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Author SHA1 Message Date
Ray Speth
d1cda15f42 Improve performance of importing phases 
Replace the O(k) implementation of Phase::speciesIndex with one that is
O(log(k)). This function is called frequently as part of Kinetics object
initialization. Optimize for the more common case where the species name is not
qualified with a phase name.
 2015-04-14 15:29:28 -04:00
Ray Speth
bde0f1466d [Thermo] Add index-based accessor for Species objects 2015-04-14 15:29:28 -04:00
Ray Speth
882a4986da Remove 'thermo' argument from Species constructor 
Since the Species object now stores its SpeciesThermoInterpType contents as a
shared_ptr, it is undesirable to have the Species constructor take this as a raw
pointer argument.
 2015-04-14 15:29:28 -04:00
Ray Speth
43952b30fc [Thermo] Use shared_ptr<Species> in ThermoPhase 2015-04-14 15:29:28 -04:00
Ray Speth
8f36e524fe Do species indexing in GeneralSpeciesThermo instead of STIT 
This means that GeneralSpeciesThermo no longer modifies the
SpeciesThermoInterpType objects, permitting them to be shared between
ThermoPhase objects.
 2015-04-14 15:29:28 -04:00
Ray Speth
5195e4f9b8 [Thermo] Use shared_ptr to STIT objects in Species and SpeciesThermo 
Exclusive ownership of the SpeciesThermoInterpType objects is no longer assumed.
 2015-04-14 15:29:28 -04:00
Ray Speth
35dbe37bf7 [Thermo] Deprecate SpeciesThermo::install 
The install_STIT method should be used instead.
 2015-04-14 15:29:28 -04:00
Ray Speth
a1599ac921 [Thermo] Add 'index' argument to GeneralSpeciesThermo::install_STIT 
This is a prerequisite to removing the species index as a property of the
SpeciesThermoInterpType object and making it independent of any specific
ThermoPhase object.
 2015-04-14 15:29:28 -04:00
Ray Speth
1dd7b214b5 [Thermo] Deprecate unused method 'getUnitsStandardConc' 
First step in resolving Issue #96
 2015-04-14 15:18:20 -04:00
Ray Speth
df971368a9 Remove some unnecessary files 2015-04-14 14:53:48 -04:00
Ray Speth
258fb8ed57 [Matlab] Add missing 'clear' functions 
Without these functions, it was impossible to use these classes
without leaking memory. Even with these functions, the memory is
released only when these functions are explicitly called, as
old-style Matlab classes have no notion of a destructor.

Fixes #252.
 2015-04-11 10:54:52 -04:00
Ray Speth
2161060743 [Matlab] Fix clear(Reactor) to delete the reactor instead of copying 2015-04-10 23:44:55 -04:00
Ray Speth
c540e67d50 [Thermo] Deprecate non-functional 'testProb' constructors 
These "test problem" constructors don't actually do anything, and most of them
can't be used because the corresponding input files don't exist.
 2015-04-09 19:04:08 -04:00
Ray Speth
23ad04f882 [Transport] Deprecate non-functional AqueousTransport class 
This class has been broken since 2009. Note the vectors m_visccoeffs,
m_condcoeffs, and m_diffcoeffs, which are used but never initialized.
 2015-04-09 18:54:05 -04:00
Ray Speth
b495262aff [Matlab] 'cleanup' now deletes all Cantera objects 
'cleanup' previously only deleted ThermoPhase, Kinetics, Transport, Domain1D,
Sim1D, and XML_Node objects, while missing all objects associated with reactor
networks (Reactor, ReactorNet, FlowDevice, Wall), MultiPhase, Func1, and
reaction paths (ReactionPathBuilder, ReactionPathDiagram).

