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338 commits

Author SHA1 Message Date
Ray Speth
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
838f435ca9 [Kinetics] Deprecate class ExchangeCurrent 
Unused duplicate of class Arrhenius
 2015-03-10 22:41:29 +00:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +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
26c6d93168 [Kinetics] Fix options for skipping undeclared species / third bodies 2015-02-26 00:13:29 +00:00
Ray Speth
70b51c797c Fix function named specified in checkReactionBalance exception message 2015-02-20 00:11:16 +00:00
Ray Speth
e545d123c2 [Kinetics] Relax tolerance on reaction element balance 
This allows use of some mechanisms with imprecise fractional product
stoichiometries.
 2015-02-20 00:11:12 +00:00
Ray Speth
efb80dfe05 Remove unnecessary delimiter lines between functions 
A single line of white space is sufficient and consistent. Also moved a couple
Doxygen strings out of source files.
 2015-01-22 00:04:24 +00:00
Ray Speth
b8a99b4b83 Remove unnecessary explicit calls to default constructors 2015-01-22 00:04:12 +00:00
Ray Speth
0ad587f50b Remove some unnecessary temporary references 2014-12-12 01:36:35 +00:00
Ray Speth
4e99746457 [Kinetics] Allow explicit specification of the sticking species 2014-11-15 19:26:37 +00:00
Ray Speth
ced2d20dd8 Use XML_Node::attrib when it is more clear than using operator[] 2014-11-15 00:47:31 +00:00
Ray Speth
5958578c40 [Kinetics] Check for negative and non-reactant reaction orders 
Allow non-reactant orders for electrochemical reactions

Allow negative orders specifically requested, e.g. by setting the
'negative_orders' option in the CTI definition of the reaction.
 2014-11-15 00:47:25 +00:00
Ray Speth
7438e791b5 Update comments in Kinetics::addReaction 2014-11-15 00:47:18 +00:00
Ray Speth
a2c415aaa5 [Kinetics] Add reactions using Reaction instead of ReactionData 
Deprecate class ReactionData and all related functions.
 2014-11-15 00:47:15 +00:00
Ray Speth
e3022a8057 [Kinetics] Check Reaction objects for orders on reversible reactions 2014-11-15 00:47:13 +00:00
Ray Speth
82fbff7a05 [Kinetics] Validate rate coefficient data for Reaction objects 2014-11-15 00:47:09 +00:00
Ray Speth
6727902c3f [Kinetics] Allow skipping third-body efficiencies when using Reaction 2014-11-15 00:47:04 +00:00
Ray Speth
ffe3eb5e5a [Kinetics] Check for undeclared species when using Reaction objects 
Skip the reaction or raise an exception based on the
'm_skipUndeclaredSpecies' flag
 2014-11-15 00:46:59 +00:00
Ray Speth
d72c2e7132 [Kinetics] Add reaction balance check to Kinetics 
This applies to reactions added using Reaction objects. Previously, the
check would only be performed for reactions added from an XML tree.
