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Author SHA1 Message Date
Ray Speth
c214d912e5 [Doc] Add labels to enable linking to Python/Matlab examples 
The labels are "py-example-scriptname.py" and "matlab-example-scriptname.m",
respectively.
 2015-05-06 21:15:02 -04:00
Ray Speth
d470486bee [Python] Reactants and products can be specified in Reaction constructor 2015-05-06 21:15:01 -04:00
Ray Speth
9824edcb86 [Python] Update docs for Species and Reaction 2015-05-06 21:15:01 -04:00
Ray Speth
646654b7d0 [Python] Fix declarations of some methods which can throw exceptions 2015-05-06 21:15:01 -04:00
Ray Speth
658ce5d73b [Python] Return 'None' if thermo or transport are undefined 2015-05-06 21:15:00 -04:00
Ray Speth
a4252480aa [Python] Add setter for Species.transport 2015-05-06 21:15:00 -04:00
Ray Speth
00ed585f18 [Python] Adding example demonstrating submechanism extraction 2015-05-06 21:14:59 -04:00
Ray Speth
092937fd06 [Kinetics] Fix handling of undeclared third bodies in Falloff reactions 2015-05-06 21:14:59 -04:00
Ray Speth
08f0fb5bf6 [1D/Examples] Use np.genfromtxt in fixed-T flame example 2015-05-06 21:14:59 -04:00
Ray Speth
27726c3072 [Python/1D] Use initial gas composition as state of flame inlet 
This eliminates the need to set the inlet temperature and composition explicitly
for configurations where only one composition needs to be specified (i.e. all
premixed configurations).
 2015-05-06 21:14:58 -04:00
Ray Speth
14b2e8f5cf [Kinetics] Fix 'skip_undeclared_species' behavior 2015-05-06 21:14:58 -04:00
Ray Speth
982846acf7 [Python] Add mechanism reduction example using Species and Reactions 2015-05-05 15:02:57 -04:00
Ray Speth
d8ed6135ea [Python] Skip undeclared third bodies when adding Reactions 
This needs to be the default behavior, since reactions can currently only be
added from the constructor.
 2015-05-05 13:47:50 -04:00
Ray Speth
26c0c3f587 [Doc] Update docs for GasTransportData 2015-05-05 11:44:34 -04:00
Ray Speth
d68c41197e [Python/Doc] Document GasTransportData 2015-05-05 11:34:07 -04:00
Ray Speth
18e2ab7c8d [Python/Doc] Document Reaction and derived classes 2015-05-05 11:34:07 -04:00
Ray Speth
fe0c864f45 [Doc] Fix missing separator before static/class methods in Sphinx docs 2015-05-05 11:00:25 -04:00
Ray Speth
ce15158bf9 [Doc] Fix CSS used for method names in Sphinx docs 
This appears to be necessary for Sphinx >= 1.3.0
 2015-05-05 11:00:25 -04:00
Ray Speth
dd62e6061e [Python] Add setters for InterfaceReaction properties 2015-05-05 11:00:25 -04:00
Ray Speth
4022e408af [Doc] Document interface reaction coverage dependencies 
Specifically, that the activation energy term is given in temperature
units.
 2015-05-05 11:00:25 -04:00
Ray Speth
be2d08f7c2 Remove a leftover debugging print statement 2015-05-05 11:00:25 -04:00
Ray Speth
4ea96b810d [Python] Document Species, SpeciesThermo, and derived classes 2015-05-05 11:00:25 -04:00
Ray Speth
9af5d5835a [Python] Handle 'charge' and 'size' arguments to class Species 2015-05-05 11:00:25 -04:00
Ray Speth
56195cc67d [Python] Fix a typo in the name of class 'CoverageDependency' 2015-05-05 11:00:25 -04:00
Ray Speth
184bff328d [Python] Add ability to get/set species transport data 2015-05-05 11:00:25 -04:00
Ray Speth
fd659c09ea [1D] Fix saving multiple flame profiles to a single XML file 
Broken by the change in b0e5b13913. Modify the save_restore test
to cover this case.
