From 2902c58f69f4917b29e956cbf044f677805a8da9 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Thu, 3 Aug 2023 09:36:47 -0500 Subject: [PATCH 1/8] [docs] Sort BibTeX entries alphabetically --- doc/doxygen/cantera.bib | 398 ++++++++++++++++++++-------------------- 1 file changed, 200 insertions(+), 198 deletions(-) diff --git a/doc/doxygen/cantera.bib b/doc/doxygen/cantera.bib index 79064de981..9479edfcab 100644 --- a/doc/doxygen/cantera.bib +++ b/doc/doxygen/cantera.bib @@ -1,3 +1,66 @@ +@article{blowers2004, + author = {P.~Blowers and R.~Masel}, + journal = {AIChE Journal}, + number = {5}, + pages = {1151--1156}, + title = {Engineering approximations for activation energies in hydrogen transfer + reactions}, + doi = {10.1002/aic.690461015}, + url = {https://dx.doi.org/10.1002/aic.690461015}, + volume = {46}, + year = {2004}} +@article{chiflikian1995, + author = {R.~V.~Chiflikian}, + journal = {Physics of Plasmas}, + number = {10}, + pages = {3902--3909}, + title = {The analog of {B}lanc's law for drift velocities of electrons in gas + mixtures in weakly ionized plasma}, + doi = {10.1063/1.871019}, + url = {https://dx.doi.org/10.1063/1.871019}, + volume = {2}, + year = {1995}} +@techreport{RADCAL, + author = {W.~L.~Grosshandler}, + institution = {National Institute of Standards and Technology}, + number = {1402}, + title = {{RADCAL}: A Narrow-Band Model for Radiation Calculations in a Combustion + Environment}, + url = {https://nvlpubs.nist.gov/nistpubs/Legacy/TN/nbstechnicalnote1402.pdf}, + year = {1993}} +@article{gudmundsson2001, + author = {J.~T.~Gudmundsson}, + journal = {Plasma Sources Science and Technology}, + number = {1}, + pages = {76}, + title = {On the effect of the electron energy distribution on the plasma + parameters of an argon discharge: a global (volume-averaged) model study}, + doi = {10.1088/0963-0252/10/1/310}, + url = {https://dx.doi.org/10.1088/0963-0252/10/1/310}, + volume = {10}, + year = {2001}} +@article{hagelaar2005, + author = {G.~J.~M.~Hagelaar and L.~C.~Pitchford}, + journal = {Plasma Sources Science and Technology}, + number = {4}, + pages = {722}, + title = {Solving the {B}oltzmann equation to obtain electron transport + coefficients and rate coefficients for fluid models}, + doi = {10.1088/0963-0252/14/4/011}, + url = {https://dx.doi.org/10.1088/0963-0252/14/4/011}, + volume = {14}, + year = {2005}} +@article{han2015, + author = {J.~Han and X.~Chen and Z.~Zhang and Z.~Li and F.~Qi and Z.~Wang and + Z.~Sun}, + journal = {Combustion Theory and Modelling}, + number = {6}, + pages = {744--772}, + title = {Numerical modelling of ion transport in flames}, + doi = {10.1080/13647830.2015.1090018}, + url = {https://dx.doi.org/10.1080/13647830.2015.1090018}, + volume = {19}, + year = {2015}} @book{kee2003, author = {R.~J.~Kee and M.~E.~Coltrin and P.~Glarborg}, publisher = {John Wiley & Sons}, @@ -11,29 +74,63 @@ @book{kee2017 doi = {10.1002/9781119186304}, url = {https://dx.doi.org/10.1002/9781119186304}, year = {2017}} -@article{zhu2006, - author = {H.~Zhu and R.~J.~Kee}, - journal = {Journal of The Electrochemical Society}, +@article{khalilpour2020, + author = {H.~Khalilpour and G.~Foroutan}, + journal = {Journal of Plasma Physics}, + number = {2}, + pages = {1--14}, + title = {The effects of electron energy distribution function on the plasma + sheath structure in the presence of charged nanoparticles}, + doi = {10.1017/S0022377820000161}, + url = {https://dx.doi.org/10.1017/S0022377820000161}, + volume = {86}, + year = {2020}} +@article{kim2019, + author = {S.~Kim, and J.~Chen and T.~Cheng and A.~Gindulyte and J.~He and S.He + and Q.~Li and B.~A.~Shoemaker and P.~A.~Thiessen, and B.~Yu and L.~Zaslavsky + and J.Zhangn and E.~E.~Bolton}, + journal = {Nucleic Acids Research}, + number = {D1}, + pages = {D1102--D1109}, + title = {{PubChem} 2019 update: improved access to chemical data}, + doi = {10.1093/nar/gky1033}, + url = {https://dx.doi.org/10.1093/nar/gky1033}, + volume = {47}, + year = {2019}} +@article{kossyi1992, + author = {I.~A.~Kossyi and A.~Y.~Kostinsky and A.~A.~Matveyev and V.~P.~Silakov}, + journal = {Plasma Sources Science and Technology}, + number = {3}, + pages = {207}, + title = {Kinetic scheme of the non-equilibrium discharge in nitrogen-oxygen + mixtures}, + doi = {10.1088/0963-0252/1/3/011}, + url = {https://dx.doi.org/10.1088/0963-0252/1/3/011}, + volume = {1}, + year = {1992}} +@conference{liu1991, + author = {Y.~Liu and B.~Rogg}, + journal = {EUROTHERM Seminars}, + pages = {114--127}, + title = {Modelling of thermally radiating diffusion flames with detailed + chemistry and transport}, + volume = {17}, + year = {1991}} +@article{lucassen2011, + author = {A.~Lucassen and N.~Labbe and P.~R.~Westmoreland and K.~Kohse-Höinghaus}, + title = {Combustion chemistry and fuel-nitrogen conversion in a laminar premixed + flame of morpholine as a model biofuel}, + journal = {Combustion and Flame}, + volume = {158}, number = {9}, - pages = {A1765--A1772}, - title = {Modeling Electrochemical Impedance Spectra in {SOFC} Button Cells with - Internal Methane Reforming}, - doi = {10.1149/1.2220065}, - url = {https://dx.doi.org/10.1149/1.2220065}, - volume = {153}, - year = {2006}} -@article{zhu2005, - author = {H.~Zhu and R.~J.~Kee and V.~M.~Janardhanan and O.~Deutschmann and - D.~G.~Goodwin}, - journal = {Journal of The Electrochemical Society}, - number = {12}, - pages = {A2427--A2439}, - title = {Modeling Elementary Heterogeneous Chemistry and Electrochemistry in - Solid-Oxide Fuel Cells}, - doi = {10.1149/1.2116607}, - url = {https://dx.doi.org/10.1149/1.2116607}, - volume = {152}, - year = {2005}} + pages = {1647--1666}, + doi = {10.1016/j.combustflame.2011.02.010}, + url = {https://dx.doi.org/10.1016/j.combustflame.2011.02.010}, + year = {2011}} +@software{BOLOS, + author = {A.~Luque}, + title = {{BOLOS}: {BOL}tzmann equation solver {O}pen {S}ource library}, + url = {https://github.com/aluque/bolos}} @article{mason1983, author = {E.~A.~Mason and A.~P.~Malinauskas}, journal = {Chemical Engineering Monographs}, @@ -41,18 +138,35 @@ @article{mason1983 publisher = {Elsevier}, title = {Gas Transport in Porous Media: the Dusty-Gas Model}, year = {1983}} -@article{veldsink1995, - author = {J.~W.~Veldsink and R.~M.~J.~van Damme and G.~F.~Versteeg and - W.~P.~M.~van Swaaij}, - journal = {Chemical Engineering Journal}, - number = {2}, - pages = {115--125}, - title = {The use of the dusty gas model for the description of mass transport - with chemical reaction in porous media}, - doi = {10.1016/0923-0467(94)02929-6}, - url = {https://dx.doi.org/10.1016/0923-0467(94)02929-6}, - volume = {57}, - year = {1995}} +@article{niemeyer2017, + author = {K.~E.~Niemeyer and N.~J.~Curtis and C.-J.~Sung}, + journal = {Journal of Computational Science}, + pages = {1--10}, + title = {{pyJac}: Analytical {J}acobian generator for chemical kinetics}, + doi = {10.1016/j.cpc.2017.02.004}, + url = {https://dx.doi.org/10.1016/j.cpc.2017.02.004}, + volume = {21}, + year = {2017}} +@article{perini2012, + author = {F.~Perini and E.~Galligani and R.~D.~Reitz}, + journal = {Energy \& Fuels}, + number = {8}, + pages = {4804--4822}, + title = {An analytical {J}acobian approach to sparse reaction kinetics for + computationally efficient combustion modeling with large reaction + mechanisms}, + doi = {10.1021/ef300747n}, + url = {https://dx.doi.org/10.1021/ef300747n}, + volume = {26}, + year = {2012}} +@phdthesis{prager2005, + author = {J.~Prager}, + school = {Technische Universität Darmstadt}, + title = {Modeling and simulation of charged species in lean methane-oxygen + flames}, + doi = {10.11588/heidok.00005889}, + url = {https://dx.doi.org/10.11588/heidok.00005889}, + year = {2005}} @article{selle1999, author = {S.~Selle and U.~Riedel}, journal = {Annals of the New York Academy of Sciences}, @@ -72,47 +186,6 @@ @conference{selle2000 doi = {10.2514/6.2000-211}, url = {https://dx.doi.org/10.2514/6.2000-211}, year = {2000}} -@article{han2015, - author = {J.~Han and X.~Chen and Z.~Zhang and Z.~Li and F.~Qi and Z.~Wang and - Z.~Sun}, - journal = {Combustion Theory and Modelling}, - number = {6}, - pages = {744--772}, - title = {Numerical modelling of ion transport in flames}, - doi = {10.1080/13647830.2015.1090018}, - url = {https://dx.doi.org/10.1080/13647830.2015.1090018}, - volume = {19}, - year = {2015}} -@article{chiflikian1995, - author = {R.~V.~Chiflikian}, - journal = {Physics of Plasmas}, - number = {10}, - pages = {3902--3909}, - title = {The analog of {B}lanc's law for drift velocities of electrons in gas - mixtures in weakly ionized plasma}, - doi = {10.1063/1.871019}, - url = {https://dx.doi.org/10.1063/1.871019}, - volume = {2}, - year = {1995}} -@article{viehland1975, - author = {L.~A.~Viehland and J.~W.~McConkey and J.~W.~Hogan}, - journal = {Atomic Data and Nuclear Data Tables}, - number = {6}, - pages = {495--514}, - title = {Tables of transport collision integrals for (n, 6, 4) ion-neutral - potentials}, - doi = {10.1016/0092-640x(75)90022-4}, - url = {https://dx.doi.org/10.1016/0092-640x(75)90022-4}, - volume = {16}, - year = {1975}} -@phdthesis{prager2005, - author = {J.~Prager}, - school = {Technische Universität Darmstadt}, - title = {Modeling and simulation of charged species in lean methane-oxygen - flames}, - doi = {10.11588/heidok.00005889}, - url = {https://dx.doi.org/10.11588/heidok.00005889}, - year = {2005}} @article{sengers1986, author = {J.~V.~Sengers and J.~T.~R.~Watson}, journal = {Journal of Physical and Chemical Reference Data}, @@ -125,28 +198,13 @@ @article{sengers1986 year = {1986}, %doi = {10.1063/1.555763}, } -@article{blowers2004, - author = {P.~Blowers and R.~Masel}, - journal = {AIChE Journal}, - number = {5}, - pages = {1151--1156}, - title = {Engineering approximations for activation energies in hydrogen transfer - reactions}, - doi = {10.1002/aic.690461015}, - url = {https://dx.doi.org/10.1002/aic.690461015}, - volume = {46}, - year = {2004}} -@article{kossyi1992, - author = {I.~A.~Kossyi and A.~Y.~Kostinsky and A.~A.~Matveyev and V.~P.~Silakov}, - journal = {Plasma Sources Science and Technology}, - number = {3}, - pages = {207}, - title = {Kinetic scheme of the non-equilibrium discharge in nitrogen-oxygen - mixtures}, - doi = {10.1088/0963-0252/1/3/011}, - url = {https://dx.doi.org/10.1088/0963-0252/1/3/011}, - volume = {1}, - year = {1992}} +@book{smith1982, + author = {W.