +++ b/include/cantera/thermo/VPStandardStateTP.h @@ -407,7 +407,7 @@ protected: public: /*! * Returns the vector of the - * gibbs function of the reference state at the current temperature + * Gibbs function of the reference state at the current temperature * of the solution and the reference pressure for the species. * units = J/kmol * diff --git a/include/cantera/thermo/WaterPropsIAPWSphi.h b/include/cantera/thermo/WaterPropsIAPWSphi.h index c549cf08c..85ecb3bfc 100644 --- a/include/cantera/thermo/WaterPropsIAPWSphi.h +++ b/include/cantera/thermo/WaterPropsIAPWSphi.h @@ -123,7 +123,7 @@ public: */ doublereal dfind(doublereal p_red, doublereal tau, doublereal deltaGuess); - //! Calculate the dimensionless gibbs free energy + //! Calculate the dimensionless Gibbs free energy doublereal gibbs_RT() const; //! Calculate the dimensionless enthalpy, h/RT diff --git a/include/cantera/thermo/WaterSSTP.h b/include/cantera/thermo/WaterSSTP.h index 290479824..7ee379c7e 100644 --- a/include/cantera/thermo/WaterSSTP.h +++ b/include/cantera/thermo/WaterSSTP.h @@ -205,21 +205,21 @@ public: //! @name Properties of the Standard State of the Species in the Solution //! @{ - //! Get the gibbs function for the species + //! Get the Gibbs function for the species //! standard states at the current T and P of the solution. /*! * @param gss Vector of length m_kk, which on return * will contain the - * standard state gibbs function for species k. + * standard state Gibbs function for species k. */ virtual void getStandardChemPotentials(doublereal* gss) const; - //!Get the nondimensional gibbs function for the species + //!Get the nondimensional Gibbs function for the species //! standard states at the current T and P of the solution. /*! * @param grt Vector of length m_kk, which on return * will contain the nondimensional - * standard state gibbs function for species k + * standard state Gibbs function for species k */ virtual void getGibbs_RT(doublereal* grt) const; @@ -288,7 +288,7 @@ public: virtual void getGibbs_RT_ref(doublereal* grt) const; /*! - * Returns the vector of the gibbs function of the reference state at the + * Returns the vector of the Gibbs function of the reference state at the * current temperature of the solution and the reference pressure for the * species. units = J/kmol * diff --git a/include/cantera/transport/AqueousTransport.h b/include/cantera/transport/AqueousTransport.h index e8654e437..5a5c2dc31 100644 --- a/include/cantera/transport/AqueousTransport.h +++ b/include/cantera/transport/AqueousTransport.h @@ -77,7 +77,7 @@ namespace Cantera * \sum_i \mathbf{j}_i = 0 * \f] * - * When there are charged species, we replace the rhs with the + * When there are charged species, we replace the RHS with the * gradient of the electrochemical potential to obtain the * modified equation * @@ -435,10 +435,10 @@ private: */ DenseMatrix m_wratkj1; - //! RHS to the stefan-maxwell equation + //! RHS to the Stefan-Maxwell equation Array2D m_B; - //! Matrix for the stefan maxwell equation. + //! Matrix for the Stefan-Maxwell equation. DenseMatrix m_A; //! Internal storage for the species LJ well depth diff --git a/include/cantera/transport/LTPspecies.h b/include/cantera/transport/LTPspecies.h index b01e61870..05c676484 100644 --- a/include/cantera/transport/LTPspecies.h +++ b/include/cantera/transport/LTPspecies.h @@ -248,7 +248,7 @@ public: * \f[ * x = A T^b \exp( - E / RT ) * \f] - * where A, b, and E are passed in the xml input file. + * where A, b, and E are passed in the XML input file. * * As an example of the input required for LTPspecies_Arrhenius * consider the following XML fragment diff --git a/include/cantera/transport/LiquidTranInteraction.h b/include/cantera/transport/LiquidTranInteraction.h index c214887c5..3abf154a0 100644 --- a/include/cantera/transport/LiquidTranInteraction.h +++ b/include/cantera/transport/LiquidTranInteraction.h @@ -448,7 +448,7 @@ protected: * \f] * where F is Faraday's constant, RT is the gas constant times the * tempurature, and V is the molar volume (basis is moles of ions) that is - * calculated by the thermophase member. X_A and X_B are the mole fractions + * calculated by the ThermoPhase member. X_A and X_B are the mole fractions * of the salts composed of cation(1) and cation(2), respectively, that share * a common anion(3). \f$\nu_{+,-}\f$ are the stoichiometric coefficients in * the dissociation reaction of the salts to the ions with charges of @@ -463,7 +463,7 @@ protected: * where the self diffusion coefficients, \f$D_i^*\f$, are temperature and * composition parameterized inputs and the derivative of the activity * coefficient, \f$\frac{\partial \gamma_B}{\partial N_B}\f$, is calculated - * by the thermophase member using the excess enthalpy and entropy upon mixing. + * by the ThermoPhase member using the excess enthalpy and entropy upon mixing. * * Finally, the deviation of the transferrence numbers from ideality, * \f$\epsilon\f$, is calculated from the mobility ratio of the cations. diff --git a/include/cantera/transport/LiquidTransport.h b/include/cantera/transport/LiquidTransport.h index 0ea78f09a..fb443a936 100644 --- a/include/cantera/transport/LiquidTransport.h +++ b/include/cantera/transport/LiquidTransport.h @@ -178,7 +178,7 @@ public: * tracer species at the current temperature and composition of the * species. Therefore, the dilute limit of transport is assumed for the * tracer species. The effective formula may be calculated from the - * stefan-maxwell formulation by adding another row for the tracer + * Stefan-Maxwell formulation by adding another row for the tracer * species, assigning all D's to be equal to the respective species D's, * and then taking the limit as the tracer species mole fraction goes to * zero. The corresponding flux equation for the tracer species k in @@ -656,14 +656,14 @@ protected: * \nabla ( \ln a_k ) \right] * \f] * - * The gradient in the activity coefficient requires the use of thermophase + * The gradient in the activity coefficient requires the use of ThermoPhase * getdlnActCoeff that calculates its change based on a change in the state * (i.e. temperature and composition