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Author SHA1 Message Date
Ray Speth
2561ab82e3 [Equil] Check index bounds for known problems in VCS_SOLVE 
See #187
 2016-05-03 15:03:52 -04:00
Ray Speth
aa5f26bda6 [Thermo] Check dynamic_cast to PDSS_Water 
Resolves #6
 2016-05-03 15:03:52 -04:00
Ray Speth
ca2a330d5f [XML] Include file name in XML-related errors 
Resolves #40
 2016-05-03 15:03:51 -04:00
Ray Speth
26b937651b [XML] Improve error message generated by XML_NoChild 2016-05-03 15:03:51 -04:00
Ray Speth
6003af01a3 [XML] Add version of XML_Node::build that takes file name directly 2016-05-03 15:03:51 -04:00
Ray Speth
c7a1a57fbd [Reactor] Eliminate re-ordering of sensitivity parameters 
Passing the full parameter vector to evalEqs for each reactor and wall
eliminates the need to re-order the parameter vector. Instead, each reactor and
wall just needs to know the indices of its sensitivity parameters, which are now
returned by ReactorNet::registerSensitivityReaction.
 2016-05-01 20:35:34 -04:00
Ray Speth
e13faa1071 [Base] Fix vec2str to actually use provided format string 2016-04-30 16:47:55 -04:00
Ray Speth
0e2ea0964b [Thermo] Add function 'resetHf298' 
Using this instead of modifyHf298 to reset the thermo data to its original
state avoids round-off errors that otherwise make modifications to the
species thermo data irreversible.
 2016-04-30 16:43:37 -04:00
Ray Speth
0f669153fb [Thermo] Remove unnecessary overrides of modifyOneHf298SS 2016-04-30 16:43:37 -04:00
Ray Speth
92e9e08097 [Test] Show largest error component in assertArrayNear 2016-04-29 22:11:17 -04:00
Ray Speth
e454c51925 [Numerics] Show messages from std::exception in CVODES residual function 2016-04-28 22:01:26 -04:00
Ray Speth
cd77a94588 [Numerics] Fix memory leak in CVodesIntegrator 
Memory allocated in CVodesIntegrator::sensInit was not being released.
 2016-04-20 14:35:57 -04:00
Ray Speth
032bb9c363 [Reactor] Move sensitivity parameter vector into FuncEval 
This eliminates the need for class FuncData, and makes it possible to
introduce sensitivity parameters which have a nominal values other than 1.0.
 2016-04-19 16:08:52 -04:00
Ray Speth
51b0e46277 [Thermo] ThermoPhase::modifyOneHf298SS always invalidates cached data 2016-04-18 22:20:06 -04:00
Ray Speth
3566542c0b [Equil] Replace PropertyCalculator with simple lambdas 2016-04-18 20:29:02 -04:00
Ray Speth
f4ad150905 [1D] Sim1D::setProfile checks range of position array 2016-04-18 20:00:15 -04:00
Ray Speth
6a928b57f9 Replace getValue with std::map.at where possible 
Deprecate the two-argument version of getValue, since the C++11 at method does
the same thing.
 2016-04-18 19:34:40 -04:00
Ray Speth
6e3812a828 [Thermo] Remove unnecessary temporary work vectors 2016-04-18 17:52:08 -04:00
Ray Speth
9e9ae783f8 Don't use a vector where a scalar will suffice 2016-04-18 15:36:23 -04:00
Ray Speth
336271c395 [Doc] Clean up redundant "@return returns ..." 2016-04-18 14:58:15 -04:00
Ray Speth
a026c6ad8b [Thermo] Add compatibility check for phases added to MultiPhase 
PureFluidPhase and WaterSSTP are not compatible with MultiPhase since they are
already multi-phase mixtures.

Resolves #306
 2016-04-18 14:40:28 -04:00
Ray Speth
32b3543cbe [Thermo] Introduce Phase::compositionChanged 
This function is called after any change in composition, and can be used by
phases to update quantities that are affected by the composition change, instead
of needing to overload all of the different functions which update the
composition.
 2016-04-17 23:58:34 -04:00
Ray Speth
ac2361ee53 [Thermo] Deprecate IdealSolidSolnPhase::referenceConcentration 2016-04-17 22:49:28 -04:00
Ray Speth
994c9d1afb [CTML] Deprecate addInteger and CTML_Version 2016-04-16 23:55:51 -04:00
Ray Speth
56f49ef444 Miscellaneous jargon cleanup 2016-04-16 22:32:49 -04:00
Ray Speth
80fcc92129 [Thermo] Deprecated constructPhaseFile and constructPhaseXML methods 
These methods were only defined for HMWSoln and IonsFromNeturalVPSSTP, and just
do the same thing as initThermoFile and importPhase (respectively).
