diff --git a/include/cantera/thermo/ConstDensityThermo.h b/include/cantera/thermo/ConstDensityThermo.h index 5153e572a..7088f8293 100644 --- a/include/cantera/thermo/ConstDensityThermo.h +++ b/include/cantera/thermo/ConstDensityThermo.h @@ -19,7 +19,7 @@ namespace Cantera //! Overloads the virtual methods of class ThermoPhase to implement the //! incompressible equation of state. /** - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * The density is assumed to be constant, no matter what the concentration of * the solution. diff --git a/include/cantera/thermo/DebyeHuckel.h b/include/cantera/thermo/DebyeHuckel.h index 18e21aff6..d133eedf7 100644 --- a/include/cantera/thermo/DebyeHuckel.h +++ b/include/cantera/thermo/DebyeHuckel.h @@ -54,9 +54,7 @@ class PDSS_Water; * The concentrations of the ionic species are assumed to obey the * electroneutrality condition. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * The standard states are on the unit molality basis. Therefore, in the * documentation below, the normal \f$ o \f$ superscript is replaced with the @@ -107,9 +105,7 @@ class PDSS_Water; * properties at a T and P where the water phase is not a stable phase, i.e., * beyond its spinodal curve. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * Chemical potentials of the solutes, \f$ \mu_k \f$, and the solvent, \f$ \mu_o * \f$, which are based on the molality form, have the following general format: @@ -127,7 +123,7 @@ class PDSS_Water; * Individual activity coefficients of ions can not be independently measured. * Instead, only binary pairs forming electroneutral solutions can be measured. * - *

Ionic Strength

+ * ### Ionic Strength * * Most of the parameterizations within the model use the ionic strength as a * key variable. The ionic strength, \f$ I\f$ is defined as follows @@ -178,8 +174,8 @@ class PDSS_Water; * \f] * * The specification of which species are weakly associated acids is made in the - * input file via the stoichIsMods XML block, where the charge for k1 - * is also specified. An example is given below: + * input file via the `stoichIsMods` XML block, where the charge for k1 is also + * specified. An example is given below: * * @code * @@ -191,27 +187,26 @@ class PDSS_Water; * \f$ I_s \f$ we need to catalog all species in the phase. This is done using * the following categories: * - * - cEST_solvent Solvent species (neutral) - * - cEST_chargedSpecies Charged species (charged) - * - cEST_weakAcidAssociated Species which can break apart into charged species. - * It may or may not be charged. These may or - * may not be be included in the - * species solution vector. - * - cEST_strongAcidAssociated Species which always breaks apart into charged species. - * It may or may not be charged. Normally, these aren't included - * in the speciation vector. - * - cEST_polarNeutral Polar neutral species - * - cEST_nonpolarNeutral Non polar neutral species + * - `cEST_solvent` Solvent species (neutral) + * - `cEST_chargedSpecies` Charged species (charged) + * - `cEST_weakAcidAssociated` Species which can break apart into charged species. + * It may or may not be charged. These may or + * may not be be included in the + * species solution vector. + * - `cEST_strongAcidAssociated` Species which always breaks apart into charged species. + * It may or may not be charged. Normally, these aren't included + * in the speciation vector. + * - `cEST_polarNeutral` Polar neutral species + * - `cEST_nonpolarNeutral` Non polar neutral species * * Polar and non-polar neutral species are differentiated, because some * additions to the activity coefficient expressions distinguish between these * two types of solutes. This is the so-called salt-out effect. * - * The type of species is specified in the electrolyteSpeciesType XML - * block. Note, this is not considered a part of the specification of the - * standard state for the species, at this time. Therefore, this information is - * put under the activityCoefficient XML block. An example is given - * below + * The type of species is specified in the `electrolyteSpeciesType` XML block. + * Note, this is not considered a part of the specification of the standard + * state for the species, at this time. Therefore, this information is put under + * the `activityCoefficient` XML block. An example is given below * * @code * @@ -233,7 +228,7 @@ class PDSS_Water; * assumed for the Debye-Huckel term. The model is set by the internal parameter * #m_formDH. We will now describe each category in its own section. * - *

Debye-Huckel Dilute Limit

+ * ### Debye-Huckel Dilute Limit * * DHFORM_DILUTE_LIMIT = 0 * @@ -253,7 +248,7 @@ class PDSS_Water; * \ln(a_o) = \frac{X_o - 1.0}{X_o} + \frac{ 2 A_{Debye} \tilde{M}_o}{3} (I)^{3/2} * \f] * - *

Bdot Formulation

+ * ### Bdot Formulation * * DHFORM_BDOT_AK = 1 * @@ -285,7 +280,7 @@ class PDSS_Water; * Additionally, Helgeson's formulation for the water activity is offered as an * alternative. * - *

Bdot Formulation with Uniform Size Parameter in the Denominator

+ * ### Bdot Formulation with Uniform Size Parameter in the Denominator * * DHFORM_BDOT_AUNIFORM = 2 * @@ -304,7 +299,7 @@ class PDSS_Water; * - \frac{\log(10)}{2} \tilde{M}_o I \sum_k{ B^{dot}_k m_k} * \f] * - *

Beta_IJ formulation

+ * ### Beta_IJ formulation * * DHFORM_BETAIJ = 3 * @@ -331,13 +326,13 @@ class PDSS_Water; * supplied to the model, in an ionicRadius XML block. * * The \f$ \beta_{j,k} \f$ parameters are binary interaction parameters. They - * are supplied to the object in an DHBetaMatrix XML block. There are - * in principle \f$ N (N-1) /2 \f$ different, symmetric interaction parameters, + * are supplied to the object in an `DHBetaMatrix` XML block. There are in + * principle \f$ N (N-1) /2 \f$ different, symmetric interaction parameters, * where \f$ N \f$ are the number of solute species in the mechanism. An example * is given below. * - * An example activityCoefficients XML block for this formulation is - * supplied below + * An example `activityCoefficients` XML block for this formulation is supplied + * below * * @code * @@ -362,7 +357,7 @@ class PDSS_Water; * * @endcode * - *

Pitzer Beta_IJ formulation

+ * ### Pitzer Beta_IJ formulation * * DHFORM_PITZER_BETAIJ = 4 * @@ -382,15 +377,14 @@ class PDSS_Water; * - \tilde{M}_o \sum_j \sum_k \beta_{j,k} m_j m_k * \f] * - *

Specification of the Debye Huckel Constants

+ * ### Specification of the Debye Huckel Constants * * In the equations above, the formulas for \f$ A_{Debye} \f$ and \f$ * B_{Debye} \f$ are needed. The DebyeHuckel object uses two methods for * specifying these quantities. The default method is to assume that \f$ * A_{Debye} \f$ is a constant, given in the initialization process, and stored * in the member double, m_A_Debye. Optionally, a full water treatment may be - * employed that makes \f$ A_{Debye} \f$ a full function of T and - * P. + * employed that makes \f$ A_{Debye} \f$ a full function of *T* and *P*. * * \f[ * A_{Debye} = \frac{F e B_{Debye}}{8 \pi \epsilon R T} {\left( C_o \tilde{M}_o \right)}^{1/2} @@ -414,10 +408,10 @@ class PDSS_Water; * - \f$ \epsilon_o \f$ is the permittivity of free space * - \f$ \rho_o \f$ is the density of the solvent in its standard state. * - * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)1/2 based on: + * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)^(1/2) based on: * - \f$ \epsilon / \epsilon_0 \f$ = 78.54 (water at 25C) * - T = 298.15 K - * - B_Debye = 3.28640E9 (kg/gmol)1/2 m-1 + * - B_Debye = 3.28640E9 (kg/gmol)^(1/2) / m * * An example of a fixed value implementation is given below. * @code @@ -442,9 +436,7 @@ class PDSS_Water; * a default water value, or through the input file. This may have to be looked * at, in the future. * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * For the time being, we have set the standard concentration for all species in * this phase equal to the default concentration of the solvent at 298 K and 1 @@ -490,9 +482,7 @@ class PDSS_Water; * * Note, this treatment may be modified in the future, as events dictate. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is NOT located in the default ThermoFactory * for %Cantera. However, a new DebyeHuckel object may be created by @@ -517,9 +507,7 @@ class PDSS_Water; * importPhase(*xm, &dhphase); * @endcode * - *
- *

XML Example

- *
+ * ## XML Example * * The phase model name for this is called StoichSubstance. It must be supplied * as the model attribute of the thermo XML element entry. Within the phase XML @@ -704,8 +692,7 @@ public: * * @param k Optional parameter indicating the species. The default is to * assume this refers to species 0. - * @return the standard Concentration in units of m3 - * kmol-1. + * @return the standard Concentration in units of m^3/kmol */ virtual doublereal standardConcentration(size_t k=0) const; @@ -864,11 +851,11 @@ public: * - \f$ \epsilon_o \f$ is the permittivity of free space. * - \f$ \rho_o \f$ is the density of the solvent in its standard state. * - * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)1/2 + * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)^(1/2) * based on: * - \f$ \epsilon / \epsilon_0 \f$ = 78.54 (water at 25C) * - T = 298.15 K - * - B_Debye = 3.28640E9 (kg/gmol)1/2 m-1 + * - B_Debye = 3.28640E9 (kg/gmol)^(1/2)/m * * @param temperature Temperature in kelvin. Defaults to -1, in which * case the temperature of the phase is assumed. @@ -992,12 +979,12 @@ protected: * The generalized concentrations can have three different forms * depending on the value of the member attribute m_formGC, which * is supplied in the constructor. - * - * - * - * - * - *
m_formGC GeneralizedConc StandardConc
0 X_k 1.0
1 X_k / V_k 1.0 / V_k
2 X_k / V_N 1.0 / V_N
+ * + * | m_formGC | GeneralizedConc | StandardConc | + * | -------- | --------------- | ------------ | + * | 0 | X_k | 1.0 | + * | 1 | X_k / V_k | 1.0 / V_k | + * | 2 | X_k / V_N | 1.0 / V_N | * * The value and form of the generalized concentration will affect reaction * rate constants involving species in this phase. diff --git a/include/cantera/thermo/FixedChemPotSSTP.h b/include/cantera/thermo/FixedChemPotSSTP.h index 1b2a7fb08..c8fad71f6 100644 --- a/include/cantera/thermo/FixedChemPotSSTP.h +++ b/include/cantera/thermo/FixedChemPotSSTP.h @@ -26,7 +26,7 @@ namespace Cantera * to pressure. This is necessary because the phase is incompressible. It uses a * zero volume approximation. * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * This class inherits from SingleSpeciesTP. It uses a single value for the * chemical potential which is assumed to be constant with respect to @@ -40,12 +40,12 @@ namespace Cantera * the chemical potential. The entropy, the heat capacity, and the molar volume * are equal to zero. * - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * All solution properties are obtained from the standard state species * functions, since there is only one species in the phase. * - * Application within Kinetics Managers + * ## Application within Kinetics Managers * * The standard concentration is equal to 1.0. This means that the kinetics * operator works on an (activities basis). Since this is a stoichiometric @@ -65,7 +65,7 @@ namespace Cantera * constant expression, since it's a stoichiometric phase, and the activity is * always equal to 1.0. * - * Instantiation of the Class + * ## 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 @@ -98,7 +98,7 @@ namespace Cantera * FixedChemPotSSTP *LiFixed = new FixedChemPotSSTP("Li", -2.3E7); * @endcode * - * XML Example + * ## XML Example * * The phase model name for this is called FixedChemPot. It must be supplied * as the model attribute of the thermo XML element entry. @@ -249,8 +249,7 @@ public: virtual doublereal logStandardConc(size_t k=0) const; //! Get the array of chemical potentials at unit activity for the species at - //! their standard states at the current T and P of the - //! solution. + //! their standard states at the current *T* and *P* of the solution. /*! * For a stoichiometric substance, there is no activity term in the chemical * potential expression, and therefore the standard chemical potential and @@ -290,7 +289,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Returns the vector of nondimensional Internal Energies of the standard - //! state species at the current T and P of the solution + //! state species at the current *T* and *P* of the solution /*! * For an incompressible, stoichiometric substance, the molar internal * energy is independent of pressure. Since the thermodynamic properties are @@ -304,7 +303,7 @@ public: virtual void getIntEnergy_RT(doublereal* urt) const; //! Get the molar volumes of each species in their standard states at the - //! current T and P of the solution. + //! current *T* and *P* of the solution. /* * units = m^3 / kmol * diff --git a/include/cantera/thermo/GibbsExcessVPSSTP.h b/include/cantera/thermo/GibbsExcessVPSSTP.h index 4520275ac..39d3dbccd 100644 --- a/include/cantera/thermo/GibbsExcessVPSSTP.h +++ b/include/cantera/thermo/GibbsExcessVPSSTP.h @@ -58,9 +58,7 @@ namespace Cantera * vector. That's one of its primary usages. In order to keep the mole fraction * vector constant, all of the setState functions are redesigned at this layer. * - *