of each species) which was first * implemented in MargulesVPSSTP.cpp (LiquidTransport.h doxygen) */ virtual void update_Grad_lnAC(); - //! Solve the stefan_maxell equations for the diffusive fluxes. + //! Solve the Stefan-Maxwell equations for the diffusive fluxes. /*! * The diffusive mass flux of species \e k is computed * using the Stefan-Maxwell equation @@ -687,7 +687,7 @@ protected: * velocities may be specified as relative to a specific species (i.e. a * solvent) all according to the `velocityBasis` input parameter. * - * The gradient in the activity coefficient requires the use of thermophase + * The gradient in the activity coefficient requires the use of ThermoPhase * getdlnActCoeff that calculates its change based on a change in the state * i.e. temperature and composition of each species. * First implemented in MargulesVPSSTP.cpp. @@ -914,7 +914,7 @@ private: */ LiquidTranInteraction* m_diffMixModel; - //! Setfan-Maxwell diffusion coefficients + //! Stefan-Maxwell diffusion coefficients DenseMatrix m_diff_Dij; //! Hydrodynamic radius for each species expressed as an appropriate subclass of LTPspecies @@ -1169,10 +1169,10 @@ private: //! Vector of activity coefficients vector_fp m_actCoeff; - //! RHS to the stefan-maxwell equation + //! RHS to the Stefan-Maxwell equation DenseMatrix m_B; - //! Matrix for the stefan maxwell equation. + //! Matrix for the Stefan-Maxwell equation. DenseMatrix m_A; //! Current Temperature -> locally stored diff --git a/include/cantera/transport/SimpleTransport.h b/include/cantera/transport/SimpleTransport.h index de782e64e..d730c6f48 100644 --- a/include/cantera/transport/SimpleTransport.h +++ b/include/cantera/transport/SimpleTransport.h @@ -75,7 +75,7 @@ namespace Cantera * \sum_i \mathbf{j}_i = 0 * \f] * - * When there are charged species, we replace the rhs with the + * When there are charged species, we replace the RHS with the * gradient of the electrochemical potential to obtain the * modified equation * diff --git a/include/cantera/transport/TransportBase.h b/include/cantera/transport/TransportBase.h index 8c4312481..6178f8fe4 100644 --- a/include/cantera/transport/TransportBase.h +++ b/include/cantera/transport/TransportBase.h @@ -316,7 +316,7 @@ public: * The self diffusion coefficient is the diffusion coefficient of a tracer * species at the current temperature and composition of the species. * Therefore, the dilute limit of transport is assumed for the tracer - * species. The effective formula may be calculated from the stefan-maxwell + * species. The effective formula may be calculated from the Stefan-Maxwell * formulation by adding another row for the tracer species, assigning all * D's to be equal to the respective species D's, and then taking the limit * as the tracer species mole fraction goes to zero. The corresponding flux @@ -372,7 +372,7 @@ public: //! Get the Electrical mobilities (m^2/V/s). /*! * This function returns the mobilities. In some formulations - * this is equal to the normal mobility multiplied by faraday's constant. + * this is equal to the normal mobility multiplied by Faraday's constant. * * Frequently, but not always, the mobility is calculated from the * diffusion coefficient using the Einstein relation diff --git a/include/cantera/transport/TransportParams.h b/include/cantera/transport/TransportParams.h index bb1210a6e..76585be9f 100644 --- a/include/cantera/transport/TransportParams.h +++ b/include/cantera/transport/TransportParams.h @@ -1,6 +1,6 @@ /** * @file TransportParams.h - * Class that holds the data that is read in from the xml file, and which is used for + * Class that holds the data that is read in from the XML file, and which is used for * processing of the transport object * (see \ref tranprops and \link Cantera::TransportParams TransportParams \endlink). */ diff --git a/interfaces/cython/cantera/ctml_writer.py b/interfaces/cython/cantera/ctml_writer.py index c23c2f6b1..e2acae6f2 100644 --- a/interfaces/cython/cantera/ctml_writer.py +++ b/interfaces/cython/cantera/ctml_writer.py @@ -283,7 +283,7 @@ def is_local_species(name): return 0 def dataset(nm): - "Set the dataset name. Invoke this to change the name of the xml file." + "Set the dataset name. Invoke this to change the name of the XML file." global _name _name = nm diff --git a/interfaces/cython/cantera/mixture.pyx b/interfaces/cython/cantera/mixture.pyx index 92186ceee..96537cdfd 100644 --- a/interfaces/cython/cantera/mixture.pyx +++ b/interfaces/cython/cantera/mixture.pyx @@ -212,7 +212,7 @@ cdef class Mixture: return self.mix.charge() def phase_charge(self, p): - """The charge of phase *p* in Coulumbs.""" + """The charge of phase *p* in Coulombs.""" return self.mix.phaseCharge(self.phase_index(p)) def phase_moles(self, p=None): diff --git a/interfaces/cython/cantera/thermo.pyx b/interfaces/cython/cantera/thermo.pyx index 9f7bd5c35..8d46eef15 100644 --- a/interfaces/cython/cantera/thermo.pyx +++ b/interfaces/cython/cantera/thermo.pyx @@ -308,7 +308,7 @@ cdef class ThermoPhase(_SolutionBase): * 'gibbs' - a slower but more robust Gibbs minimization solver * 'vcs' - the VCS non-ideal equilibrium solver * "auto" - The element potential solver will be tried first, then - if it fails the gibbs solver will be tried. + if it fails the Gibbs solver will be tried. :param rtol: the relative error tolerance. :param maxsteps: diff --git a/platform/posix/SConscript b/platform/posix/SConscript index 22a1fbbc6..01cf9bc1a 100644 --- a/platform/posix/SConscript +++ b/platform/posix/SConscript @@ -73,7 +73,7 @@ else: localenv['mak_boost_libs'] = ' '.join('-l%s' % s for s in localenv['boost_libs']) pc_libs += localenv['boost_libs'] -# Handle blas/lapack linkage +# Handle BLAS/LAPACK linkage localenv['mak_have_blas_lapack_dir'] = '1' if localenv['blas_lapack_dir'] else '0' if localenv['blas_lapack_dir']: diff --git a/src/base/application.h b/src/base/application.h index fac5cda6e..ae0d3ad67 100644 --- a/src/base/application.h +++ b/src/base/application.h @@ -412,7 +412,7 @@ protected: std::map options; //! Current value of tmp_dir std::string tmp_dir; - //! Current vector of xml file trees that have been previously parsed + //! Current vector of XML file trees that have been previously parsed //! The second element of the value is used to store the last-modified time //! for the file, to enable change detection. std::map > xmlfiles; diff --git a/src/base/ctml.cpp b/src/base/ctml.cpp index 0fdc8c3db..f9fd0235a 100644 --- a/src/base/ctml.cpp +++ b/src/base/ctml.cpp @@ -331,7 +331,7 @@ size_t getFloatArray(const Cantera::XML_Node& node, std::vector & v, vector ll = node.getChildren(nodeName); if (ll.size() == 0) { throw CanteraError("getFloatArray", - "wrong xml element type/name: was expecting " + "wrong XML element type/name: was expecting " + nodeName + "but accessed " + node.name()); } else { readNode = ll[0]; diff --git a/src/equil/BasisOptimize.cpp b/src/equil/BasisOptimize.cpp index 19c44012c..f1496b7bf 100644 --- a/src/equil/BasisOptimize.cpp +++ b/src/equil/BasisOptimize.cpp @@ -278,7 +278,7 @@ size_t Cantera::BasisOptimize(int* usedZeroedSpecies, bool doFormRxn, * C will be an nc x nc matrix made up of the formula * vectors for the components. Each component's formula * vector is a column. The rows are the elements. - * n rhs's will be solved for. Thus, B is an nc x n + * n RHS's will be solved for. Thus, B is an nc x n * matrix. * * BIG PROBLEM 1/21/99: diff --git a/src/equil/ChemEquil.cpp b/src/equil/ChemEquil.cpp index 6d6758aeb..283800e32 100644 --- a/src/equil/ChemEquil.cpp +++ b/src/equil/ChemEquil.cpp @@ -429,7 +429,7 @@ int ChemEquil::equilibrate(thermo_t& s, const char* XYstr, size_t mm = m_mm; size_t nvar = mm + 1; - DenseMatrix jac(nvar, nvar); // jacobian + DenseMatrix jac(nvar, nvar); // Jacobian vector_fp x(nvar, -102.0); // solution vector vector_fp res_trial(nvar, 0.0); // residual @@ -585,7 +585,7 @@ int ChemEquil::equilibrate(thermo_t& s, const char* XYstr, * Do a better estimate of the element potentials. * We have found that the current estimate may not be good * enough to avoid drastic numerical issues associated with - * the use of a numerically generated jacobian. + * the use of a numerically generated Jacobian. * * The Brinkley algorithm assumes a constant T, P system * and uses a linearized analytical Jacobian that turns out @@ -693,7 +693,7 @@ int ChemEquil::equilibrate(thermo_t& s, const char* XYstr, } return 0; } - // compute the residual and the jacobian using the current + // compute the residual and the Jacobian using the current // solution vector equilResidual(s, x, elMolesGoal, res_trial, xval, yval); f = 0.5*dot(res_trial.begin(), res_trial.end(), res_trial.begin()); diff --git a/src/equil/vcs_MultiPhaseEquil.cpp b/src/equil/vcs_MultiPhaseEquil.cpp index 17333aceb..02a052577 100644 --- a/src/equil/vcs_MultiPhaseEquil.cpp +++ b/src/equil/vcs_MultiPhaseEquil.cpp @@ -785,7 +785,7 @@ int vcs_Cantera_to_vprob(Cantera::MultiPhase* mphase, for (size_t iphase = 0; iphase < totNumPhases; iphase++) { /* - * Get the thermophase object - assume volume phase + * Get the ThermoPhase object - assume volume phase */ Cantera::ThermoPhase* tPhase = &(mphase->phase(iphase)); size_t nelem = tPhase->nElements(); @@ -1066,7 +1066,7 @@ int vcs_Cantera_to_vprob(Cantera::MultiPhase* mphase, VolPhase->setMolesFromVCS(VCS_STATECALC_OLD, VCS_DATA_PTR(vprob->w)); /* - * Now, calculate a sample naught gibbs free energy calculation + * Now, calculate a sample naught Gibbs free energy calculation * at the specified temperature. */ double R = vcsUtil_gasConstant(vprob->m_VCS_UnitsFormat); diff --git a/src/equil/vcs_TP.cpp b/src/equil/vcs_TP.cpp index dc31821f0..b54111982 100644 --- a/src/equil/vcs_TP.cpp +++ b/src/equil/vcs_TP.cpp @@ -63,7 +63,7 @@ int VCS_SOLVE::vcs_evalSS_TP(int ipr, int ip1, double Temp, double pres) * comes into play in calculating the ideal equation of state * contributions, and other equations of state also. Therefore, * we will emulate the VCS_UNITS_KELVIN case, here by changing - * the initial gibbs free energy units to Kelvin before feeding + * the initial Gibbs free energy units to Kelvin before feeding * them to the cpc_ts_GStar_calc() routine. Then, we will revert * them back to unitless at the end of this routine. */ diff --git a/src/equil/vcs_VolPhase.cpp b/src/equil/vcs_VolPhase.cpp index 46a0bebba..29f6ebbf0 100644 --- a/src/equil/vcs_VolPhase.cpp +++ b/src/equil/vcs_VolPhase.cpp @@ -815,7 +815,7 @@ void vcs_VolPhase::_updateLnActCoeffJac() void vcs_VolPhase::sendToVCS_LnActCoeffJac(Cantera::Array2D& np_LnACJac_VCS) { /* - * update the Ln Act Coeff jacobian entries with respect to the + * update the Ln Act Coeff Jacobian entries with respect to the * mole number of species in the phase -> we always assume that * they are out of date. */ diff --git a/src/equil/vcs_phaseStability.cpp b/src/equil/vcs_phaseStability.cpp index 9499a5cff..eae49b7f7 100644 --- a/src/equil/vcs_phaseStability.cpp +++ b/src/equil/vcs_phaseStability.cpp @@ -514,7 +514,7 @@ double VCS_SOLVE::vcs_phaseStabilityTest(const size_t iph) minNumberIterations = 1; } - // We will do a full newton calculation later, but for now, ... + // We will do a full Newton calculation later, but for now, ... bool doSuccessiveSubstitution = true; double funcPhaseStability; vector X_est(nsp, 0.0); diff --git a/src/equil/vcs_solve_TP.cpp b/src/equil/vcs_solve_TP.cpp index 7c56523cf..4d11d0993 100644 --- a/src/equil/vcs_solve_TP.cpp +++ b/src/equil/vcs_solve_TP.cpp @@ -1736,7 +1736,7 @@ double VCS_SOLVE::vcs_minor_alt_calc(size_t kspec, size_t irxn, bool* do_delete, } /* - * get the diagonal of the activity coefficient jacobian + * get the diagonal of the activity coefficient Jacobian */ s = m_np_dLnActCoeffdMolNum(kspec,kspec) / (m_tPhaseMoles_old[iph]); /* @@ -2821,7 +2821,7 @@ L_END_LOOP: * coefficients. CX + B = 0 * C will be an nc x nc matrix made up of the formula * vectors for the components. - * n rhs's will be solved for. Thus, B is an nc x n + * n RHS's will be solved for. Thus, B is an nc x n * matrix. * * BIG PROBLEM 1/21/99: diff --git a/src/kinetics/KineticsFactory.cpp b/src/kinetics/KineticsFactory.cpp index 1719c75f9..7445e5fed 100644 --- a/src/kinetics/KineticsFactory.cpp +++ b/src/kinetics/KineticsFactory.cpp @@ -24,7 +24,7 @@ Kinetics* KineticsFactory::newKinetics(XML_Node& phaseData, vector