 2016-04-16 22:08:39 -04:00
Ray Speth
111b4909c9 [Thermo] Deprecate class SemiconductorPhase 
Can't be constructed from ThermoFactory, and constructor from file is not
implemented. Also, the getChemPotentials method uses the m_work array, which is
never initialized because the private method initLengths() is never called.

See #267
 2016-04-16 21:06:49 -04:00
Ray Speth
f583bd4530 [Doc] Convert HTML tags to Markdown in Doxygen docs 2016-04-16 20:58:38 -04:00
Ray Speth
aa3780b094 [Thermo] Reference source of formula used in WaterPropsIAPWS::psat_est 2016-04-16 17:44:09 -04:00
Ray Speth
af19481b65 [Doc] Remove some incorrect copy/pasted docstrings 2016-04-16 17:26:49 -04:00
Ray Speth
9c907af1b8 [Python] Add ThermoPhase.set_equivalence_ratio 2016-04-16 16:22:06 -04:00
Ray Speth
1ba5f6b879 [Kinetics] Allow adding species after reactions for homogeneous kinetics 
This enables incremental mechanism construction for gas phase kinetics. For
surface kinetics, adding new species changes the kinetics species index of
existing species in other phases, so this feature is disabled.
 2016-04-16 11:52:08 -04:00
Ray Speth
9c4a0baa55 [Thermo] Simplify adding species for most phase types 
Where possible, extend arrays as species are added rather than requiring a
later call to initThermo(). For phases that do not require any data except
that which is included in the Species objects themselves (notably, this
includes IdealGasPhase), species can now be added dynamically without
affecting the phase state.
 2016-04-15 20:56:24 -04:00
Ray Speth
7ee47585ae [Test] Fix compiler warnings in tests 2016-04-15 17:33:11 -04:00
Ray Speth
1f231d1dd0 [Kinetics] Eliminate need for 'finalize' method 
All reaction-sized arrays are now allocated as reactions are added, which means
that the finalize() method is unnecessary and reactions can be continuously
added, even after the Kinetics object has been used for rate calculations.
 2016-04-15 17:05:10 -04:00
Ray Speth
4428a62f3c [Thermo] Add ability to modify species data for existing Phase objects 2016-04-15 15:32:38 -04:00
Ray Speth
13fa0c7a4f Add invalidateCache() function to ThermoPhase and Kinetics 
This can be used to invalidate cached data after a change to underlying data
such as species thermo coefficients or reaction rate coefficients. Needs to be
user-accessible so that dependent objects can be updated manually.
 2016-04-15 15:32:38 -04:00
Ray Speth
eda9fc8f23 [Equil] Add vcs_VolPhase::eos_name; deprecate string16_EOSType 2016-04-15 15:31:23 -04:00
Ray Speth
5bf57795fc [Doc] Add slicing and dict-based compositions to Python tutorial 2016-04-15 13:00:48 -04:00
Ray Speth
fb346d85bc [Doc] Add detailed descriptions to classes ChebyshevRate and Plog 
The descriptions are essentially taken from the CTI guide (reactions.rst)
 2016-04-15 12:31:19 -04:00
Ray Speth
7124385292 [Test] Make deprecation warnings fatal in test suites 
This ensures that deprecated methods aren't being called anywhere in the test
suite, without having to manually scan the test output for warning messages.
 2016-04-15 12:04:08 -04:00
Ray Speth
9a848fbd0e [Equil] Deprecate unused internal VCS functions 2016-04-14 23:29:33 -04:00
Ray Speth
70824559ce [Test/Equil] Update tests to sometimes use VCS 'estimate_equil' option 2016-04-14 21:51:53 -04:00
Ray Speth
ef441e4182 [CTML] Deprecate getFloatDefaultUnits 
This function is unnecessarily complicated and rarely needed.
 2016-04-14 19:41:44 -04:00
Ray Speth
a288d5c6f7 [1D] Make Jacobian atol independent of compiler optimizations 
If compiling with -funsafe-math-optimizations, this method of attempting to
calculate the floating point epsilon value would fail.
 2016-04-14 19:00:00 -04:00
Ray Speth
f2b68d8c34 [Examples] General cleanup of C++ flamespeed example 2016-04-14 15:31:50 -04:00
Ray Speth
b50ef03838 [Examples] Update C++ flamespeed to use current best-practices 
Wider, uniform initial grid; initial profiles with zero-gradient section
on both ends of the domain; skip initial fixed-temperature solve.
 2016-04-14 15:31:49 -04:00
Ray Speth
c0c9a4ef31 [Test] Add more tests of DenseMatrix 2016-04-13 21:11:05 -04:00
Ray Speth
7af1b4b60f [Numerics] Fix invalid memory access in DenseMatrix increment 
This method now works for rectangular matrices
 2016-04-13 21:11:05 -04:00
Ray Speth
bd24aeb926 [Numerics] Fix DenseMatrix::mult to work for rectangular matrices 2016-04-13 21:11:05 -04:00