- * Activity Concentrations: Relationship of ThermoPhase to %Kinetics Expressions - *

+ * ### Activity Concentrations: Relationship of ThermoPhase to %Kinetics Expressions * * As explained in a similar discussion in the ThermoPhase class, the actual * units used in kinetics expressions must be specified in the ThermoPhase class @@ -78,9 +76,7 @@ namespace Cantera * activities appear directly in kinetics expressions involving species in * underlying GibbsExcessVPSSTP phases. * - *

- * SetState Strategy - *

+ * ### SetState Strategy * * All setState functions that set the internal state of the ThermoPhase object * are overloaded at this level, so that a current mole fraction vector is diff --git a/include/cantera/thermo/HMWSoln.h b/include/cantera/thermo/HMWSoln.h index 494727243..a926f2dee 100644 --- a/include/cantera/thermo/HMWSoln.h +++ b/include/cantera/thermo/HMWSoln.h @@ -85,9 +85,7 @@ class WaterProps; * The concentrations of the ionic species are assumed to obey the * electroneutrality condition. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * The solvent is assumed to be liquid water. A real model for liquid water * (IAPWS 1995 formulation) is used as its standard state. All standard state @@ -148,9 +146,7 @@ class WaterProps; * properties at a T and P where the water phase is not a stable phase, i.e., * beyond its spinodal curve. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * Chemical potentials of the solutes, \f$ \mu_k \f$, and the solvent, \f$ \mu_o * \f$, which are based on the molality form, have the following general format: @@ -174,7 +170,7 @@ class WaterProps; * applied, all other standard state properties of ionic species contain * meaningful information. * - *

Ionic Strength

+ * ### Ionic Strength * * Most of the parameterizations within the model use the ionic strength as a * key variable. The ionic strength, \f$ I\f$ is defined as follows @@ -186,7 +182,7 @@ class WaterProps; * \f$ m_k \f$ is the molality of the kth species. \f$ z_k \f$ is the charge of * the kth species. Note, the ionic strength is a defined units quantity. The * molality has defined units of gmol kg-1, and therefore the ionic strength has - * units of sqrt( gmol kg-1). + * units of sqrt(gmol/kg). * * In some instances, from some authors, a different formulation is used for the * ionic strength in the equations below. The different formulation is due to @@ -225,8 +221,8 @@ class WaterProps; * \f] * * The specification of which species are weakly associated acids is made in the - * input file via the stoichIsMods XML block, where the charge for k1 - * is also specified. An example is given below: + * input file via the `stoichIsMods` XML block, where the charge for k1 is also + * specified. An example is given below: * * @code * @@ -238,27 +234,26 @@ class WaterProps; * \f$ I_s \f$ we need to catalog all species in the phase. This is done using * the following categories: * - * - cEST_solvent : Solvent species (neutral) - * - cEST_chargedSpecies Charged species (charged) - * - cEST_weakAcidAssociated Species which can break apart into charged species. - * It may or may not be charged. These may or - * may not be be included in the - * species solution vector. - * - cEST_strongAcidAssociated Species which always breaks apart into charged species. - * It may or may not be charged. Normally, these - * aren't included in the speciation vector. - * - cEST_polarNeutral Polar neutral species - * - cEST_nonpolarNeutral Non polar neutral species + * - `cEST_solvent` Solvent species (neutral) + * - `cEST_chargedSpecies` Charged species (charged) + * - `cEST_weakAcidAssociated` Species which can break apart into charged species. + * It may or may not be charged. These may or + * may not be be included in the + * species solution vector. + * - `cEST_strongAcidAssociated` Species which always breaks apart into charged species. + * It may or may not be charged. Normally, these + * aren't included in the speciation vector. + * - `cEST_polarNeutral` Polar neutral species + * - `cEST_nonpolarNeutral` Non polar neutral species * * Polar and non-polar neutral species are differentiated, because some * additions to the activity coefficient expressions distinguish between these * two types of solutes. This is the so-called salt-out effect. * - * The type of species is specified in the electrolyteSpeciesType XML - * block. Note, this is not considered a part of the specification of the - * standard state for the species, at this time. Therefore, this information is - * put under the activityCoefficient XML block. An example is given - * below + * The type of species is specified in the `electrolyteSpeciesType` XML block. + * Note, this is not considered a part of the specification of the standard + * state for the species, at this time. Therefore, this information is put under + * the `activityCoefficient` XML block. An example is given below * * @code * @@ -276,7 +271,7 @@ class WaterProps; * given the "chargedSpecies" default category. A neutral solute species is put * into the "nonpolarNeutral" category by default. * - *

Specification of the Excess Gibbs Free Energy

+ * ### 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$, defined as the deviation of the total @@ -317,22 +312,22 @@ class WaterProps; * \end{array} * \f] * - * a is a subscript over all anions, c is a subscript extending - * over all cations, and i is a subscript that extends over all anions - * and cations. n is a subscript that extends only over neutral solute - * molecules. The second line contains cross terms where cations affect cations - * and/or cation/anion pairs, and anions affect anions or cation/anion pairs. - * Note part of the coefficients, \f$ \Phi_{c{c'}} \f$ and \f$ \Phi_{a{a'}} \f$ - * stem from the theory of unsymmetrical mixing of electrolytes with different - * charges. This theory depends on the total ionic strength of the solution, and + * *a* is a subscript over all anions, *c* is a subscript extending over all + * cations, and *i* is a subscript that extends over all anions and cations. + * *n* is a subscript that extends only over neutral solute molecules. The + * second line contains cross terms where cations affect cations and/or + * cation/anion pairs, and anions affect anions or cation/anion pairs. Note part + * of the coefficients, \f$ \Phi_{c{c'}} \f$ and \f$ \Phi_{a{a'}} \f$ stem from + * the theory of unsymmetrical mixing of electrolytes with different charges. + * This theory depends on the total ionic strength of the solution, and * therefore, \f$ \Phi_{c{c'}} \f$ and \f$ \Phi_{a{a'}} \f$ will depend on - * I, the ionic strength. \f$ B_{ca}\f$ is a strong function of the - * total ionic strength, I, of the electrolyte. The rest of the - * coefficients are assumed to be independent of the molalities or ionic - * strengths. However, all coefficients are potentially functions of the - * temperature and pressure of the solution. + * *I*, the ionic strength. \f$ B_{ca}\f$ is a strong function of the + * total ionic strength, *I*, of the electrolyte. The rest of the coefficients + * are assumed to be independent of the molalities or ionic strengths. However, + * all coefficients are potentially functions of the temperature and pressure + * of the solution. * - * A is the Debye-Huckel constant. Its specification is described in its + * *A* is the Debye-Huckel constant. Its specification is described in its * own section below. * * \f$ I\f$ is the ionic strength of the solution, and is given by: @@ -382,7 +377,7 @@ class WaterProps; * were fit to experimental data. For 2-2 electrolytes, \f$ \alpha^{(1)}_{ca} = * 1.4\ kg^{1/2}\ gmol^{-1/2}\f$ is used in combination with either \f$ * \alpha^{(2)}_{ca} = 12\ kg^{1/2}\ gmol^{-1/2}\f$ or \f$ \alpha^{(2)}_{ca} = k - * A_\psi \f$, where k is a constant. For electrolytes other than 2-2 + * A_\psi \f$, where *k* is a constant. For electrolytes other than 2-2 * electrolytes the \f$ \beta^{(2)}_{ca} g(\alpha^{(2)}_{ca} \sqrt{I}) \f$ term * is not used in the fitting procedure; it is only used for divalent metal * solfates and other high-valence electrolytes which exhibit significant @@ -405,7 +400,7 @@ class WaterProps; * multicomponent systems with just binary and minor ternary contributions, * which can be independently measured in binary or ternary subsystems. * - *

Multicomponent Activity Coefficients for Solutes

+ * ### Multicomponent Activity Coefficients for Solutes * * The formulas for activity coefficients of solutes may be obtained by taking * the following derivative of the excess Gibbs Free Energy formulation @@ -415,13 +410,13 @@ class WaterProps; * \ln(\gamma_k^\triangle) = \frac{d\left( \frac{G^{ex}}{M_o n_o RT} \right)}{d(m_k)}\Bigg|_{n_i} * \f] * - * In the formulas below the following conventions are used. The subscript - * M refers to a particular cation. The subscript X refers to a - * particular anion, whose activity is being currently evaluated. the subscript - * a refers to a summation over all anions in the solution, while the - * subscript c refers to a summation over all cations in the solutions. + * In the formulas below the following conventions are used. The subscript *M* + * refers to a particular cation. The subscript X refers to a particular anion, + * whose activity is being currently evaluated. the subscript *a* refers to a + * summation over all anions in the solution, while the subscript *c* refers to + * a summation over all cations in the solutions. * - * The activity coefficient for a particular cation M is given by + * The activity coefficient for a particular cation *M* is given by * * \f[ * \ln(\gamma_M^\triangle) = -z_M^2(F) + \sum_a m_a \left( 2 B_{Ma} + Z C_{Ma} \right) @@ -431,7 +426,7 @@ class WaterProps; * + 2 \sum_n m_n \lambda_{nM} * \f] * - * The activity coefficient for a particular anion X is given by + * The activity coefficient for a particular anion *X* is given by * * \f[ * \ln(\gamma_X^\triangle) = -z_X^2(F) + \sum_a m_c \left( 2 B_{cX} + Z C_{cX} \right) @@ -475,13 +470,13 @@ class WaterProps; * \frac{2\left(1 - \left(1 + x + \frac{x^2}{2} \right)\exp(-x) \right)}{x^2} * \f] * - * The activity coefficient for neutral species N is given by + * The activity coefficient for neutral species *N* is given by * * \f[ * \ln(\gamma_N^\triangle) = 2 \left( \sum_i m_i \lambda_{iN}\right) * \f] * - *

Activity of the Water Solvent

+ * ### Activity of the Water Solvent * * The activity for the solvent water,\f$ a_o \f$, is not independent and must * be determined either from the Gibbs-Duhem relation or from taking the @@ -543,7 +538,7 @@ class WaterProps; * \Phi^{\phi}_{a{a'}} = \Phi_{a{a'}} + I \frac{d\Phi_{a{a'}}}{dI} * \f] * - *

