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566 commits

Author SHA1 Message Date
Ray Speth
91f3a2b073 Fix statements that called the assignment operator twice 2014-10-03 01:45:41 +00:00
Ray Speth
79461c34e8 [Thermo] Add default value for 'id' argument of 'newPhase' 2014-09-27 00:09:11 +00:00
Ray Speth
4baccc732c [Thermo] Simplify interface for adding elements to a Phase 
Phase::addElements(string name, ...) is the single entry point for adding
elements. It always perform the uniqueness check, and can do the extra
additional work required to add elements to a phase that already has species,
removing the need for "freezing" the phase's elements. Parsing the XML tree for
elements is now handled in "installElements". The variant element-adding methods
are deprecated.
 2014-09-27 00:09:05 +00:00
Ray Speth
473827a8a6 [Thermo] Check to make sure parameterizations are of the correct type 2014-09-27 00:09:02 +00:00
Ray Speth
1cb688150e [Thermo] Fix SpeciesThermoDuo to pass on the parameterization type 2014-09-27 00:08:59 +00:00
Ray Speth
a8f4c76097 [Thermo] Check to make sure thermo data is installed for all species 2014-09-27 00:08:54 +00:00
Ray Speth
89888e6697 [Thermo] Fix derived classes to always call parent's initThermo() 
Remove unnecessary reimplementations that only called the parent's method.
 2014-09-27 00:08:46 +00:00
Ray Speth
f46b61a740 Make "string&" arguments "const string&" 
This way, these functions can accept constant strings, including string
literals.
 2014-09-26 13:45:12 +00:00
Ray Speth
5ecdc1a4e1 [Equil] Deprecate VCS 'UseCanteraCalls' flag 
When this flag is removed, the behavior will be as if the flag's value were
'true'.
 2014-09-24 23:17:58 +00:00
Ray Speth
ca68fbc075 Rename Cabinet member variables to avoid using reserved identifiers 
Names containing double underscores are reserved for the C++ implementation.
 2014-09-24 23:17:50 +00:00
Ray Speth
8e7588671f [Cython/Reactor] Print messages from exceptions raised in Python callbacks 
Unlike the normal case for CallbackError, where the error message is visible
when it is re-raised in Python, errors occuring during reactor network
integration aren't necessarily terminal, so they can't simply be re-raised after
returning to Python. But we still want to display the information they contain,
so we need to extract that information from the Python exception objects in the
what() function that is called by cvodes_rhs.
 2014-09-23 02:20:41 +00:00
Ray Speth
09db5a498a [Thermo] Add getMass/MoleFractionsByName functions with thresholds 
This makes it easier to set the composition of a phase based on the composition
of another phase with a different set of species. The threshold argument allows
species with negligible concentrations to be skipped.

Deprecate the unused getMoleFractionsByName function that didn't return a
value.
 2014-09-18 22:58:59 +00:00
Ray Speth
1ea0122c15 [Transport] Check for invalid 'geometry' flags 
For those cases where the number of atoms in a molecule precludes certain
geometries, check to make sure that that the geometry flag is set
appropriately.
 2014-09-15 18:05:00 +00:00
Ray Speth
2fc09337c0 Deprecate XML_Node::operator() 2014-09-15 18:04:57 +00:00
Ray Speth
a837dfdc6d [1D] Add 'clearStats' function for clearing accumulated solver stats 2014-09-07 21:17:00 +00:00
Ray Speth
959cbb7d7a Remove unimplemented method MultiPhaseEquil::printInfo 2014-09-07 21:16:57 +00:00
Ray Speth
f4e277573d [Doc] Improve description of CTI format and CTI/CTML relationship 2014-09-07 21:16:49 +00:00
Harry Moffat
42a934a37e InterfaceKinetics rewrite -> next iteration. Addition of Affinity input terms. 2014-09-03 16:46:53 +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
6a07722675 [Thermo] Remove unnecessarily overridden methods in PureFluidPhase 2014-09-02 22:34:25 +00:00
Ray Speth
0886de8650 Include CVodes error text in resulting CanteraErrors 
Failures in 'integrate' and 'advance' now include the error text provided by
CVodes directly, rather than just the numerical error code. This is especially
helpful in cases where the direct output from CVodes to stderr is lost
(e.g. when running from the Matlab GUI).
