Documentation updates

doc/sphinx/yaml/reactions.rst

@@ -26,6 +26,7 @@ The fields common to all ``reaction`` entries are:
     - :ref:`chemically-activated <sec-yaml-chemically-activated>`
     - :ref:`pressure-dependent-Arrhenius <sec-yaml-pressure-dependent-Arrhenius>`
     - :ref:`Chebyshev <sec-yaml-Chebyshev>`
+    - :ref:`two-temperature-plasma <sec-yaml-two-temperature-plasma>`
     - :ref:`Blowers-Masel <sec-yaml-Blowers-Masel>`
     - :ref:`surface-Blowers-Masel <sec-yaml-surface-Blowers-Masel>`
 
@@ -286,6 +287,26 @@ Example::
     type: Blowers-Masel
     rate-constant: {A: 3.87e+04 cm^2/mol/s, b: 2.7, Ea0: 6260.0 cal/mol, w: 1e9 cal/mol}
 
+.. _sec-yaml-two-temperature-plasma:
+
+``two-temperature-plasma``
+--------------------------
+
+A reaction involving an electron as one of the reactants, where the electron temperature
+may differ from the gas temperature as `described here <https://cantera.org/science/reactions.html#two-temperature-plasma-reactions>`__.
+
+Includes the fields of an :ref:`sec-yaml-elementary` reaction, except that the
+``rate-constant`` field is a mapping with the fields:
+
+``A``
+    The pre-exponential factor
+``b``
+    The temperature exponent, which is applied to the electron temperature
+``Ea_T``
+    The activation energy term :math:`E_{a,g}` that is related to the gas temperature
+``Ea_Te``
+    The activation energy term :math:`E_{a,e}` that is related to the electron
+    temperature
 
 .. _sec-yaml-interface-reaction:
 
@@ -312,7 +333,7 @@ Includes the fields of an :ref:`sec-yaml-elementary` reaction plus:
 
 ``coverage-dependencies``
     A mapping of species names to coverage dependence parameters, where these
-    parameters are contained in a mapping with the fields:
+    parameters are contained in either a mapping with the fields:
 
     ``a``
         Coefficient for exponential dependence on the coverage
@@ -324,17 +345,24 @@ Includes the fields of an :ref:`sec-yaml-elementary` reaction plus:
         Activation energy dependence on coverage, which uses the same sign convention
         as the leading-order activation energy term
 
+    or a list containing the three elements above, in the given order.
+
     Note that parameters ``a``, ``m`` and ``E`` correspond to parameters
     :math:`\eta_{ki}`, :math:`\mu_{ki}` and :math:`\epsilon_{ki}` in Eq 11.113 of
     [Kee, R. J., Coltrin, M. E., & Glarborg, P.(2003). Chemically reacting flow:
     theory and practice. John Wiley & Sons], respectively.
 
-Example::
+Examples::
 
-    equation: 2 H(s) => H2 + 2 Pt(s)
-    rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea: 67400 J/mol}
-    coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}
+    - equation: 2 H(s) => H2 + 2 Pt(s)
+      rate-constant: {A: 3.7e21 cm^2/mol/s, b: 0, Ea: 67400 J/mol}
+      coverage-dependencies: {H(s): {a: 0, m: 0, E: -6000 J/mol}}
 
+    - equation: CH4 + PT(S) + O(S) => CH3(S) + OH(S)
+      rate-constant: {A: 5.0e+18, b: 0.7, Ea: 4.2e+04}
+      coverage-dependencies:
+        O(S): [0, 0, 8000]
+        PT(S): [0, -1.0, 0]
 
 .. _sec-yaml-electrochemical-reaction:
 

interfaces/cython/cantera/examples/transport/dusty_gas.py

@@ -6,7 +6,7 @@
 create a transport manager that implements the Dusty Gas model and use it to
 compute the multicomponent diffusion coefficients and thermal conductivity.
 
-Requires:  cantera >= 2.5.0
+Requires:  cantera >= 2.6.0
 """
 
 import cantera as ct

interfaces/cython/cantera/reaction.pyx

@@ -131,8 +131,9 @@ cdef class ArrheniusRateBase(ReactionRate):
     def _cinit(self, input_data, **kwargs):
         """
         Helper function called by __cinit__. The method is used as a uniform interface
-        for object construction. A separate method is necessary as Cython does not
-        support overloading of special methods such as __cinit__.
+        for object construction. A separate method is necessary as default argument
+        values to __cinit__ defined in derived classes are not available in the base
+        class's __cinit__ (which gets called first).
         """
         if self._reaction_rate_type is None:
             raise TypeError(
@@ -286,12 +287,11 @@ cdef class TwoTempPlasmaRate(ArrheniusRateBase):
         k_f = A T_e^b \exp(-\tfrac{E_{a,g}}{RT}) \exp(\tfrac{E_{a,e}(T_e - T)}{R T T_e})
 
     where :math:`A` is the
-    `pre_exponential_factor <ArrheniusTypeRate.pre_exponential_factor>`,
-    :math:`b` is the `temperature_exponent <ArrheniusTypeRate.temperature_exponent>`,
+    `pre_exponential_factor <ArrheniusRateBase.pre_exponential_factor>`,
+    :math:`b` is the `temperature_exponent <ArrheniusRateBase.temperature_exponent>`,
     :math:`E_{a,g}` (``Ea_gas``) is the
-    `activation_energy <ArrheniusTypeRate.activation_energy>`, and
-    :math:`E_{a,e}` (``Ea_electron``) is the
-    `activation_electron_energy <ArrheniusTypeRate.activation_electron_energy>`.
+    `activation_energy <ArrheniusRateBase.activation_energy>`, and
+    :math:`E_{a,e}` (``Ea_electron``) is the `activation_electron_energy`.
     """
     _reaction_rate_type = "two-temperature-plasma"
 

samples/cxx/jacobian/derivative_speed.cpp

@@ -1,7 +1,11 @@
 /*!
  * @file derivative_speed.cpp
  *
- * Benchmark tests for derivative evaluations
+ * Benchmark derivative evaluations
+ *
+ * Calculate derivatives of reaction rates of progress and species production and
+ * destruction rates with respect to temperature, pressure, molar concentration,
+ * and mole fractions. Time evaluation for different chemical mechanisms.
  */
 
 // This file is part of Cantera. See License.txt in the top-level directory or