Fixes #251.
 2015-04-08 23:08:42 -04:00
Ray Speth
f59bcdf057 [Thermo/Doc] Fix incorrect SurfPhase docstrings 
These docstrings were just copied from unimplemented virtual methods in class
ThermoPhase.
 2015-04-08 19:44:16 -04:00
Ray Speth
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
7fdef37e4b Replace Google Code URLs 2015-04-07 18:24:55 -04:00
Ray Speth
7ff9836648 [Doc] Update compilation instructions to reflect Github migration 2015-04-07 18:20:47 -04:00
Ray Speth
2c26e50244 Update README formatting and resource locations 2015-04-07 18:06:05 -04:00
Ray Speth
6545481928 Move README to README.rst so Github will format it nicely 2015-04-07 18:01:06 -04:00
Ray Speth
eb18f34f47 [Python] Fix class docstrings of composite classes 
These were being hidden by incorrectly placed __slots__ attributes (the
docstring must appear first).
 2015-04-07 17:58:26 -04:00
Ray Speth
a981622981 [Python] Add transport_model override option to Solution constructor 
This keyword argument allows the transport model specified in a CTI/XML file to
be overridden when creating the object. Can be used to speed up Solution
initialization by specifying 'transport_model=None', which is especially useful
for large mechanisms where transport initialization scales as species number
squared.
 2015-04-07 17:58:26 -04:00
Ray Speth
79b3a8ae39 [ck2cti] Allow arbitrary reactant stoichiometries 
There is no reason to disallow more than 3 reactants
 2015-04-07 17:58:26 -04:00
Ray Speth
c757c3bc76 Add include guard to smart_ptr.h 2015-03-10 22:41:53 +00:00
Ray Speth
57856254f7 Change Python module URL to point to cantera.org 2015-03-10 22:41:49 +00:00
Ray Speth
d5aba63018 Update 'AUTHORS' file to acknowledge additional contributors 2015-03-10 22:41:45 +00:00
Ray Speth
8780ef68b0 [Doc] Update supported software versions 2015-03-10 22:41:41 +00:00
Ray Speth
6898976218 [Doc] Update compilation documentation 2015-03-10 22:41:37 +00:00
Ray Speth
a609631981 [Doc] Add glossary defining various abbreviations 2015-03-10 22:41:33 +00:00
Ray Speth
838f435ca9 [Kinetics] Deprecate class ExchangeCurrent 
Unused duplicate of class Arrhenius
 2015-03-10 22:41:29 +00:00
Ray Speth
4890cccb03 [Doc] Update phase report examples to show compact species output 2015-03-10 22:41:23 +00:00
Ray Speth
86f0058a0c [Doc] Fix some inconsistencies in the Python tutorial 
Resolves Issue 255.
 2015-03-10 22:41:19 +00:00
Ray Speth
ab2beb4c64 [Reactor] Check that contents are assigned before starting integration 2015-02-28 00:24:38 +00:00
Ray Speth
eca79a5332 [Examples/1D] Use uniform initial grids in flame simulation examples 2015-02-28 00:24:32 +00:00
Ray Speth
603e321a37 [Cython] Fix treatment of writelogendl() 
Both writelog and writelogendl should be passed through PySys_WriteStdout to
ensure that they are printed in the correct order. Problems with this were
identified in the 1D solver log when using Python 3.
 2015-02-28 00:24:29 +00:00
Ray Speth
5534c15bc5 [Examples] Use IdealGasConstPressureReactor in sensitivity example 2015-02-28 00:24:25 +00:00
Ray Speth
ff3a1cc385 [Cython/Reactor] Fix setting reactor name through the constructor 
This parameter wasn't being passed from Reactor to ReactorBase
 2015-02-28 00:24:22 +00:00
Ray Speth
a15cb7d95c [Doc] Improve OS X installation instructions 
Reflect changes due to 10.10 and current Xcode versions. Improve organization
and describe some steps in greater detail. Thanks to Ingmar Schoegl for
suggesting some of the improvements.

Resolves Issue 254.
 2015-02-28 00:24:19 +00:00
Ray Speth
88dcff9c47 [Doc] Update instructions for installing Windows dependencies with pip 2015-02-28 00:24:15 +00:00
Ray Speth
7cdeedb91b [Transport] Provide transitional 'TransportFactory::initTransport' 
There are user-provided classes derived from GasTransport which still call this
method, so a version of it that calls the new method for initializing
GasTransport objects needs to be provided until after Cantera 2.2.
 2015-02-26 21:59:37 +00:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
5592a52e0f Remove unnecessary use of 'extern' 2015-02-26 21:54:11 +00:00
Ray Speth
cf3ad30537 [Kinetics] Changing a rate multiplier invalidates existing ROPs 2015-02-26 21:54:04 +00:00
Ray Speth
cc17716182 Cleanup trailing whitespace 2015-02-26 21:52:52 +00:00
Ray Speth
72e0d650b4 [ck2cti] Automatically add the 'negative_A' flag where necessary 2015-02-26 00:13:39 +00:00
Ray Speth
74f1cf05b1 [ck2cti] Narrow implicit end-of-section test 
Assume that the new section label must be the first word on a line
 2015-02-26 00:13:34 +00:00
Ray Speth
26c6d93168 [Kinetics] Fix options for skipping undeclared species / third bodies 2015-02-26 00:13:29 +00:00
Ray Speth
e3c598a619 [Doc] Fix formatting problem in OS X installation instructions 2015-02-25 19:48:38 +00:00
Ray Speth
60c221c845 [Kinetics] Combine ThirdBodyMgr and Enhanced3BConc as ThirdBodyCalc 
The old classes are now deprecated. The name change was needed to avoid
collisions with no-longer-necessary template parameter.
 2015-02-20 23:44:41 +00:00