diff --git a/doc/doxygen/Doxyfile b/doc/doxygen/Doxyfile index dc8647d52..66b52325b 100644 --- a/doc/doxygen/Doxyfile +++ b/doc/doxygen/Doxyfile @@ -36,12 +36,6 @@ PROJECT_NAME = Cantera PROJECT_NUMBER = 2.4.0b1 -# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) -# base path where the generated documentation will be put. -# If a relative path is entered, it will be relative to the location -# where doxygen was started. If left blank the current directory will be used. - - # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. # If a relative path is entered, it will be relative to the location @@ -640,8 +634,7 @@ EXCLUDE_SYMBOLS = std::* EXAMPLE_PATH = samples \ data/inputs \ - doc/doxygen \ - doc/sphinx/cxx-guide + doc/doxygen # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp diff --git a/interfaces/cython/cantera/ck2cti.py b/interfaces/cython/cantera/ck2cti.py index 122f7528b..98cf448b8 100644 --- a/interfaces/cython/cantera/ck2cti.py +++ b/interfaces/cython/cantera/ck2cti.py @@ -822,7 +822,7 @@ class Sri(object): """ A kinetic model of a phenomenological rate coefficient k(T, P) using the "SRI" formulation of the blending function :math:`F` using either 3 or - 5 parameters. See :ref:`sec-sri-falloff`. + 5 parameters. See https://cantera.org/science/reactions.html#sec-sri-falloff. The attributes are: diff --git a/interfaces/cython/cantera/ctml_writer.py b/interfaces/cython/cantera/ctml_writer.py index 26068e22e..d30953b96 100644 --- a/interfaces/cython/cantera/ctml_writer.py +++ b/interfaces/cython/cantera/ctml_writer.py @@ -536,21 +536,22 @@ class species(object): convenient. Required parameter. :param atoms: The atomic composition, specified by a string containing - space-delimited : pairs. The number of atoms may be + space-delimited ``:`` pairs. The number of atoms may be either an integer or a floating-point number. :param note: A user-defined comment. Not evaluated by Cantera itself. :param thermo: The parameterization to use to compute the reference-state thermodynamic properties. This must be one of the entry types - described in :ref:`sec-thermo-models`. To specify multiple - parameterizations, each for a different temperature range, + described in https://cantera.org/science/science-species.html#sec-thermo-models. + To specify multiple parameterizations, each for a different temperature range, group them in parentheses. :param transport: An entry specifying parameters to compute this species' contribution to the transport properties. This must be one of the - entry types described in :ref:`sec-species-transport-models`, and - must be consistent with the transport model of the phase into which + entry types described in + https://cantera.org/science/science-species.html#species-transport-coefficients, + and must be consistent with the transport model of the phase into which the species is imported. To specify parameters for multiple transport models, group the entries in parentheses. :param size: @@ -1146,9 +1147,10 @@ class reaction(object): stoichiometric coefficients. Given as a string of key:value pairs, e.g. ``"CH4:0.25 O2:1.5"``. :param options: Processing options, as described in - :ref:`sec-reaction-options`. May be one or more (as a list) of the - following: 'skip', 'duplicate', 'negative_A', 'negative_orders', - 'nonreactant_orders'. + https://cantera.org/tutorials/cti/reactions.html#options. + May be one or more (as a list) of the + following: ``'skip'``, ``'duplicate'``, ``'negative_A'``,`` 'negative_orders'``, + ``'nonreactant_orders'``. """ self._id = id self._e = equation @@ -1372,7 +1374,7 @@ class three_body_reaction(reaction): four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: Processing options, as described in - :ref:`sec-reaction-options`. + https://cantera.org/tutorials/cti/reactions.html#options. """ reaction.__init__(self, equation, kf, id, '', options) self._type = 'threeBody' @@ -1462,7 +1464,8 @@ class falloff_reaction(pdep_reaction): four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: - Processing options, as described in :ref:`sec-reaction-options`. + Processing options, as described in + https://cantera.org/tutorials/cti/reactions.html#options. """ kf2 = (kf, kf0) reaction.__init__(self, equation, kf2, id, '', options) @@ -1505,7 +1508,8 @@ class chemically_activated_reaction(pdep_reaction): four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: - Processing options, as described in :ref:`sec-reaction-options`. + Processing options, as described in + https://cantera.org/tutorials/cti/reactions.html#options. """ reaction.