th) { /* - * Look for a child of the xml element phase called + * Look for a child of the XML element phase called * "kinetics". It has an attribute name "model". * Store the value of that attribute in the variable kintype */ diff --git a/src/kinetics/importKinetics.cpp b/src/kinetics/importKinetics.cpp index cac20a5ed..9de0f1a21 100644 --- a/src/kinetics/importKinetics.cpp +++ b/src/kinetics/importKinetics.cpp @@ -104,8 +104,8 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp, /* * 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. + * the XML tree for these children based on the value of rp, + * and store the XML element pointer here. */ if (rp == 1) { rptype = "reactants"; @@ -196,7 +196,7 @@ bool getReagents(const XML_Node& rxn, Kinetics& kin, int rp, } /** - * getArrhenius() parses the xml element called Arrhenius. + * 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. @@ -565,7 +565,7 @@ bool installReactionArrays(const XML_Node& p, Kinetics& kin, int itot = 0; /* * Search the children of the phase element for the - * xml element named reactionArray. If we can't find it, + * XML element named reactionArray. If we can't find it, * then return signaling having not found any reactions. * Apparently, we allow multiple reactionArray elements here * Each one will be processed sequentially, with the @@ -578,17 +578,17 @@ bool installReactionArrays(const XML_Node& p, Kinetics& kin, } for (size_t n = 0; n < rarrays.size(); n++) { /* - * Go get a reference to the current xml element, + * Go get a reference to the current XML element, * reactionArray. We will process this element now. */ const XML_Node& rxns = *rarrays[n]; /* * The reactionArray element has an attribute called, - * datasrc. The value of the attribute is the xml + * datasrc. The value of the attribute is the XML * element comprising the top of the * tree of reactions for the phase. * Find this datasrc element starting with the root - * of the current xml node. + * of the current XML node. */ const XML_Node* rdata = get_XML_Node(rxns["datasrc"], &rxns.root()); /* diff --git a/src/kinetics/solveSP.cpp b/src/kinetics/solveSP.cpp index be20c47cd..50765511b 100644 --- a/src/kinetics/solveSP.cpp +++ b/src/kinetics/solveSP.cpp @@ -243,13 +243,13 @@ int solveSP::solveSurfProb(int ifunc, doublereal time_scale, doublereal TKelvin, } } else { /* make steady state calc a step of 1 million seconds to - prevent singular jacobians for some pathological cases */ + prevent singular Jacobians for some pathological cases */ inv_t = 1.0e-6; } deltaT = 1.0/inv_t; /* - * Call the routine to numerically evaluation the jacobian + * Call the routine to numerically evaluation the Jacobian * and residual for the current iteration. */ resjac_eval(m_Jac, DATA_PTR(m_resid), DATA_PTR(m_CSolnSP), @@ -801,7 +801,7 @@ void solveSP::print_header(int ioflag, int ifunc, doublereal time_scale, printf("\n SOLVESP Called to calculate steady state residual\n"); printf(" from a good initial guess\n"); } else if (ifunc == SFLUX_JACOBIAN) { - printf("\n SOLVESP Called to calculate steady state jacobian\n"); + printf("\n SOLVESP Called to calculate steady state Jacobian\n"); printf(" from a good initial guess\n"); } else if (ifunc == SFLUX_TRANSIENT) { printf("\n SOLVESP Called to integrate surface in time\n"); diff --git a/src/numerics/BEulerInt.cpp b/src/numerics/BEulerInt.cpp index 5c0ab114a..03a95b39d 100644 --- a/src/numerics/BEulerInt.cpp +++ b/src/numerics/BEulerInt.cpp @@ -274,7 +274,7 @@ void BEulerInt::computeResidWts(GeneralMatrix& jac) * We compute residual weights here, which we define as the L_0 norm * of the Jacobian Matrix, weighted by the solution weights. * This is the proper way to guage the magnitude of residuals. However, - * it does need the evaluation of the jacobian, and the implementation + * it does need the evaluation of the Jacobian, and the implementation * below is slow, but doesn't take up much memory. * * Here a small weighting indicates that the change in solution is @@ -461,7 +461,7 @@ static void print_lvl1_summary( * * This routine is used in numerical differencing schemes in order * to avoid roundoff errors resulting in creating Jacobian terms. - * Note: This is a slow routine. However, jacobian errors may cause + * Note: This is a slow routine. However, Jacobian errors may cause * loss of convergence. Therefore, in practice this routine * has proved cost-effective. */ @@ -497,7 +497,7 @@ void BEulerInt::beuler_jac(GeneralMatrix& J, double* const f, if (m_jacFormMethod & BEULER_JAC_ANAL) { /******************************************************************** - * Call the function to get a jacobian. + * Call the function to get a Jacobian. */ m_func->evalJacobian(time_curr, delta_t_n, CJ, y, ydot, J, f); m_nJacEval++; @@ -507,7 +507,7 @@ void BEulerInt::beuler_jac(GeneralMatrix& J, double* const f, * Generic algorithm to calculate a numerical Jacobian */ /* - * Calculate the current value of the rhs given the + * Calculate the current value of the RHS given the * current conditions. */ @@ -1030,7 +1030,7 @@ double BEulerInt::step(double t_max) calc_ydot(m_order, &m_y_n[0], &m_ydot_n[0]); /* - * Calculate CJ, the coefficient for the jacobian corresponding to the + * Calculate CJ, the coefficient for the Jacobian corresponding to the * derivative of the residual wrt to the acceleration vector. */ if (m_order < 2) { @@ -1780,7 +1780,7 @@ int BEulerInt::solve_nonlinear_problem(double* const y_comm, num_newt_its); } else { if (loglevel > 1) { - printf("\t\t\tSolving system with old jacobian\n"); + printf("\t\t\tSolving system with old Jacobian\n"); } } @@ -1794,7 +1794,7 @@ int BEulerInt::solve_nonlinear_problem(double* const y_comm, num_backtracks += i_backtracks; /* - * Impose the minimum number of newton iterations critera + * Impose the minimum number of Newton iterations critera */ if (num_newt_its < m_min_newt_its) { if (m == 1) { @@ -1802,7 +1802,7 @@ int BEulerInt::solve_nonlinear_problem(double* const y_comm, } } /* - * Impose max newton iteration + * Impose max Newton iteration */ if (num_newt_its > 20) { m = -1; diff --git a/src/numerics/CVodeInt.cpp