Temperature and Pressure Dependence of the Pitzer Parameters

+ * ### Temperature and Pressure Dependence of the Pitzer Parameters * * In general most of the coefficients introduced in the previous section may * have a temperature and pressure dependence. The temperature and pressure @@ -609,10 +604,9 @@ class WaterProps; * and \f$ C^{\phi}_{MX} \f$ coefficients described above. * There are 2 coefficients for each term. * - * The temperature dependence is specified in an attributes field in the - * activityCoefficients XML block, called TempModel . - * Permissible values for that attribute are CONSTANT, COMPLEX1, and - * LINEAR. + * The temperature dependence is specified in an attributes field in the + * `activityCoefficients` XML block, called `TempModel`. Permissible values for + * that attribute are `CONSTANT`, `COMPLEX1`, and `LINEAR`. * * The specification of the binary interaction between a cation and an anion is * given by the coefficients, \f$ B_{MX}\f$ and \f$ C_{MX}\f$ The specification @@ -620,15 +614,14 @@ class WaterProps; * \f$\beta^{(1)}_{MX} \f$, \f$\beta^{(2)}_{MX} \f$, \f$\alpha^{(1)}_{MX} \f$, * and \f$\alpha^{(2)}_{MX} \f$. \f$ C_{MX}\f$ is calculated from * \f$C^{\phi}_{MX} \f$ from the formula above. All of the underlying - * coefficients are specified in the XML element block binarySaltParameters - * , which has the attribute cation and anion to - * identify the interaction. XML elements named beta0, beta1, beta2, Cphi, - * Alpha1, Alpha2 within each binarySaltParameters block - * specify the parameters. Within each of these blocks multiple parameters - * describing temperature or pressure dependence are serially listed in the - * order that they appear in the equation in this document. An example of the - * beta0 block that fits the COMPLEX1 temperature - * dependence given above is + * coefficients are specified in the XML element block `binarySaltParameters`, + * which has the attribute `cation` and `anion` to identify the interaction. XML + * elements named `beta0, beta1, beta2, Cphi, Alpha1, Alpha2` within each + * `binarySaltParameters` block specify the parameters. Within each of these + * blocks multiple parameters describing temperature or pressure dependence are + * serially listed in the order that they appear in the equation in this + * document. An example of the `beta0` block that fits the `COMPLEX1` + * temperature dependence given above is * * @code * @@ -645,13 +638,13 @@ class WaterProps; * + q_4^{{\beta}0} \ln \left( \frac{T}{T_r} \right) * \f] * - * This same COMPLEX1 temperature - * dependence given above is used for the following parameters: + * This same `COMPLEX1` temperature dependence given above is used for the + * following parameters: * \f$ \beta^{(0)}_{MX} \f$, \f$ \beta^{(1)}_{MX} \f$, * \f$ \beta^{(2)}_{MX} \f$, \f$ \Theta_{cc'} \f$, \f$\Theta_{aa'} \f$, * \f$ \Psi_{c{c'}a} \f$ and \f$ \Psi_{ca{a'}} \f$. * - *

Like-Charged Binary Ion Parameters and the Mixing Parameters

+ * ### Like-Charged Binary Ion Parameters and the Mixing Parameters * * The previous section contained the functions, \f$ \Phi_{c{c'}} \f$, * \f$ \Phi_{a{a'}} \f$ and their derivatives wrt the ionic strength, \f$ @@ -699,11 +692,10 @@ class WaterProps; * numerical integration. * * The \f$ \Theta_{ij} \f$ term is a constant that is specified by the XML - * element thetaCation and thetaAnion , which has the - * attribute cation1 , cation2 and anion1 , - * anion2 respectively to identify the interaction. No temperature or - * pressure dependence of this parameter is currently allowed. An example of the - * block is presented below. + * element `thetaCation` and `thetaAnion`, which has the attribute `cation1`, + * `cation2` and `anion1`, `anion2` respectively to identify the interaction. No + * temperature or pressure dependence of this parameter is currently allowed. An + * example of the block is presented below. * * @code * @@ -711,7 +703,7 @@ class WaterProps; * * @endcode * - *

Ternary Pitzer Parameters

+ * ### Ternary Pitzer Parameters * * The \f$ \Psi_{c{c'}a} \f$ and \f$ \Psi_{ca{a'}} \f$ terms represent ternary * interactions between two cations and an anion and two anions and a cation, @@ -719,18 +711,16 @@ class WaterProps; * absolute size. Currently these parameters do not have any dependence on * temperature, pressure, or ionic strength. * - * Their values are input using the XML element psiCommonCation and - * psiCommonAnion . The species id's are specified in attribute fields - * in the XML element. The fields cation, anion1, and - * anion2 are used for psiCommonCation. The fields - * anion, cation1 and cation2 are used for - * psiCommonAnion. An example block is given below. The Theta - * field below is a duplicate of the thetaAnion field mentioned - * above. The two fields are input into the same block for convenience, and - * because their data are highly correlated, in practice. It is an error for the - * two blocks to specify different information about thetaAnion (or thetaCation) - * in different blocks. It's ok to specify duplicate but consistent information - * in multiple blocks. + * Their values are input using the XML element `psiCommonCation` and + * `psiCommonAnion`. The species id's are specified in attribute fields in the + * XML element. The fields `cation`, `anion1`, and `anion2` are used for + * `psiCommonCation`. The fields `anion`, `cation1` and `cation2` are used for + * `psiCommonAnion`. An example block is given below. The `Theta` field below is + * a duplicate of the `thetaAnion` field mentioned above. The two fields are + * input into the same block for convenience, and because their data are highly + * correlated, in practice. It is an error for the two blocks to specify + * different information about thetaAnion (or thetaCation) in different blocks. + * It's ok to specify duplicate but consistent information in multiple blocks. * * @code * @@ -739,18 +729,17 @@ class WaterProps; * * @endcode * - *

Treatment of Neutral Species

+ * ### Treatment of Neutral Species * * Binary virial-coefficient-like interactions between two neutral species may * be specified in the \f$ \lambda_{mn} \f$ terms that appear in the formulas * above. Currently these interactions are independent of temperature, pressure, * and ionic strength. Also, currently, the neutrality of the species are not * checked. Therefore, this interaction may involve charged species in the - * solution as well. The identity of the species is specified by the - * species1 and species2 attributes to the XML - * lambdaNeutral node. These terms are symmetrical; species1 - * and species2 may be reversed and the term will be the same. An - * example is given below. + * solution as well. The identity of the species is specified by the `species1` + * and `species2` attributes to the XML `lambdaNeutral` node. These terms are + * symmetrical; `species1` and `species2` may be reversed and the term will be + * the same. An example is given below. * * @code * @@ -758,13 +747,12 @@ class WaterProps; * * @endcode * - *

Example of the Specification of Parameters for the Activity - * Coefficients

+ * ## Example of the Specification of Parameters for the Activity Coefficients * * An example is given below. * - * An example activityCoefficients XML block for this formulation is - * supplied below + * An example `activityCoefficients` XML block for this formulation is supplied + * below * * @code * @@ -823,16 +811,16 @@ class WaterProps; * * @endcode * - *

Specification of the Debye-Huckel Constant

+ * ### Specification of the Debye-Huckel Constant * * In the equations above, the formula for \f$ A_{Debye} \f$ is needed. The * HMWSoln object uses two methods for specifying these quantities. The default * method is to assume that \f$ A_{Debye} \f$ is a constant, given in the * initialization process, and stored in the member double, m_A_Debye. * Optionally, a full water treatment may be employed that makes - * \f$ A_{Debye} \f$ a full function of T and P and creates - * nontrivial entries for the excess heat capacity, enthalpy, and excess volumes - * of solution. + * \f$ A_{Debye} \f$ a full function of *T* and *P* and creates nontrivial + * entries for the excess heat capacity, enthalpy, and excess volumes of + * solution. * * \f[ * A_{Debye} = \frac{F e B_{Debye}}{8 \pi \epsilon R T} {\left( C_o \tilde{M}_o \right)}^{1/2} @@ -860,11 +848,11 @@ class WaterProps; * - \f$ \epsilon_o \f$ is the permittivity of free space. * - \f$ \rho_o \f$ is the density of the solvent in its standard state. * - * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)1/2 + * Nominal value at 298 K and 1 atm = 1.172576 (kg/gmol)^(1/2) * based on: * - \f$ \epsilon / \epsilon_0 \f$ = 78.54 (water at 25C) * - T = 298.15 K - * - B_Debye = 3.28640E9 (kg/gmol)1/2 m-1 + * - B_Debye = 3.28640E9 (kg/gmol)^(1/2) / m * * An example of a fixed value implementation is given below. * @code @@ -886,7 +874,7 @@ class WaterProps; * * @endcode * - *

Temperature and Pressure Dependence of the Activity Coefficients

+ * ### Temperature and Pressure Dependence of the Activity Coefficients * * Temperature dependence of the activity coefficients leads to nonzero terms * for the excess enthalpy and entropy of solution. This means that the partial @@ -949,9 +937,7 @@ class WaterProps; * s_update_d2lnMolalityActCoeff_dT2(), and the first derivative of the log * activity coefficients wrt pressure, s_update_dlnMolalityActCoeff_dP(). * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * For the time being, we have set the standard concentration for all solute * species in this phase equal to the default concentration of the solvent at @@ -965,10 +951,10 @@ class WaterProps; * basis (kmol /m3). The concentration will be modified by the activity * coefficients. * - * For example, a bulk-phase binary reaction between liquid solute species - * j and k, producing a new liquid solute species l would - * have the following equation for its rate of progress variable, \f$ R^1 \f$, - * which has units of kmol m-3 s-1. + * For example, a bulk-phase binary reaction between liquid solute species *j* + * and *k*, producing a new liquid solute species *l* would have the following + * equation for its rate of progress variable, \f$ R^1 \f$, which has units of + * kmol m-3 s-1. * * \f[ * R^1 = k^1 C_j^a C_k^a = k^1 (C^o_o \tilde{M}_o a_j) (C^o_o \tilde{M}_o a_k) @@ -980,24 +966,24 @@ class WaterProps; * C_j^a = C^o_o \tilde{M}_o a_j \quad and \quad C_k^a = C^o_o \tilde{M}_o a_k * \f] * - * \f$ C_j^a \f$ is the activity concentration of species j, and - * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^o_o \f$ - * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ has - * units of kg solvent per gmol solvent and is equal to + * \f$ C_j^a \f$ is the activity concentration of species *j*, and + * \f$ C_k^a \f$ is the activity concentration of species *k*. \f$ C^o_o \f$ is + * the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ has units + * of kg solvent per gmol solvent and is equal to * * \f[ * \tilde{M}_o = \frac{M_o}{1000} * \f] * - * \f$ a_j \f$ is the activity of species j at the current temperature - * and pressure and concentration of the liquid phase is given by the molality - * based activity coefficient multiplied by the molality of the jth species. + * \f$ a_j \f$ is the activity of species *j* at the current temperature and + * pressure and concentration of the liquid phase is given by the molality based + * activity coefficient multiplied by the molality of the jth species. * * \f[ * a_j = \gamma_j^\triangle m_j = \gamma_j^\triangle \frac{n_j}{\tilde{M}_o n_o} * \f] * - * \f$k^1 \f$ has units of m3 kmol-1 s-1. + * \f$k^1 \f$ has units of m^3/kmol/s. * * Therefore the generalized activity concentration of a solute species has the following form * @@ -1030,13 +1016,11 @@ class WaterProps; * k^{-1} = k^1 K^{o,1} C_o \tilde{M}_o * \f] * - * \f$ k^{-1} \f$ has units of s-1. + * \f$ k^{-1} \f$ has units of 1/s. * * Note, this treatment may be modified in the future, as events dictate. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is now located in the default ThermoFactory * for %Cantera. The following code snippet may be used to initialize the phase @@ -1067,9 +1051,7 @@ class WaterProps; * importPhase(*xm, &dhphase); * @endcode * - *
- *