~R.~Smith and R.~W.~Missen}, + publisher = {Wiley}, + address = {New York}, + isbn = {978-0471093473}, + title = {Chemical Reaction Equilibrium Analysis: Theory and Algorithms}, + year = {1982}} @article{tsang1991, author = {W.~Tsang and J.~T.~Herron}, journal = {Journal of Physical and Chemical Reference Data}, @@ -158,54 +216,29 @@ @article{tsang1991 url = {https://dx.doi.org/10.1063/1.555890}, volume = {20}, year = {1991}} -@article{lucassen2011, - author = {A.~Lucassen and N.~Labbe and P.~R.~Westmoreland and K.~Kohse-Höinghaus}, - title = {Combustion chemistry and fuel-nitrogen conversion in a laminar premixed - flame of morpholine as a model biofuel}, - journal = {Combustion and Flame}, - volume = {158}, - number = {9}, - pages = {1647--1666}, - doi = {10.1016/j.combustflame.2011.02.010}, - url = {https://dx.doi.org/10.1016/j.combustflame.2011.02.010}, - year = {2011}} -@article{gudmundsson2001, - author = {J.~T.~Gudmundsson}, - journal = {Plasma Sources Science and Technology}, - number = {1}, - pages = {76}, - title = {On the effect of the electron energy distribution on the plasma - parameters of an argon discharge: a global (volume-averaged) model study}, - doi = {10.1088/0963-0252/10/1/310}, - url = {https://dx.doi.org/10.1088/0963-0252/10/1/310}, - volume = {10}, - year = {2001}} -@article{khalilpour2020, - author = {H.~Khalilpour and G.~Foroutan}, - journal = {Journal of Plasma Physics}, +@article{veldsink1995, + author = {J.~W.~Veldsink and R.~M.~J.~van Damme and G.~F.~Versteeg and + W.~P.~M.~van Swaaij}, + journal = {Chemical Engineering Journal}, number = {2}, - pages = {1--14}, - title = {The effects of electron energy distribution function on the plasma - sheath structure in the presence of charged nanoparticles}, - doi = {10.1017/S0022377820000161}, - url = {https://dx.doi.org/10.1017/S0022377820000161}, - volume = {86}, - year = {2020}} -@article{hagelaar2005, - author = {G.~J.~M.~Hagelaar and L.~C.~Pitchford}, - journal = {Plasma Sources Science and Technology}, - number = {4}, - pages = {722}, - title = {Solving the {B}oltzmann equation to obtain electron transport - coefficients and rate coefficients for fluid models}, - doi = {10.1088/0963-0252/14/4/011}, - url = {https://dx.doi.org/10.1088/0963-0252/14/4/011}, - volume = {14}, - year = {2005}} -@software{BOLOS, - author = {A.~Luque}, - title = {{BOLOS}: {BOL}tzmann equation solver {O}pen {S}ource library}, - url = {https://github.com/aluque/bolos}} + pages = {115--125}, + title = {The use of the dusty gas model for the description of mass transport + with chemical reaction in porous media}, + doi = {10.1016/0923-0467(94)02929-6}, + url = {https://dx.doi.org/10.1016/0923-0467(94)02929-6}, + volume = {57}, + year = {1995}} +@article{viehland1975, + author = {L.~A.~Viehland and J.~W.~McConkey and J.~W.~Hogan}, + journal = {Atomic Data and Nuclear Data Tables}, + number = {6}, + pages = {495--514}, + title = {Tables of transport collision integrals for (n, 6, 4) ion-neutral + potentials}, + doi = {10.1016/0092-640x(75)90022-4}, + url = {https://dx.doi.org/10.1016/0092-640x(75)90022-4}, + volume = {16}, + year = {1975}} @article{wagner2002, author = {W.~Wagner and A.~Pru\ss}, journal = {Journal of Physical and Chemical Reference Data}, @@ -217,57 +250,26 @@ @article{wagner2002 url = {https://dx.doi.org/10.1063/1.1461829}, volume = {31}, year = {2002}} -@article{kim2019, - author = {S.~Kim, and J.~Chen and T.~Cheng and A.~Gindulyte and J.~He and S.He - and Q.~Li and B.~A.~Shoemaker and P.~A.~Thiessen, and B.~Yu and L.~Zaslavsky - and J.Zhangn and E.~E.~Bolton}, - journal = {Nucleic Acids Research}, - number = {D1}, - pages = {D1102--D1109}, - title = {{PubChem} 2019 update: improved access to chemical data}, - doi = {10.1093/nar/gky1033}, - url = {https://dx.doi.org/10.1093/nar/gky1033}, - volume = {47}, - year = {2019}} -@conference{liu1991, - author = {Y.~Liu and B.~Rogg}, - journal = {EUROTHERM Seminars}, - pages = {114--127}, - title = {Modelling of thermally radiating diffusion flames with detailed - chemistry and transport}, - volume = {17}, - year = {1991}} -@techreport{RADCAL, - author = {W.~L.~Grosshandler}, - institution = {National Institute of Standards and Technology}, - number = {1402}, - title = {{RADCAL}: A Narrow-Band Model for Radiation Calculations in a Combustion - Environment}, - url = {https://nvlpubs.nist.gov/nistpubs/Legacy/TN/nbstechnicalnote1402.pdf}, - year = {1993}} -@book{smith1982, - author = {W.~R.~Smith and R.~W.~Missen}, - publisher = {Wiley}, - title = {Chemical Reaction Equilibrium Analysis: Theory and Algorithms}, - year = {1982}} -@article{perini2012, - author = {F.~Perini and E.~Galligani and R.~D.~Reitz}, - journal = {Energy \& Fuels}, - number = {8}, - pages = {4804--4822}, - title = {An analytical {J}acobian approach to sparse reaction kinetics for - computationally efficient combustion modeling with large reaction - mechanisms}, - doi = {10.1021/ef300747n}, - url = {https://dx.doi.org/10.1021/ef300747n}, - volume = {26}, - year = {2012}} -@article{niemeyer2017, - author = {K.~E.~Niemeyer and N.~J.~Curtis and C.-J.~Sung}, - journal = {Journal of Computational Science}, - pages = {1--10}, - title = {{pyJac}: Analytical {J}acobian generator for chemical kinetics}, - doi = {10.1016/j.cpc.2017.02.004}, - url = {https://dx.doi.org/10.1016/j.cpc.2017.02.004}, - volume = {21}, - year = {2017}} +@article{zhu2006, + author = {H.~Zhu and R.~J.~Kee}, + journal = {Journal of The Electrochemical Society}, + number = {9}, + pages = {A1765--A1772}, + title = {Modeling Electrochemical Impedance Spectra in {SOFC} Button Cells with + Internal Methane Reforming}, + doi = {10.1149/1.2220065}, + url = {https://dx.doi.org/10.1149/1.2220065}, + volume = {153}, + year = {2006}} +@article{zhu2005, + author = {H.~Zhu and R.~J.~Kee and V.~M.~Janardhanan and O.~Deutschmann and + D.~G.~Goodwin}, + journal = {Journal of The Electrochemical Society}, + number = {12}, + pages = {A2427--A2439}, + title = {Modeling Elementary Heterogeneous Chemistry and Electrochemistry in + Solid-Oxide Fuel Cells}, + doi = {10.1149/1.2116607}, + url = {https://dx.doi.org/10.1149/1.2116607}, + volume = {152}, + year = {2005}} From 901cbb60ffc597a1cbefcd3ee9e7a147f0b9a6bb Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Wed, 2 Aug 2023 13:00:06 -0500 Subject: [PATCH 2/8] [docs] Replace remaining Doxygen commands --- include/cantera/base/Array.h | 6 +- include/cantera/base/global.h | 12 +-- include/cantera/base/utilities.h | 4 +- include/cantera/equil/MultiPhase.h | 42 +++++----- include/cantera/equil/MultiPhaseEquil.h | 2 +- include/cantera/equil/vcs_VolPhase.h | 4 +- include/cantera/kinetics/Kinetics.h | 2 +- include/cantera/kinetics/ReactionPath.h | 10 +-- include/cantera/kinetics/StoichManager.h | 6 +- include/cantera/numerics/BandMatrix.h | 6 +- include/cantera/numerics/DenseMatrix.h | 8 +- include/cantera/numerics/Func1.h | 92 ++++++++++----------- include/cantera/numerics/Integrator.h | 2 +- include/cantera/oneD/Domain1D.h | 4 +- include/cantera/oneD/StFlow.h | 4 +- include/cantera/thermo/MultiSpeciesThermo.h | 4 +- include/cantera/thermo/Phase.h | 14 ++-- include/cantera/thermo/PlasmaPhase.h | 2 +- include/cantera/thermo/ThermoPhase.h | 8 +- include/cantera/transport/GasTransport.h | 2 +- include/cantera/transport/MixTransport.h | 6 +- include/cantera/transport/Transport.h | 4 +- samples/cxx/bvp/BoundaryValueProblem.h | 10 +-- 23 files changed, 127 insertions(+), 127 deletions(-) diff --git a/include/cantera/base/Array.h b/include/cantera/base/Array.h index 142fe2945c..d9841bfa9b 100644 --- a/include/cantera/base/Array.h +++ b/include/cantera/base/Array.h @@ -52,7 +52,7 @@ class Array2D //! Constructor. /*! - * Create an \c m by \c n array, and initialize all elements to \c v. + * Create an @c m by @c n array, and initialize all elements to @c v. * * @param m Number of rows * @param n Number of columns @@ -62,8 +62,8 @@ class Array2D //! Constructor. /*! - * Create an \c m by \c n array, initialized with the contents of the array - * \c values. + * Create an @c m by @c n array, initialized with the contents of the array + * @c values. * * @param m Number of rows * @param n Number of columns diff --git a/include/cantera/base/global.h b/include/cantera/base/global.h index 02d45e6d8e..ee43737936 100644 --- a/include/cantera/base/global.h +++ b/include/cantera/base/global.h @@ -39,13 +39,13 @@ class AnyMap; * for input files along a path that includes platform-specific default * locations, and possibly user-specified locations: * - * - The current directory \c "." is always searched first. Then, on Windows, the + * - The current directory @c "." is always searched first. Then, on Windows, the * registry is checked to find the %Cantera installation directory, and the - * \c data subdirectory of the installation directory will be added to the search + * @c data subdirectory of the installation directory will be added to the search * path. - * - On any platform, if environment variable \c CANTERA_DATA is set to a directory + * - On any platform, if environment variable @c CANTERA_DATA is set to a directory * name or a list of directory names separated with the OS-dependent path - * separator (that is, \c ";" on Windows, \c ":" elsewhere), then these directories + * separator (that is, @c ";" on Windows, @c ":" elsewhere), then these directories * will be added to the search path. * - Finally, the location where the data files were installed when %Cantera was * built is added to the search path. @@ -116,7 +116,7 @@ bool usingSharedLibrary(); //! @{ //! Returns the %Cantera version. This function is used to access the version from a -//! library, rather than the \c CANTERA_VERSION macro that is available at compile time. +//! library, rather than the @c CANTERA_VERSION macro that is available at compile time. //! @since New in %Cantera 3.0 string version(); @@ -130,7 +130,7 @@ string gitCommit(); //! preprocessor macro is defined. bool debugModeEnabled(); -//! Returns true if %Cantera was compiled with C++ \c HDF5 support. +//! Returns true if %Cantera was compiled with C++ @c HDF5 support. //! @since New in %Cantera 3.0. bool usesHDF5(); diff --git a/include/cantera/base/utilities.h b/include/cantera/base/utilities.h index c5f6eedc6f..26d0c3ea81 100644 --- a/include/cantera/base/utilities.h +++ b/include/cantera/base/utilities.h @@ -29,7 +29,7 @@ namespace Cantera //! Templated Inner product of two vectors of length 4. /*! - * If either \a x or \a y has length greater than 4, only the first 4 elements + * If either @e x or @e y has length greater than 4, only the first 4 elements * will be used. * * @param x first reference to the templated class V @@ -44,7 +44,7 @@ inline double dot4(const V& x, const V& y) //! Templated Inner product of two vectors of length 5 /*! - * If either \a x or \a y has length greater than 4, only the first 4 elements + * If either @e x or @e y has length greater than 4, only the first 4 elements * will be used. * * @param x first reference to the templated class V diff --git a/include/cantera/equil/MultiPhase.h b/include/cantera/equil/MultiPhase.h index f42862a47d..0971fe117d 100644 --- a/include/cantera/equil/MultiPhase.h +++ b/include/cantera/equil/MultiPhase.h @@ -113,7 +113,7 @@ class MultiPhase */ string elementName(size_t m) const; - //! Returns the index of the element with name \a name. + //! Returns the index of the element with name @e name. /*! * @param name String name of the global element */ @@ -133,14 +133,14 @@ class MultiPhase //! which take an array pointer. void checkSpeciesArraySize(size_t kk) const; - //! Name of species with global index \a kGlob + //! Name of species with global index @e kGlob /*! * @param kGlob global species index */ string speciesName(const size_t kGlob) const; - //! Returns the Number of atoms of global element \a mGlob in - //! global species \a kGlob. + //! Returns the Number of atoms of global element @e mGlob in + //! global species @e kGlob. /*! * @param kGlob global species index * @param mGlob global element index @@ -151,7 +151,7 @@ class MultiPhase //! Returns the global Species mole fractions. /*! * Write the array of species mole - * fractions into array \c x. The mole fractions are + * fractions into array @c x. The mole fractions are * normalized to sum to one in each phase. * * @param x vector of mole fractions. Length = number of global species. @@ -211,14 +211,14 @@ class MultiPhase //! which take an array pointer. void checkPhaseArraySize(size_t mm) const; - //! Returns the moles of global species \c k. units = kmol + //! Returns the moles of global species @c k. units = kmol /*! * @param kGlob Global species index k */ double speciesMoles(size_t kGlob) const; - //! Return the global index of the species belonging to phase number \c p - //! with local index \c k within the phase. + //! Return the global index of the species belonging to phase number @c p + //! with local index @c k within the phase. /*! * @param k local index of the species within the phase * @param p index of the phase @@ -227,8 +227,8 @@ class MultiPhase return m_spstart[p] + k; } - //! Return the global index of the species belonging to phase name \c phaseName - //! with species name \c speciesName + //! Return the global index of the species belonging to phase name @c phaseName + //! with species name @c speciesName /*! * @param speciesName Species Name * @param phaseName Phase Name @@ -257,15 +257,15 @@ class MultiPhase //! Total charge summed over all phases (Coulombs). double charge() const; - //! Charge (Coulombs) of phase with index \a p. + //! Charge (Coulombs) of phase with index @e p. /*! * The net charge is computed as @f[ Q_p = N_p \sum_k F z_k X_k @f] - * where the sum runs only over species in phase \a p. + * where the sum runs only over species in phase @e p. * @param p index of the phase for which the charge is desired. */ double phaseCharge(size_t p) const; - //! Total moles of global element \a m, summed over all phases. + //! Total moles of global element @e m, summed over all phases. /*! * @param m Index of the global element */ @@ -273,7 +273,7 @@ class MultiPhase //! Returns a vector of Chemical potentials. /*! - * Write into array \a mu the chemical potentials of all species + * Write into array @e mu the chemical potentials of all species * [J/kmol]. The chemical potentials are related to the activities by * * @f$ @@ -287,16 +287,16 @@ class MultiPhase //! Returns a vector of Valid chemical potentials. /*! - * Write into array \a mu the chemical potentials of all species with + * Write into array @e mu the chemical potentials of all species with * thermo data valid for the current temperature [J/kmol]. For other - * species, set the chemical potential to the value \a not_mu. If \a + * species, set the chemical potential to the value @e not_mu. If @e * standard is set to true, then the values returned are standard chemical * potentials. * * This method is designed for use in computing chemical equilibrium by * Gibbs minimization. For solution phases (more than one species), this * does the same thing as getChemPotentials. But for stoichiometric - * phases, this writes into array \a mu the user-specified value \a not_mu + * phases, this writes into array @e mu the user-specified value @e not_mu * instead of the chemical potential if the temperature is outside the * range for which the thermo data for the one species in the phase are * valid. The need for this arises since many condensed phases have thermo @@ -307,7 +307,7 @@ class MultiPhase * result in spurious chemical potentials, and can lead to condensed * phases appearing when in fact they should be absent. * - * By setting \a not_mu to a large positive value, it is possible to force + * By setting @e not_mu to a large positive value, it is possible to force * routines which seek to minimize the Gibbs free energy of the mixture to * zero out any phases outside the temperature range for which their * thermo data are valid. @@ -316,7 +316,7 @@ class MultiPhase * for which the thermo data is not valid * @param mu Vector of chemical potentials. length = Global species, * units = J kmol-1 - * @param standard If this method is called with \a standard set to true, + * @param standard If this method is called with @e standard set to true, * then the composition-independent standard chemical * potentials are returned instead of the composition- * dependent chemical potentials. @@ -426,7 +426,7 @@ class MultiPhase return m_phase.size(); } - //! Return true is species \a kGlob is a species in a multicomponent + //! Return true is species @e kGlob is a species in a multicomponent //! solution phase. /*! * @param kGlob index of the global species @@ -506,7 +506,7 @@ class MultiPhase */ void getElemAbundances(double* elemAbundances) const; - //! Return true if the phase \a p has valid thermo data for the current + //! Return true if the phase @e p has valid thermo data for the current //! temperature. /*! * @param p Index of the phase. diff --git a/include/cantera/equil/MultiPhaseEquil.h b/include/cantera/equil/MultiPhaseEquil.h index cf432f9364..2962f3a8b3 100644 --- a/include/cantera/equil/MultiPhaseEquil.h +++ b/include/cantera/equil/MultiPhaseEquil.h @@ -96,7 +96,7 @@ class MultiPhaseEquil //! The component species are taken to be the first M species in array //! 'species' that have linearly-independent compositions. //! - //! @param order On entry, vector \a order should contain species index + //! @param order On entry, vector @e order should contain species index //! numbers in the order of decreasing desirability as a component. //! For example, if it is desired to choose the components from among //! the major species, this array might list species index numbers in diff --git a/include/cantera/equil/vcs_VolPhase.h b/include/cantera/equil/vcs_VolPhase.h index f313b22109..231b311bfd 100644 --- a/include/cantera/equil/vcs_VolPhase.h +++ b/include/cantera/equil/vcs_VolPhase.h @@ -423,13 +423,13 @@ class vcs_VolPhase //! Returns the number of element constraints size_t nElemConstraints() const; - //! Name of the element constraint with index \c e. + //! Name of the element constraint with index @c e. /*! * @param e Element index. */ string elementName(const size_t e) const; - //! Type of the element constraint with index \c e. + //! Type of the element constraint with index @c e. /*! * @param e Element index. */ diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h index 5f3181c31d..52d18ff8c7 100644 --- a/include/cantera/kinetics/Kinetics.h +++ b/include/cantera/kinetics/Kinetics.h @@ -419,7 +419,7 @@ class Kinetics * @f] * For example, if this method is called with the array of standard-state * molar Gibbs free energies for the species, then the values returned in - * array \c deltaProperty would be the standard-state Gibbs free energies of + * array @c deltaProperty would be the standard-state Gibbs free energies of * reaction for each reaction. * * @param property Input vector of property value. Length: #m_kk. diff --git a/include/cantera/kinetics/ReactionPath.h b/include/cantera/kinetics/ReactionPath.h index 7901063484..7b0378b850 100644 --- a/include/cantera/kinetics/ReactionPath.h +++ b/include/cantera/kinetics/ReactionPath.h @@ -84,7 +84,7 @@ class Path typedef map rxn_path_map; /** - * Constructor. Construct a one-way path from \c begin to \c end. + * Constructor. Construct a one-way path from @c begin to @c end. */ Path(SpeciesNode* begin, SpeciesNode* end); @@ -114,7 +114,7 @@ class Path } /** - * If \c n is one of the nodes this path connects, then + * If @c n is one of the nodes this path connects, then * the other node is returned. Otherwise zero is returned. */ SpeciesNode* otherNode(SpeciesNode* n) { @@ -171,12 +171,12 @@ class ReactionPathDiagram return m_flxmax; } - //! The net flow from node \c k1 to node \c k2 + //! The net flow from node @c k1 to node @c k2 double netFlow(size_t k1, size_t k2) { return flow(k1, k2) - flow(k2, k1); } - //! The one-way flow from node \c k1 to node \c k2 + //! The one-way flow from node @c k1 to node @c k2 double flow(size_t k1, size_t k2) { return (m_paths[k1][k2] ? m_paths[k1][k2]->flow() : 0.0); } @@ -190,7 +190,7 @@ class ReactionPathDiagram /** * Export the reaction path diagram. This method writes to stream - * \c s the commands for the 'dot' program in the \c GraphViz + * @c s the commands for the 'dot' program in the @c GraphViz * package from AT&T. (GraphViz may be downloaded from www.graphviz.org.) * * To generate a postscript reaction path diagram from the output of this diff --git a/include/cantera/kinetics/StoichManager.h b/include/cantera/kinetics/StoichManager.h