 2014-08-28 16:55:41 +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
08fe85b4cd Check for fenv.h availability. Apparently, MS visual doesn't have C99 support before 2013, so previous commit didn't compile on MSVISUAL. 
If fenv.h not available, program now error exits if fenv functions are requested.
 2014-08-26 17:55:44 +00:00
Harry Moffat
3a6d72346d Made a member public for now, until further development is done. 2014-08-21 23:27:12 +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
0d9b7d7868 Updated doxygen make generation capability. 
Started to modify doxygen content to get rid of the large number of warnings.
 2014-08-21 00:48:04 +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
fcbf41ac73 Changed the default to not crop the printout of any small numbers. 2014-08-12 22:45:53 +00:00
Harry Moffat
e129d02d93 Added in real number overflow exception control. 
There are a series of activity coefficients for published battery models
 which actually overflows. Cantera was treating this as a nonerror and changing
the return results without comment. This is not correct. Made the behavior a
user controlled capability.
 2014-08-05 23:42:24 +00:00
Harry Moffat
cdec2e90c7 Fixes need to restore capability to solve banded systems with nonlinear solver 2014-08-05 23:11:58 +00:00
Steven DeCaluwe
ccc4dda228 Adding helper functions to HighPressureGasTransport.cpp 2014-08-05 15:01:13 +00:00
Ray Speth
907bbd8b79 Allow importing phases from XML or CTI strings 2014-07-30 16:59:51 +00:00
Ray Speth
a22a767be1 Fix some compiler warnings 2014-07-30 16:59:45 +00:00
Ray Speth
56ccc667df Fix some uninitialized member variables 2014-07-30 16:59:39 +00:00
Ray Speth
063c2a261a Eliminate redundancy between get_XML_File and get_CTML_Tree 
get_CTML_Tree and getCtmlTree are now deprecated in favor of get_XML_File
 2014-07-30 16:58:55 +00:00
Steven DeCaluwe
9c3ac51818 Adding cpp and header files for HighPressureGasTransport module 2014-07-28 21:04:11 +00:00
Steven DeCaluwe
14019cfd2e Adding HighPressureGas transport module. 2014-07-28 21:02:18 +00:00
Ray Speth
67539df9f2 Fix #includes to work with Visual Studio 2013 2014-07-25 18:32:57 +00:00
Ray Speth
1e078d4fd3 [Kinetics] Change temperatures used for P-log validation 
For rate expressions with negative activation energies, evaluating at
unphysically low temperatures (e.g. 1 K) could lead to overflows in calculating
exp(Ea/RT) that are not indicative of problems at more reasonable temperatures.
 2014-07-25 18:32:37 +00:00
Ray Speth
1cd82d40af Remove 'SQUARE' and 'DSIGN' macros 2014-07-25 18:32:29 +00:00
Ray Speth
884dd36b9c [Reactor] Remove unused reactor connectivity calculation 2014-07-18 15:14:12 +00:00
Ray Speth
1b1703cc56 [Reactor] Remove unused variable ReactorBase::m_init 2014-07-18 15:14:07 +00:00
Ray Speth
d46bc31d2c Simplify SolveSP printing functions 
Remove unused arguments. Merge printIteration and PrintFinal.
 2014-07-10 22:36:54 +00:00
Ray Speth
45f6e84ebf Improved error messages that just reported 'confused' 2014-07-10 22:36:43 +00:00
Ray Speth
5ebdb7e924 Use execeptions to simplify usage of ElemRearrange 2014-07-10 22:36:36 +00:00
Ray Speth
bd14358a68 [1D] Remove empty overrides of Domain1D::_finalize 2014-07-10 22:36:06 +00:00
Ray Speth
c4beab316f Remove unnecessary class forward declarations 2014-07-10 22:34:44 +00:00