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1744 commits

Author SHA1 Message Date
Ray Speth
bbe2e1c79b [Python] Add access to properties of simple reaction types 
This includes ElementaryReaction and ThirdBodyReaction
 2015-04-23 18:10:15 -04:00
Ray Speth
3ad02817c5 [Kinetics] Refactor KineticsFactory::newKinetics 
Eliminate redundant implementations, eliminate unnecessary static arrays,
and fix cases which were missing in the newKinetics(string) version.
 2015-04-22 14:08:24 -04:00
Ray Speth
25953f94d4 [Transport] Make transport XML node optional 
The default is equivalent to specifying <transport model="None">
 2015-04-22 14:08:24 -04:00
Ray Speth
a4ba47594c [Python] Add functions for creating Species objects from CTI/XML 2015-04-22 14:08:24 -04:00
Ray Speth
f3eaef1675 [CTI] Strip leading whitespace when converting CTI strings 
Leading whitespace would normally result in a Python IndentationError.
 2015-04-20 18:34:39 -04:00
Ray Speth
b0e5b13913 Remove redundant, unnamed root XML node from parsed documents 
XML_Node::build will make that node the root node (i.e. the 'ctml' node)
of the tree, instead of giving that node a child node containing the actual
root node.
 2015-04-20 18:34:39 -04:00
Ray Speth
39b93d3690 Allow XML documents without an XML declaration node 2015-04-20 18:34:38 -04:00
Ray Speth
96cf312ec6 [Thermo] Always add species using Species objects 
Deprecate the non-Species-based addSpecies and addUniqueSpecies
functions.
 2015-04-20 18:34:38 -04:00
Ray Speth
2ca603838d [Thermo] Extract 'newSpecies(XML_Node&) from thermo initialization 
VPStandardStateTP phases now use the same pathway for adding species as
other phase in importPhase. Deprecate the now-unused 'installSpecies'
function.
 2015-04-20 18:34:37 -04:00
Ray Speth
d27b9ef9b1 [Thermo] Species size defaults to 1.0 
This mostly affects surface phases, where a species size of 0 causes
several problems.
 2015-04-20 18:34:37 -04:00
Ray Speth
a471e4316a [Thermo] Phase::addSpecies takes shared_ptr by value 
This helps to clarify that addSpecies stores a copy of the shared_ptr.
 2015-04-20 18:34:37 -04:00
Ray Speth
a63874e4b4 [Transport] Refactor TransportData initialization 2015-04-20 18:34:36 -04:00
Ray Speth
71f912d211 [Python] Add basic access to Species objects 2015-04-17 19:06:43 -04:00
Ray Speth
aee6cc14ac [Transport] Remove 'name' variable from TransportData 
This was used only for validation error messages, but in that case we can just
use the Species object which is available during validation.
 2015-04-17 19:06:43 -04:00
Ray Speth
7d170a9989 [Thermo] newSpeciesThermoInterpType argument is the 'thermo' XML node 
No data from the outer 'species' node is needed to instantiate the
SpeciesThermoInterpType object, so this function can just take the 'thermo' node
directly.
 2015-04-17 19:06:43 -04:00
Ray Speth
1b0970a494 [Thermo] Remove species name argument from STIT factory functions 
This argument was used only in error messages, which can be reported more
uniformly if implemented at a higher level.
 2015-04-17 19:06:43 -04:00
Ray Speth
ec1d7d7382 Fix compilier warnings about unused variables 2015-04-14 16:08:10 -04:00
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
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
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
838f435ca9 [Kinetics] Deprecate class ExchangeCurrent 
Unused duplicate of class Arrhenius
 2015-03-10 22:41:29 +00:00
Ray Speth
ab2beb4c64 [Reactor] Check that contents are assigned before starting integration 2015-02-28 00:24:38 +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
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
26c6d93168 [Kinetics] Fix options for skipping undeclared species / third bodies 2015-02-26 00:13:29 +00:00
Ray Speth
dab74d2d10 [Thermo] Deprecate mean_Y and sum_xlogQ methods of class Phase 2015-02-20 23:44:36 +00:00
Ray Speth
2ed8552939 [Thermo] Add a version of Phase::mean_X that takes vector_fp 
This simplifies all internal calls to this function
 2015-02-20 23:44:21 +00:00
Ray Speth
0ad8d45baf [Thermo] Deprecate classes PseudoBinaryVPSSTP and electrodeElectron 2015-02-20 23:43:29 +00:00
Ray Speth
09ce99dc83 [Thermo] Eliminate redundant assignment of m_kk 
m_kk is automatically set as species are added to a phase.
 2015-02-20 23:43:12 +00:00
Ray Speth
42e7061bd8 [Thermo] Remove unnecessary counter variables 
These counter variables just stored the length of another std::vector
member variable.
 2015-02-20 23:43:04 +00:00
Ray Speth
17bb09a2da [Equil] Remove unused member variables from VCS_SPECIES_THERMO 2015-02-20 23:42:54 +00:00
Ray Speth
999a6e4615 [Thermo] Add missing variable to GeneralSpeciesThermo copy constructor 
(and assignment operator)
 2015-02-20 00:11:37 +00:00
Ray Speth
b4492cb8a3 [Thermo] Whitespace cleanup in MaskellSolidSolnPhase 2015-02-20 00:11:30 +00:00
Ray Speth
d7cbb30086 Eliminate unnecessary manual memory management of XML_Node 
This also eliminates memory leaks that would occur if an exception were raised
in these methods.
 2015-02-20 00:11:19 +00:00
Ray Speth
70b51c797c Fix function named specified in checkReactionBalance exception message 2015-02-20 00:11:16 +00:00
Ray Speth
e545d123c2 [Kinetics] Relax tolerance on reaction element balance 
This allows use of some mechanisms with imprecise fractional product
stoichiometries.
 2015-02-20 00:11:12 +00:00
Ray Speth
79cf2dcba7 Remove empty comment blocks 2015-02-20 00:11:05 +00:00
Thomas Fiala
4bc4fda90c Add C++ and Cython support for computing elemental mass/mole fractions 2015-02-17 23:23:51 +00:00