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Author SHA1 Message Date
Ray Speth
822cdc7d38 [Thermo] Always use PDSS_ConstVol for constant volume standard state 
Remove the redundant (and questionable) implementation of this from the
PDSS_SSVol class. Also fix some values in PDSS_SSVol that were not updated
except in the constant volume case.
 2017-08-13 23:59:49 -04:00
Ray Speth
4c630fc592 [Thermo] Make PDSS_HKFT constructible without XML 
Also fixes PDSS_HKFT to actually make use of the units specified for each input
constant.
 2017-08-13 23:59:49 -04:00
Ray Speth
0ca788bd69 [Thermo] Look up standard entropy when adding undefined elements 2017-08-13 23:59:49 -04:00
Bryan W. Weber
c88ddce0d6 [Test/1D] Test getRefineCriteria 2017-08-09 18:46:47 -04:00
Bryan W. Weber
4b44c66182 [1D/Cython] Adds Python interface to getRefineCriteria 2017-08-09 18:46:47 -04:00
Bryan W. Weber
bce4210e1b [1D] Adds getRefineCriteria function 2017-08-09 18:46:47 -04:00
Ray Speth
572af616e7 [Thermo] Remove optional debug printing from HMWSoln 2017-08-07 21:47:10 -04:00
Ray Speth
e9f08fc58e [Thermo] Move implementation of HMWSoln into a single file 2017-08-07 21:33:02 -04:00
Ray Speth
3790115b99 [Thermo] Make HMWSolution constructible without XML 2017-08-07 21:32:15 -04:00
Ray Speth
4b69c7f265 [Thermo] Remove unused ionic radius from HMWSoln 2017-08-07 20:58:18 -04:00
Ray Speth
d07908f9c9 [Thermo] Clean up HMWSoln variables used in cutoff calculation 2017-08-07 20:58:18 -04:00
Ray Speth
1bd950fef5 [XML] Make searches for child nodes case insensitive 2017-08-07 20:58:17 -04:00
Ray Speth
6ca782030d [Thermo] Remove unused data from HMWSoln 
The model implemented does not use the weak acid / "electrolyte species type"
concept, so there is no reason to read data about this from the input file.
 2017-08-07 20:57:34 -04:00
Ray Speth
cfc3b728f5 [Thermo] Remove m_formGC and m_formPitzer switches from HMWSoln 
These switches only had one possible value, so were not actually useful.
 2017-08-07 20:57:34 -04:00
Ray Speth
e33fe6904d [Thermo] Solvent is always the first species 
No useful capabilities are provided by allowing the solvent species to vary, and
there are many places where the solvent was already implicitly assumed to be the
first species.
 2017-08-07 20:57:34 -04:00
Ray Speth
e3afaf5e61 [Thermo] Make IonsFromNeutral constructible without XML 2017-08-07 20:57:34 -04:00
Ray Speth
7fab7f3cd3 Add boolean and integer types to AnyMap 2017-08-07 20:57:34 -04:00
Ray Speth
c85ba586d2 [Thermo] Remove unused variable MolarityIonicVPSSTP::indexSpecialSpecies_ 2017-08-07 20:57:34 -04:00
Ray Speth
4856d1328b [Thermo] Make IonsFromNeutralVPSSTP::neutralMoleculePhase_ a shared_ptr 
Also make it non-public and add getters and setters
 2017-08-07 20:57:34 -04:00
Ray Speth
338b21694f [Test] Add regression checks to IonsFromNeutralConstructor.fromXML 2017-08-07 20:57:34 -04:00
Ray Speth
aa02d24235 [Thermo] Allow instantiation of IdealSolidSolnPhase without XML 2017-08-07 20:57:34 -04:00
Ray Speth
8a4142d4bc [Python] Raise exception when setting composition with empty array 2017-08-07 15:39:13 -04:00
Ray Speth
4c489c175d [Kinetics] Fix duplicate reaction check to handle unchanged species 2017-08-02 16:46:24 -04:00
Ray Speth
513b43200c [Kinetics] Fix indexing error in Kinetics::checkDuplicates 2017-08-02 16:46:24 -04:00
Ray Speth
45891a2118 [CI] Use system Python 3 on Travis 2017-07-31 21:15:36 -04:00
Ray Speth
9e5da87a2a [CI] Force Travis builds to use Trusty 2017-07-31 21:15:32 -04:00
Ray Speth
3f69f6ac8a [SCons] Make issues importing NumPy easier to diagnose 2017-07-31 17:26:09 -04:00
Ray Speth
3d03795c4f [Python] Set minimum NumPy version to 1.8.1. 
Minimum set based on a regression in NumPy 1.8.0 which affects the SolutionArray
class.