XML Example

- *
+ * ## XML Example * * The phase model name for this is called StoichSubstance. It must be supplied * as the model attribute of the thermo XML element entry. Within the phase XML @@ -1420,8 +1402,7 @@ public: * * The consequence of this is that the standard concentrations have unequal * units between the solvent and the solute. However, both the solvent and - * the solute activity concentrations will have the same units of kmol - * kg-3. + * the solute activity concentrations will have the same units of kmol/kg^3. * * This means that the kinetics operator essentially works on an generalized * concentration basis (kmol / m3), with units for the kinetic rate constant @@ -1430,9 +1411,9 @@ public: * coefficients. * * For example, a bulk-phase binary reaction between liquid solute species - * j and k, producing a new liquid solute species l - * would have the following equation for its rate of progress variable, \f$ - * R^1 \f$, which has units of kmol m-3 s-1. + * *j* and *k*, producing a new liquid solute species *l* would have the + * following equation for its rate of progress variable, \f$ R^1 \f$, which + * has units of kmol m-3 s-1. * * \f[ * R^1 = k^1 C_j^a C_k^a = k^1 (C^o_o \tilde{M}_o a_j) (C^o_o \tilde{M}_o a_k) @@ -1444,17 +1425,17 @@ public: * C_j^a = C^o_o \tilde{M}_o a_j \quad and \quad C_k^a = C^o_o \tilde{M}_o a_k * \f] * - * \f$ C_j^a \f$ is the activity concentration of species j, and - * \f$ C_k^a \f$ is the activity concentration of species k. \f$ C^o_o \f$ - * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ - * has units of kg solvent per gmol solvent and is equal to + * \f$ C_j^a \f$ is the activity concentration of species *j*, and + * \f$ C_k^a \f$ is the activity concentration of species *k*. \f$ C^o_o \f$ + * is the concentration of water at 298 K and 1 atm. \f$ \tilde{M}_o \f$ has + * units of kg solvent per gmol solvent and is equal to * * \f[ * \tilde{M}_o = \frac{M_o}{1000} * \f] * * \f$ a_j \f$ is - * the activity of species j at the current temperature and pressure + * the activity of species *j* at the current temperature and pressure * and concentration of the liquid phase is given by the molality based * activity coefficient multiplied by the molality of the jth species. * @@ -1462,7 +1443,7 @@ public: * a_j = \gamma_j^\triangle m_j = \gamma_j^\triangle \frac{n_j}{\tilde{M}_o n_o} * \f] * - * \f$k^1 \f$ has units of m3 kmol-1 s-1. + * \f$k^1 \f$ has units of m^3/kmol/s. * * Therefore the generalized activity concentration of a solute species has * the following form @@ -1480,8 +1461,7 @@ public: * * @param k Optional parameter indicating the species. The default is to * assume this refers to species 0. - * @returns the standard Concentration in units of m3 - * kmol-1. + * @returns the standard Concentration in units of m^3/kmol. * * @param k Species index */ @@ -1885,12 +1865,12 @@ private: * The generalized concentrations can have three different forms * depending on the value of the member attribute m_formGC, which * is supplied in the constructor. - * - * - * - * - * - *
m_formGC GeneralizedConc StandardConc
0 X_k 1.0
1 X_k / V_k 1.0 / V_k
2 X_k / V_N 1.0 / V_N
+ * + * | m_formGC | GeneralizedConc | StandardConc | + * | -------- | --------------- | ------------ | + * | 0 | X_k | 1.0 | + * | 1 | X_k / V_k | 1.0 / V_k | + * | 2 | X_k / V_N | 1.0 / V_N | * * The value and form of the generalized concentration will affect reaction * rate constants involving species in this phase. diff --git a/include/cantera/thermo/IdealGasPhase.h b/include/cantera/thermo/IdealGasPhase.h index f3f8c1e04..b552ebdcc 100644 --- a/include/cantera/thermo/IdealGasPhase.h +++ b/include/cantera/thermo/IdealGasPhase.h @@ -28,9 +28,7 @@ namespace Cantera * current mass fraction vector and temperature and the desired pressure, and * then set the density. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * It is assumed that the reference state thermodynamics may be obtained by a * pointer to a populated species thermodynamic property manager class in the @@ -100,16 +98,14 @@ namespace Cantera * where R is the molar gas constant. For a complete list of physical constants * used within %Cantera, see \ref physConstants . * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The activity of a species defined in the phase is given by the ideal gas law: * \f[ * a_k = X_k * \f] - * where \f$ X_k \f$ is the mole fraction of species k. The chemical - * potential for species k is equal to + * where \f$ X_k \f$ is the mole fraction of species *k*. The chemical potential + * for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \log(X_k) @@ -121,33 +117,31 @@ namespace Cantera * \mu_k(T,P) = \mu^{ref}_k(T, P) + R T \log(\frac{P X_k}{P_{ref}}) * \f] * - * The partial molar entropy for species k is given by the following relation, + * The partial molar entropy for species *k* is given by the following relation, * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(\frac{P X_k}{P_{ref}}) * \f] * - * The partial molar enthalpy for species k is + * The partial molar enthalpy for species *k* is * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) = h^{ref}_k(T) * \f] * - * The partial molar Internal Energy for species k is + * The partial molar Internal Energy for species *k* is * * \f[ * \tilde{u}_k(T,P) = u^o_k(T,P) = u^{ref}_k(T) * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{Cp}_k(T,P) = Cp^o_k(T,P) = Cp^{ref}_k(T) * \f] * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / C^s_k, \f$ where \f$ * C^s_k \f$ is a standard concentration defined below and \f$ a_k \f$ are @@ -160,8 +154,7 @@ namespace Cantera * C^a_k = C^s_k X_k = \frac{P}{R T} X_k * \f] * - * The standard concentration for species k is independent of k - * and equal to + * The standard concentration for species *k* is independent of *k* and equal to * * \f[ * C^s_k = C^s = \frac{P}{R T} @@ -245,9 +238,7 @@ namespace Cantera * * \f$k^{-1} \f$ has units of s-1. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is located in the default ThermoFactory for * %Cantera. A new IdealGasPhase may be created by the following code snippet: @@ -267,9 +258,8 @@ namespace Cantera * IdealGasPhase *silaneGas = new IdealGasPhase(*xs); * @endcode * - *
- *

XML Example

- *
+ * ## XML Example + * * An example of an XML Element named phase setting up a IdealGasPhase * object named silane is given below. * diff --git a/include/cantera/thermo/IdealMolalSoln.h b/include/cantera/thermo/IdealMolalSoln.h index b5f81ebd7..09da4e880 100644 --- a/include/cantera/thermo/IdealMolalSoln.h +++ b/include/cantera/thermo/IdealMolalSoln.h @@ -51,12 +51,11 @@ namespace Cantera * The standard concentrations can have three different forms depending on the * value of the member attribute m_formGC, which is supplied in the XML file. * - * - * - * - * - * - *
m_formGC ActivityConc StandardConc
0 \f$ {m_k}/ { m^{\Delta}}\f$ \f$ 1.0 \f$
1 \f$ m_k / (m^{\Delta} V_k)\f$ \f$ 1.0 / V_k \f$
2 \f$ m_k / (m^{\Delta} V^0_0)\f$ \f$ 1.0 / V^0_0\f$
+ * | m_formGC | ActivityConc | StandardConc | + * | -------- | -------------------------------- | ------------------ | + * | 0 | \f$ {m_k}/ { m^{\Delta}}\f$ | \f$ 1.0 \f$ | + * | 1 | \f$ m_k / (m^{\Delta} V_k)\f$ | \f$ 1.0 / V_k \f$ | + * | 2 | \f$ m_k / (m^{\Delta} V^0_0)\f$ | \f$ 1.0 / V^0_0\f$ | * * \f$ V^0_0 \f$ is the solvent standard molar volume. \f$ m^{\Delta} \f$ is a * constant equal to a molality of \f$ 1.0 \quad\mbox{gm kmol}^{-1} \f$. @@ -442,12 +441,11 @@ protected: * the value of the member attribute m_formGC, which is supplied in the XML * file. * - * - * - * - * - * - *
m_formGC ActivityConc StandardConc
0 \f$ {m_k}/ { m^{\Delta}}\f$ \f$ 1.0 \f$
1 \f$ m_k / (m^{\Delta} V_k)\f$ \f$ 1.0 / V_k \f$
2 \f$ m_k / (m^{\Delta} V^0_0)\f$ \f$ 1.0 / V^0_0\f$
+ * | m_formGC | ActivityConc | StandardConc | + * | -------- | -------------------------------- | ------------------ | + * | 0 | \f$ {m_k}/ { m^{\Delta}}\f$ | \f$ 1.0 \f$ | + * | 1 | \f$ m_k / (m^{\Delta} V_k)\f$ | \f$ 1.0 / V_k \f$ | + * | 2 | \f$ m_k / (m^{\Delta} V^0_0)\f$ | \f$ 1.0 / V^0_0\f$ | */ int m_formGC; diff --git a/include/cantera/thermo/IdealSolidSolnPhase.h b/include/cantera/thermo/IdealSolidSolnPhase.h index eaf269784..84acfb3ae 100644 --- a/include/cantera/thermo/IdealSolidSolnPhase.h +++ b/include/cantera/thermo/IdealSolidSolnPhase.h @@ -296,8 +296,8 @@ public: * For this implementation the activity is defined to be the mole fraction * of the species. The generalized concentration is defined to be equal to * the mole fraction divided by the partial molar volume. The generalized - * concentrations for species in this phase therefore have units of kmol - * m-3. Rate constants must reflect this fact. + * concentrations for species in this phase therefore have units of + * kmol/m^3. Rate constants must reflect this fact. * * On a general note, the following must be true. For an ideal solution, the * generalized concentration must consist of the mole fraction multiplied by @@ -328,8 +328,7 @@ public: * generalized concentration. In many cases, this quantity will be the * same for all species in a phase. However, for this case, we will return * a distinct concentration for each species. This is the inverse of the - * species molar volume. Units for the standard concentration are kmol - * m-3. + * species molar volume. Units for the standard concentration are kmol/m^3. * * @param k Species number: this is a require parameter, a change from the * ThermoPhase base class, where it was an optional parameter. @@ -388,9 +387,9 @@ public: * \f[ * \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. + * 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 - * species k at the reference pressure, \f$P_{ref}\f$. + * species *k* at the reference pressure, \f$P_{ref}\f$. * * @param mu Output vector of dimensionless chemical potentials. * Length = m_kk. @@ -481,14 +480,14 @@ public: } //! Get the array of nondimensional Enthalpy functions for the standard - //! state species at the current T and P of the solution. + //! state species at the current *T* and *P* of the solution. /*! * We assume an incompressible constant partial molar volume here: * \f[ * h^0_k(T,P) = h^{ref}_k(T) + (P - P_{ref}) * V_k * \f] - * where \f$V_k\f$ is the molar volume of pure species k. - * \f$ h^{ref}_k(T)\f$ is the enthalpy of the pure species k at the + * where \f$V_k\f$ is the molar volume of pure species *k*. + * \f$ h^{ref}_k(T)\f$ is the enthalpy of the pure species *k* at the * reference pressure, \f$P_{ref}\f$. * * @param hrt Vector of length m_kk, which on return hrt[k] will contain the @@ -514,8 +513,8 @@ public: * \f[ * \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_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 species k + * 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 species *k* * at the reference pressure, \f$P_{ref}\f$. * * @param grt Vector of length m_kk, which on return sr[k] will contain the @@ -524,15 +523,15 @@ public: virtual void getGibbs_RT(doublereal* grt) const; /** - * Get the Gibbs functions for the pure species at the current T and - * P of the solution. We assume an incompressible constant partial - * molar volume here: + * Get the Gibbs functions for the pure species at the current *T* and *P* + * of the solution. We assume an incompressible constant partial molar + * volume here: * \f[ * \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_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 species k - * at the reference pressure, \f$P_{ref}\f$. + * 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 species *k* at + * the reference pressure, \f$P_{ref}\f$. * * @param gpure Output vector of Gibbs functions for species. Length: m_kk. */ @@ -546,9 +545,9 @@ public: * \f[ * Cp^0_k(T,P) = Cp^{ref}_k(T) * \f] - * where \f$V_k\f$ is the molar volume of pure species k. + * where \f$V_k\f$ is the molar volume of pure species *k*. * \f$ Cp^{ref}_k(T)\f$ is the constant pressure heat capacity of species - * k at the reference pressure, \f$p_{ref}\f$. + * *k* at the reference pressure, \f$p_{ref}\f$. * * @param cpr Vector of length m_kk, which on return cpr[k] will contain the * nondimensional constant pressure heat capacity for species k. @@ -648,12 +647,11 @@ protected: /** * Format for the generalized concentrations. * - * - * - * - * - * - *
m_formGC GeneralizedConc StandardConc
0 (default) X_k 1.0
1 X_k / V_k 1.0 / V_k
2 X_k / V_N 1.0 / V_N
+ * | m_formGC | GeneralizedConc | StandardConc | + * | ----------- | --------------- | ------------ | + * | 0 (default) | X_k | 1.0 | + * | 1 | X_k / V_k | 1.0 / V_k | + * | 2 | X_k / V_N | 1.0 / V_N | * * The value and form of the generalized concentration will affect * reaction rate constants involving species in this phase. diff --git a/include/cantera/thermo/LatticePhase.h b/include/cantera/thermo/LatticePhase.h index e7f165cad..6cb2d9b50 100644 --- a/include/cantera/thermo/LatticePhase.h +++ b/include/cantera/thermo/LatticePhase.h @@ -28,7 +28,7 @@ namespace Cantera * The density of matrix sites is given by the variable \f$ C_o \f$, which has * SI units of kmol m-3. * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * It is assumed that the reference state thermodynamics may be obtained by a * pointer to a populated species thermodynamic property manager class (see @@ -67,9 +67,7 @@ namespace Cantera * V^o_k(T,P) = \frac{1.0}{C_o} * \f] * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The activity of species \f$ k \f$ defined in the phase, \f$ a_k \f$, is given * by the ideal solution law: @@ -78,33 +76,32 @@ namespace Cantera * a_k = X_k , * \f] * - * where \f$ X_k \f$ is the mole fraction of species k. The chemical - * potential for species k is equal to + * where \f$ X_k \f$ is the mole fraction of species *k*. The chemical potential + * for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \log(X_k) * \f] * - * The partial molar entropy for species k is given by the following - * relation, + * The partial molar entropy for species *k* is given by the following relation, * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(X_k) * \f] * - * The partial molar enthalpy for species k is + * The partial molar enthalpy for species *k* is * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) = h^{ref}_k(T) + \left( \frac{P - P_{ref}}{C_o} \right) * \f] * - * The partial molar Internal Energy for species k is + * The partial molar Internal Energy for species *k* is * * \f[ * \tilde{u}_k(T,P) = u^o_k(T,P) = u^{ref}_k(T) * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{Cp}_k(T,P) = Cp^o_k(T,P) = Cp^{ref}_k(T) @@ -126,9 +123,7 @@ namespace Cantera * only has a weak dependence on the enthalpy, and doesn't effect the molar * concentration. * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ C^a_k = a_k = X_k \f$. \f$ C^s_k \f$, * the standard concentration, is defined to be equal to one. \f$ a_k \f$ are @@ -141,7 +136,7 @@ namespace Cantera * C^a_k = C^s_k X_k = X_k * \f] * - * The standard concentration for species k is identically one + * The standard concentration for species *k* is identically one * * \f[ * C^s_k = C^s = 1.0 @@ -183,9 +178,7 @@ namespace Cantera * K_c \f$, using the second and third part of the above expression as a * definition for the concentration equilibrium constant. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is located in the default ThermoFactory for * %Cantera. A new LatticePhase object may be created by the following code @@ -208,9 +201,7 @@ namespace Cantera * * The XML file used in this example is listed in the next section * - *
- *

