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723 commits

Author SHA1 Message Date
Ray Speth
0562f18100 [Reactor] Wall coverages may be set using a compositionMap or string 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
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
6648b9ec34 [Kinetics] Falloff initialization checks for correct number of parameters 2015-04-29 22:12:00 -04:00
Ray Speth
c371751f65 Remove obsolete references to Subversion 2015-04-29 18:06:40 -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
a9c6eb6fda [Kinetics] Add methods for inspecting ChebyshevRate objects 2015-04-24 18:53:02 -04:00
Ray Speth
b12c90b315 [Doc] Add missing docstrings for ChebyshevRate and Plog 2015-04-24 18:13:46 -04:00
Ray Speth
d3d303c4e9 [Kinetics] Add Plog::rates() for informational purposes 2015-04-24 16:43:37 -04:00
Ray Speth
4151c10884 [Kinetics] Simplify Plog by using Arrhenius objects internally 2015-04-24 14:49:42 -04:00
Ray Speth
d2418c0c2a [Kinetics] Add methods for inspecting Falloff objects 2015-04-23 18:10:15 -04:00
Ray Speth
9d4a3e0f75 [Kinetics] Reaction objects have Falloff objects 
This approach actually makes use of the fact that we have a Falloff type.
 2015-04-23 18:10:15 -04:00
Ray Speth
873724c135 [Kinetics] Move member function definitions out of Falloff.h 2015-04-23 18:10:15 -04:00
Ray Speth
bbe2e1c79b [Python] Add access to properties of simple reaction types 
This includes ElementaryReaction and ThirdBodyReaction
 2015-04-23 18:10:15 -04:00
Ray Speth
a4ba47594c [Python] Add functions for creating Species objects from CTI/XML 2015-04-22 14:08:24 -04:00
Ray Speth
b0e5b13913 Remove redundant, unnamed root XML node from parsed documents 
XML_Node::build will make that node the root node (i.e. the 'ctml' node)
of the tree, instead of giving that node a child node containing the actual
root node.
 2015-04-20 18:34:39 -04:00
Ray Speth
96cf312ec6 [Thermo] Always add species using Species objects 
Deprecate the non-Species-based addSpecies and addUniqueSpecies
functions.
 2015-04-20 18:34:38 -04:00
Ray Speth
2ca603838d [Thermo] Extract 'newSpecies(XML_Node&) from thermo initialization 
VPStandardStateTP phases now use the same pathway for adding species as
other phase in importPhase. Deprecate the now-unused 'installSpecies'
function.
 2015-04-20 18:34:37 -04:00
Ray Speth
d27b9ef9b1 [Thermo] Species size defaults to 1.0 
This mostly affects surface phases, where a species size of 0 causes
several problems.
 2015-04-20 18:34:37 -04:00
Ray Speth
a471e4316a [Thermo] Phase::addSpecies takes shared_ptr by value 
This helps to clarify that addSpecies stores a copy of the shared_ptr.
 2015-04-20 18:34:37 -04:00
Ray Speth
a63874e4b4 [Transport] Refactor TransportData initialization 2015-04-20 18:34:36 -04:00
Ray Speth
aee6cc14ac [Transport] Remove 'name' variable from TransportData 
This was used only for validation error messages, but in that case we can just
use the Species object which is available during validation.
 2015-04-17 19:06:43 -04:00
Ray Speth
7d170a9989 [Thermo] newSpeciesThermoInterpType argument is the 'thermo' XML node 
No data from the outer 'species' node is needed to instantiate the
SpeciesThermoInterpType object, so this function can just take the 'thermo' node
directly.
 2015-04-17 19:06:43 -04:00
Ray Speth
1b0970a494 [Thermo] Remove species name argument from STIT factory functions 
This argument was used only in error messages, which can be reported more
uniformly if implemented at a higher level.
 2015-04-17 19:06:43 -04:00
Ray Speth
ec1d7d7382 Fix compilier warnings about unused variables 2015-04-14 16:08:10 -04:00
Ray Speth
d1cda15f42 Improve performance of importing phases 
Replace the O(k) implementation of Phase::speciesIndex with one that is
O(log(k)). This function is called frequently as part of Kinetics object
initialization. Optimize for the more common case where the species name is not
qualified with a phase name.
