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636 commits

Author SHA1 Message Date
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
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
39b751d655 [Equil] Always use the member function versions of 'equilibrate' 
The various free functions are deprecated, along with the now unnecessary
headers 'equil.h' and 'equilibrium.h'.
 2014-11-08 00:53:45 +00:00
Ray Speth
8c934ab678 [Equil] Implement equilibrate as a method of MultiPhase 
This differs from the current equilibrate method in that it can use either of
the multiphase equilibrium solvers.
 2014-11-08 00:53:42 +00:00
Ray Speth
e16e998dd7 [Equil] Implement equilibrate as a method of ThermoPhase 
The Cython interface now calls this equilibrate function.

Unlike the free function 'equilibrate', this new equilibrate method actually
does what the documentation describes regarding the 'solver' argument. This
means that there are cases where failures of the MultiphaseEquil solver were
previously being hidden by a subsequent successful solution using the ChemEquil
solver. These tests have been marked as known failures.
 2014-11-08 00:53:39 +00:00
Ray Speth
4bcbe862a9 Fix copy constructor and assignment operator for SpeciesThermo classes 2014-11-08 00:53:36 +00:00
Ray Speth
363d3ec3f0 Remove HMWSoln 'testProb' constructor 
This constructor was used only in HMW_test_1, and it just set the same
parameters that were already read from the XML input file.
 2014-11-08 00:53:33 +00:00
Ray Speth
eb71d8cdd0 Deprecate "copyData" method of array classes 2014-11-08 00:53:30 +00:00
Ray Speth
8b8a95a2ff Deprecate unused stringUtils functions 2014-11-07 02:14:57 +00:00
Ray Speth
07f8d520ee Improved implementation of parseCompString 
Improvements:

- Tolerate formatting irregularities such as spaces befpre or after the colon
  (e.g. 'H2: 1.0')

- Allow names containing commas and semicolons

- Detect errors such as no value being supplied for the last element (e.g. 'H2')

- Single implementation handles both the case where a list of valid names is
  supplied and when any name is allowed
 2014-11-07 02:14:52 +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
7eb726d3d9 [Kinetics] Remove unnecessary copy constructors and assignment operators 
The data members of C1, C2, C3, C_AnyN, and StoichManagerN are all copyable and
assignable, so it's better to just let the compiler supply these.
 2014-11-01 00:13:52 +00:00
Ray Speth
fd777096b2 [Kinetics] Remove unused variables from StoichManagerN 2014-11-01 00:13:51 +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
fbe8a7cd3f Make common interface to shared_ptr available 
Use configure-time checks to find an available implementation of shared_ptr from
the standard library (C++11), TR1 (C++03), or Boost.
 2014-11-01 00:13:39 +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
79d9accaa9 [Kinetics] Clean up documentation of Falloff classes 2014-10-30 21:10:07 +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
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
Ray Speth
584c57d569 [Kinetics] move "reaction type" up to Kinetics 2014-10-22 21:48:15 +00:00
Ray Speth
d65dbe3da2 [Kinetics] Move common Kinetics features up to the base class 2014-10-22 21:48:11 +00:00
Ray Speth
e7236df51f Formatting cleanup of InterfaceKinetics 2014-10-22 21:48:09 +00:00
Ray Speth
a208c54d1c Add a version of XML_Node::getChildren with a simpler interface 2014-10-22 21:48:04 +00:00
Ray Speth
7d9a6eeefc Deprecate class SpeciesThermoFactory 2014-10-17 23:44:56 +00:00
Ray Speth
4dd3e1d2bc Use Species objects when adding species from XML 2014-10-17 23:44:47 +00:00