XML Example

- *
+ * ## XML Example * * An example of an XML Element named phase setting up a LatticePhase object * named "O_lattice_SiO2" is given below. @@ -412,9 +403,7 @@ public: * * @param k Optional parameter indicating the species. The default is to * assume this refers to species 0. - * @return - * Returns the standard Concentration in units of - * m3 kmol-1. + * @return Returns the standard Concentration in units of m^3/kmol. * * @param k Species index */ @@ -504,8 +493,8 @@ public: //@{ //! Get the nondimensional Enthalpy functions for the species standard - //! states at their standard states at the current T and P of - //! the solution. + //! states at their standard states at the current *T* and *P* of the + //! solution. /*! * A small pressure dependent term is added onto the reference state enthalpy * to get the pressure dependence of this term. @@ -525,7 +514,7 @@ public: virtual void getEnthalpy_RT(doublereal* hrt) const; //! Get the array of nondimensional Entropy functions for the species - //! standard states at the current T and P of the solution. + //! standard states at the current *T* and *P* of the solution. /*! * The entropy of the standard state is defined as independent of * pressure here. @@ -545,7 +534,7 @@ public: virtual void getEntropy_R(doublereal* sr) const; //! Get the nondimensional Gibbs functions for the species standard states - //! at the current T and P of the solution. + //! at the current *T* and *P* of the solution. /*! * The standard Gibbs free energies are obtained from the enthalpy and * entropy formulation. @@ -560,8 +549,7 @@ public: virtual void getGibbs_RT(doublereal* grt) const; //! Get the nondimensional Heat Capacities at constant pressure for the - //! species standard states at the current T and P of the - //! solution + //! species standard states at the current *T* and *P* of the solution /*! * The heat capacity of the standard state is independent of pressure * @@ -580,7 +568,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Get the molar volumes of the species standard states at the current - //! T and P of the solution. + //! *T* and *P* of the solution. /*! * units = m^3 / kmol * diff --git a/include/cantera/thermo/LatticeSolidPhase.h b/include/cantera/thermo/LatticeSolidPhase.h index af237589b..45ea6262f 100644 --- a/include/cantera/thermo/LatticeSolidPhase.h +++ b/include/cantera/thermo/LatticeSolidPhase.h @@ -34,9 +34,7 @@ namespace Cantera * routine getMoleFraction() and setMoleFraction() have been redefined to use * this convention. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * The standard state properties are calculated in the normal way for each of * the sublattices. The normal way here means that a thermodynamic polynomial in @@ -44,9 +42,7 @@ namespace Cantera * pressure dependence is assumed. All of these properties are on a Joules per * kmol of sublattice constituent basis. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The sum over the LatticePhase objects is carried out by weighting each * LatticePhase object value with the molar density (kmol m-3) of its @@ -74,9 +70,7 @@ namespace Cantera * sublattice will have a weight of 1.0 associated with it. The S sublattice * will have a weight of 2.0 associated with it. * - *
- *