 2015-04-14 15:29:28 -04:00
Ray Speth
bde0f1466d [Thermo] Add index-based accessor for Species objects 2015-04-14 15:29:28 -04:00
Ray Speth
882a4986da Remove 'thermo' argument from Species constructor 
Since the Species object now stores its SpeciesThermoInterpType contents as a
shared_ptr, it is undesirable to have the Species constructor take this as a raw
pointer argument.
 2015-04-14 15:29:28 -04:00
Ray Speth
43952b30fc [Thermo] Use shared_ptr<Species> in ThermoPhase 2015-04-14 15:29:28 -04:00
Ray Speth
8f36e524fe Do species indexing in GeneralSpeciesThermo instead of STIT 
This means that GeneralSpeciesThermo no longer modifies the
SpeciesThermoInterpType objects, permitting them to be shared between
ThermoPhase objects.
 2015-04-14 15:29:28 -04:00
Ray Speth
5195e4f9b8 [Thermo] Use shared_ptr to STIT objects in Species and SpeciesThermo 
Exclusive ownership of the SpeciesThermoInterpType objects is no longer assumed.
 2015-04-14 15:29:28 -04:00
Ray Speth
35dbe37bf7 [Thermo] Deprecate SpeciesThermo::install 
The install_STIT method should be used instead.
 2015-04-14 15:29:28 -04:00
Ray Speth
a1599ac921 [Thermo] Add 'index' argument to GeneralSpeciesThermo::install_STIT 
This is a prerequisite to removing the species index as a property of the
SpeciesThermoInterpType object and making it independent of any specific
ThermoPhase object.
 2015-04-14 15:29:28 -04:00
Ray Speth
1dd7b214b5 [Thermo] Deprecate unused method 'getUnitsStandardConc' 
First step in resolving Issue #96
 2015-04-14 15:18:20 -04:00
Ray Speth
c540e67d50 [Thermo] Deprecate non-functional 'testProb' constructors 
These "test problem" constructors don't actually do anything, and most of them
can't be used because the corresponding input files don't exist.
 2015-04-09 19:04:08 -04:00
Ray Speth
23ad04f882 [Transport] Deprecate non-functional AqueousTransport class 
This class has been broken since 2009. Note the vectors m_visccoeffs,
m_condcoeffs, and m_diffcoeffs, which are used but never initialized.
 2015-04-09 18:54:05 -04:00
Ray Speth
f59bcdf057 [Thermo/Doc] Fix incorrect SurfPhase docstrings 
These docstrings were just copied from unimplemented virtual methods in class
ThermoPhase.
 2015-04-08 19:44:16 -04:00
Ray Speth
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
c757c3bc76 Add include guard to smart_ptr.h 2015-03-10 22:41:53 +00:00
Ray Speth
838f435ca9 [Kinetics] Deprecate class ExchangeCurrent 
Unused duplicate of class Arrhenius
 2015-03-10 22:41:29 +00:00
Ray Speth
603e321a37 [Cython] Fix treatment of writelogendl() 
Both writelog and writelogendl should be passed through PySys_WriteStdout to
ensure that they are printed in the correct order. Problems with this were
identified in the 1D solver log when using Python 3.
 2015-02-28 00:24:29 +00:00
Ray Speth
7cdeedb91b [Transport] Provide transitional 'TransportFactory::initTransport' 
There are user-provided classes derived from GasTransport which still call this
method, so a version of it that calls the new method for initializing
GasTransport objects needs to be provided until after Cantera 2.2.
 2015-02-26 21:59:37 +00:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
5592a52e0f Remove unnecessary use of 'extern' 2015-02-26 21:54:11 +00:00
Ray Speth
cf3ad30537 [Kinetics] Changing a rate multiplier invalidates existing ROPs 2015-02-26 21:54:04 +00:00
Ray Speth
cc17716182 Cleanup trailing whitespace 2015-02-26 21:52:52 +00:00
Ray Speth
60c221c845 [Kinetics] Combine ThirdBodyMgr and Enhanced3BConc as ThirdBodyCalc 
The old classes are now deprecated. The name change was needed to avoid
collisions with no-longer-necessary template parameter.
 2015-02-20 23:44:41 +00:00