__init__(self, equation, (kLow, kHigh), id, '', options) self._type = 'chemAct' @@ -1636,7 +1640,8 @@ class surface_reaction(reaction): four-digit numeric string beginning with 0001 for the first reaction in the file. :param options: - Processing options, as described in :ref:`sec-reaction-options`. + Processing options, as described in + https://cantera.org/tutorials/cti/reactions.html#options. :param beta: Charge transfer coefficient: A number between 0 and 1 which, for a charge transfer reaction, determines how much of the electric @@ -1735,14 +1740,15 @@ class phase(object): The elements. A string of element symbols. :param species: The species. A string or sequence of strings in the format - described in :ref:`sec-defining-species`. + described in https://cantera.org/tutorials/cti/phases.html#defining-the-species. :param note: A user-defined comment. Not evaluated by Cantera itself. :param reactions: The homogeneous reactions. If omitted, no reactions will be included. A string or sequence of strings in the format described - in :ref:`sec-declaring-reactions`. This field is not allowed for - stoichiometric_solid and stoichiometric_liquid entries. + in https://cantera.org/tutorials/cti/phases.html#defining-the-reactions. + This field is not allowed for ``stoichiometric_solid`` and + ``stoichiometric_liquid`` entries. :param kinetics: The kinetics model. Optional; if omitted, the default model for the phase type will be used. @@ -2352,7 +2358,7 @@ class ideal_interface(phase): :param reactions: The heterogeneous reactions at this interface. If omitted, no reactions will be included. A string or sequence of strings in the - format described in :ref:`sec-declaring-reactions`. + format described in https://cantera.org/tutorials/cti/phases.html#declaring-the-reactions. :param site_density: The number of adsorption sites per unit area. :param phases: diff --git a/interfaces/cython/cantera/reactor.pyx b/interfaces/cython/cantera/reactor.pyx index 6f75b1c6b..eaf842e04 100644 --- a/interfaces/cython/cantera/reactor.pyx +++ b/interfaces/cython/cantera/reactor.pyx @@ -983,19 +983,20 @@ cdef class ReactorNet: The sensitivities are returned in an array with dimensions *(n_vars, n_sensitivity_params)*, unless no timesteps have been taken, in which case the shape is *(0, n_sensitivity_params)*. The order of the - variables (i.e. rows) is: + variables (i.e., rows) is: `Reactor` or `IdealGasReactor`: - - 0 - mass - - 1 - volume - - 2 - internal energy or temperature - - 3+ - mass fractions of the species + - 0 - mass + - 1 - volume + - 2 - internal energy or temperature + - 3+ - mass fractions of the species `ConstPressureReactor` or `IdealGasConstPressureReactor`: - - 0 - mass - - 1 - enthalpy or temperature - - 2+ - mass fractions of the species + + - 0 - mass + - 1 - enthalpy or temperature + - 2+ - mass fractions of the species """ cdef np.ndarray[np.double_t, ndim=2] data = \ np.empty((self.n_vars, self.n_sensitivity_params)) diff --git a/interfaces/matlab/toolbox/@Interface/Interface.m b/interfaces/matlab/toolbox/@Interface/Interface.m index d9b2f46bd..e6cd1e434 100644 --- a/interfaces/matlab/toolbox/@Interface/Interface.m +++ b/interfaces/matlab/toolbox/@Interface/Interface.m @@ -1,7 +1,7 @@ function s = Interface(src, id, p1, p2, p3, p4) % INTERFACE Interface class constructor. % s = Interface(src, id, p1, p2, p3, p4) -% See :ref:`sec-interfaces`. +% See https://cantera.org/tutorials/cti/phases.html#interfaces. % % See also: :mat:func:`importEdge`, :mat:func:`importInterface` % diff --git a/interfaces/matlab/toolbox/importEdge.m b/interfaces/matlab/toolbox/importEdge.m index 08da014ef..acb4b6aea 100644 --- a/interfaces/matlab/toolbox/importEdge.m +++ b/interfaces/matlab/toolbox/importEdge.m @@ -1,7 +1,8 @@ function s = importEdge(file, name, phase1, phase2, phase3, phase4) % IMPORTEDGE Import edges between phases. % s = importEdge(file, name, phase1, phase2, phase3, phase4) -% Supports up to four neighbor phases. See :ref:`sec-interfaces` +% Supports up to four neighbor phases. See +% https://cantera.org/tutorials/cti/phases.html#interfaces % % :param file: % File containing phases diff --git a/interfaces/matlab/toolbox/importInterface.m b/interfaces/matlab/toolbox/importInterface.m index 3ae973b75..aec75cfe1 100644 --- a/interfaces/matlab/toolbox/importInterface.m +++ b/interfaces/matlab/toolbox/importInterface.m @@ -1,7 +1,7 @@ function s = importInterface(file, name, phase1, phase2) % IMPORTINTERFACE Import an interface between phases. % s = importInterface(file, name, phase1, phase2) -% See :ref:`sec-interfaces`. +% See https://cantera.org/tutorials/cti/phases.html#interfaces. % % :param file: % CTI or CTML file containing the interface