 2015-05-02 21:24:51 -04:00
Ray Speth
decf251a8b Improve error messages generated by XML_NoChild and XML_TagMismatch 2015-05-02 20:07:46 -04:00
Ray Speth
c1fda5ca3c [Python] Wall coverages can be set using a dict or string 2015-05-02 20:07:46 -04:00
Ray Speth
0562f18100 [Reactor] Wall coverages may be set using a compositionMap or string 2015-05-02 20:07:45 -04:00
Ray Speth
31491c82cc [Python] Interface.coverages can be set using a string or dict 2015-05-02 20:07:45 -04:00
Ray Speth
522c563810 [Thermo] Surface coverages can be set using a compositionMap 2015-05-02 20:07:44 -04:00
Ray Speth
9e4e73da90 [Python] Convert both dicts and strings to compositionMap 2015-05-02 20:07:44 -04:00
Ray Speth
f4715c671f [Python] Add method for setting Chebyshev rate coefficient parameters 2015-05-02 20:07:36 -04:00
Ray Speth
7a21855574 [Kinetics] Switch parameter order in ChebyshevRate constructor 
The usual order of arguments is temperature then pressure.
 2015-04-30 22:34:25 -04:00
Ray Speth
6458b0c50d [Python] Enable direct construction of PlogReaction 2015-04-30 22:32:11 -04:00
Ray Speth
2fff28f37c [Kinetics] Fix Plog::rates to suppress all artificial rates 2015-04-30 19:24:16 -04:00
Ray Speth
a6038b32f6 [Python] Add functions for constructing falloff / chemact reactions 2015-04-29 22:48:44 -04:00
Ray Speth
6648b9ec34 [Kinetics] Falloff initialization checks for correct number of parameters 2015-04-29 22:12:00 -04:00
Ray Speth
0a2b4816ef [Python] Add setters for constructing elementary and third-body reactions 
This allows creating reactions of these types without needing an XML or
CTI input file.
 2015-04-29 19:35:13 -04:00
Ray Speth
498f53c350 [Python] Allow direct creation of derived-type Reaction objects 2015-04-29 19:32:35 -04:00
Ray Speth
c371751f65 Remove obsolete references to Subversion 2015-04-29 18:06:40 -04:00
Ray Speth
c1304e9ee6 Add support for Sundials 2.6 
Resolves #256.
 2015-04-29 18:03:17 -04:00
Ray Speth
a1e4735743 [Python] Fix premature deallocation when slicing Solution objects 
Testing the value of self.parent in _SolutionBase.__dealloc__ was ineffective
because this attribute can already be cleared when __dealloc__ is called,
causing the borrowed C++ objects to be deleted prematurely. A C data member
needs to be used to determine whether this object is responsible for deleting
the underlying C++ objects.
 2015-04-29 14:38:45 -04:00
Ray Speth
25c2d6c781 [Python] Enable creation of Kinetics objects from Reaction objects 2015-04-29 13:05:12 -04:00
Ray Speth
23642ded3c [Kinetics] Use current site density sticking reaction rate coefficient 
The conversion of sticking coefficients to Arrhenius expressions includes the
site density on the surface phase, which may not be set when the reaction is
being added to the Kinetics object. We now defer the calculation of this
dependency until the rate coefficient is being evaluated so that the current
value for the site density can be used.
 2015-04-29 11:55:07 -04:00
Ray Speth
bc4c71f8ee [Thermo] Ensure that site density is always positive 
A site density of zero causes divide-by-zero errors in SurfPhase and
EdgePhase. This change makes it possible to initialize SurfPhase and
EdgePhase objects without XML phase descriptions.
 2015-04-28 17:13:11 -04:00
Ray Speth
c994917bae [Kinetics] Add functions for creating Reaction objects from CTI/XML 2015-04-28 17:13:11 -04:00
Ray Speth
b6ac3ce995 [CTI] Allow CTI files containing only reaction definitions 
The reactions in these files can be referenced by other CTI/XML files, or used
directly to create Reaction objects. The absence of a phase definition requires
that either (a) all reactions are in bulk phases, or (b) the rate constants are
given in kmol, meter, second units since it is impossible to determine the
dimensionality of the concentration for each species.
 2015-04-28 17:13:11 -04:00
Ray Speth
caf71b839c [ctml] Refactor 'stick' to be a class instead of a function 
This has no impact on the normal use case, but helps separate some properties
which are not relevant for bulk-phase reactions.
 2015-04-28 17:13:11 -04:00
Ray Speth
4049bb4bb2 Fix out-of-bounds memory access in CvodesIntegrator::getErrorInfo 
Out-of-bounds memory was being accessed in cases where the system had fewer
state variables than the specified maximum number of error estimates to display.
 2015-04-28 17:13:11 -04:00