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Author SHA1 Message Date
Ray Speth
8bee138553 [Kinetics] Add access to reactant and product strings 
In C++, these are the reactantString() and productString() methods.  In Python,
these are the 'reactants' and 'products' properties.

Resolves Issue 110.
 2014-06-20 18:45:17 +00:00
Ray Speth
a470502932 [Transport] Replace transport_log.xml with regular text logging 
Write plain text to the common Cantera logger to be more consistent with the
verbose/debug logging from other parts of Cantera. This simplifies several of
the transport initialization functions, and eliminates the need for class
XML_Writer.
 2014-06-20 18:44:59 +00:00
Ray Speth
284c0d0345 Remove unimplemented 'potentialEnergy' methods from IdealMolalSoln 2014-06-20 18:44:53 +00:00
Ray Speth
3349a28d38 Update some deprecation warnings. 2014-06-20 18:44:39 +00:00
Ray Speth
e778afad32 Remove deprecated functions 2014-06-20 18:44:33 +00:00
Ray Speth
63dd02073c [Doc] Fix a few Doxygen warnings 2014-06-20 18:44:23 +00:00
Ray Speth
147d630f48 [Doc] Remove references to nonexistent source file 'importCTML.cpp' 2014-06-20 18:43:51 +00:00
Ray Speth
7064fd1964 [Cython/Examples] Add reactor example with ODEs implemented in Python 2014-06-20 18:43:47 +00:00
Ray Speth
fc9ba22772 [Cython] Add methods for setting unnormalized mass/mole fractions 2014-06-20 18:43:42 +00:00
Ray Speth
a33eca6684 [Python/Samples] Add Peridic CSTR example to Python module 
Translated from the Matlab sample
 2014-06-16 22:01:54 +00:00
Ray Speth
dd297256ff [Matlab/Samples] Update to use IdealGasReactor 2014-06-16 22:01:31 +00:00
Ray Speth
049c9a1960 [Matlab/Samples] Fix broken default argument checks 
There are no classes named 'GasMix' or (lowercase) 'solution', so these checks
would always fail and the input argument would always be silently ignored.
 2014-06-16 22:01:13 +00:00
Ray Speth
6c3fdb7963 [Matlab/Samples] Remove duplicate examples 
'ignite2.m' was essentially a duplicate of 'ignite.m'
'ignite3.m' was essentially a duplicate of 'ignite_uv.m'
 2014-06-16 22:00:46 +00:00
Ray Speth
fd0db67172 [Matlab/Samples] Move reactor ODE functions into samples directory 
These functions are used by some of the examples, and show how custom
reactor-like models can be implemented in Matlab. They are useful mostly as a
basis for user modifications.
 2014-06-16 22:00:41 +00:00
Ray Speth
b4826c9b9c [Matlab/Reactor] Use 'nonorm' when setting mass fractions 2014-06-16 22:00:30 +00:00
Ray Speth
01987b4438 [Thermo] Implement missing SurfPhase functions 
Adding the entropy_mole, cp_mole, and cv_mole functions fixes the silent failure
of the report() function for surface phases.
 2014-06-16 22:00:25 +00:00
Ray Speth
6ffbaa5f77 [Reactor] Remove unneeded variables from ReactorBase 2014-06-10 16:23:43 +00:00
Ray Speth
48101ea1f4 [Reactor] Remove unneeded functions from ReactorBase 2014-06-10 16:23:24 +00:00
Ray Speth
8b5ca80303 [Reactor] Implement reactor network reinitialization 
Adds ReactorNet::reinitialize, which skips all one-time initialization and
re-uses the same CVODES integrator. The Reactor::syncState() method is
introduced for applying new initial conditions for individual Reactor objects.

This approach increases efficiency when solving many similar problems with short
integration times, for example when being used as the chemistry term integrator
in an operator-split CFD code.
 2014-06-10 16:23:03 +00:00
Ray Speth
1437aade8c [Reactor] Refactor updateState and getInitialConditions implementations 
Extract common parts related to surface species
 2014-06-10 16:22:46 +00:00
Ray Speth
67de2fa793 [Reactor] Refactor re-implementations of Reactor::initialize 
The base class methods does almost all the initialization needed for the derived
classes, so call that first and then do any additional steps needed.
 2014-06-10 16:22:37 +00:00
Ray Speth
0da063cdef [Reactor] Refactor wall / surface chemistry evaluation 
This creates a single implementation of the calculation of the contributions of
walls and surface chemistry to the governing equations for all reactor types.