Specification of Solution Density Properties

- *
+ * ### Specification of Solution Density Properties * * Currently, molar density is not a constant within the object, even though the * species molar volumes are a constant. The basic idea is that a swelling of @@ -149,7 +143,7 @@ public: * \tilde h(T,P) = {\sum_n \theta_n \tilde h_n(T,P) } * \f] * - * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. + * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. * * units J/kmol */ @@ -164,8 +158,7 @@ public: * \tilde u(T,P) = {\sum_n \theta_n \tilde u_n(T,P) } * \f] * - * \f$ \tilde u_n(T,P) \f$ is the internal energy of the nth - * lattice. + * \f$ \tilde u_n(T,P) \f$ is the internal energy of the nth lattice. * * units J/kmol */ @@ -180,7 +173,7 @@ public: * \tilde s(T,P) = \sum_n \theta_n \tilde s_n(T,P) * \f] * - * \f$ \tilde s_n(T,P) \f$ is the molar entropy of the nth lattice. + * \f$ \tilde s_n(T,P) \f$ is the molar entropy of the nth lattice. * * units J/kmol/K */ @@ -196,7 +189,7 @@ public: * \tilde h(T,P) = {\sum_n \theta_n \tilde h_n(T,P) } * \f] * - * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. + * \f$ \tilde h_n(T,P) \f$ is the enthalpy of the nth lattice. * * units J/kmol */ @@ -212,7 +205,7 @@ public: * \tilde c_{p,n}(T,P) = \frac{\sum_n C_n \tilde c_{p,n}(T,P) }{C_T}, * \f] * - * \f$ \tilde c_{p,n}(T,P) \f$ is the heat capacity of the nth lattice. + * \f$ \tilde c_{p,n}(T,P) \f$ is the heat capacity of the nth lattice. * * units J/kmol/K */ @@ -228,7 +221,7 @@ public: * \tilde c_{v,n}(T,P) = \frac{\sum_n C_n \tilde c_{v,n}(T,P) }{C_T}, * \f] * - * \f$ \tilde c_{v,n}(T,P) \f$ is the heat capacity of the nth lattice. + * \f$ \tilde c_{v,n}(T,P) \f$ is the heat capacity of the nth lattice. * * units J/kmol/K */ @@ -396,8 +389,8 @@ public: virtual void getPartialMolarVolumes(doublereal* vbar) const; //! Get the array of standard state chemical potentials at unit activity for - //! the species at their standard states at the current T and - //! P of the solution. + //! the species at their standard states at the current *T* and *P* of the + //! solution. /*! * These are the standard state chemical potentials \f$ \mu^0_k(T,P) \f$. * The values are evaluated at the current temperature and pressure of the diff --git a/include/cantera/thermo/MargulesVPSSTP.h b/include/cantera/thermo/MargulesVPSSTP.h index 18ed00be3..120ce3e26 100644 --- a/include/cantera/thermo/MargulesVPSSTP.h +++ b/include/cantera/thermo/MargulesVPSSTP.h @@ -25,9 +25,7 @@ namespace Cantera * * The independent unknowns are pressure, temperature, and mass fraction. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * All species are defined to have standard states that depend upon both the * temperature and the pressure. The Margules approximation assumes symmetric @@ -36,15 +34,13 @@ namespace Cantera * don't think it prevents, however, some species from being dilute in the * solution. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The molar excess Gibbs free energy is given by the following formula which is - * a sum over interactions i. 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. + * a sum over interactions *i*. 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. * * \f[ * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) @@ -81,47 +77,44 @@ namespace Cantera * where * \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and * \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ and where - * \f$ X_k \f$ is the mole fraction of species k. + * \f$ X_k \f$ is the mole fraction of species *k*. * * This object inherits from the class VPStandardStateTP. Therefore, the * specification and calculation of all standard state and reference state * values are handled at that level. Various functional forms for the standard - * state are permissible. The chemical potential for species k is equal - * to + * state are permissible. The chemical potential for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) * \f] * - * The partial molar entropy for species k is given by + * The partial molar entropy for species *k* is given by * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] * - * The partial molar enthalpy for species k is given by + * The partial molar enthalpy for species *k* is given by * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * - * The partial molar volume for species k is + * The partial molar volume for species *k* is * * \f[ * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} * \f] * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / C^s_k, \f$ where * \f$ C^s_k \f$ is a standard concentration defined below and \f$ a_k \f$ are @@ -134,7 +127,7 @@ namespace Cantera * C^a_k = C^s_k X_k = \frac{P}{R T} X_k * \f] * - * The standard concentration for species k is independent of k and equal to + * The standard concentration for species *k* is independent of *k* and equal to * * \f[ * C^s_k = C^s = \frac{P}{R T} diff --git a/include/cantera/thermo/MetalSHEelectrons.h b/include/cantera/thermo/MetalSHEelectrons.h index 0cc76b6db..a1f00e10e 100644 --- a/include/cantera/thermo/MetalSHEelectrons.h +++ b/include/cantera/thermo/MetalSHEelectrons.h @@ -23,9 +23,9 @@ namespace Cantera //! aqueous electrolyte, that are consistent with the SHE reference electrode. /*! * The class is based on the electron having a chemical potential equal to one- - * half of the entropy of the H2 gas at the system pressure + * half of the entropy of the H2 gas at the system pressure * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * This class inherits from SingleSpeciesTP. It is assumed that the reference * state thermodynamics may be obtained by a pointer to a populated species @@ -73,12 +73,12 @@ namespace Cantera * u^o_k(T,P) = h^o_k(T) - R T * \f] * - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * All solution properties are obtained from the standard state species * functions, since there is only one species in the phase. * - * %Application within Kinetics Managers + * ## %Application within Kinetics Managers * * The standard concentration is equal to 1.0. This means that the kinetics * operator works on an activities basis. Since this is a stoichiometric @@ -90,7 +90,7 @@ namespace Cantera * is equal to 1/2 of the H2 gas chemical potential, and the voltage assigned to * the electron, which is the voltage of the metal. * - * Instantiation of the Class + * ## Instantiation of the Class * * The constructor for this phase is located in the default ThermoFactory for * %Cantera. A new MetalSHEelectrons object may be created by the following code @@ -119,7 +119,7 @@ namespace Cantera * MetalSHEelectrons *eMetal = new MetalSHEelectrons("MetalSHEelectrons_default.xml", ""); * @endcode * - * XML Example + * ## XML Example * * The phase model name for this is called MetalSHEelectrons. It must be * supplied as the model attribute of the thermo XML element entry. Within the @@ -275,8 +275,7 @@ public: virtual doublereal logStandardConc(size_t k=0) const; //! Get the array of chemical potentials at unit activity for the species at - //! their standard states at the current T and P of the - //! solution. + //! their standard states at the current *T* and *P* of the solution. /*! * For a stoichiometric substance, there is no activity term in the chemical * potential expression, and therefore the standard chemical potential and @@ -301,7 +300,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Returns the vector of nondimensional Internal Energies of the standard - //! state species at the current T and P of the solution + //! state species at the current *T* and *P* of the solution /*! * For an incompressible, stoichiometric substance, the molar internal * energy is independent of pressure. Since the thermodynamic properties are diff --git a/include/cantera/thermo/MineralEQ3.h b/include/cantera/thermo/MineralEQ3.h index 8922d786f..de187c4cc 100644 --- a/include/cantera/thermo/MineralEQ3.h +++ b/include/cantera/thermo/MineralEQ3.h @@ -26,7 +26,7 @@ namespace Cantera * This class inherits from SingleSpeciesTP class. EQ's parameterization is * mapped onto the Shomate polynomial class. * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * This class inherits from SingleSpeciesTP. It is assumed that the reference * state thermodynamics may be obtained by a pointer to a populated species @@ -61,12 +61,12 @@ namespace Cantera * standard state Gibbs free energy is obtained from the enthalpy and entropy * functions. * - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * All solution properties are obtained from the standard state species * functions, since there is only one species in the phase. * - * %Application within Kinetics Managers + * ## %Application within Kinetics Managers * * The standard concentration is equal to 1.0. This means that the kinetics * operator works on an (activities basis). Since this is a stoichiometric @@ -187,8 +187,7 @@ public: virtual doublereal logStandardConc(size_t k=0) const; //! Get the array of chemical potentials at unit activity for the species at - //! their standard states at the current T and P of the - //! solution. + //! their standard states at the current *T* and *P* of the solution. /*! * For a stoichiometric substance, there is no activity term in the chemical * potential expression, and therefore the standard chemical potential and @@ -213,7 +212,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Returns the vector of nondimensional Internal Energies of the standard - //! state species at the current T and P of the solution + //! state species at the current *T* and *P* of the solution /*! * For an incompressible, stoichiometric substance, the molar internal * energy is independent of pressure. Since the thermodynamic properties are diff --git a/include/cantera/thermo/MixedSolventElectrolyte.h b/include/cantera/thermo/MixedSolventElectrolyte.h index b0ec6bcc1..f254bb279 100644 --- a/include/cantera/thermo/MixedSolventElectrolyte.h +++ b/include/cantera/thermo/MixedSolventElectrolyte.h @@ -23,9 +23,7 @@ namespace Cantera * * The independent unknowns are pressure, temperature, and mass fraction. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * All species are defined to have standard states that depend upon both the * temperature and the pressure. The Margules approximation assumes symmetric @@ -34,15 +32,13 @@ namespace Cantera * don't think it prevents, however, some species from being dilute in the * solution. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The molar excess Gibbs free energy is given by the following formula which is - * a sum over interactions i. 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. + * a sum over interactions *i*. 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. * * \f[ * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) @@ -78,47 +74,44 @@ namespace Cantera * \f] * where \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and * \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ and where \f$ X_k \f$ is the mole - * fraction of species k. + * fraction of species *k*. * * This object inherits from the class VPStandardStateTP. Therefore, the * specification and calculation of all standard state and reference state * values are handled at that level. Various functional forms for the standard - * state are permissible. The chemical potential for species k is equal - * to + * state are permissible. The chemical potential for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) * \f] * - * The partial molar entropy for species k is given by the following relation, + * The partial molar entropy for species *k* is given by the following relation, * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] * - * The partial molar enthalpy for species k is given by + * The partial molar enthalpy for species *k* is given by * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * - * The partial molar volume for species k is + * The partial molar volume for species *k* is * * \f[ * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} * \f] * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / C^s_k, \f$ where * \f$ C^s_k \f$ is a standard concentration defined below and \f$ a_k \f$ are @@ -131,8 +124,7 @@ namespace Cantera * C^a_k = C^s_k X_k = \frac{P}{R T} X_k * \f] * - * The standard concentration for species k is independent of k - * and equal to + * The standard concentration for species *k* is independent of *k* and equal to * * \f[ * C^s_k = C^s = \frac{P}{R T} diff --git a/include/cantera/thermo/MixtureFugacityTP.h b/include/cantera/thermo/MixtureFugacityTP.h index bdea15983..1572bed81 100644 --- a/include/cantera/thermo/MixtureFugacityTP.h +++ b/include/cantera/thermo/MixtureFugacityTP.h @@ -157,7 +157,7 @@ public: virtual void getStandardChemPotentials(doublereal* mu) const; //! Get the nondimensional Enthalpy functions for the species at their - //! standard states at the current T and P of the solution. + //! standard states at the current *T* and *P* of the solution. /*! * For all objects with the Mixture Fugacity approximation, we define the * standard state as an ideal gas at the current temperature and pressure @@ -169,7 +169,7 @@ public: virtual void getEnthalpy_RT(doublereal* hrt) const; //! Get the array of nondimensional Enthalpy functions for the standard - //! state species at the current T and P of the solution. + //! state species at the current *T* and *P* of the solution. /*! * For all objects with the Mixture Fugacity approximation, we define the * standard state as an ideal gas at the current temperature and pressure of @@ -233,7 +233,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Get the molar volumes of each species in their standard states at the - //! current T and P of the solution. + //! current *T* and *P* of the solution. /*! * For all objects with the Mixture Fugacity approximation, we define the * standard state as an ideal gas at the current temperature and pressure of diff --git a/include/cantera/thermo/MolalityVPSSTP.h b/include/cantera/thermo/MolalityVPSSTP.h index 6ad2d99c0..bb290d09e 100644 --- a/include/cantera/thermo/MolalityVPSSTP.h +++ b/include/cantera/thermo/MolalityVPSSTP.h @@ -36,7 +36,7 @@ namespace Cantera * member function, ThermoPhase::activityConvention() that indicates which * convention the activities are based on. The default is to assume activities * are based on the molar convention. However, classes which derive from the - * MolalityVPSSTP class return cAC_CONVENTION_MOLALITY from this member + * MolalityVPSSTP class return `cAC_CONVENTION_MOLALITY` from this member * function. * * The molality of a solute, \f$ m_i \f$, is defined as @@ -50,7 +50,7 @@ namespace Cantera * \f] * * where \f$ M_o \f$ is the molecular weight of the solvent. The molality has - * units of gmol kg-1. For the solute, the molality may be considered + * units of gmol/kg. For the solute, the molality may be considered * as the amount of gmol's of solute per kg of solvent, a natural experimental * quantity. * @@ -69,9 +69,9 @@ namespace Cantera * X_i = \frac{m_i}{L^{sum}} * \f] * where \f$ X_o \f$ is the mole fraction of solvent, and \f$ X_o \f$ is the - * mole fraction of solute i. Thus, the molality scale and the mole - * fraction scale offer a one-to-one mapping between each other, except in the - * limit of a zero solvent mole fraction. + * mole fraction of solute *i*. Thus, the molality scale and the mole fraction + * scale offer a one-to-one mapping between each other, except in the limit of a + * zero solvent mole fraction. * * The standard states for thermodynamic objects that derive from MolalityVPSSTP * are on the unit molality basis. Chemical potentials of the solutes, \f$ \mu_k @@ -128,7 +128,7 @@ namespace Cantera * functions which return activities return the molality-based activities. The * reason for this convention has been discussed in supporting memos. However, * it's important because the term in the equation above is non-trivial. For - * example it's equal to 2.38 kcal gmol-1 for water at 298 K. + * example it's equal to 2.38 kcal/gmol for water at 298 K. * * In order to prevent a singularity, this class includes the concept of a * minimum value for the solvent mole fraction. All calculations involving the @@ -166,7 +166,7 @@ namespace Cantera * defined as the raw unscaled activity coefficients produced by the underlying * objects. * - *

SetState Strategy

+ * ### SetState Strategy * * The MolalityVPSSTP object does not have a setState strategy concerning the * molalities. It does not keep track of whether the molalities have changed. diff --git a/include/cantera/thermo/PDSS.h b/include/cantera/thermo/PDSS.h index d779c9f4d..c23ba981a 100644 --- a/include/cantera/thermo/PDSS.h +++ b/include/cantera/thermo/PDSS.h @@ -160,7 +160,7 @@ class VPSSMgr; * recalculates the standard state when the setState functions for temperature * and pressure are called. * - *

