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Author SHA1 Message Date
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
af19481b65 [Doc] Remove some incorrect copy/pasted docstrings 2016-04-16 17:26:49 -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
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
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
ef441e4182 [CTML] Deprecate getFloatDefaultUnits 
This function is unnecessarily complicated and rarely needed.
 2016-04-14 19:41:44 -04:00
Ray Speth
bd24aeb926 [Numerics] Fix DenseMatrix::mult to work for rectangular matrices 2016-04-13 21:11:05 -04:00
Ray Speth
9ed23a57ab Move non-trivial functions out of header files 2016-04-08 19:13:09 -04:00
Ray Speth
b7f9f230a7 [Equil] Replace (vcs_)print_stringTrunc with usage of cppformat 2016-04-06 23:08:37 -04:00
Ray Speth
511a39fc73 [Equil] Standardize VCS solver to always use MKS units 2016-04-05 12:52:01 -04:00
Ray Speth
a60217cfc6 [Equil] Make better use of local variables 2016-04-05 12:52:01 -04:00
Ray Speth
4c5301d6cd [1D] Initialize number-of-steps counter at start of solve 
Fixes the enforcement of the maximum number of steps constraint if solve() is
called again after an exception.
 2016-03-28 17:13:24 -04:00
Ray Speth
2e3726fe5f [Thermo] Mark overrides of ThermoPhase methods as virtual consistently 2016-03-28 00:01:39 -04:00
Ray Speth
bec0c88e32 [Thermo] Remove unnecessary overloads of getElectrochemPotentials 2016-03-27 23:18:26 -04:00
Ray Speth
0995725a13 [1D] Deprecate unused methods of Domain1D 2016-03-27 22:19:38 -04:00
Ray Speth
1aa28f9310 Let the constructor for std::string do its job 2016-03-27 22:19:38 -04:00
Ray Speth
9c632cf123 [1D] Remove unused / unimplemented methods from StFlow 2016-03-27 22:19:37 -04:00
Ray Speth
b56094b183 [1D/Examples] eliminate unnecessary setting of tolerances 
For most problems, these new default tolerances for both time stepping and
steady state solves are more likely to converge than tighter tolerances, but
still give well-resolved results. Tighter tolerances are required in some cases,
e.g. when evaluating sensitivity coefficients by finite difference.
 2016-03-27 17:07:36 -04:00
Ray Speth
5e35ca5486 [1D] Allow replacing flow domain grid after creating Sim1D 
This makes it possible to try solving on a different grid if the initial
solution attempt fails without needing to recreate the Sim1D object.
 2016-03-27 17:07:36 -04:00
Ray Speth
f13e2715bb [1D] Add accessor functions for steady and relative tolerances 
The existing functions for getting tolerances are difficult to use because
they return the tolerances based on the steady/unsteady mode of the solver
which the user shouldn't have to care about (and can't easily set).
 2016-03-27 17:07:36 -04:00
Ray Speth
80b8cd7e2b [1D] Remove Bdry1D::m_nv which shadowed Domain1D::m_nv 2016-03-27 17:07:36 -04:00
Ray Speth
9f3821db82 [1D] Use most prevalent species to impose sum-of-mass-fractions constraint 
Previously, the first species was always used, which could cause problems with
negative mass fractions in cases where the first species has a mass fraction
near zero.
 2016-03-27 17:07:36 -04:00
Ray Speth
b99ba44f13 Fix SurfPhase::setCoveragesNoNorm to retain negative coverages 
This prevents Jacobian singularities due to (trivial) negative coverages,
e.g. in ReactingSurf1D.
 2016-03-27 17:07:36 -04:00
Ray Speth
af5bbf74a4 [1D] Improve Jacobian evaluation for ReactingSurf1D 
Don't normalize coverages when evaluating the residual normally -- only as part
of recovering from a failed timestep, like what is done in StFlow.
 2016-03-27 17:07:36 -04:00
Ray Speth
81074b2b4a [1D] Add function for restoring last successful steady-state solution 2016-03-27 17:07:36 -04:00
Ray Speth
29b704916c [1D] Set limit on number of timesteps without reaching steady state 2016-03-27 17:07:36 -04:00
Ray Speth
532e132788 [1D] Add accessors for solver statistics 
Previously, this information was only available in the text output of the
'showStats' function.
 2016-03-27 17:07:35 -04:00
Ray Speth
11b665b00a [1D] Keep track of number of time steps taken before each steady-state solve 2016-03-27 17:07:35 -04:00
Ray Speth
318fa04cf7 [1D] Reset negative species concentrations after a failed time step 2016-03-27 17:07:35 -04:00
Ray Speth
832ee88692 [1D] Add ability to access last successful timestepped solution 
This can be helpful when debugging 1D solver failures.
 2016-03-25 12:21:19 -04:00
Ray Speth
73246130fa [1D] Fix docstrings for OneDim::eval and StFlow::eval 2016-03-25 12:21:19 -04:00
Ray Speth
d20ab891e8 [1D] add function for getting info about a solution component 2016-03-25 12:21:19 -04:00
imitrichev
8b3557ee4d Clarified surface coverage modification equation 
Now it is shown it is identical to equation from Sphinx cti
module docs (eq. also used in Surface CHEMKIN)

Resolves #322
 2016-03-06 19:11:16 -05:00
pwcnorthrop
125d2e0e23 Add RedlichKisterVPSSTP::s_update_dlnActCoeff_dlnX_diag() 
Fixes bug in RedlichKisterVPSSTP::getlnActCoeffdlnX_diag() which would always return 0

Resolves #293
 2016-02-17 23:34:36 -05:00
Ray Speth
b55c8fe813 Replace overly-specific exception types with CanteraError 
Deprecate exception types which are now unused.
 2016-02-04 19:34:26 -05:00
Ray Speth
f44b5fed57 Replace usage of int2str with cppformat and deprecate int2str 2016-02-04 19:11:49 -05:00
Ray Speth
f91afda8cb Replace usage of fp2str with cppformat and deprecate fp2str 2016-02-04 19:11:45 -05:00
Ray Speth
84ede11e6a Remove unimplemented method SimpleTransport::updateViscosities_C 2016-02-02 23:14:35 -05:00
Bryan W. Weber
97697e09e1 Overwritten -> Overridden 2016-01-25 13:14:50 -05:00
Bryan W. Weber
63cfed1503 Add functions to set property pairs specified in Sub.cpp 
Add functions to set the unimplemented property pairs specified
in the Substance::Set function of Sub.cpp
 2016-01-25 13:07:34 -05:00
Bryan W. Weber
31316b7079 Switch PureFluidPhase to use double instead of doublereal 2016-01-25 13:07:34 -05:00
Bryan W. Weber
9970b4bcc5 Fix typo in ThermoPhase.h 2016-01-25 13:07:34 -05:00
Bryan W. Weber
28e8fa1d2d Whitespace fixup in comments in ThermoPhase.h 2016-01-25 13:07:34 -05:00