 2014-06-10 16:21:56 +00:00
Ray Speth
54c14c3ac1 Remove orphaned 'Cantera_legacy.h' file 2014-06-10 16:21:46 +00:00
Ray Speth
2b9f3b9913 Remove unused Doxygen input files 2014-06-10 16:21:37 +00:00
Ray Speth
1ea1e705f3 Remove redundant 'NotImplemented' exception class 2014-06-10 16:21:16 +00:00
Ray Speth
2558ec222d [Test] Use 'assertIn' and 'assertNotIn' where possible 2014-06-10 16:21:01 +00:00
Ray Speth
7f83a49e07 [Test] Fix some incorrect assertions 2014-06-10 16:20:53 +00:00
Ray Speth
baa787f7ac [Test] Use context handler form for 'assertRaises' 2014-06-10 16:20:31 +00:00
Ray Speth
be9882a765 [ck2cti] Import the resulting mechanism to complete validation 
This relaxes the need to perform redundant validation in ck2cti.
 2014-06-06 00:18:18 +00:00
Ray Speth
c29ae666c0 [CTI] Allow non-integer atomicity 
This allows specification of lumped species with average compositions,
such as C10.6H21.8.
 2014-06-06 00:18:13 +00:00
Ray Speth
83e38480d6 Throw exceptions instead of calling std::exit after an error 
By throwing an exception, Cantera is better behaved when used within other
applications, e.g. as in the case of the Matlab and Python interfaces.
 2014-06-06 00:17:58 +00:00
Ray Speth
40290736e0 [Reactor/Samples] Cleanup of kinetics1.cpp 
Change this example to use IdealGasConstPressure reactor, which
is the preferred reactor model for this kind of simulation.
 2014-06-06 00:17:53 +00:00
Ray Speth
51d0654e47 [Reactor] Add IdealGas reactor types to zerodim.h 2014-06-06 00:17:49 +00:00
Ray Speth
a583949457 [Reactor] ReactorNet::addReactor takes a reference instead of a pointer 
This reflects how the function is usually used. The old signature is now
deprecated, as is the extra argument for transfering "ownership" to the
ReactorNet object.
 2014-06-06 00:17:41 +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
Harry Moffat
f2130b5e3f Added a missing function 2014-06-05 22:41:55 +00:00
Harry Moffat
f3a0092b42 Fixed a error introduced by Speth that caused the brine phase pop problems to fail. 2014-06-05 22:40:20 +00:00
Ray Speth
ea3f74eb27 [Thermo] 'report' only prints species with non-trivial mole fractions 
The threshold for printing species is a new, optional parameter to the
'report' function. If any species are excluded, the total number of
minor species and their aggregate mass and mole fraction are printed.
 2014-06-03 16:54:15 +00:00
Ray Speth
dbfe428437 Fix compiler warnings 
These were mostly related to changes from r2957.
 2014-06-03 16:53:40 +00:00
Ray Speth
d38e4553ec Eliminate 'goto' in VCS_SOLVE::vcs_inest 2014-06-03 16:53:34 +00:00
Ray Speth
b5396837b2 Make use of std::min, std::max, and clip 2014-06-03 16:52:43 +00:00
Ray Speth
d3667cae3c [Doc] Fix reference that wasn't being parsed correctly 2014-06-03 16:52:22 +00:00
Ray Speth
a5d735f047 [Reactor] Disable verbose output by default, even in "debug mode" 2014-06-03 16:52:09 +00:00
Ray Speth
0e9ca0fc4b [Reactor] Eliminate tracking of Reservoirs by ReactorNet 
Since Reservoirs don't have any equations to solve, there is no reason to add
them to a ReactorNet.
 2014-06-03 16:52:00 +00:00
Ray Speth
2d1003271d [Reactor] Replace ReactorNet::m_size with m_start 
A small simplification since the offset into the global solution vector is
usually what we're interested in.
 2014-06-03 16:51:47 +00:00
Ray Speth
fb588d873b Remove deprecated / unfinished 'spectra' classes 2014-05-30 19:23:37 +00:00
Ray Speth
46a36c11cb Eliminate redundant VCS vector functions 
These functions just duplicated features of the standard library.
 2014-05-30 19:23:25 +00:00
Ray Speth
c6cefd6df8 Replace IntStarStar with Array2D 2014-05-30 19:23:16 +00:00
Ray Speth
b569b842d0 Replace DoubleStarStar with Array2D 2014-05-30 19:23:03 +00:00
Ray Speth
3e39423a42 [Doc] Fix name of 'ck2cti' in man page 2014-05-30 19:22:58 +00:00