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1082 commits

Author SHA1 Message Date
Ingmar Schoegl
197c69a476 [YAML] preserve zero in Troe T2 input 2019-11-10 22:56:20 -05:00
Ray Speth
d4f9717c1c [Input] Fix handling of global Motz-Wise flag in cti2yaml 2019-11-09 11:53:16 -05:00
Bryan W. Weber
efb246d73a [cti2yaml] Add failing test of Motz-Wise option 
The global Motz-Wise option is not added to the phase specification
 2019-11-09 11:53:16 -05:00
Ingmar Schoegl
21de00c549 [Kinetics] update unit tests to probe falloff type 2019-11-08 15:18:26 -05:00
Ingmar Schoegl
e2bfba328c [Kinetics] deprecate magic numbers for falloff reactions 2019-11-08 15:18:26 -05:00
Ingmar Schoegl
91c7bf14d7 [Base] finalize introduction of Solution object in C++ layer 2019-11-08 15:12:36 -05:00
Ray Speth
ce47733c42 [Test] Fix coverage consistency issue in getMixDiffCoeffsMole 2019-11-02 15:43:05 -04:00
Ray Speth
71ba021467 Add sticking coefficients to CTI API docs 2019-11-02 10:42:35 -04:00
CyberDrudge
65f7b16f01 Implemented function to list data files 
Update function to list data files