index d32e94e9fb..0f930a3d6f 100644 --- a/include/cantera/kinetics/StoichManager.h +++ b/include/cantera/kinetics/StoichManager.h @@ -37,7 +37,7 @@ namespace Cantera * @f] * * where @f$ \nu^{(p)_{k,i}} @f$ is the product-side stoichiometric - * coefficient of species \a k in reaction \a i. This could be done by + * coefficient of species @e k in reaction @e i. This could be done by * straightforward matrix multiplication, but would be inefficient, since most * of the matrix elements of @f$ \nu^{(p)}_{k,i} @f$ are zero. We could do * better by using sparse-matrix algorithms to compute this product. @@ -563,7 +563,7 @@ inline static void _scale(InputIter begin, InputIter end, * @f] * To understand the operations performed by this class, let @f$ N_{k,i} @f$ * denote the stoichiometric coefficient of species k on one side (reactant or - * product) in reaction i. Then \b N is a sparse K by I matrix of stoichiometric + * product) in reaction i. Then @b N is a sparse K by I matrix of stoichiometric * coefficients. * * The following matrix operations may be carried out with a vector S of length @@ -576,7 +576,7 @@ inline static void _scale(InputIter begin, InputIter end, * * The actual implementation, however, does not compute these quantities by * matrix multiplication. A faster algorithm is used that makes use of the fact - * that the \b integer-valued N matrix is very sparse, and the non-zero terms + * that the @b integer-valued N matrix is very sparse, and the non-zero terms * are small positive integers. * @f[ * S_k = R_{i1} + \dots + R_{iM} diff --git a/include/cantera/numerics/BandMatrix.h b/include/cantera/numerics/BandMatrix.h index 8d89583b37..c4b92d0f30 100644 --- a/include/cantera/numerics/BandMatrix.h +++ b/include/cantera/numerics/BandMatrix.h @@ -38,14 +38,14 @@ class BandMatrix : public GeneralMatrix public: //! Base Constructor /*! - * Create an \c 0 by \c 0 matrix, and initialize all elements to \c 0. + * Create an @c 0 by @c 0 matrix, and initialize all elements to @c 0. */ BandMatrix(); ~BandMatrix(); //! Creates a banded matrix and sets all elements to zero /*! - * Create an \c n by \c n banded matrix, and initialize all elements to \c v. + * Create an @c n by @c n banded matrix, and initialize all elements to @c v. * * @param n size of the square matrix * @param kl band size on the lower portion of the matrix @@ -131,7 +131,7 @@ class BandMatrix : public GeneralMatrix //! Return the number of rows of storage needed for the band storage size_t ldim() const; - //! Multiply A*b and write result to \c prod. + //! Multiply A*b and write result to @c prod. virtual void mult(const double* b, double* prod) const; virtual void leftMult(const double* const b, double* const prod) const; diff --git a/include/cantera/numerics/DenseMatrix.h b/include/cantera/numerics/DenseMatrix.h index 9e5205aec7..ca10ddf854 100644 --- a/include/cantera/numerics/DenseMatrix.h +++ b/include/cantera/numerics/DenseMatrix.h @@ -59,7 +59,7 @@ class DenseMatrix : public Array2D //! Constructor. /*! - * Create an \c n by \c m matrix, and initialize all elements to \c v. + * Create an @c n by @c m matrix, and initialize all elements to @c v. * * @param n New number of rows * @param m New number of columns @@ -93,7 +93,7 @@ class DenseMatrix : public Array2D virtual void mult(const double* b, double* prod) const; - //! Multiply A*B and write result to \c prod. + //! Multiply A*B and write result to @c prod. /*! * Take this matrix to be of size NxM. * @param[in] b DenseMatrix B of size MxP @@ -188,7 +188,7 @@ int solve(DenseMatrix& A, double* b, size_t nrhs=1, size_t ldb=0); */ int solve(DenseMatrix& A, DenseMatrix& b); -//! Multiply \c A*b and return the result in \c prod. Uses BLAS routine DGEMV. +//! Multiply @c A*b and return the result in @c prod. Uses BLAS routine DGEMV. /*! * @f[ * prod_i = sum^N_{j = 1}{A_{ij} b_j} @@ -200,7 +200,7 @@ int solve(DenseMatrix& A, DenseMatrix& b); */ void multiply(const DenseMatrix& A, const double* const b, double* const prod); -//! Multiply \c A*b and add it to the result in \c prod. Uses BLAS routine DGEMV. +//! Multiply @c A*b and add it to the result in @c prod. Uses BLAS routine DGEMV. /*! * @f[ * prod_i += sum^N_{j = 1}{A_{ij} b_j} diff --git a/include/cantera/numerics/Func1.h b/include/cantera/numerics/Func1.h index da68133a74..15d16335f5 100644 --- a/include/cantera/numerics/Func1.h +++ b/include/cantera/numerics/Func1.h @@ -49,39 +49,39 @@ class TimesConstant1; //! Simple functors implement standard mathematical expressions with a single //! parameter. //! The following simple functor types are implemented: -//! - \c "sin" (class Sin1), \c "cos" (class Cos1), -//! - \c "exp" (class Exp1), \c "log" (class Log1), -//! - \c "pow" (class Pow1), -//! - \c "constant" (class Const1). +//! - @c "sin" (class Sin1), @c "cos" (class Cos1), +//! - @c "exp" (class Exp1), @c "log" (class Log1), +//! - @c "pow" (class Pow1), +//! - @c "constant" (class Const1). //! @ingroup func1 //! @defgroup func1advanced Advanced Functors //! Advanced functors implement expressions that require multiple parameters. //! The following advanced functor types are implemented: -//! - \c "tabulated-linear" and \c "tabulated-previous" (class Tabulated1), -//! - \c "polynomial" (class Poly1), -//! - \c "Fourier" (class Fourier1), -//! - \c "Gaussian" (class Gaussian1), -//! - \c "Arrhenius" (class Arrhenius1). +//! - @c "tabulated-linear" and @c "tabulated-previous" (class Tabulated1), +//! - @c "polynomial" (class Poly1), +//! - @c "Fourier" (class Fourier1), +//! - @c "Gaussian" (class Gaussian1), +//! - @c "Arrhenius" (class Arrhenius1). //! @ingroup func1 //! @defgroup func1compound Compound Functors //! Compound functors implement expressions that are composed of other functors. //! The following compound functor types are implemented: -//! - \c "sum" (class Sum1), -//! - \c "diff" (class Diff1), -//! - \c "product" (class Product1), -//! - \c "ratio" (class Ratio1), -//! - \c "composite" (class Composite1), +//! - @c "sum" (class Sum1), +//! - @c "diff" (class Diff1), +//! - @c "product" (class Product1), +//! - @c "ratio" (class Ratio1), +//! - @c "composite" (class Composite1), //! @ingroup func1 //! @defgroup func1modified Modified Functors //! Modified functors implement expressions that involve one functor and //! a single parameter. //! The following modified functor types are implemented: -//! - \c "times-constant" (class TimesConstant1), -//! - \c "plus-constant" (class PlusConstant1), -//! - \c "periodic" (class Periodic1). +//! - @c "times-constant" (class TimesConstant1), +//! - @c "plus-constant" (class PlusConstant1), +//! - @c "periodic" (class Periodic1). //! @ingroup func1 //! @defgroup func1helper Helper Functions @@ -264,9 +264,9 @@ shared_ptr newTimesConstFunction(shared_ptr f1, double c); //! @ingroup func1helper shared_ptr newPlusConstFunction(shared_ptr f1, double c); -//! Implements the \c sin() function. +//! Implements the @c sin() function. /*! - * The functor class with type \c "sin" returns @f$ f(x) = \cos(\omega x) @f$, + * The functor class with type @c "sin" returns @f$ f(x) = \cos(\omega x) @f$, * where the argument @f$ x @f$ is in radians. * @param omega Frequency @f$ \omega @f$ (default=1.0) * @ingroup func1simple @@ -313,9 +313,9 @@ class Sin1 : public Func1 }; -//! Implements the \c cos() function. +//! Implements the @c cos() function. /*! - * The functor class with type \c "cos" returns @f$ f(x) = \cos(\omega x) @f$, + * The functor class with type @c "cos" returns @f$ f(x) = \cos(\omega x) @f$, * where the argument @f$ x @f$ is in radians. * @param omega Frequency @f$ \omega @f$ (default=1.0) * @ingroup func1simple @@ -359,9 +359,9 @@ class Cos1 : public Func1 }; -//! Implements the \c exp() (exponential) function. +//! Implements the @c exp() (exponential) function. /*! - * The functor class with type \c "exp" returns @f$ f(x) = \exp(a x) @f$. + * The functor class with type @c "exp" returns @f$ f(x) = \exp(a x) @f$. * @param a Factor (default=1.0) * @ingroup func1simple */ @@ -403,9 +403,9 @@ class Exp1 : public Func1 }; -//! Implements the \c log() (natural logarithm) function. +//! Implements the @c log() (natural logarithm) function. /*! - * The functor class with type \c "log" returns @f$ f(x) = \log(a x) @f$. + * The functor class with type @c "log" returns @f$ f(x) = \log(a x) @f$. * @param a Factor (default=1.0) * @ingroup func1simple * @since New in %Cantera 3.0 @@ -433,9 +433,9 @@ class Log1 : public Func1 virtual string write(const string& arg) const; }; -//! Implements the \c pow() (power) function. +//! Implements the @c pow() (power) function. /*! - * The functor class with type \c "pow" returns @f$ f(x) = x^n @f$. + * The functor class with type @c "pow" returns @f$ f(x) = x^n @f$. * @param n Exponent * @ingroup func1simple */ @@ -477,12 +477,12 @@ class Pow1 : public Func1 //! Implements a tabulated function. /*! - * The functor class is based on tabulated arrays \c tvals and \c fvals, where - * \c tvals contain independent variables and \c fvals are corresponding function + * The functor class is based on tabulated arrays @c tvals and @c fvals, where + * @c tvals contain independent variables and @c fvals are corresponding function * values. Depending on configuration, the function is either interpolated linearly - * between the tabulated points (type \c "tabulated-linear" ; default), or yields + * between the tabulated points (type @c "tabulated-linear" ; default), or yields * the last tabulated value until a new tabulated time value is reached (type - * \c "tabulated-previous" ). + * @c "tabulated-previous" ). * @ingroup func1advanced */ class Tabulated1 : public Func1 @@ -503,8 +503,8 @@ class Tabulated1 : public Func1 Tabulated1(const vector& params); //! Set the interpolation method - //! @param method Evaluation method. If \c "linear" (default), a linear - //! interpolation between tabulated values is used; if \c "previous", the + //! @param method Evaluation method. If @c "linear" (default), a linear + //! interpolation between tabulated values is used; if @c "previous", the //! last tabulated value is held until a new tabulated time value is reached. //! @since New in %Cantera 3.0 void setMethod(const string& method); @@ -533,7 +533,7 @@ class Tabulated1 : public Func1 //! Implements a constant. /*! - * The