Thread Safety

+ * ### Thread Safety * * These classes are designed such that they are not thread safe when called by * themselves. The reason for this is that they sometimes use shared diff --git a/include/cantera/thermo/PDSS_IonsFromNeutral.h b/include/cantera/thermo/PDSS_IonsFromNeutral.h index cf8fcd461..8b2af0f66 100644 --- a/include/cantera/thermo/PDSS_IonsFromNeutral.h +++ b/include/cantera/thermo/PDSS_IonsFromNeutral.h @@ -92,12 +92,11 @@ public: * \frac{\mu^o_k}{RT} = \sum_{m}{ \alpha_{m , k} \frac{\mu^o_{m}}{RT}} + ( 1 - \delta_{k,sp}) 2.0 \ln{2.0} * \f] * - * m is the neutral molecule species index. \f$ \alpha_{m , k} \f$ is - * the stoiciometric coefficient for the neutral molecule, m, that - * creates the thermodynamics for the ionic species k. A factor \f$ - * 2.0 \ln{2.0} \f$ is added to all ions except for the species ionic - * species, which in this case is the single anion species, with species - * index sp. + * *m* is the neutral molecule species index. \f$ \alpha_{m , k} \f$ is the + * stoiciometric coefficient for the neutral molecule, *m*, that creates the + * thermodynamics for the ionic species *k*. A factor \f$ 2.0 \ln{2.0} \f$ + * is added to all ions except for the species ionic species, which in this + * case is the single anion species, with species index *sp*. */ virtual doublereal gibbs_RT() const; virtual doublereal cp_R() const; diff --git a/include/cantera/thermo/PDSS_SSVol.h b/include/cantera/thermo/PDSS_SSVol.h index 742bad270..23165dd52 100644 --- a/include/cantera/thermo/PDSS_SSVol.h +++ b/include/cantera/thermo/PDSS_SSVol.h @@ -57,9 +57,9 @@ namespace Cantera * {\rho}^o_k(T,P) = \frac{M_k}{V^o_k(T,P)} = a_0 + a_1 T + a_2 T^2 + a_3 T^3 + a_4 T^4 * \f] * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * - * The standard molar Gibbs free energy for species k is determined from + * The standard molar Gibbs free energy for species *k* is determined from * the enthalpy and entropy expressions * * \f[ @@ -94,14 +94,14 @@ namespace Cantera * {\left(\frac{d{C}^o_{p,k}}{dP}\right)}_T = - T {\left(\frac{{d}^2{V}^o_k}{{dT}^2}\right)}_T * \f] * - * The standard molar Internal Energy for species k is determined from the following - * relation. + * The standard molar Internal Energy for species *k* is determined from the + * following relation. * * \f[ * U^o_k(T,P) = H^o_k(T,P) - p V^o_k * \f] * - * XML Example + * ## XML Example * * An example of the specification of a standard state for the LiCl molten salt * which employs a constant molar volume expression. diff --git a/include/cantera/thermo/PhaseCombo_Interaction.h b/include/cantera/thermo/PhaseCombo_Interaction.h index bf593f426..df2fd3f8d 100644 --- a/include/cantera/thermo/PhaseCombo_Interaction.h +++ b/include/cantera/thermo/PhaseCombo_Interaction.h @@ -45,9 +45,7 @@ namespace Cantera * phase behaves more like a series of phases. That's why we named it * PhaseCombo. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * All species are defined to have standard states that depend upon both the * temperature and the pressure. The Margules approximation assumes symmetric @@ -56,16 +54,14 @@ namespace Cantera * don't think it prevents, however, some species from being dilute in the * solution. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The molar excess Gibbs free energy is given by the following formula which is - * a sum over interactions i. 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 ideal solution's mixing term. + * a sum over interactions *i*. 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 ideal solution's mixing term. * * \f[ * G^E = \sum_i \left( H_{Ei} - T S_{Ei} \right) - \sum_i \left( n_i R T \ln{X_i} \right) @@ -100,48 +96,44 @@ namespace Cantera * * where \f$ g^E_{o,i} = h_{o,i} - T s_{o,i} \f$ and * \f$ g^E_{1,i} = h_{1,i} - T s_{1,i} \f$ and where \f$ X_k \f$ is the mole - * fraction of species k. + * fraction of species *k*. * * This object inherits from the class VPStandardStateTP. Therefore, the * specification and calculation of all standard state and reference state * values are handled at that level. Various functional forms for the standard - * state are permissible. The chemical potential for species k is equal - * to + * state are permissible. The chemical potential for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) * \f] * - * The partial molar entropy for species k is given by the following - * relation, + * The partial molar entropy for species *k* is given by the following relation, * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] * - * The partial molar enthalpy for species k is given by + * The partial molar enthalpy for species *k* is given by * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * - * The partial molar volume for species k is + * The partial molar volume for species *k* is * * \f[ * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} * \f] * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / C^s_k, \f$ where * \f$ C^s_k \f$ is a standard concentration defined below and \f$ a_k \f$ are @@ -154,8 +146,7 @@ namespace Cantera * C^a_k = C^s_k X_k = \frac{P}{R T} X_k * \f] * - * The standard concentration for species k is independent of k - * and equal to + * The standard concentration for species *k* is independent of *k* and equal to * * \f[ * C^s_k = C^s = \frac{P}{R T} @@ -240,9 +231,7 @@ namespace Cantera * * \f$k^{-1} \f$ has units of s-1. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is located in the default ThermoFactory for * %Cantera. A new PhaseCombo_Interaction object may be created by the following @@ -271,9 +260,8 @@ namespace Cantera * PhaseCombo_Interaction *LiFeS_X_solid = new PhaseCombo_Interaction(*xs); * @endcode * - *
- *

XML Example

- *
+ * ## XML Example + * * An example of an XML Element named phase setting up a PhaseCombo_Interaction * object named LiFeS_X is given below. * diff --git a/include/cantera/thermo/RedlichKisterVPSSTP.h b/include/cantera/thermo/RedlichKisterVPSSTP.h index 4cf8f3b3b..b2e149a33 100644 --- a/include/cantera/thermo/RedlichKisterVPSSTP.h +++ b/include/cantera/thermo/RedlichKisterVPSSTP.h @@ -26,9 +26,7 @@ namespace Cantera * * The independent unknowns are pressure, temperature, and mass fraction. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * All species are defined to have standard states that depend upon both the * temperature and the pressure. The Redlich-Kister approximation assumes @@ -37,15 +35,13 @@ namespace Cantera * solution. I don't think it prevents, however, some species from being dilute * in the solution. * - *
- *

