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347 commits

Author SHA1 Message Date
Ray Speth
d545a2e598 Deprecate 'testProb' constructors 
These constructors should be removed and any useful test code they
contain incorporated into new or existing tests.
 2013-06-17 14:20:09 +00:00
Ray Speth
dd10230ce1 Deprecate unused VCS functions 2013-06-17 14:20:05 +00:00
Ray Speth
1c7c4938e9 Deprecate getNamedStringValue 2013-06-17 14:20:01 +00:00
Ray Speth
9c542981f1 Deprecate getUnitsStandardConc 2013-06-17 14:19:54 +00:00
Ray Speth
94800445a1 Allow derived classes of MultiTransport 2013-06-14 23:06:21 +00:00
Ray Speth
496dfe31ce Remove extraneous constructor for XML_Node 2013-06-13 22:50:35 +00:00
Ray Speth
112d9b5093 Remove unusable KINETICS_WITH_INTERMEDIATE_ZEROED_PHASES macro 2013-06-13 22:50:26 +00:00
Ray Speth
75e586da0f Remove unusable CHEMKIN_COMPATIBILITY_MODE macro 2013-06-13 22:50:21 +00:00
Ray Speth
9740980c5d Deprecate class GRI_30_Kinetics 2013-06-13 22:50:14 +00:00
Ray Speth
d4be0e605b Remove header for unimplemented 'Crystal' class 2013-06-13 22:50:07 +00:00
Ray Speth
ca8d131092 Fix a few missing includes in header files 
These header files had implicit dependencies on other header files, which are
now made explicit.
 2013-06-13 22:50:03 +00:00
Ray Speth
843f2ad337 Deprecate ctml::getFloats 2013-06-06 15:33:11 +00:00
Ray Speth
18a102c91f Deprecate unused spectroscopy-related classes 2013-06-06 15:33:05 +00:00
Ray Speth
305e4eec54 Deprecate Kinetics::activationEnergies 2013-06-06 15:33:00 +00:00
Ray Speth
a972a7f558 Deprecate class Elements 2013-06-06 15:32:56 +00:00
Ray Speth
a6614b87bb [Doxygen] Fix some incorrect/missing "@file" commands 2013-06-06 15:32:30 +00:00
Ray Speth
11170a0e32 Deprecate class AqueousKinetics 2013-06-05 17:09:59 +00:00
Ray Speth
8757836d64 Deprecate stripLTWScstring 2013-06-05 17:09:54 +00:00
Ray Speth
2483e39ae5 Allow tests to suppress deprecation warnings 
This prevents certain tests from failing comparisons with blessed output files.
 2013-06-05 17:09:46 +00:00
Ray Speth
64bfdcc952 Deprecate support for Sundials 2.2 and 2.3. 2013-06-05 17:09:30 +00:00
Ray Speth
b888df70c4 Clean up Doxygen docs for some liquid transport related classes 2013-06-05 17:09:21 +00:00
Ray Speth
d253fc0d63 Eliminate redundant standard library includes 2013-06-05 17:08:13 +00:00
Ray Speth
be1e95576e Resolve some Doxygen warnings 2013-06-05 03:09:13 +00:00
Ray Speth
f75ba112f9 Clean up Doxygen docs for 1D simulation classes 2013-06-05 03:09:03 +00:00
Ray Speth
00da5bead5 Remove some dead code 2013-06-03 22:17:19 +00:00
Ray Speth
8d004658d7 Update Doxygen docs for other Reactor-related classes 2013-06-03 22:17:12 +00:00
Ray Speth
5a94876c91 Update Doxygen docs for class ReactorBase and descendants 2013-06-03 22:17:05 +00:00
Ray Speth
5c2b5cbde0 Update Doxygen docs for class ReactorNet 
Adding a docstring for the class means this class is finally included in the
Doxygen-generated documentation.
 2013-06-03 22:17:01 +00:00
Ray Speth
0fc6861892 Clean up Doxygen docs for LiquidTranInteraction and descendants 2013-06-03 22:16:52 +00:00
Ray Speth
6a1ebcd9d7 Clean up Doxygen docs for TransportParams and descendants 2013-06-03 22:16:46 +00:00
Ray Speth
a8fea51046 Clean up Doxygen docs for TransportFactory 2013-06-03 22:16:41 +00:00
Ray Speth
098a87cdcd Clean up Doxygen documentation for class Transport and descendants 2013-06-03 22:16:29 +00:00
Ray Speth
f8ac8ea7c3 Remove the DEPRECATED macro 
This macro was not a reliable way of marking deprecated features. Future
deprecation warnings will be issued at runtime using the warn_deprecated
function.
 2013-05-31 15:56:11 +00:00
Ray Speth
c1cfdffccc Add "warn_deprecated" function 
This function can be used for issuing runtime deprecation warnings
 2013-05-31 15:56:06 +00:00
Ray Speth
e059b5c60c Eliminate unnecessary use of reinterpret_cast 2013-05-31 15:55:48 +00:00
Ray Speth
1ed172a4d4 [Kinetics] Lazy evaluation of temperature-dependent terms in rate expression 
This interacts well with the new formulations for the Reactor governing
equations where T is an independent variable, which means that the
temperature-dependent terms do not need to be updated when computing the
Jacobian terms involving derivative with respect to composition.
 2013-05-29 00:11:52 +00:00
Ray Speth
190c4bf8ce Cleaned up Doxygen documentation in other "numerics" classes 2013-05-29 00:11:40 +00:00
Ray Speth
eadf4e3fdd Cleaned up Doxygen documentation for Sundials wrapper classes 2013-05-29 00:11:32 +00:00
Ray Speth
e9daef3313 Cleaned up Doxygen Documentation for matrix classes 
BandMatrix, DenseMatrix, SquareMatrix, and GeneralMatrix
 2013-05-29 00:11:22 +00:00
Ray Speth
7e8276809f Cleaned up Doxygen documentation for class BEulerInt 2013-05-29 00:11:17 +00:00
Ray Speth
0dba3d47a6 [Reactor] Converted ConstPressureReactor to (m,T,Yk) as independent variables 
Parallels the change of independent variables for Reactor introduced in r2295.
 2013-05-29 00:11:12 +00:00
Ray Speth
a59309e81e [Reactor] Independent variables for Reactor are now T,V, and Yk 
This formulation for the reactor's governing equations significantly improves
the performance of integrator, mostly by improving the quality of the
Jacobian. The effect is small for smaller mechanisms (GRI 3.0) but can lead to
order-of-magnitude improvements for mechanisms with hundreds or thousands of
species.