b/src/numerics/CVodeInt.cpp index 100614f3f..eb0e56753 100644 --- a/src/numerics/CVodeInt.cpp +++ b/src/numerics/CVodeInt.cpp @@ -7,7 +7,7 @@ #include "CVodeInt.h" using namespace std; -// cvode includes +// CVODE includes #include "../../ext/cvode/include/llnltyps.h" #include "../../ext/cvode/include/llnlmath.h" #include "../../ext/cvode/include/cvode.h" @@ -21,7 +21,7 @@ using namespace std; extern "C" { /** - * Function called by cvode to evaluate ydot given y. The cvode + * Function called by CVODE to evaluate ydot given y. The CVODE * integrator allows passing in a void* pointer to access * external data. This pointer is cast to a pointer to a instance * of class FuncEval. The equations to be integrated should be @@ -39,7 +39,7 @@ extern "C" { } /** - * Function called by cvode to evaluate the Jacobian matrix. + * Function called by CVODE to evaluate the Jacobian matrix. * (temporary) * @ingroup odeGroup */ diff --git a/src/numerics/CVodeInt.h b/src/numerics/CVodeInt.h index b06918b01..d6fc775a1 100644 --- a/src/numerics/CVodeInt.h +++ b/src/numerics/CVodeInt.h @@ -25,8 +25,8 @@ public: }; /** - * Wrapper class for 'cvode' integrator from LLNL. - * The unmodified cvode code is in directory ext/cvode. + * Wrapper class for 'CVODE' integrator from LLNL. + * The unmodified CVODE code is in directory ext/cvode. * * @see FuncEval.h. Classes that use CVodeInt: * ImplicitChem, ImplicitSurfChem, Reactor @@ -35,7 +35,7 @@ class CVodeInt : public Integrator { public: /*! - * Constructor. Default settings: dense jacobian, no user-supplied + * Constructor. Default settings: dense Jacobian, no user-supplied * Jacobian function, Newton iteration. */ CVodeInt(); diff --git a/src/numerics/CVodesIntegrator.cpp b/src/numerics/CVodesIntegrator.cpp index e11677839..7e1420093 100644 --- a/src/numerics/CVodesIntegrator.cpp +++ b/src/numerics/CVodesIntegrator.cpp @@ -47,7 +47,7 @@ public: extern "C" { /** - * Function called by cvodes to evaluate ydot given y. The cvode + * Function called by cvodes to evaluate ydot given y. The CVODE * integrator allows passing in a void* pointer to access * external data. This pointer is cast to a pointer to a instance * of class FuncEval. The equations to be integrated should be @@ -289,7 +289,7 @@ void CVodesIntegrator::initialize(double t0, FuncEval& func) * Specify the method and the iteration type: * Cantera Defaults: * CV_BDF - Use BDF methods - * CV_NEWTON - use newton's method + * CV_NEWTON - use Newton's method */ m_cvode_mem = CVodeCreate(m_method, m_iter); if (!m_cvode_mem) { diff --git a/src/numerics/NonlinearSolver.cpp b/src/numerics/NonlinearSolver.cpp index 339884525..cfb428677 100644 --- a/src/numerics/NonlinearSolver.cpp +++ b/src/numerics/NonlinearSolver.cpp @@ -1067,7 +1067,7 @@ int NonlinearSolver::doAffineNewtonSolve(const doublereal* const y_curr, const } vector_fp delyH(neq_); - // First recalculate the scaled residual. It got wiped out doing the newton solve + // First recalculate the scaled residual. It got wiped out doing the Newton solve if (m_rowScaling) { for (size_t n = 0; n < neq_; n++) { delyH[n] = -m_rowScales[n] * m_resid[n]; @@ -1405,23 +1405,23 @@ void NonlinearSolver::descentComparison(doublereal time_curr, doublereal* ydot0 * HKM These have been shown to exactly match up. * The steepest direction is always largest even when there are variable solution weights * - * HKM When a hessian is used with junk on the diagonal, funcDecreaseNewtExp2 is no longer accurate as the + * HKM When a Hessian is used with junk on the diagonal, funcDecreaseNewtExp2 is no longer accurate as the * direction gets significantly shorter with increasing condition number. This suggests an algorithm where the - * newton step from the Hessian should be increased so as to match funcDecreaseNewtExp2 = funcDecreaseNewt2. - * This roughly equals the ratio of the norms of the hessian and newton steps. This increased Newton step can + * Newton step from the Hessian should be increased so as to match funcDecreaseNewtExp2 = funcDecreaseNewt2. + * This roughly equals the ratio of the norms of the Hessian and Newton steps. This increased Newton step can * then be used with the trust region double dogleg algorithm. */ if ((s_print_DogLeg && m_print_flag >= 3) || (doDogLeg_ && m_print_flag >= 5)) { - printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir (expected) = %g\n", funcDecreaseSDExp); - printf("\t\t descentComparison: initial rate of decrease of func in cauchy dir = %g\n", funcDecreaseSD); - printf("\t\t descentComparison: initial rate of decrease of func in newton dir (expected) = %g\n", funcDecreaseNewtExp2); - printf("\t\t descentComparison: initial rate of decrease of func in newton dir = %g\n", funcDecreaseNewt2); + printf("\t\t descentComparison: initial rate of decrease of func in Cauchy dir (expected) = %g\n", funcDecreaseSDExp); + printf("\t\t descentComparison: initial rate of decrease of func in Cauchy dir = %g\n", funcDecreaseSD); + printf("\t\t descentComparison: initial rate of decrease of func in Newton dir (expected) = %g\n", funcDecreaseNewtExp2); + printf("\t\t descentComparison: initial rate of decrease of func in Newton dir = %g\n", funcDecreaseNewt2); } if ((s_print_DogLeg && m_print_flag >= 3) || (doDogLeg_ && m_print_flag >= 4)) { - printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir (expected) = %g\n", ResidDecreaseSDExp_); - printf("\t\t descentComparison: initial rate of decrease of Resid in cauchy dir = %g\n", ResidDecreaseSD_); - printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir (expected) = %g\n", ResidDecreaseNewtExp_); - printf("\t\t descentComparison: initial rate of decrease of Resid in newton dir = %g\n", ResidDecreaseNewt_); + printf("\t\t descentComparison: initial rate of decrease of Resid in Cauchy dir (expected) = %g\n", ResidDecreaseSDExp_); + printf("\t\t descentComparison: initial rate of decrease of Resid in Cauchy dir = %g\n", ResidDecreaseSD_); + printf("\t\t descentComparison: initial rate of decrease of Resid in Newton dir (expected) = %g\n", ResidDecreaseNewtExp_); + printf("\t\t descentComparison: initial rate of decrease of Resid in Newton dir = %g\n", ResidDecreaseNewt_); } if ((s_print_DogLeg && m_print_flag >= 5) || (doDogLeg_ && m_print_flag >= 5)) { @@ -1459,7 +1459,7 @@ void NonlinearSolver::setupDoubleDogleg() * (grad f)T H (grad f) (grad f)T H-1 (grad f) */ /* - * This hasn't worked. so will do it heuristically. One issue is that the newton + * This hasn't worked. so will do it heuristically. One issue is that the Newton * direction is not the inverse of the Hessian times the gradient. The Hessian * is the matrix squared. Until I have the inverse of the Hessian from QR factorization * I may not be able to do it this way. @@ -1467,8 +1467,8 @@ void NonlinearSolver::setupDoubleDogleg() /* * Heuristic algorithm - Find out where on the Newton line the residual is the same - * as the residual at the cauchy point. Then, go halfway to - * the newton point and call that Nuu. + * as the residual at the Cauchy point. Then, go halfway to + * the Newton point and call that Nuu. * Maybe we need to check that the linearized residual is * monotonic along that line. However, we haven't needed to yet. */ @@ -2443,15 +2443,15 @@ int NonlinearSolver::decideStep(const doublereal time_curr, int leg, doublereal // Calculate the initial (R**2 * neq) value for the old function doublereal normResid0_2 = m_normResid_0 * m_normResid_0 * neq_; - // Calculate the distance to the cauchy point + // Calculate the distance to the Cauchy point doublereal cauchyDistanceNorm = solnErrorNorm(DATA_PTR(deltaX_CP_)); - // This is the expected initial rate of decrease in the cauchy direction. + // This is the expected initial rate of decrease in the Cauchy direction. // -> This is Eqn. 29 = Rhat dot Jhat dy / || d || doublereal funcDecreaseSDExp = RJd_norm_ / cauchyDistanceNorm * lambdaStar_; if (funcDecreaseSDExp > 0.0) { if (m_print_flag >= 5) { - printf("\t\tdecideStep(): Unexpected condition -> cauchy slope is positive\n"); + printf("\t\tdecideStep(): Unexpected condition -> Cauchy slope is positive\n"); } } @@ -2711,7 +2711,7 @@ int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal* const y_c } } else { if (m_print_flag > 1) { - printf("\t solve_nonlinear_problem(): Solving system with old jacobian\n"); + printf("\t solve_nonlinear_problem(): Solving system with old Jacobian\n"); } } /* @@ -2736,7 +2736,7 @@ int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal* const y_c } /* - * Scale the matrix and the rhs, if they aren't already scaled + * Scale the matrix and the RHS, if they aren't already scaled * Figure out and store the residual scaling factors. */ scaleMatrix(jac, DATA_PTR(m_y_n_curr), DATA_PTR(m_ydot_n_curr), time_curr, num_newt_its); @@ -2873,12 +2873,12 @@ int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal* const y_c /* - * Impose the minimum number of newton iterations criteria + * Impose the minimum number of Newton iterations criteria */ if (num_newt_its < m_min_newt_its) { if (retnDamp > NSOLN_RETN_CONTINUE) { if (m_print_flag > 2) { - printf("\t solve_nonlinear_problem(): Damped Newton successful (m=%d) but minimum newton" + printf("\t solve_nonlinear_problem(): Damped Newton successful (m=%d) but minimum Newton" "iterations not attained. Resolving ...\n", retnDamp); } retnDamp = NSOLN_RETN_CONTINUE; @@ -2886,12 +2886,12 @@ int NonlinearSolver::solve_nonlinear_problem(int SolnType, doublereal* const y_c } /* - * Impose max newton iteration + * Impose max Newton iteration */ if (num_newt_its > maxNewtIts_) { retnDamp = NSOLN_RETN_MAXIMUMITERATIONSEXCEEDED; if (m_print_flag > 1) { - printf("\t solve_nonlinear_problem(): Damped newton unsuccessful (max newts exceeded) sfinal = %g\n", + printf("\t solve_nonlinear_problem(): Damped Newton unsuccessful (max newts exceeded) sfinal = %g\n", stepNorm_1); } } @@ -3173,7 +3173,7 @@ void NonlinearSolver::print_solnDelta_norm_contrib(const doublereal* const step_ * * This routine is used in numerical differencing schemes in order * to avoid roundoff errors resulting in creating Jacobian terms. - * Note: This is a slow routine. However, jacobian errors may cause + * Note: This is a slow routine. However, Jacobian errors may cause * loss of convergence. Therefore, in practice this routine has proved cost-effective. * * @param a Value of a @@ -3213,7 +3213,7 @@ int NonlinearSolver::beuler_jac(GeneralMatrix& J, doublereal* const f, J.clearFactorFlag(); if (m_jacFormMethod == NSOLN_JAC_ANAL) { /******************************************************************** - * Call the function to get a jacobian. + * Call the function to get a Jacobian. */ info = m_func->evalJacobian(time_curr, delta_t_n, CJ, y, ydot, J, f); m_nJacEval++; @@ -3227,7 +3227,7 @@ int NonlinearSolver::beuler_jac(GeneralMatrix& J, doublereal* const f, * Generic algorithm to calculate a numerical Jacobian */ /* - * Calculate the current value of the rhs given the + * Calculate the current value of the RHS given the * current conditions. */ @@ -3254,7 +3254,7 @@ int NonlinearSolver::beuler_jac(GeneralMatrix& J, doublereal* const f, if (m_print_flag >= 7) { if (retn != 1) { printf("\t\t beuler_jac ERROR! calcDeltaSolnVariables() returned an error flag\n"); - printf("\t\t We will bail from the nonlinear solver after calculating the jacobian"); + printf("\t\t We will bail from the nonlinear solver after calculating the Jacobian"); } if (neq_ < 20) { printf("\t\tUnk m_ewt y dyVector ResN\n"); @@ -3354,7 +3354,7 @@ int NonlinearSolver::beuler_jac(GeneralMatrix& J, doublereal* const f, if (m_print_flag >= 7) { if (retn != 1) { printf("\t\t beuler_jac ERROR! calcDeltaSolnVariables() returned an error flag\n"); - printf("\t\t We will bail from the nonlinear solver after calculating the jacobian"); + printf("\t\t We will bail from the nonlinear solver after calculating the Jacobian"); } if (neq_ < 20) { printf("\t\tUnk m_ewt y dyVector ResN\n"); @@ -3460,7 +3460,7 @@ int NonlinearSolver::beuler_jac(GeneralMatrix& J, doublereal* const f, } } /* - * Make a copy of the data. Note, this jacobian copy occurs before any matrix scaling operations. + * Make a copy of the data. Note, this Jacobian copy occurs before any matrix scaling operations. * It's the raw matrix producted by this routine. */ *jacCopyPtr_ = J; diff --git a/src/numerics/solveProb.cpp b/src/numerics/solveProb.cpp index 96decf715..9a0147de7 100644 --- a/src/numerics/solveProb.cpp +++ b/src/numerics/solveProb.cpp @@ -185,13 +185,13 @@ int solveProb::solve(int ifunc, doublereal time_scale, } } else { /* make steady state calc a step of 1 million seconds to - prevent singular jacobians for some pathological cases */ + prevent singular Jacobians for some pathological cases */ inv_t = 1.0e-6; } deltaT = 1.0/inv_t; /* - * Call the routine to numerically evaluation the jacobian + * Call the routine to numerically evaluation the Jacobian * and residual for the current iteration. */ resjac_eval(m_JacCol, DATA_PTR(m_resid), DATA_PTR(m_CSolnSP), @@ -215,7 +215,7 @@ int solveProb::solve(int ifunc, doublereal time_scale, if (m_ioflag > 1) { printIterationHeader(m_ioflag, damp, inv_t, t_real, iter, do_time); /* - * Print out the residual and jacobian + * Print out the residual and Jacobian */ printResJac(m_ioflag, m_neq, m_Jac, DATA_PTR(m_resid), DATA_PTR(m_wtResid), resid_norm); @@ -618,7 +618,7 @@ void solveProb::print_header(int ioflag, int ifunc, doublereal time_scale, printf("\n SOLVEPROB Called to calculate steady state residual\n"); printf(" from a good initial guess\n"); } else if (ifunc == SOLVEPROB_JACOBIAN) { - printf("\n SOLVEPROB Called to calculate steady state jacobian\n"); + printf("\n SOLVEPROB Called to calculate steady state Jacobian\n"); printf(" from a good initial guess\n"); } else if (ifunc == SOLVEPROB_TRANSIENT) { printf("\n SOLVEPROB Called to integrate surface in time\n"); diff --git a/src/thermo/DebyeHuckel.cpp b/src/thermo/DebyeHuckel.cpp index 96440c84f..42bf6e220 100644 --- a/src/thermo/DebyeHuckel.cpp +++ b/src/thermo/DebyeHuckel.cpp @@ -507,7 +507,7 @@ void DebyeHuckel::getPartialMolarVolumes(doublereal* vbar) const void DebyeHuckel::getPartialMolarCp(doublereal* cpbar) const { /* - * Get the nondimensional gibbs standard state of the + * Get the nondimensional Gibbs standard state of the * species at the T and P of the solution. */ getCp_R(cpbar); @@ -906,7 +906,7 @@ void DebyeHuckel::initThermoXML(XML_Node& phaseNode, const std::string& id_) if (m_formDH == DHFORM_BDOT_AK) { /* * Define a string-string map, and interpret the - * value of the xml element as binary pairs separated + * value of the XML element as binary pairs separated * by colons, e.g.: * Na+:3.0 * Cl-:4.0 diff --git a/src/thermo/Elements.cpp b/src/thermo/Elements.cpp index a1800b5c5..c1d707ff0 100644 --- a/src/thermo/Elements.cpp +++ b/src/thermo/Elements.cpp @@ -516,7 +516,7 @@ 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"); + "phase XML node doesn't have \"elementArray\" XML Node"); } XML_Node& elements = phase.child("elementArray"); vector enames; diff --git a/src/thermo/GibbsExcessVPSSTP.cpp b/src/thermo/GibbsExcessVPSSTP.cpp index 96a994add..b80adf50c 100644 --- a/src/thermo/GibbsExcessVPSSTP.cpp +++ b/src/thermo/GibbsExcessVPSSTP.cpp @@ -7,7 +7,7 @@ * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based upon expressions - * for the excess gibbs free energy expressed as a function of + * for the excess Gibbs free energy expressed as a function of * the mole fractions. */ /* diff --git a/src/thermo/HMWSoln.cpp b/src/thermo/HMWSoln.cpp index e2c16723a..e36670a5e 100644 --- a/src/thermo/HMWSoln.cpp +++ b/src/thermo/HMWSoln.cpp @@ -806,7 +806,7 @@ void HMWSoln::getPartialMolarVolumes(doublereal* vbar) const void HMWSoln::getPartialMolarCp(doublereal* cpbar) const { /* - * Get the nondimensional gibbs standard state of the + * Get the nondimensional Gibbs standard state of the * species at the T and P of the solution. */ getCp_R(cpbar); diff --git a/src/thermo/IdealMolalSoln.cpp b/src/thermo/IdealMolalSoln.cpp index 5a7dddf64..33ba92c0c 100644 --- a/src/thermo/IdealMolalSoln.cpp +++ b/src/thermo/IdealMolalSoln.cpp @@ -468,7 +468,7 @@ void IdealMolalSoln::getPartialMolarVolumes(doublereal* vbar) const void IdealMolalSoln::getPartialMolarCp(doublereal* cpbar) const { /* - * Get the nondimensional gibbs standard state of the + * Get the nondimensional Gibbs standard state of the * species at the T and P of the solution. */ getCp_R(cpbar); diff --git a/src/thermo/IonsFromNeutralVPSSTP.cpp b/src/thermo/IonsFromNeutralVPSSTP.cpp index af9bb2866..b3a7ecf6d 100644 --- a/src/thermo/IonsFromNeutralVPSSTP.cpp +++ b/src/thermo/IonsFromNeutralVPSSTP.cpp @@ -8,7 +8,7 @@ * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based upon expressions - * for the excess gibbs free energy expressed as a function of + * for the excess Gibbs free energy expressed as a function of * the mole fractions. */ /* diff --git a/src/thermo/MargulesVPSSTP.cpp b/src/thermo/MargulesVPSSTP.cpp index 482b9d411..62fd7aa6f 100644 --- a/src/thermo/MargulesVPSSTP.cpp +++ b/src/thermo/MargulesVPSSTP.cpp @@ -1,7 +1,7 @@ /** * @file MargulesVPSSTP.cpp * Definitions for ThermoPhase object for phases which - * employ excess gibbs free energy formulations related to Margules + * employ excess Gibbs free energy formulations related to Margules * expansions (see \ref thermoprops * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). */ diff --git a/src/thermo/MixedSolventElectrolyte.cpp b/src/thermo/MixedSolventElectrolyte.cpp index 39f04216a..0a6ed5507 100644 --- a/src/thermo/MixedSolventElectrolyte.cpp +++ b/src/thermo/MixedSolventElectrolyte.cpp @@ -1,7 +1,7 @@ /** * @file MixedSolventElectrolyte.cpp * Definitions for ThermoPhase object for phases which - * employ excess gibbs free energy formulations related to Margules + * employ excess Gibbs free energy formulations related to Margules * expansions (see \ref thermoprops * and class \link Cantera::MargulesVPSSTP MargulesVPSSTP\endlink). */ diff --git a/src/thermo/MixtureFugacityTP.cpp b/src/thermo/MixtureFugacityTP.cpp index 0a498ab5e..ab69e52aa 100644 --- a/src/thermo/MixtureFugacityTP.cpp +++ b/src/thermo/MixtureFugacityTP.cpp @@ -769,7 +769,7 @@ doublereal MixtureFugacityTP::calculatePsat(doublereal TKelvin, doublereal& mola * The key requirement is to find an initial pressure where both the liquid and the gas exist. This * is not as easy as it sounds, and it gets exceedingly hard as