Specification of Solution Thermodynamic Properties

- *
+ * ## Specification of Solution Thermodynamic Properties * * The molar excess Gibbs free energy is given by the following formula which is - * a sum over interactions i. 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 Redlich-Kister formulation - * for a phase that has more than 2 species. + * a sum over interactions *i*. 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 Redlich-Kister formulation for a phase that has + * more than 2 species. * * \f[ * G^E = \sum_{i} G^E_{i} @@ -89,43 +85,39 @@ namespace Cantera * This object inherits from the class VPStandardStateTP. Therefore, the * specification and calculation of all standard state and reference state * values are handled at that level. Various functional forms for the standard - * state are permissible. The chemical potential for species k is equal - * to + * state are permissible. The chemical potential for species *k* is equal to * * \f[ * \mu_k(T,P) = \mu^o_k(T, P) + R T \ln(\gamma_k X_k) * \f] * - * The partial molar entropy for species k is given by the following - * relation, + * The partial molar entropy for species *k* is given by the following relation, * * \f[ * \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln( \gamma_k X_k ) * - R T \frac{d \ln(\gamma_k) }{dT} * \f] * - * The partial molar enthalpy for species k is given by + * The partial molar enthalpy for species *k* is given by * * \f[ * \tilde{h}_k(T,P) = h^o_k(T,P) - R T^2 \frac{d \ln(\gamma_k)}{dT} * \f] * - * The partial molar volume for species k is + * The partial molar volume for species *k* is * * \f[ * \tilde V_k(T,P) = V^o_k(T,P) + R T \frac{d \ln(\gamma_k) }{dP} * \f] * - * The partial molar Heat Capacity for species k is + * The partial molar Heat Capacity for species *k* is * * \f[ * \tilde{C}_{p,k}(T,P) = C^o_{p,k}(T,P) - 2 R T \frac{d \ln( \gamma_k )}{dT} * - R T^2 \frac{d^2 \ln(\gamma_k) }{{dT}^2} * \f] * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * \f$ C^a_k\f$ are defined such that \f$ a_k = C^a_k / C^s_k, \f$ where * \f$ C^s_k \f$ is a standard concentration defined below and \f$ a_k \f$ are @@ -138,8 +130,7 @@ namespace Cantera * C^a_k = C^s_k X_k = \frac{P}{R T} X_k * \f] * - * The standard concentration for species k is independent of k - * and equal to + * The standard concentration for species *k* is independent of *k* and equal to * * \f[ * C^s_k = C^s = \frac{P}{R T} diff --git a/include/cantera/thermo/SingleSpeciesTP.h b/include/cantera/thermo/SingleSpeciesTP.h index c5519461e..758393044 100644 --- a/include/cantera/thermo/SingleSpeciesTP.h +++ b/include/cantera/thermo/SingleSpeciesTP.h @@ -203,7 +203,7 @@ public: virtual void getPureGibbs(doublereal* gpure) const; //! Get the molar volumes of each species in their standard states at the - //! current T and P of the solution. + //! current *T* and *P* of the solution. /*! * units = m^3 / kmol * diff --git a/include/cantera/thermo/StoichSubstance.h b/include/cantera/thermo/StoichSubstance.h index 4a0907a24..8fb4973b1 100644 --- a/include/cantera/thermo/StoichSubstance.h +++ b/include/cantera/thermo/StoichSubstance.h @@ -25,7 +25,7 @@ namespace Cantera * to pressure. This is necessary because the phase is incompressible. It uses a * constant volume approximation. * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * This class inherits from SingleSpeciesTP. It is assumed that the reference * state thermodynamics may be obtained by a pointer to a populated species @@ -60,12 +60,12 @@ namespace Cantera * standard state Gibbs free energy is obtained from the enthalpy and entropy * functions. * - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * All solution properties are obtained from the standard state species * functions, since there is only one species in the phase. * - * Application within Kinetics Managers + * ## Application within Kinetics Managers * * The standard concentration is equal to 1.0. This means that the kinetics * operator works on an (activities basis). Since this is a stoichiometric @@ -85,7 +85,7 @@ namespace Cantera * constant expression, since it's a stoichiometric phase and the activity is * always equal to 1.0. * - * Instantiation of the Class + * ## Instantiation of the Class * * The constructor for this phase is NOT located in the default ThermoFactory * for %Cantera. However, a new StoichSubstance may be created by @@ -104,7 +104,7 @@ namespace Cantera * importPhase(*xm, &solid); * @endcode * - * XML Example + * ## XML Example * * The phase model name for this is called StoichSubstance. It must be supplied * as the model attribute of the thermo XML element entry. Within the phase XML @@ -246,9 +246,8 @@ public: virtual doublereal standardConcentration(size_t k=0) const; virtual doublereal logStandardConc(size_t k=0) const; - //! Get the array of chemical potentials at unit activity for the species - //! at their standard states at the current T and P of the - //! solution. + //! Get the array of chemical potentials at unit activity for the species at + //! their standard states at the current *T* and *P* of the solution. /*! * For a stoichiometric substance, there is no activity term in the chemical * potential expression, and therefore the standard chemical potential and @@ -273,7 +272,7 @@ public: virtual void getCp_R(doublereal* cpr) const; //! Returns the vector of nondimensional Internal Energies of the standard - //! state species at the current T and P of the solution + //! state species at the current *T* and *P* of the solution /*! * For an incompressible, stoichiometric substance, the molar internal * energy is independent of pressure. Since the thermodynamic properties diff --git a/include/cantera/thermo/SurfPhase.h b/include/cantera/thermo/SurfPhase.h index 8c1c14ba0..249afd574 100644 --- a/include/cantera/thermo/SurfPhase.h +++ b/include/cantera/thermo/SurfPhase.h @@ -27,7 +27,7 @@ namespace Cantera * The density of surface sites is given by the variable \f$ n_0 \f$, * which has SI units of kmol m-2. * - * Specification of Species Standard State Properties + * ## Specification of Species Standard State Properties * * It is assumed that the reference state thermodynamics may be obtained by a * pointer to a populated species thermodynamic property manager class (see @@ -37,8 +37,8 @@ namespace Cantera * Pressure is defined as an independent variable in this phase. However, it has * no effect on any quantities, as the molar concentration is a constant. * - * Therefore, The standard state internal energy for species k is - * equal to the enthalpy for species k. + * Therefore, The standard state internal energy for species *k* is equal to the + * enthalpy for species *k*. * * \f[ * u^o_k = h^o_k @@ -48,14 +48,14 @@ namespace Cantera * are independent of pressure. The standard state Gibbs free energy is obtained * from the enthalpy and entropy functions. * - * Specification of Solution Thermodynamic Properties + * ## Specification of Solution Thermodynamic Properties * * The activity of species defined in the phase is given by * \f[ * a_k = \theta_k * \f] * - * The chemical potential for species k is equal to + * The chemical potential for species *k* is equal to * \f[ * \mu_k(T,P) = \mu^o_k(T) + R T \log(\theta_k) * \f] @@ -63,7 +63,7 @@ namespace Cantera * Pressure is defined as an independent variable in this phase. However, it has * no effect on any quantities, as the molar concentration is a constant. * - * The internal energy for species k is equal to the enthalpy for species k + * The internal energy for species k is equal to the enthalpy for species *k* * \f[ * u_k = h_k * \f] @@ -75,7 +75,7 @@ namespace Cantera * s_k(T,P) = s^o_k(T) - R \log(\theta_k) * \f] * - * %Application within Kinetics Managers + * ## %Application within Kinetics Managers * * The activity concentration,\f$ C^a_k \f$, used by the kinetics manager, is equal to * the actual concentration, \f$ C^s_k \f$, and is given by the following @@ -84,12 +84,12 @@ namespace Cantera * C^a_k = C^s_k = \frac{\theta_k n_0}{s_k} * \f] * - * The standard concentration for species k is: + * The standard concentration for species *k* is: * \f[ * C^0_k = \frac{n_0}{s_k} * \f] * - * Instantiation of the Class + * ## Instantiation of the Class * * The constructor for this phase is located in the default ThermoFactory * for %Cantera. A new SurfPhase may be created by the following code snippet: @@ -109,7 +109,7 @@ namespace Cantera * SurfPhase *diamond100TP = new SurfPhase(*xs); * @endcode * - * XML Example + * ## XML Example * * An example of an XML Element named phase setting up a SurfPhase object named * diamond_100 is given below. diff --git a/include/cantera/thermo/ThermoPhase.h b/include/cantera/thermo/ThermoPhase.h index e3f4eec9c..fdfffbd7c 100644 --- a/include/cantera/thermo/ThermoPhase.h +++ b/include/cantera/thermo/ThermoPhase.h @@ -542,8 +542,7 @@ public: //@{ //! Get the array of chemical potentials at unit activity for the species at - //! their standard states at the current T and P of the - //! solution. + //! their standard states at the current *T* and *P* of the solution. /*! * These are the standard state chemical potentials \f$ \mu^0_k(T,P) * \f$. The values are evaluated at the current temperature and pressure of @@ -557,7 +556,7 @@ public: } //! Get the nondimensional Enthalpy functions for the species at their - //! standard states at the current T and P of the solution. + //! standard states at the current *T* and *P* of the solution. /*! * @param hrt Output vector of nondimensional standard state enthalpies. * Length: m_kk. @@ -567,7 +566,7 @@ public: } //! Get the array of nondimensional Entropy functions for the standard state - //! species at the current T and P of the solution. + //! species at the current *T* and *P* of the solution. /*! * @param sr Output vector of nondimensional standard state entropies. * Length: m_kk. @@ -577,7 +576,7 @@ public: } //! Get the nondimensional Gibbs functions for the species in their standard - //! states at the current T and P of the solution. + //! states at the current *T* and *P* of the solution. /*! * @param grt Output vector of nondimensional standard state Gibbs free * energies. Length: m_kk. @@ -587,7 +586,7 @@ public: } //! Get the Gibbs functions for the standard state of the species at the - //! current T and P of the solution + //! current *T* and *P* of the solution /*! * Units are Joules/kmol * @param gpure Output vector of standard state Gibbs free energies. @@ -598,7 +597,7 @@ public: } //! Returns the vector of nondimensional Internal Energies of the standard - //! state species at the current T and P of the solution + //! state species at the current *T* and *P* of the solution /*! * @param urt output vector of nondimensional standard state internal energies * of the species. Length: m_kk. @@ -608,7 +607,7 @@ public: } //! Get the nondimensional Heat Capacities at constant pressure for the - //! species standard states at the current T and P of the + //! species standard states at the current *T* and *P* of the //! solution /*! * @param cpr Output vector of nondimensional standard state heat @@ -619,7 +618,7 @@ public: } //! Get the molar volumes of the species standard states at the current - //! T and P of the solution. + //! *T* and *P* of the solution. /*! * units = m^3 / kmol * @@ -702,7 +701,7 @@ public: } //! Get the molar volumes of the species reference states at the current - //! T and P_ref of the solution. + //! *T* and *P_ref* of the solution. /*! * units = m^3 / kmol * @@ -1612,8 +1611,8 @@ public: * units = 1 / kmol * * dlnActCoeffdlnN[ ld * k + m] will contain the derivative of log - * act_coeff for the mth species with respect to the - * number of moles of the kth species. + * act_coeff for the *m*-th species with respect to the number of moles of + * the *k*-th species. * * \f[ * \frac{d \ln(\gamma_m) }{d \ln( n_k ) }\Bigg|_{n_i} diff --git a/include/cantera/thermo/WaterProps.h b/include/cantera/thermo/WaterProps.h index 0b9dd1013..4cb1a340c 100644 --- a/include/cantera/thermo/WaterProps.h +++ b/include/cantera/thermo/WaterProps.h @@ -23,8 +23,8 @@ class PDSS_Water; /** * @defgroup relatedProps Electric Properties of Phases * - *

Treatment of the %Phase Potential and the electrochemical potential of - * a species

+ * ### Treatment of the %Phase Potential and the electrochemical potential of + * a species * * The electrochemical potential of species *k* in a phase *p*, \f$ \zeta_k \f$, * is related to the chemical potential via the following equation, @@ -65,7 +65,7 @@ class PDSS_Water; * drop between phases. This effect is used within the InterfaceKinetics and * EdgeKinetics kinetics objects classes. * - *

Electrothermochemical Properties of Phases of Matter.

+ * ### Electrothermochemical Properties of Phases of Matter * * The following classes are used to compute the electrical and * electrothermochemical properties of phases of matter. The main property diff --git a/include/cantera/thermo/WaterSSTP.h b/include/cantera/thermo/WaterSSTP.h index ba350827f..46e6a32ff 100644 --- a/include/cantera/thermo/WaterSSTP.h +++ b/include/cantera/thermo/WaterSSTP.h @@ -27,9 +27,7 @@ class WaterProps; * Thermodynamic Properties of Ordinary Water Substance for General and * Scientific Use," J. Phys. Chem. Ref. Dat, 31, 387, 2002. * - *
- *

Specification of Species Standard State Properties

- *
+ * ## Specification of Species Standard State Properties * * The offsets used in the steam tables are different than NIST's. They assume * u_liq(TP) = 0.0, s_liq(TP) = 0.0, where TP is the triple point conditions: @@ -62,15 +60,11 @@ class WaterProps; * * So(1bar) = S(P0) + RT ln(1bar/P0) * - *
- *

%Application within Kinetics Managers

- *
+ * ## %Application within Kinetics Managers * * This is unimplemented. * - *
- *

Instantiation of the Class

- *
+ * ## Instantiation of the Class * * The constructor for this phase is NOT located in the default ThermoFactory * for %Cantera. However, a new WaterSSTP object may be created by the following @@ -95,9 +89,7 @@ class WaterProps; * importPhase(*xm, &water); * @endcode * - *
- *

XML Example

- *
+ * ## XML Example * * An example of an XML Element named phase setting up a WaterSSTP object with * id "water" is given below. diff --git a/include/cantera/transport/SimpleTransport.h b/include/cantera/transport/SimpleTransport.h index 2dac430be..1bc1b4cba 100644 --- a/include/cantera/transport/SimpleTransport.h +++ b/include/cantera/transport/SimpleTransport.h @@ -85,7 +85,7 @@ namespace Cantera * With this formulation we may solve for the diffusion velocities, without * having to worry about what the mass averaged velocity is. * - *

Viscosity Calculation

+ * ## Viscosity Calculation * * The viscosity calculation may be broken down into two parts. In the first * part, the viscosity of the pure species are calculated In the second part, a @@ -106,7 +106,7 @@ namespace Cantera * \mu = \sum_k {\mu_k X_k} * \f] * - *

Calculate of the Binary Diffusion Coefficients

+ * ## Calculate of the Binary Diffusion Coefficients * * The binary diffusion coefficients are obtained from the pure species * diffusion coefficients using an additive process @@ -115,7 +115,7 @@ namespace Cantera * D_{i,j} = \frac{1}{2} \left( D^0_i(T) + D^0_j(T) \right) * \f] * - *

Electrical Mobilities

+ * ## Electrical Mobilities * * The mobility \f$ \mu^e_k \f$ is calculated from the diffusion coefficient * using the Einstein relation. @@ -127,7 +127,7 @@ namespace Cantera * The diffusion coefficients, \f$ D_k \f$ , is calculated from a call to the * mixture diffusion coefficient routine. * - *

Species Diffusive Fluxes

+ * ## Species Diffusive Fluxes * * The diffusive mass flux of species \e k is computed from the following * formula @@ -161,7 +161,7 @@ namespace Cantera * \rho V_c = - \sum_j {c^T M_j D_j \nabla X_j} + \sum_j F C^T M_j \frac{D_j}{ R T } X_j z_j \nabla V * \f] * - *

Species Diffusional Velocities

+ * ## Species Diffusional Velocities * * Species diffusional velocities are calculated from the species diffusional * fluxes, within this object, using the following formula for the diffusional diff --git a/include/cantera/transport/TransportBase.h b/include/cantera/transport/TransportBase.h index aaf704ff8..d3aa74abc 100644 --- a/include/cantera/transport/TransportBase.h +++ b/include/cantera/transport/TransportBase.h @@ -96,9 +96,7 @@ const VelocityBasis VB_SPECIES_3 = 3; * this class. Class Transport is meant to be used as a base class only. It is * possible to instantiate it, but its methods throw exceptions if called. * - *
- *

Relationship of the Transport class to the ThermoPhase Class

- *
+ * ## Relationship of the Transport class to the ThermoPhase Class * * This section describes how calculations are carried out within the Transport * class. The Transport class and derived classes of the the Transport class @@ -119,9 +117,7 @@ const VelocityBasis VB_SPECIES_3 = 3; * implicitly assumed that the underlying state within the ThermoPhase object * has not changed its values. * - *
- *

Diffusion Fluxes and their Relationship to Reference Velocities

- *
+ * ## Diffusion Fluxes and their Relationship to Reference Velocities * * The diffusion fluxes must be referenced to a particular reference fluid * velocity. Most typical is to reference the diffusion fluxes to the mass @@ -588,7 +584,7 @@ public: //! Return a vector of Thermal diffusion coefficients [kg/m/sec]. /*! * The thermal diffusion coefficient \f$ D^T_k \f$ is defined so that the - * diffusive mass flux of species k induced by the local temperature + * diffusive mass flux of species *k* induced by the local temperature * gradient is given by the following formula: * * \f[