 2014-11-15 00:46:57 +00:00
Ray Speth
e2f15e97d4 [Kinetics] Add duplicate reaction checks using Reaction objects 2014-11-15 00:46:54 +00:00
Ray Speth
c39b93c424 [Kinetics] Automatically generate reaction equation strings 2014-11-11 00:12:28 +00:00
Ray Speth
f51ed2aa02 [Kinetics] Add factory functions for Reaction classes 2014-11-11 00:12:26 +00:00
Ray Speth
69650b8ec2 [Kinetics] InterfaceReaction supports sticking coefficients 2014-11-11 00:12:13 +00:00
Ray Speth
c4e6790fda [Kinetics] Implement addReaction from Reaction for InterfaceKinetics 2014-11-11 00:12:08 +00:00
Ray Speth
b19d7342fa [Kinetics] Refactor InterfaceKinetics::addReaction 2014-11-11 00:12:03 +00:00
Ray Speth
e4d2ed9b78 [Kinetics] Add SurfaceArrhenius constructor from Arrhenius 2014-11-11 00:11:59 +00:00
Ray Speth
028bca0d73 [Kinetics] Implement addReaction from Reaction for AqueousKinetics 2014-11-11 00:11:55 +00:00
Ray Speth
be585aab3e [Kinetics] Implement direct constructor for ChebyshevRate 2014-11-11 00:11:33 +00:00
Ray Speth
191e9bcc42 [Kinetics] Implement direct constructor for P-log reactions 2014-11-11 00:11:31 +00:00
Ray Speth
b4afcd3e8e [Kinetics] Implement addReaction using Reaction objects for GasKinetics 
This covers elementary, third-body, and falloff reaction types
 2014-11-11 00:11:25 +00:00
Ray Speth
c0944f1700 [Kinetics] Basic implementation of class Reaction and descendants 2014-11-11 00:11:17 +00:00
Ray Speth
24c509f539 [Kinetics] Fix some cases where duplicate reactions were not detected 
Also add several tests which check that the various kinds of duplicate
reactions are being identified as errors or allowed as intended.
 2014-11-07 02:15:03 +00:00
Ray Speth
37f71bd912 [Kinetics] Deprecate 'reactants' and 'products' methods 
These methods are rarely used, and they expose a now-unused internal data
structure that isn't even correct for all reactions.
 2014-11-07 02:14:50 +00:00
Ray Speth
b2afb1a7a9 [Kinetics] Handle stoichiometry and reaction order in StoichManagerN 
In the previous implementation, the higher-level classes were making unnecessary
assumptions about the optimizations used in StoichManagerN for reactions with
unity stoichometric coefficients.
 2014-11-01 00:13:49 +00:00
Ray Speth
557ffffc5b [Kinetics] Combine ReactionStoichMgr with class Kinetics 
Class ReactionStoichMgr is now deprecated, as all of its functions were just
pass-throughs between Kinetics and StoichManagerN.
 2014-11-01 00:13:46 +00:00
Ray Speth
f1387be98a Formatting cleanup of importKinetics 2014-11-01 00:13:44 +00:00
Ray Speth
50a08db7c0 [Kinetics] Move some function definitions out of RxnRates.h 
The performance-sensitive update_C and updateRC methods remain in the header
file.
 2014-11-01 00:13:42 +00:00
Ray Speth
06732a6581 [Kinetics] Merge SRI5 and SRI3 implementations 2014-10-30 21:10:12 +00:00
Ray Speth
9c008a753b [Kinetics] Merge Troe3 and Troe4 implementations 2014-10-30 21:10:09 +00:00
Ray Speth
d1295a5249 [Kinetics] Make Falloff class declarations public 2014-10-30 21:10:04 +00:00
Ray Speth
3b71d75ada [Kinetics] Add class BulkKinetics 
This class serves as a common base for GasKinetics and AqueousKinetics,
eliminating most of the redundancy between the two classes.
 2014-10-30 21:09:59 +00:00
Ray Speth
6f0fb5cf8d [Kinetics] Refactor and deprecate installReagents 2014-10-29 23:32:27 +00:00
Ray Speth
a8659c86cc [Kinetics] Removed unnecessary initializations 2014-10-29 23:32:24 +00:00
Ray Speth
3ab37254eb [Kinetics] Move m_rfn and m_rkcn up to Kinetics 2014-10-29 23:32:19 +00:00
Ray Speth
987bb8f115 [Kinetics] Remove unused variable 'm_fwdOrder' 2014-10-29 23:32:16 +00:00
Ray Speth
ba87385c86 [Kinetics] Finish deprecating duplicate "reactionNumber" function 
Remove the private implementations outright.
 2014-10-29 23:32:12 +00:00
Ray Speth
d5262e8bee [Kinetics] Move stoich manager and related functions up to Kinetics 2014-10-29 23:32:07 +00:00
Ray Speth
6287c2c311 [Kinetics] Remove unused m_index member of Kinetics classes 2014-10-22 21:48:19 +00:00