the critical temperature is approached * from below. - * Once we have this initial state, then we seek to equilibrate the gibbs free energies of the + * Once we have this initial state, then we seek to equilibrate the Gibbs free energies of the * gas and liquid and use the formula * * dp = VdG diff --git a/src/thermo/MolarityIonicVPSSTP.cpp b/src/thermo/MolarityIonicVPSSTP.cpp index e69a7d3bb..0b00330cb 100644 --- a/src/thermo/MolarityIonicVPSSTP.cpp +++ b/src/thermo/MolarityIonicVPSSTP.cpp @@ -1,14 +1,14 @@ /** * @file MolarityIonicVPSSTP.cpp * Definitions for intermediate ThermoPhase object for phases which - * employ excess gibbs free energy formulations + * employ excess Gibbs free energy formulations * (see \ref thermoprops * and class \link Cantera::MolarityIonicVPSSTP MolarityIonicVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based upon expressions - * for the excess gibbs free energy expressed as a function of + * for the excess Gibbs free energy expressed as a function of * the mole fractions. */ /* diff --git a/src/thermo/NasaThermo.h b/src/thermo/NasaThermo.h index 25852df43..7887c24f8 100644 --- a/src/thermo/NasaThermo.h +++ b/src/thermo/NasaThermo.h @@ -1,6 +1,6 @@ /** * @file NasaThermo.h - * Header for the 2 regime 7 coefficient Nasa thermodynamic + * 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). diff --git a/src/thermo/PseudoBinaryVPSSTP.cpp b/src/thermo/PseudoBinaryVPSSTP.cpp index 53f6ed233..ab06fed17 100644 --- a/src/thermo/PseudoBinaryVPSSTP.cpp +++ b/src/thermo/PseudoBinaryVPSSTP.cpp @@ -1,14 +1,14 @@ /** * @file PseudoBinaryVPSSTP.cpp * Definitions for intermediate ThermoPhase object for phases which - * employ excess gibbs free energy formulations + * employ excess Gibbs free energy formulations * (see \ref thermoprops * and class \link Cantera::PseudoBinaryVPSSTP PseudoBinaryVPSSTP\endlink). * * Header file for a derived class of ThermoPhase that handles * variable pressure standard state methods for calculating * thermodynamic properties that are further based upon expressions - * for the excess gibbs free energy expressed as a function of + * for the excess Gibbs free energy expressed as a function of * the mole fractions. */ /* diff --git a/src/thermo/RedlichKisterVPSSTP.cpp b/src/thermo/RedlichKisterVPSSTP.cpp index bb5882696..824bfe392 100644 --- a/src/thermo/RedlichKisterVPSSTP.cpp +++ b/src/thermo/RedlichKisterVPSSTP.cpp @@ -1,7 +1,7 @@ /** * @file RedlichKisterVPSSTP.cpp * Definitions for ThermoPhase object for phases which - * employ excess gibbs free energy formulations related to RedlichKister + * employ excess Gibbs free energy formulations related to RedlichKister * expansions (see \ref thermoprops * and class \link Cantera::RedlichKisterVPSSTP RedlichKisterVPSSTP\endlink). * diff --git a/src/thermo/ThermoFactory.cpp b/src/thermo/ThermoFactory.cpp index 3dd3266c9..7a9347f48 100644 --- a/src/thermo/ThermoFactory.cpp +++ b/src/thermo/ThermoFactory.cpp @@ -326,7 +326,7 @@ bool importPhase(XML_Node& phase, ThermoPhase* th, /* * In this section of code, we get the reference to the - * phase xml tree within the ThermoPhase object. Then, + * phase XML tree within the ThermoPhase object. Then, * we clear it and fill it with the current information that * we are about to use to construct the object. We will then * be able to resurrect the information later by calling xml(). @@ -500,7 +500,7 @@ void installElements(Phase& th, const XML_Node& phaseNode) // get the declared element names if (!phaseNode.hasChild("elementArray")) { throw CanteraError("installElements", - "phase xml node doesn't have \"elementArray\" XML Node"); + "phase XML node doesn't have \"elementArray\" XML Node"); } XML_Node& elements = phaseNode.child("elementArray"); vector enames; diff --git a/src/thermo/VPSSMgrFactory.cpp b/src/thermo/VPSSMgrFactory.cpp index c099c7674..fb1425fd5 100644 --- a/src/thermo/VPSSMgrFactory.cpp +++ b/src/thermo/VPSSMgrFactory.cpp @@ -42,8 +42,8 @@ mutex_t VPSSMgrFactory::vpss_species_thermo_mutex; * of species XML nodes underneath it. * @param has_nasa_idealGas Boolean indicating that one species has a NASA ideal gas standard state * @param has_nasa_constVol Boolean indicating that one species has a NASA ideal solution standard state - * @param has_shomate_idealGas Boolean indicating that one species has a shomate ideal gas standard state - * @param has_shomate_constVol Boolean indicating that one species has a shomate ideal solution standard state + * @param has_shomate_idealGas Boolean indicating that one species has a Shomate ideal gas standard state + * @param has_shomate_constVol Boolean indicating that one species has a Shomate ideal solution standard state * @param has_simple_idealGas Boolean indicating that one species has a simple ideal gas standard state * @param has_simple_constVol Boolean indicating that one species has a simple ideal solution standard state * @param has_water Boolean indicating that one species has a water standard state diff --git a/src/transport/LTPspecies.cpp b/src/transport/LTPspecies.cpp index 1d68c005c..95430b1f7 100644 --- a/src/transport/LTPspecies.cpp +++ b/src/transport/LTPspecies.cpp @@ -28,7 +28,7 @@ public: } }; -//! Parses the xml element called Arrhenius. +//! Parses the XML element called Arrhenius. /*! * The Arrhenius expression is * \f[ diff --git a/src/transport/TransportParams.cpp b/src/transport/TransportParams.cpp index 7c9e8105c..11362886b 100644 --- a/src/transport/TransportParams.cpp +++ b/src/transport/TransportParams.cpp @@ -1,6 +1,6 @@ /** * @file TransportParams.cpp - * Class that holds the data that is read in from the xml file, and which is used for + * Class that holds the data that is read in from the XML file, and which is used for * processing of the transport object * (see \ref tranprops and \link Cantera::TransportParams TransportParams \endlink). */ diff --git a/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml b/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml index 42a499ff3..d035375fc 100644 --- a/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml +++ b/test_problems/VCSnonideal/NaCl_equil/HMW_NaCl.xml @@ -116,7 +116,7 @@