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331 commits

Author SHA1 Message Date
Ray Speth
5214672ab3 Merge namespace ctml with namespace Cantera 2015-05-27 18:09:07 -04:00
Ray Speth
1c878c16de Fix issues indicated by compiler warnings 2015-05-26 11:42:20 -04:00
Ray Speth
341b137766 [Doc] Capitalize proper nouns and acronyms 2015-05-25 20:58:44 -04:00
Ray Speth
51c8d7365a [Doc] Fix spelling errors 2015-05-25 20:57:19 -04:00
Ray Speth
522c563810 [Thermo] Surface coverages can be set using a compositionMap 2015-05-02 20:07:44 -04:00
Ray Speth
bc4c71f8ee [Thermo] Ensure that site density is always positive 
A site density of zero causes divide-by-zero errors in SurfPhase and
EdgePhase. This change makes it possible to initialize SurfPhase and
EdgePhase objects without XML phase descriptions.
 2015-04-28 17:13:11 -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
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
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
ecb6242b79 Fix spelling errors 2015-04-08 19:36:55 -04:00
Ray Speth
2e53890adf Minor cleanup of constructors and destructors 2015-02-26 21:58:42 +00:00
Ray Speth
cc17716182 Cleanup trailing whitespace 2015-02-26 21:52:52 +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
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
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
Ray Speth
71d57330b6 [Thermo] Deprecate methods of IdealGasPhase that only worked for StatMech 2015-02-12 04:04:51 +00:00
Ray Speth
7acf0378c6 [Thermo] Improve usage of local variables 
Also eliminate some unnecessary temporary variables.
 2015-02-12 04:04:18 +00:00
Ray Speth
efb80dfe05 Remove unnecessary delimiter lines between functions 
A single line of white space is sufficient and consistent. Also moved a couple
Doxygen strings out of source files.
 2015-01-22 00:04:24 +00:00
Ray Speth
b8a99b4b83 Remove unnecessary explicit calls to default constructors 2015-01-22 00:04:12 +00:00
Ray Speth
0a3332aa43 [Thermo] Add simpler constructors for SpeciesThermoInterpType objects 
These objects do not need to know the index of the species within the phase, so
the new constructors do not take that as an argument.

For the NASA polynomial constructors, the order of the coefficients arrays in
the new constructors has been modified to match the conventional ordering of the
coefficients as written in thermo database files.
 2015-01-22 00:04:06 +00:00
Ray Speth
ad1cd8c7bb Remove unnecessary numerical constants 2015-01-15 21:15:07 +00:00
Ray Speth
2a50dc50f7 [Thermo] Add accessor for Species objects 2015-01-08 23:36:24 +00:00
Ray Speth
8022e9e01e [Transport] Add gas phase transport parameters to Species objects 2015-01-08 23:36:22 +00:00
Ray Speth
ba42bc6da2 [Doc] Remove suppression of Doxygen autolinking 
In those cases where the name is actually a reference to the class, we actually
want Doxygen to apply formatting to the name and link to the class's
documentation, so we shouldn't suppress that behavior with the prepended '%'.
 2014-12-05 23:33:24 +00:00