Since this set of variables corresponds to the intrinsic state variables used
for IdealGasPhase objects, we also eliminate the need to iterate when setting
the state of the thermo object.

Additionally, by using temperature as an independent variable, the
temperature-dependent parts of the kinetic rate expressions do not need to be
recomputed while updating the Jacobian (this optimization is not currently
implemented).
 2013-05-23 19:33:16 +00:00
Ray Speth
3850e0329d Fix preprocessor directives so that AssertFinite is always defined 
It is a no-op when "NDEBUG" is defined.
 2013-05-07 19:36:54 +00:00
Ray Speth
259ceaa9a6 Added assertions to check that some variables remain finite 2013-05-06 20:05:53 +00:00
Ray Speth
47598a197f Removed mdp_allo.h and mdp_allo.cpp from Cantera proper 2013-04-29 18:05:35 +00:00
Ray Speth
09def59948 Eliminated use of mdp functions in BEulerInt 2013-04-29 18:05:31 +00:00
Ray Speth
2c58b7237a Moved the "checkFinite" function into the Cantera namespace 2013-04-29 18:05:22 +00:00
Ray Speth
0a059d406a Eliminated unnecessary empty destructors from derived classes 
See http://www.parashift.com/c++-faq-lite/virtual-dtors.html
 2013-04-29 18:04:23 +00:00
Ray Speth
7fa9a9eb63 Added interface to LAPACK linear least squares solver, DGELSS 2013-04-24 21:47:53 +00:00
Ray Speth
ee74c80afc Fixed a number of "shadowed variable" compiler warnings 2013-04-18 22:08:36 +00:00