functor class with type \c "constant" returns @f$ f(x) = a @f$. + * The functor class with type @c "constant" returns @f$ f(x) = a @f$. * @param a Constant * @ingroup func1simple */ @@ -580,7 +580,7 @@ class Const1 : public Func1 /** * Implements the sum of two functions. - * The functor class with type \c "sum" returns @f$ f(x) = f_1(x) + f_2(x) @f$. + * The functor class with type @c "sum" returns @f$ f(x) = f_1(x) + f_2(x) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param f2 Functor @f$ f_2(x) @f$ * @ingroup func1compound @@ -651,7 +651,7 @@ class Sum1 : public Func1 /** * Implements the difference of two functions. - * The functor class with type \c "diff" returns @f$ f(x) = f_1(x) - f_2(x) @f$. + * The functor class with type @c "diff" returns @f$ f(x) = f_1(x) - f_2(x) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param f2 Functor @f$ f_2(x) @f$ * @ingroup func1compound @@ -724,7 +724,7 @@ class Diff1 : public Func1 /** * Implements the product of two functions. - * The functor class with type \c "product" returns @f$ f(x) = f_1(x) f_2(x) @f$. + * The functor class with type @c "product" returns @f$ f(x) = f_1(x) f_2(x) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param f2 Functor @f$ f_2(x) @f$ * @ingroup func1compound @@ -794,7 +794,7 @@ class Product1 : public Func1 /** * Implements the product of a function and a constant. - * The functor class with type \c "times-constant" returns @f$ f(x) = a f_1(x) @f$. + * The functor class with type @c "times-constant" returns @f$ f(x) = a f_1(x) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param a Constant @f$ a @f$ * @ingroup func1modified @@ -874,7 +874,7 @@ class TimesConstant1 : public Func1 /** * Implements the sum of a function and a constant. - * The functor class with type \c "plus-constant" returns @f$ f(x) = f_1(x) + a @f$. + * The functor class with type @c "plus-constant" returns @f$ f(x) = f_1(x) + a @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param a Constant @f$ a @f$ * @ingroup func1modified @@ -940,7 +940,7 @@ class PlusConstant1 : public Func1 /** * Implements the ratio of two functions. - * The functor class with type \c "ratio" returns @f$ f(x) = f_1(x) / f_2(x) @f$. + * The functor class with type @c "ratio" returns @f$ f(x) = f_1(x) / f_2(x) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param f2 Functor @f$ f_2(x) @f$ * @ingroup func1compound @@ -1009,7 +1009,7 @@ class Ratio1 : public Func1 /** * Implements a composite function. - * The functor class with type \c "composite" returns @f$ f(x) = f_1\left(f_2(x)\right) @f$. + * The functor class with type @c "composite" returns @f$ f(x) = f_1\left(f_2(x)\right) @f$. * @param f1 Functor @f$ f_1(x) @f$ * @param f2 Functor @f$ f_2(x) @f$ * @ingroup func1compound @@ -1081,7 +1081,7 @@ class Composite1 : public Func1 /** * Implements a Gaussian function. - * The functor class with type \c "Gaussian" returns + * The functor class with type @c "Gaussian" returns * @f[ * f(t) = A e^{-[(t - t_0)/\tau]^2} * @f] @@ -1159,8 +1159,8 @@ class Gaussian : public Gaussian1 /** - * Implements a polynomial of degree \e n. - * The functor class with type \c "polynomial" returns + * Implements a polynomial of degree @e n. + * The functor class with type @c "polynomial" returns * @f[ * f(x) = a_n x^n + \dots + a_1 x + a_0 * @f] @@ -1215,7 +1215,7 @@ class Poly1 : public Func1 /** * Implements a Fourier cosine/sine series. - * The functor class with type \c "Fourier" returns + * The functor class with type @c "Fourier" returns * @f[ * f(t) = \frac{A_0}{2} + * \sum_{n=1}^N A_n \cos (n \omega t) + B_n \sin (n \omega t) @@ -1281,7 +1281,7 @@ class Fourier1 : public Func1 /** * Implements a sum of Arrhenius terms. - * The functor class with type \c "Arrhenius" returns + * The functor class with type @c "Arrhenius" returns * @f[ * f(T) = \sum_{n=1}^N A_n T^b_n \exp(-E_n/T) * @f] diff --git a/include/cantera/numerics/Integrator.h b/include/cantera/numerics/Integrator.h index ae72eaf29f..0253f09092 100644 --- a/include/cantera/numerics/Integrator.h +++ b/include/cantera/numerics/Integrator.h @@ -333,7 +333,7 @@ class Integrator // defined in Integrators.cpp //! Create new Integrator object -//! @param itype Integration mode; either \c CVODE or \c IDA +//! @param itype Integration mode; either @c CVODE or @c IDA //! @ingroup odeGroup Integrator* newIntegrator(const string& itype); diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h index 0a4af429f0..95e6c17a89 100644 --- a/include/cantera/oneD/Domain1D.h +++ b/include/cantera/oneD/Domain1D.h @@ -207,7 +207,7 @@ class Domain1D m_name[n] = name; } - //! index of component with name \a name. + //! index of component with name @e name. virtual size_t componentIndex(const string& name) const; void setBounds(size_t n, double lower, double upper) { @@ -536,7 +536,7 @@ class Domain1D */ virtual void _getInitialSoln(double* x); - //! Initial value of solution component \a n at grid point \a j. + //! Initial value of solution component @e n at grid point @e j. virtual double initialValue(size_t n, size_t j); /** diff --git a/include/cantera/oneD/StFlow.h b/include/cantera/oneD/StFlow.h index ddfad4c35f..8cb26fbe09 100644 --- a/include/cantera/oneD/StFlow.h +++ b/include/cantera/oneD/StFlow.h @@ -216,8 +216,8 @@ class StFlow : public Domain1D virtual size_t getSolvingStage() const; //! Solving stage mode for handling ionized species (used by IonFlow specialization) - //! - \c stage=1: the fluxes of charged species are set to zero - //! - \c stage=2: the electric field equation is solved, and the drift flux for + //! - @c stage=1: the fluxes of charged species are set to zero + //! - @c stage=2: the electric field equation is solved, and the drift flux for //! ionized species is evaluated virtual void setSolvingStage(const size_t stage); diff --git a/include/cantera/thermo/MultiSpeciesThermo.h b/include/cantera/thermo/MultiSpeciesThermo.h index 82ccb0a161..8c5fb81b7b 100644 --- a/include/cantera/thermo/MultiSpeciesThermo.h +++ b/include/cantera/thermo/MultiSpeciesThermo.h @@ -99,7 +99,7 @@ class MultiSpeciesThermo //! Minimum temperature. /*! * If no argument is supplied, this method returns the minimum temperature - * for which \e all parameterizations are valid. If an integer index k is + * for which @e all parameterizations are valid. If an integer index k is * supplied, then the value returned is the minimum temperature for * species k in the phase. * @@ -110,7 +110,7 @@ class MultiSpeciesThermo //! Maximum temperature. /*! * If no argument is supplied, this method returns the maximum temperature - * for which \e all parameterizations are valid. If an integer index k is + * for which @e all parameterizations are valid. If an integer index k is * supplied, then the value returned is the maximum temperature for * parameterization k. * diff --git a/include/cantera/thermo/Phase.h b/include/cantera/thermo/Phase.h index 1e7072e7a8..7322decd06 100644 --- a/include/cantera/thermo/Phase.h +++ b/include/cantera/thermo/Phase.h @@ -218,7 +218,7 @@ class Phase //! which take an array pointer. void checkElementArraySize(size_t mm) const; - //! Number of atoms of element \c m in species \c k. + //! Number of atoms of element @c m in species @c k. //! @param k species index //! @param m element index double nAtoms(size_t k, size_t m) const; @@ -357,7 +357,7 @@ class Phase //! @{ //! Set the species mole fractions by name. - //! Species not listed by name in \c xMap are set to zero. + //! Species not listed by name in @c xMap are set to zero. //! @param xMap map from species names to mole fraction values. void setMoleFractionsByName(const Composition& xMap); @@ -367,12 +367,12 @@ class Phase void setMoleFractionsByName(const string& x); //! Set the species mass fractions by name. - //! Species not listed by name in \c yMap are set to zero. + //! Species not listed by name in @c yMap are set to zero. //! @param yMap map from species names to mass fraction values. void setMassFractionsByName(const Composition& yMap); //! Set the species mass fractions by name. - //! Species not listed by name in \c x are set to zero. + //! Species not listed by name in @c x are set to zero. //! @param x String containing a composition map void setMassFractionsByName(const string& x); @@ -458,9 +458,9 @@ class Phase //! @} end group set thermo state - //! Molecular weight of species \c k. - //! @param k index of species \c k - //! @returns the molecular weight of species \c k. + //! Molecular weight of species @c k. + //! @param k index of species @c k + //! @returns the molecular weight of species @c k. double molecularWeight(size_t k) const; //! Copy the vector of molecular weights into vector weights. diff --git a/include/cantera/thermo/PlasmaPhase.h b/include/cantera/thermo/PlasmaPhase.h index 85c9bdd997..f3384928b6 100644 --- a/include/cantera/thermo/PlasmaPhase.h +++ b/include/cantera/thermo/PlasmaPhase.h @@ -80,7 +80,7 @@ class PlasmaPhase: public IdealGasPhase //! Set electron energy levels. //! @param levels The vector of electron energy levels (eV). //! Length: #m_nPoints. - //! @param length The length of the \p levels. + //! @param length The length of the @c levels. void setElectronEnergyLevels(const double* levels, size_t length); //! Get electron energy levels. diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h index bd0d446892..a8a7989571 100644 --- a/include/cantera/thermo/ThermoPhase.h +++ b/include/cantera/thermo/ThermoPhase.h @@ -152,8 +152,8 @@ class ThermoPhase : public Phase //! or phase are valid. /*! * If no argument is supplied, the value returned will be the lowest - * temperature at which the data for \e all species are valid. Otherwise, - * the value will be only for species \a k. This function is a wrapper that + * temperature at which the data for @e all species are valid. Otherwise, + * the value will be only for species @e k. This function is a wrapper that * calls the species thermo minTemp function. * * @param k index of the species. Default is -1, which will return the max @@ -205,8 +205,8 @@ class ThermoPhase : public Phase //! are valid. /*! * If no argument is supplied, the value returned will be the highest - * temperature at which the data for \e all species are valid. Otherwise, - * the value will be only for species \a k. This function is a wrapper that + * temperature at which the