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66 commits

Author SHA1 Message Date
Ray Speth
9e9f03288a [Kinetics] Implement modifyReaction for InterfaceKinetics 2015-05-08 11:07:41 -04:00
Ray Speth
14b2e8f5cf [Kinetics] Fix 'skip_undeclared_species' behavior 2015-05-06 21:14:58 -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
eb088793e6 [Kinetics] Fix indices used in calculating coverage-dependent rates 
The coverage dependent rate calculation is passed the array of coverages,
which include only the interface species, so the species index in the
interface phase is what is needed here.
 2015-04-26 11:42:21 -04:00
Ray Speth
ec1d7d7382 Fix compilier warnings about unused variables 2015-04-14 16:08:10 -04:00
Ray Speth
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
cc17716182 Cleanup trailing whitespace 2015-02-26 21:52:52 +00:00
Ray Speth
4e99746457 [Kinetics] Allow explicit specification of the sticking species 2014-11-15 19:26:37 +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
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
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
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
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
a74fda8ad2 Introduce 'getValue' to avoid making std::map members mutable 2014-10-03 01:45:49 +00:00
Harry Moffat
021c8f9880 InterfaceKinetics rewrite -> addition of BV and Affinity reactions, next interation. 2014-09-03 04:55:27 +00:00
Ray Speth
002c158761 Cleanup include statements 
Move includes from header to implementation files where possible, and remove
unnecessary includes.
 2014-08-28 16:54:13 +00:00
Harry Moffat
979bdffe6e InterfaceKinetics rewrite -> implementation of BV and affinity reactions 
next iteration
 2014-08-26 20:55:38 +00:00
Harry Moffat
e6863bfdae InterfaceKinetics rewite: added rmcVector and identifyMetalPhases routine. 
added utility to clean tests. tests don't rerun when they should!
 2014-08-21 21:40:26 +00:00
Harry Moffat
69c09709d1 Interfacekinetics rewrite: 
Decided to break out an ElectrodeKinetics object for now. We'll see how it goes.
 2014-08-21 00:49:41 +00:00
Harry Moffat
81556ea8aa Rewrite of InterfaceKinetics - next iteration. 2014-08-14 00:00:00 +00:00
Harry Moffat
6741d8f7c6 InterfaceKinetics rewrite -> addition of general BV reactions and affinity formulation. 2014-08-12 23:02:47 +00:00
Harry Moffat
199cd4ceba Changes in InterfaceKinetics to allow for downstream hooks to add in the capability to model 
arbitrarily fit open circuit potentials for intercalating electrodes.
 2014-06-05 22:43:41 +00:00
Ray Speth
b5396837b2 Make use of std::min, std::max, and clip 2014-06-03 16:52:43 +00:00
Ray Speth
789574ac80 Remove commented-out code 2014-05-27 02:52:21 +00:00
Harry Moffat
675df76b1c Fixed a long standing problem with the combination of storred XML files and duplicator functions. 
Now the complete XML file is storred within the ThermPhase object starting with the root node.
This is needed for later processing of kinetics and transport mechanisms when the ThermoPhase
file is duplicated and the original file is deleted.

xml() is now a const function, and still returns the same pointer.
setXMLdata() is a new function will stores the xml data.
 2014-05-20 19:02:20 +00:00
John Hewson
b84f19c439 In InterfaceKinetics added some comments and clarified function names. 
Formerly getExchangeCurrentQuantities() is now
updateExchangeCurrentQuantities().  This method updates things like
m_StandardConc for computing reaction rates.

Formerly applyExchangeCurrentDensityFormulation() is now
convertExchangeCurrentDensityFormulation().  This method converts
rate expressions from A/m2 to kmol/m2/s.
 2014-04-22 22:25:59 +00:00
Ray Speth
95eb7ab3ba Remove newline after '::' in member function definitions 
This inconsistency makes it hard to directly search the code for a specific
member function definition.
 2014-03-24 04:03:09 +00:00
Ray Speth
e1a49487b7 [Kinetics] Remove deprecated getActivationEnergies function 
Resolves Issue 147.
 2013-12-16 23:21:52 +00:00
Ray Speth
112d9b5093 Remove unusable KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES macro 2013-06-13 22:50:26 +00:00
Ray Speth
305e4eec54 Deprecate Kinetics::activationEnergies 2013-06-06 15:33:00 +00:00
Ray Speth
d253fc0d63 Eliminate redundant standard library includes 2013-06-05 17:08:13 +00:00
Ray Speth
d103ec8d2f Cleaned up Doxygen documentation for class Kinetics and descendants 2013-04-12 23:05:20 +00:00
Ray Speth
e04e59cdd3 Removed extraneous parentheses around arguments to 'return' 
'return' is a keyword, not a function, so these parens are unnecessary.
 2013-02-14 01:03:48 +00:00
Ray Speth
6d6e237f07 Removed unnecessary checks surrounding delete operations 2013-02-14 01:03:32 +00:00
Ray Speth
a25c1a43b3 [Kinetics] Fixed crashes when reaction mechanism contains no reactions 
Make sure several arrays are never of length zero so that taking &v[0]
is always well-defined.
 2013-02-14 01:02:18 +00:00
Ray Speth
7da738d238 Re-applied consistent formatting to trunk 
Applied using: astyle -n --style=kr --add-brackets --indent=spaces=4
--indent-col1-comments --unpad-paren --pad-header --align-pointer=type
--lineend=linux
 2013-02-07 23:40:59 +00:00
Ray Speth
50327a665f Moved some function implementations out of InterfaceKinetics.h 
This gets rid of some (mostly spurious) warnings generated by MSVC
 2013-01-11 22:56:33 +00:00
Ray Speth
46a8b3052f Use size_t instead of int in InterfaceKinetics 2012-12-26 23:56:07 +00:00
Harry Moffat
ea25de7fe7 Continuing transfering LiquidTransport changes, doing bugfixes, and 
qualifying against our testsuite.
 2012-12-15 00:49:14 +00:00
Harry Moffat
c6f7abbf2f Fixed a serious error in InterfaceKinetics that had crept into this branch. 
Started upgrade/update of equilibrium solver
       - Fixed numerical jacobian calculation of the ln activity coefficients.
 2012-11-29 02:18:05 +00:00