This makes Trusty Tahr (14.04) the oldest supported version of Ubuntu (using the
Ubuntu-provided NumPy package).

Resolves #445.
 2017-07-30 14:39:57 -04:00
Ray Speth
d4338249fb [Thermo] Remove debug exception from Phase::entropyElement298 
Returning the special value ENTROPY298_UNKNOWN is (apparently) the expected
behavior if no actual value was provided, and should not result in an exception.
 2017-07-30 14:28:18 -04:00
Ray Speth
8d953a9424 [Python] Make Python module compatible with Cython 0.26 
Cython 0.26 unexpectedly removed automatic conversions of C++ containers to
Python containers. Explicit casting provides the old behavior.

Fixes #465
 2017-07-30 14:28:18 -04:00
Ray Speth
3676672eec [Thermo] Allow instantiation of LatticeSolidPhase without XML 2017-07-17 23:41:44 -04:00
Ray Speth
04f10972c8 [Thermo] Store sub-lattices as shared_ptr in LatticeSolidPhase 
Also eliminates undefined behavior associated with unchecked cast to
LatticePhase*, since, at least in the Li7Si3_ls.xml example file, the
sub-lattices can be represented as other ThermoPhase types,
e.g. StoichSubstance.
 2017-07-17 23:41:44 -04:00
Ray Speth
d744bd9fb8 [Thermo] Allow instantiation of LatticePhase without XML 2017-07-17 23:41:44 -04:00
Ray Speth
6bfd82e0be [Thermo] Remove unused "vacancy species" from LatticePhase 2017-07-17 23:41:44 -04:00
Ray Speth
f3ba29f0bc [Thermo] Fix default molar volume in LatticePhase 
Molar volume is the inverse of molar "site" density
 2017-07-17 23:41:44 -04:00
Ray Speth
37be501a68 [Test] Modify DebyeHuckel test to utilize PDSS_Water class 2017-07-17 23:41:44 -04:00
Ray Speth
a5b0bdf695 [Python] Make activity coefficients and activities accessible 2017-07-17 23:41:44 -04:00
Ray Speth
90d18dd337 Remove some unused, inaccessible variables 2017-07-17 23:41:44 -04:00
Ray Speth
9c084d5c84 Fix compiler warnings associated with AnyMap 2017-07-17 23:41:44 -04:00
Ray Speth
f69ef44600 [Thermo] Allow instantiation of MargulesVPSSTP without XML 2017-07-17 23:41:44 -04:00
Ray Speth
4818c87344 [Thermo] Remove unused members of MargulesVPSSTP 2017-07-17 23:41:44 -04:00
Ray Speth
44b24ca873 [ctml_writer] Fix handling of third body names containing parentheses 
Replace the heuristic used to remove the third body terms from the
reactant and product lists to handle species names that include
parentheses.
 2017-07-12 09:16:24 -04:00
Ray Speth
6d591b82ef [ck2cti] Fix reactions with pathologically named third bodies 
This changes the order in which tokens are identified to be strictly
descending in length, so that third bodies are identified correctly
even when the third body expression could potentially be interpreted
as containing a standalone species name.
 2017-07-12 09:16:24 -04:00
Richard West
55a8910686 A failing unit test for chemkin files with weird names in PDep rates. 
Reactions of the type
 A (+B) <=> C (+B)
ought to work, as long as they are provided a pressure-dependent rate
expression. This commit adds three examples to the test file. The first
works OK, the second two cause problems.

(For what it's worth, this currently crashes the official chemkin.
 Or at least the parentheses do; I've not tested the plus.
 Ansys have created a defect record and say they will fix the issue.)
 2017-07-12 09:16:24 -04:00
Tilman Bremer
b41038f84b stylevalue 'setlinewidth' is deprecated, replaced it together with the whole style argument by 'penwidth' 2017-07-11 18:59:03 -04:00
Bryan W. Weber
35ac1acfa8 Clarify Valve coefficient vs function 2017-07-11 18:26:55 -04:00
Bryan W. Weber
fec6c34ed8 Remove more references to importPhase in Matlab docs 2017-07-11 18:26:55 -04:00
Bryan W. Weber
05809bb027 Fix small typos in docs 2017-07-11 18:26:55 -04:00
Steven DeCaluwe
04be9888ed Update importKinetics to identify unspecified electrochemical reactions 
Add test coverage for beta default value for electrochem reactions
 2017-07-06 18:14:09 -04:00
Bryan W. Weber
6bf74d179b
Handle bad representations of geometry flags 
If geometry flags are specified rather that can't be cast to integers,
intercept the ValueError raised by Python and raise a more sensible
exception.

Fixes #446
 2017-06-14 17:39:52 -04:00