data for @e all species are valid. Otherwise, + * the value will be only for species @e k. This function is a wrapper that * calls the species thermo maxTemp function. * * @param k index of the species. Default is -1, which will return the min diff --git a/include/cantera/transport/GasTransport.h b/include/cantera/transport/GasTransport.h index 34a7d4ee44..d0ebb26054 100644 --- a/include/cantera/transport/GasTransport.h +++ b/include/cantera/transport/GasTransport.h @@ -33,7 +33,7 @@ class GasTransport : public Transport * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. * @f] * - * Here @f$ \mu_k @f$ is the viscosity of pure species \e k, and + * Here @f$ \mu_k @f$ is the viscosity of pure species @e k, and * * @f[ * \Phi_{k,j} = \frac{\left[1 diff --git a/include/cantera/transport/MixTransport.h b/include/cantera/transport/MixTransport.h index 24baf935d8..e912386f6e 100644 --- a/include/cantera/transport/MixTransport.h +++ b/include/cantera/transport/MixTransport.h @@ -27,7 +27,7 @@ namespace Cantera * \mu = \sum_k \frac{\mu_k X_k}{\sum_j \Phi_{k,j} X_j}. * @f] * - * Here @f$ \mu_k @f$ is the viscosity of pure species \e k, and + * Here @f$ \mu_k @f$ is the viscosity of pure species @e k, and * * @f[ * \Phi_{k,j} = \frac{\left[1 @@ -102,7 +102,7 @@ class MixTransport : public GasTransport * \mu^e_k = \frac{F D_k}{R T} * @f] * - * @param mobil Returns the mobilities of the species in array \c mobil. + * @param mobil Returns the mobilities of the species in array @c mobil. * The array must be dimensioned at least as large as the * number of species. */ @@ -127,7 +127,7 @@ class MixTransport : public GasTransport /*! * Units for the returned fluxes are kg m-2 s-1. * - * The diffusive mass flux of species \e k is computed from + * The diffusive mass flux of species @e k is computed from * @f[ * \vec{j}_k = -n M_k D_k \nabla X_k. * @f] diff --git a/include/cantera/transport/Transport.h b/include/cantera/transport/Transport.h index c2adfaead8..cbcf67dd38 100644 --- a/include/cantera/transport/Transport.h +++ b/include/cantera/transport/Transport.h @@ -339,7 +339,7 @@ class Transport * \mu^e_k = \frac{F D_k}{R T} * @f] * - * @param mobil_e Returns the mobilities of the species in array \c + * @param mobil_e Returns the mobilities of the species in array @c * mobil_e. The array must be dimensioned at least as large as * the number of species. */ @@ -361,7 +361,7 @@ class Transport * \mu^f_k = \frac{D_k}{R T} * @f] * - * @param mobil_f Returns the mobilities of the species in array \c mobil. + * @param mobil_f Returns the mobilities of the species in array @c mobil. * The array must be dimensioned at least as large as the * number of species. * diff --git a/samples/cxx/bvp/BoundaryValueProblem.h b/samples/cxx/bvp/BoundaryValueProblem.h index 86f10fd2cc..0b49e973af 100644 --- a/samples/cxx/bvp/BoundaryValueProblem.h +++ b/samples/cxx/bvp/BoundaryValueProblem.h @@ -106,7 +106,7 @@ class BoundaryValueProblem : public Cantera::Domain1D } /** - * Set parameters and options for solution component \a n. + * Set parameters and options for solution component @e n. * This method should be invoked for each solution component * before calling 'solve'. The parameter values should first * be set by creating an instance of class Component, and @@ -185,8 +185,8 @@ class BoundaryValueProblem : public Cantera::Domain1D } /** - * Initial value of solution component \a n at initial grid - * point \a j. The default is zero for all components at all + * Initial value of solution component @e n at initial grid + * point @e j. The default is zero for all components at all * grid points. Overload in derived classes to specify other * choices for initial values. */ @@ -263,7 +263,7 @@ class BoundaryValueProblem : public Cantera::Domain1D } /** - * First derivative of component \a n at point \a j. The derivative + * First derivative of component @e n at point @e j. The derivative * is formed to the right of point j, using values at point j * and point j + 1. */ @@ -272,7 +272,7 @@ class BoundaryValueProblem : public Cantera::Domain1D } /** - * First derivative of component \a n at point \a j. The derivative + * First derivative of component @e n at point @e j. The derivative * is formed to the left of point j, using values at point j * and point j - 1. */ From 162c3d271801b292d158768915f01a2c0ff3780f Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Wed, 2 Aug 2023 19:17:13 -0500 Subject: [PATCH 3/8] [docs] Add Doxygen eqnarray --- include/cantera/kinetics/BlowersMaselRate.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/include/cantera/kinetics/BlowersMaselRate.h b/include/cantera/kinetics/BlowersMaselRate.h index fdf49b198a..592f1ea97c 100644 --- a/include/cantera/kinetics/BlowersMaselRate.h +++ b/include/cantera/kinetics/BlowersMaselRate.h @@ -43,12 +43,12 @@ struct BlowersMaselData : public ReactionData * The Blowers Masel approximation @cite blowers2004 adjusts the activation energy * based on enthalpy change of a reaction: * - * \f{eqnarray*}{ - * E_a &=& 0\; \text{if }\Delta H < -4E_0 \\ - * E_a &=& \Delta H\; \text{if }\Delta H > 4E_0 \\ + * @f{eqnarray*}{ + * E_a &=& 0\; &\text{if }\Delta H < -4E_0 \\ + * E_a &=& \Delta H\; &\text{if }\Delta H > 4E_0 \\ * E_a &=& \frac{(w + \Delta H / 2)(V_P - 2w + - * \Delta H)^2}{(V_P^2 - 4w^2 + (\Delta H)^2)}\; \text{Otherwise} - * \f} + * \Delta H)^2}{(V_P^2 - 4w^2 + (\Delta H)^2)}\; &\text{otherwise} + * @f} * where * @f[ * V_P = \frac{2w (w + E_0)}{w - E_0}, From f243f0022da6267c6ebbaf1cf595594e9f0aa441 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Wed, 2 Aug 2023 19:21:43 -0500 Subject: [PATCH 4/8] Remove % in group definition string --- include/cantera/base/global.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/cantera/base/global.h b/include/cantera/base/global.h index ee43737936..c0092c43ee 100644 --- a/include/cantera/base/global.h +++ b/include/cantera/base/global.h @@ -100,7 +100,7 @@ void appdelete(); //! @copydoc Application::thread_complete void thread_complete(); -//! @defgroup globalSettings Global %Cantera Settings +//! @defgroup globalSettings Global Cantera Settings //! @brief Functions for accessing global %Cantera settings. //! @ingroup globalData From c0cf097f36e6ecf1fe9161bec054afc443745ae5 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Thu, 3 Aug 2023 10:21:26 -0500 Subject: [PATCH 5/8] [docs] Fix LaTeX log/ln/exp --- doc/doxygen/thermoprops.dox | 8 +++--- include/cantera/equil/vcs_solve.h | 2 +- include/cantera/kinetics/Falloff.h | 2 +- include/cantera/kinetics/Kinetics.h | 4 +-- include/cantera/thermo/ConstCpPoly.h | 2 +- include/cantera/thermo/DebyeHuckel.h | 10 +++---- include/cantera/thermo/GibbsExcessVPSSTP.h | 2 +- include/cantera/thermo/HMWSoln.h | 8 +++--- include/cantera/thermo/IdealSolidSolnPhase.h | 14 ++++----- include/cantera/thermo/LatticePhase.h | 4 +-- include/cantera/thermo/LatticeSolidPhase.h | 2 +- include/cantera/thermo/MolalityVPSSTP.h | 30 ++++++++++---------- 12 files changed, 44 insertions(+), 44 deletions(-) diff --git a/doc/doxygen/thermoprops.dox b/doc/doxygen/thermoprops.dox index d20cab627c..960e78f844 100644 --- a/doc/doxygen/thermoprops.dox +++ b/doc/doxygen/thermoprops.dox @@ -362,19 +362,19 @@ * activity coefficients: * * @f[ - * \mu_k = \mu_k^\triangle(T,P) + R T ln(a_k^{\triangle}) = - * \mu_k^\triangle(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) + * \mu_k = \mu_k^\triangle(T,P) + R T \ln(a_k^{\triangle}) = + * \mu_k^\triangle(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) * @f] * * And, the solvent employs the following convention * @f[ - * \mu_o = \mu^o_o(T,P) + RT ln(a_o) + * \mu_o = \mu^o_o(T,P) + RT \ln(a_o) * @f] * * where @f$ a_o @f$ is often redefined in terms of the osmotic coefficient @f$ \phi @f$. * * @f[ - * \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} + * \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} * @f] * * %ThermoPhase classes which employ the molality based convention are all derived diff --git a/include/cantera/equil/vcs_solve.h b/include/cantera/equil/vcs_solve.h index c81a3ef723..b7743278c2 100644 --- a/include/cantera/equil/vcs_solve.h +++ b/include/cantera/equil/vcs_solve.h @@ -820,7 +820,7 @@ class VCS_SOLVE * We are checking the equation: * * sum_u = sum_j_comp [ sigma_i_j * u_j ] - * = u_i_O + log((AC_i * W_i)/m_tPhaseMoles_old) + * = u_i_O + \log((AC_i * W_i)/m_tPhaseMoles_old) * * by first evaluating: * diff --git a/include/cantera/kinetics/Falloff.h b/include/cantera/kinetics/Falloff.h index 2c0336a343..22196a9f12 100644 --- a/include/cantera/kinetics/Falloff.h +++ b/include/cantera/kinetics/Falloff.h @@ -395,7 +395,7 @@ class TroeRate final : public FalloffRate * where * @f[ P_r = \frac{k_0 [M]}{k_{\infty}} @f] * - * @f[ F = {\left( a \; exp(\frac{-b}{T}) + exp(\frac{-T}{c})\right)}^n + * @f[ F = {\left( a \; \exp(\frac{-b}{T}) + \exp(\frac{-T}{c})\right)}^n * \; d \; T^e @f] * where * @f[ n = \frac{1.0}{1.0 + (\log_{10} P_r)^2} @f] diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h index 52d18ff8c7..1eeb2fbaa4 100644 --- a/include/cantera/kinetics/Kinetics.h +++ b/include/cantera/kinetics/Kinetics.h @@ -60,7 +60,7 @@ class AnyMap; //! quantities internally, and re-evaluate them only when the temperature has //! actually changed. Or a manager designed for use with reaction mechanisms //! with a few repeated activation energies might precompute the terms @f$ -//! exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each +//! \exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each //! reaction. There are many other possible 'management styles', each of which //! might be better suited to some reaction mechanisms than others. //! @@ -401,7 +401,7 @@ class Kinetics * total number of reactions. * * @f[ - * Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ] + * Kc_i = \exp [ \Delta G_{ss,i} ] \prod(Cs_k) \exp(\sum_k \nu_{k,i} F \phi_n) * @f] * * @param kc Output vector containing the equilibrium constants. diff --git a/include/cantera/thermo/ConstCpPoly.h b/include/cantera/thermo/ConstCpPoly.h index 98a5162442..4a51375446 100644 --- a/include/cantera/thermo/ConstCpPoly.h +++ b/include/cantera/thermo/ConstCpPoly.h @@ -30,7 +30,7 @@ namespace Cantera * \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R) * @f] * @f[ - * \frac{s^0(T)}{R} = (s0\_R + (log(T) - log(T_0)) * Cp0\_R) + * \frac{s^0(T)}{R} = (s0\_R + (log(T) - \log(T_0)) * Cp0\_R) * @f] * * This parameterization takes 4 input values. These are: diff --git a/include/cantera/thermo/DebyeHuckel.h b/include/cantera/thermo/DebyeHuckel.h index da65ec8132..241388a862 100644 --- a/include/cantera/thermo/DebyeHuckel.h +++ b/include/cantera/thermo/DebyeHuckel.h @@ -103,10 +103,10 @@ class PDSS_Water; * @f$, which are based on the molality form, have the following general format: * * @f[ - * \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) + * \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) * @f] * @f[ - * \mu_o = \mu^o_o(T,P) + RT ln(a_o) + * \mu_o = \mu^o_o(T,P) + RT \ln(a_o) * @f] * * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient @@ -443,7 +443,7 @@ class DebyeHuckel : public MolalityVPSSTP * pure species phases which exhibit zero volume expansivity: * @f[ * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - * - \hat R \sum_k X_k log(X_k) + * - \hat R \sum_k X_k \log(X_k) * @f] * The reference-state pure-species entropies * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the @@ -532,7 +532,7 @@ class DebyeHuckel : public MolalityVPSSTP * solution. * * @f[ - * \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} m_k) + * \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} m_k) * @f] * * @param mu Output vector of species chemical @@ -575,7 +575,7 @@ class DebyeHuckel : public MolalityVPSSTP * For this phase, the partial molar entropies are equal to the SS species * entropies plus the ideal solution contribution: * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R log(M0 * molality[k]) + * \bar s_k(T,P) = \hat s^0_k(T) - R \log(M0 * molality[k]) * @f] * @f[ * \bar s_{solvent}(T,P) = \hat s^0_{solvent}(T) diff --git a/include/cantera/thermo/GibbsExcessVPSSTP.h b/include/cantera/thermo/GibbsExcessVPSSTP.h index 60ed803245..ca870b1096 100644 --- a/include/cantera/thermo/GibbsExcessVPSSTP.h +++ b/include/cantera/thermo/GibbsExcessVPSSTP.h @@ -47,7 +47,7 @@ namespace Cantera * format: * * @f[ - * \mu_k = \mu^o_k(T,P) + R T ln( \gamma_k X_k ) + * \mu_k = \mu^o_k(T,P) + R T \ln( \gamma_k X_k ) * @f] * * where @f$ \gamma_k^{\triangle} @f$ is a molar based activity coefficient for diff --git a/include/cantera/thermo/HMWSoln.h b/include/cantera/thermo/HMWSoln.h index 2dd4278a74..80fec0c519 100644 --- a/include/cantera/thermo/HMWSoln.h +++ b/include/cantera/thermo/HMWSoln.h @@ -129,10 +129,10 @@ class WaterProps; * @f$, which are based on the molality form, have the following general format: * * @f[ - * \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) + * \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) * @f] * @f[ - * \mu_o = \mu^o_o(T,P) + RT ln(a_o) + * \mu_o = \mu^o_o(T,P) + RT \ln(a_o) * @f] * * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient @@ -835,7 +835,7 @@ class HMWSoln : public MolalityVPSSTP * exhibit zero volume expansivity: * @f[ * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - * - \hat R \sum_k X_k log(X_k) + * - \hat R \sum_k X_k \log(X_k) * @f] * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$ * are computed by the species thermodynamic property manager. The pure @@ -1038,7 +1038,7 @@ class HMWSoln : public MolalityVPSSTP * species in solution. * * @f[ - * \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} m_k) + * \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} m_k) * @f] * * @param mu Output vector of species chemical diff --git a/include/cantera/thermo/IdealSolidSolnPhase.h b/include/cantera/thermo/IdealSolidSolnPhase.h index c22ba2ea24..fa24023df2 100644 --- a/include/cantera/thermo/IdealSolidSolnPhase.h +++ b/include/cantera/thermo/IdealSolidSolnPhase.h @@ -89,7 +89,7 @@ class IdealSolidSolnPhase : public ThermoPhase * partial molar volume solution mixture with pure species phases which * exhibit zero volume expansivity: * @f[ - * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k log(X_k) + * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \log(X_k) * @f] * The reference-state pure-species entropies * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the species thermodynamic @@ -104,7 +104,7 @@ class IdealSolidSolnPhase : public ThermoPhase * 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) + * \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 * @f$ \hat g^0_k(T) @f$ are computed by the species thermodynamic @@ -280,11 +280,11 @@ class IdealSolidSolnPhase : public ThermoPhase * This function returns a vector of chemical potentials of the * species in solution. * @f[ - * \mu_k = \mu^{ref}_k(T) + V_k * (p - p_o) + R T ln(X_k) + * \mu_k = \mu^{ref}_k(T) + V_k * (p - p_o) + R T \ln(X_k) * @f] * or another way to phrase this is * @f[ - * \mu_k = \mu^o_k(T,p) + R T ln(X_k) + * \mu_k = \mu^o_k(T,p) + R T \ln(X_k) * @f] * where @f$ \mu^o_k(T,p) = \mu^{ref}_k(T) + V_k * (p - p_o) @f$ * @@ -297,7 +297,7 @@ class IdealSolidSolnPhase : public ThermoPhase * chemical potentials at the current T and P * @f$ \mu_k / \hat R T @f$. * @f[ - * \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_k + RT ln(X_k) + * \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_k + RT \ln(X_k) * @f] * where @f$ V_k @f$ is the molar volume of pure species *k*. * @f$ \mu^{ref}_k(T) @f$ is the chemical potential of pure @@ -337,8 +337,8 @@ class IdealSolidSolnPhase : public ThermoPhase * solution. Units: J/kmol/K. For this phase, the partial molar entropies * are equal to the pure species entropies plus the ideal solution * contribution. - * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R log(X_k) + * @f[ + * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h index 761013174a..a51446611a 100644 --- a/include/cantera/thermo/LatticePhase.h +++ b/include/cantera/thermo/LatticePhase.h @@ -227,7 +227,7 @@ class LatticePhase : public ThermoPhase * For an ideal, constant partial molar volume solution mixture with * pure species phases which exhibit zero volume expansivity: * @f[ - * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k log(X_k) + * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \log(X_k) * @f] * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$ * are computed by the species thermodynamic property manager. The pure @@ -395,7 +395,7 @@ class LatticePhase : public ThermoPhase * are equal to the pure species entropies plus the ideal solution * contribution. * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R log(X_k) + * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species diff --git a/include/cantera/thermo/LatticeSolidPhase.h b/include/cantera/thermo/LatticeSolidPhase.h index acbc34cebf..ad9a9ac671 100644 --- a/include/cantera/thermo/LatticeSolidPhase.h +++ b/include/cantera/thermo/LatticeSolidPhase.h @@ -364,7 +364,7 @@ class LatticeSolidPhase : public ThermoPhase * are equal to the pure species entropies plus the ideal solution * contribution. * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R log(X_k) + * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species diff --git a/include/cantera/thermo/MolalityVPSSTP.h b/include/cantera/thermo/MolalityVPSSTP.h index 4acafeac0d..63433a70a4 100644 --- a/include/cantera/thermo/MolalityVPSSTP.h +++ b/include/cantera/thermo/MolalityVPSSTP.h @@ -35,8 +35,8 @@ namespace Cantera * using the following formula * * @f[ - * ln(\gamma_k^{s2}) = ln(\gamma_k^{s1}) - * + \frac{z_k}{z_j} \left( ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right) + * \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1}) + * + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right) * @f] * * where j is any one species. @@ -52,15 +52,15 @@ const int PHSCALE_PITZER = 0; * using the following formula * * @f[ - * ln(\gamma_k^{s2}) = ln(\gamma_k^{s1}) - * + \frac{z_k}{z_j} \left( ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right) + * \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1}) + * + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right) * @f] * * where j is any one species. For the NBS scale, j is equal to the Cl- species * and * * @f[ - * ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} + * \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} * @f] * * This is the NBS pH scale, which is used in all conventional pH measurements. @@ -123,10 +123,10 @@ const int PHSCALE_NBS = 1; * have the following general format: * * @f[ - * \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) + * \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle}) * @f] * @f[ - * \mu_o = \mu^o_o(T,P) + RT ln(a_o) + * \mu_o = \mu^o_o(T,P) + RT \ln(a_o) * @f] * * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient @@ -137,7 +137,7 @@ const int PHSCALE_NBS = 1; * solvent, @f$ a_o @f$, is further reexpressed in terms of an osmotic * coefficient, @f$ \phi @f$. * @f[ - * \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} + * \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} * @f] * * MolalityVPSSTP::osmoticCoefficient() returns the value of @f$ \phi @f$. Note @@ -195,15 +195,15 @@ const int PHSCALE_NBS = 1; * using the following formula * * @f[ - * ln(\gamma_k^{s2}) = ln(\gamma_k^{s1}) - * + \frac{z_k}{z_j} \left( ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right) + * \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1}) + * + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right) * @f] * * where j is any one species. For the NBS scale, j is equal to the Cl- species * and * * @f[ - * ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} + * \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} * @f] * * The Pitzer scale doesn't actually change anything. The pitzer scale is @@ -453,15 +453,15 @@ class MolalityVPSSTP : public VPStandardStateTP * s2 using the following formula * * @f[ - * ln(\gamma_k^{s2}) = ln(\gamma_k^{s1}) - * + \frac{z_k}{z_j} \left( ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right) + * \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1}) + * + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right) * @f] * * where j is any one species. For the NBS scale, j is equal to the Cl- * species and * * @f[ - * ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} + * \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}} * @f] * * @param acMolality Output vector containing the molality based activity @@ -472,7 +472,7 @@ class MolalityVPSSTP : public VPStandardStateTP //! Calculate the osmotic coefficient /*! * @f[ - * \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} + * \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i} * @f] * * Note there are a few of definitions of the osmotic coefficient floating From 5d4a343cc942146a67ed82d76c1cfc7607b40581 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Thu, 3 Aug 2023 10:58:40 -0500 Subject: [PATCH 6/8] [docs] Fix ConstCpPoly docstring Use same syntax as on Cantera science section --- include/cantera/thermo/ConstCpPoly.h | 39 +++++++++++++--------------- 1 file changed, 18 insertions(+), 21 deletions(-) diff --git a/include/cantera/thermo/ConstCpPoly.h b/include/cantera/thermo/ConstCpPoly.h index 4a51375446..7da643a528 100644 --- a/include/cantera/thermo/ConstCpPoly.h +++ b/include/cantera/thermo/ConstCpPoly.h @@ -24,21 +24,21 @@ namespace Cantera * thermodynamic functions for the species. * * @f[ - * \frac{c_p(T)}{R} = Cp0\_R + * \hat{c}_p^\circ(T) = \hat{c}_p^\circ(T^\circ) * @f] * @f[ - * \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R) + * \hat{h}^\circ(T) = \hat{h}^\circ\left(T_0\right) + * + \hat{c}_p^\circ \left(T-T^\circ\right) * @f] * @f[ - * \frac{s^0(T)}{R} = (s0\_R + (log(T) - \log(T_0)) * Cp0\_R) + * \hat{s}^\circ(T) = \hat{s}^\circ(T_0) + * + \hat{c}_p^\circ \ln{\left(\frac{T}{T^\circ}\right)} * @f] * - * This parameterization takes 4 input values. These are: - * - c[0] = @f$ T_0 @f$ (Kelvin) - * - c[1] = @f$ H_k^o(T_0, p_{ref}) @f$ (J/kmol) - * - c[2] = @f$ S_k^o(T_0, p_{ref}) @f$ (J/kmol K) - * - c[3] = @f$ {Cp}_k^o(T_0, p_{ref}) @f$ (J(kmol K) - * + * This parameterization takes 4 input values @f$ T^\circ @f$, + * @f$ \hat{h}^\circ(T^\circ) @f$, @f$ \hat{s}^\circ(T^\circ) @f$ and + * @f$ \hat{c}_p^\circ(T^\circ) @f$, see setParameters(). The default value of + * @f$ T^\circ @f$ is 298.15 K; the default value for the other parameters is 0.0. * @ingroup spthermo */ class ConstCpPoly: public SpeciesThermoInterpType @@ -52,20 +52,17 @@ class ConstCpPoly: public SpeciesThermoInterpType * @param thigh Maximum temperature * @param pref reference pressure (Pa). * @param coeffs Vector of coefficients used to set the parameters for - * the standard state for species n. There are 4 - * coefficients for the ConstCpPoly parameterization. - * - c[0] = @f$ T_0 @f$ (Kelvin) - * - c[1] = @f$ H_k^o(T_0, p_{ref}) @f$ (J/kmol) - * - c[2] = @f$ S_k^o(T_0, p_{ref}) @f$ (J/kmol K) - * - c[3] = @f$ {Cp}_k^o(T_0, p_{ref}) @f$ (J(kmol K) + * the standard state for species n. Contains 4 parameters + * in the order of setParameters() arguments. */ ConstCpPoly(double tlow, double thigh, double pref, const double* coeffs); /** - * @param t0 @f$ T_0 @f$ [K] - * @param h0 @f$ h_k^o(T_0, p_{ref}) @f$ [J/kmol] - * @param s0 @f$ s_k^o(T_0, p_{ref}) @f$ [J/kmol/K] - * @param cp0 @f$ c_{p,k}^o(T_0, p_{ref}) @f$ [J/kmol/K] + * Set ConstCpPoly parameters. + * @param t0 @f$ T^\circ @f$ [K] + * @param h0 @f$ \hat{h}^\circ(T^\circ) @f$ [J/kmol] + * @param s0 @f$ \hat{s}^\circ(T^\circ) @f$ [J/kmol/K] + * @param cp0 @f$ \hat{c}_p^\circ(T^\circ) @f$ [J/kmol/K] */ void setParameters(double t0, double h0, double s0, double cp0); @@ -99,7 +96,7 @@ class ConstCpPoly: public SpeciesThermoInterpType protected: //! Base temperature - double m_t0 = 0.0; + double m_t0 = 298.15; //! Dimensionless value of the heat capacity double m_cp0_R = 0.0; //! dimensionless value of the enthalpy at t0 @@ -107,7 +104,7 @@ class ConstCpPoly: public SpeciesThermoInterpType //! Dimensionless value of the entropy at t0 double m_s0_R = 0.0; //! log of the t0 value - double m_logt0 = 0.0; + double m_logt0 = log(298.15); //! Original value of h0_R, restored by calling resetHf298() double m_h0_R_orig = 0.0; }; From 7fdd04457ce2b92ed54b5f8a3eb6e9badb5aadbe Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Thu, 3 Aug 2023 12:56:49 -0500 Subject: [PATCH 7/8] [docs] Fix new Doxygen warnings --- include/cantera/equil/vcs_VolPhase.h | 4 ++-- include/cantera/thermo/Mu0Poly.h | 1 - 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/include/cantera/equil/vcs_VolPhase.h b/include/cantera/equil/vcs_VolPhase.h index 231b311bfd..531878c58b 100644 --- a/include/cantera/equil/vcs_VolPhase.h +++ b/include/cantera/equil/vcs_VolPhase.h @@ -252,7 +252,7 @@ class vcs_VolPhase /** * 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) * @@ -261,7 +261,7 @@ class vcs_VolPhase */ void sendToVCS_LnActCoeffJac(Array2D& LnACJac_VCS); - //! Set the pointer for Cantera's ThermoPhase parameter + //! Set the pointer for %Cantera's ThermoPhase parameter /*! * When we first initialize the ThermoPhase object, we read the state of the * ThermoPhase into vcs_VolPhase object. diff --git a/include/cantera/thermo/Mu0Poly.h b/include/cantera/thermo/Mu0Poly.h index b80fb7d218..f09d6c9558 100644 --- a/include/cantera/thermo/Mu0Poly.h +++ b/include/cantera/thermo/Mu0Poly.h @@ -93,7 +93,6 @@ class Mu0Poly: public SpeciesThermoInterpType * - coeffs[6] = @f$ T_3 @f$ (Kelvin) * - coeffs[7] = @f$ \mu^o(T_3) @f$ (J/kmol) * - ........ - * . */ Mu0Poly(double tlow, double thigh, double pref, const double* coeffs); From 61fbbe52bfaf296dbe2b1e765b51f1aa310e28f2 Mon Sep 17 00:00:00 2001 From: Ingmar Schoegl Date: Sun, 6 Aug 2023 08:46:45 -0500 Subject: [PATCH 8/8] Replace \log by \ln --- include/cantera/equil/vcs_solve.h | 2 +- include/cantera/thermo/DebyeHuckel.h | 4 ++-- include/cantera/thermo/HMWSoln.h | 2 +- include/cantera/thermo/IdealSolidSolnPhase.h | 6 +++--- include/cantera/thermo/LatticePhase.h | 4 ++-- include/cantera/thermo/LatticeSolidPhase.h | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-) diff --git a/include/cantera/equil/vcs_solve.h b/include/cantera/equil/vcs_solve.h index b7743278c2..af603eb0e3 100644 --- a/include/cantera/equil/vcs_solve.h +++ b/include/cantera/equil/vcs_solve.h @@ -820,7 +820,7 @@ class VCS_SOLVE * We are checking the equation: * * sum_u = sum_j_comp [ sigma_i_j * u_j ] - * = u_i_O + \log((AC_i * W_i)/m_tPhaseMoles_old) + * = u_i_O + \ln((AC_i * W_i)/m_tPhaseMoles_old) * * by first evaluating: * diff --git a/include/cantera/thermo/DebyeHuckel.h b/include/cantera/thermo/DebyeHuckel.h index 241388a862..82d10c10bf 100644 --- a/include/cantera/thermo/DebyeHuckel.h +++ b/include/cantera/thermo/DebyeHuckel.h @@ -443,7 +443,7 @@ class DebyeHuckel : public MolalityVPSSTP * pure species phases which exhibit zero volume expansivity: * @f[ * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - * - \hat R \sum_k X_k \log(X_k) + * - \hat R \sum_k X_k \ln(X_k) * @f] * The reference-state pure-species entropies * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the @@ -575,7 +575,7 @@ class DebyeHuckel : public MolalityVPSSTP * For this phase, the partial molar entropies are equal to the SS species * entropies plus the ideal solution contribution: * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R \log(M0 * molality[k]) + * \bar s_k(T,P) = \hat s^0_k(T) - R \ln(M0 * molality[k]) * @f] * @f[ * \bar s_{solvent}(T,P) = \hat s^0_{solvent}(T) diff --git a/include/cantera/thermo/HMWSoln.h b/include/cantera/thermo/HMWSoln.h index 80fec0c519..642c61a45f 100644 --- a/include/cantera/thermo/HMWSoln.h +++ b/include/cantera/thermo/HMWSoln.h @@ -835,7 +835,7 @@ class HMWSoln : public MolalityVPSSTP * exhibit zero volume expansivity: * @f[ * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - * - \hat R \sum_k X_k \log(X_k) + * - \hat R \sum_k X_k \ln(X_k) * @f] * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$ * are computed by the species thermodynamic property manager. The pure diff --git a/include/cantera/thermo/IdealSolidSolnPhase.h b/include/cantera/thermo/IdealSolidSolnPhase.h index fa24023df2..b06f6353fe 100644 --- a/include/cantera/thermo/IdealSolidSolnPhase.h +++ b/include/cantera/thermo/IdealSolidSolnPhase.h @@ -89,7 +89,7 @@ class IdealSolidSolnPhase : public ThermoPhase * partial molar volume solution mixture with pure species phases which * exhibit zero volume expansivity: * @f[ - * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \log(X_k) + * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \ln(X_k) * @f] * The reference-state pure-species entropies * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the species thermodynamic @@ -104,7 +104,7 @@ class IdealSolidSolnPhase : public ThermoPhase * 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) + * \hat g(T, P) = \sum_k X_k \hat g^0_k(T,P) + \hat R T \sum_k X_k \ln(X_k) * @f] * The reference-state pure-species Gibbs free energies * @f$ \hat g^0_k(T) @f$ are computed by the species thermodynamic @@ -338,7 +338,7 @@ class IdealSolidSolnPhase : public ThermoPhase * are equal to the pure species entropies plus the ideal solution * contribution. * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) + * \bar s_k(T,P) = \hat s^0_k(T) - R \ln(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h index a51446611a..b298dc4a95 100644 --- a/include/cantera/thermo/LatticePhase.h +++ b/include/cantera/thermo/LatticePhase.h @@ -227,7 +227,7 @@ class LatticePhase : public ThermoPhase * For an ideal, constant partial molar volume solution mixture with * pure species phases which exhibit zero volume expansivity: * @f[ - * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \log(X_k) + * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T) - \hat R \sum_k X_k \ln(X_k) * @f] * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$ * are computed by the species thermodynamic property manager. The pure @@ -395,7 +395,7 @@ class LatticePhase : public ThermoPhase * are equal to the pure species entropies plus the ideal solution * contribution. * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) + * \bar s_k(T,P) = \hat s^0_k(T) - R \ln(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species diff --git a/include/cantera/thermo/LatticeSolidPhase.h b/include/cantera/thermo/LatticeSolidPhase.h index ad9a9ac671..0eaafdb71d 100644 --- a/include/cantera/thermo/LatticeSolidPhase.h +++ b/include/cantera/thermo/LatticeSolidPhase.h @@ -364,7 +364,7 @@ class LatticeSolidPhase : public ThermoPhase * are equal to the pure species entropies plus the ideal solution * contribution. * @f[ - * \bar s_k(T,P) = \hat s^0_k(T) - R \log(X_k) + * \bar s_k(T,P) = \hat s^0_k(T) - R \ln(X_k) * @f] * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at * the reference pressure, @f$ P_{ref} @f$, are computed by the species