Follow Style Guidelines

Add doc for listing files
 2019-11-01 22:18:59 -04:00
Ray Speth
a5b28ba799 [Input] Fix conversion of Ion transport in cti2yaml 2019-11-01 22:16:45 -04:00
Ray Speth
bddb339198 [Input] Fix handling of skip_undeclared_third_bodies in cti2yaml 2019-11-01 22:16:45 -04:00
Bryan W. Weber
69393e9307 [cti2yaml] Add failing ch4_ion test 2019-11-01 22:16:45 -04:00
Ingmar Schoegl
54c12fc59c [Thermo] add support for concentration string in findIsomers 2019-10-29 21:26:57 -04:00
Ingmar Schoegl
4f42164443 [Thermo] add unit tests for add_species_alias and find_isomers 2019-10-29 21:26:57 -04:00
Ingmar Schoegl
3ef99f966c [Thermo] add functions findIsomer/addSpeciesAlias 2019-10-29 21:26:57 -04:00
Ingmar Schoegl
a85396ef11 [Input/Scons] make gri30 consistent with latest online version 
Updated version keeps input and thermo separate, which requires minor
changes in the build scripts.
 2019-10-29 21:00:36 -04:00
Ingmar Schoegl
1e01054bf5 [Thermo] eliminate SolutionArray._extra_arrays 2019-10-25 15:06:31 -04:00
Ingmar Schoegl
cd67962004 [Thermo] add ability to sort SolutionArray objects 2019-10-25 15:06:31 -04:00
Ingmar Schoegl
76901b7f50 [ReactorNet] improve handling of max_time_step 
* implement ReactorNet::maxTimeStep to allow for external queries
* implement getter/setter for property ReactorNet.max_time_step
* deprecate ReactorNet.set_max_time_step
 2019-10-24 20:31:54 -04:00
Ray Speth
a221c632f4 [Test] Add tests for ck2yaml 2019-10-23 13:54:59 -04:00
Ray Speth
5cca4f22df [Input] Preserve comment after last reaction in ck2yaml 2019-10-23 13:54:59 -04:00
Ray Speth
8665eda3c1 [Input] Fix error message for unrecognized section in ck2yaml 2019-10-23 13:54:59 -04:00
Ray Speth
a085bc1f43 [Input] Check that all species have thermo before writing YAML file 2019-10-23 13:54:59 -04:00
Ray Speth
6c8adf47b3 [Input] Normalize YAML reaction equation for Chebyshev reactions 
Fix the reaction equation to always include the (+M). Previously, if the (+M)
was omitted, an invalid reaction string was generated.
 2019-10-23 13:54:59 -04:00
Ingmar Schoegl
ee41824b1e [SpeciesThermo] address review comments 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
650db397b2 [SpeciesThermo] load piecewise-Gibbs from YAML 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
d43774e721 [SpeciesThermo] enable cython constructors for Nasa9PolyMultiTempRegion 
Further:
* Add unit tests for ShomatePoly2 and Mu0Poly
 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
cb0e1f1509 [SpeciesThermo] add unit tests 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
cf8d2efa09 [SpeciesThermo] assign nCoeffs in C++ layer 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
5ab15e15ce [SpeciesThermo] add initial Cython classes 
- n_coeffs remains to be addressed (needed: number of zones)
 2019-10-23 13:53:56 -04:00
Ingmar Schoegl
dc66407cf2 [Thermo] address code review comments 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
7c08e17f08 [Thermo] deprecate Phase::id and Phase::setID 
* Merge usage of 'id' and 'name' in the context of Phase objects
* Raise deprecation warnings for Phase::id and Phase::setID
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
6e5d45273a [Thermo] replace 'phase_id' by 'name' 
* 'name' corresponds to the YAML entry
* rename Solution keyword 'phaseid' to 'name' (instead of 'phase_id')
* rename ck2yaml argument '--id' to '--name' (instead of '--phase-id')
* ensure that C++ Phase::m_id is always the same as Phase::m_name
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
5928d63746 [Thermo] address discussion and review comments 
* rename C++ object to 'Solution' (from 'SolutionBase')
* remove 'phaseID' from 'Solution' ('id' remains assigned to 'Phase')
* remove 'type' from C++ object (no polymorphism anticipated)
* assign 'name' to 'Solution' (link back from 'Phase' until deprecated)
* clarify 'phase' as 'phase_id' in Python interface
* address various feedback in review comments
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
b5e4f25454 [Input] rename --id to --phase in ck2yaml options 
The option --phase is consistent with the resulting yaml entry in 'phases'.
The --id option is still supported, with a warning being issued.
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
3bf09fbd7f [Base] rename Base.h/.cpp to SolutionBase.h/.cpp 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
af04f97d0e [Base] use FutureWarning for deprecated keywords 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
fef352b9d5 [Base] update docstrings for Solution and Interface objects 
* Reflects changes to `phase` and `adjacent` keyword
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
d8e09a9550 [Base] clarify keyword arguments of _SolutionBase initializers 
* Replace `phaseid` by `phase`
* Replace `phases` by `adjacent`
* Add deprecation warnings and update unit tests
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
dbac2fc79c [Base] replace Solution property ID by phase in Python 
* Clarifies the meaning of ID
* Creates a PEP8 compliant attribute that does not conflict with
a built-in function name that is also consistent with the YAML entry.
* Change associated member function names in C++ SolutionBase
* Deprecate `ID` in Python (to be removed after Cantera 2.5)
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
b926a31faf [Base] break out thermo/kinetics manager types to Python 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
f71954ac96 [Base] associate phase ID with SolutionBase object 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
b5137d40a3 [Base] remove redundant unique_name attribute 
* Resolve conflation of gas.ID and gas.name in unit tests
* Also fixes #691
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
799ef81518 [Base] link managers back to SolutionBase 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
486e2ba9b8 [Base] add unit test probing methods of C++ SolutionBase 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
afd36b1c1e [Base] create SolutionBase object in C++ 
* Add Base.h/Base.cpp with definition of SolutionBase
* Link C++ object into Cython interface
* Add unique_name and type attributes to Cython _SolutionBase
 2019-10-23 13:45:29 -04:00
Ingmar Schoegl
fe7be79552 [Thermo] improve error messages 
Incorporate reviewer suggestions for error messages (user feedback) in
PureFluid.TPX setter and SolutionArray.restore_data
 2019-10-02 22:16:55 -04:00
Ingmar Schoegl
074fd2cd74 [Thermo] adopt review comments for SolutionBase.restore_data 2019-10-02 22:16:55 -04:00
Ingmar Schoegl
2b61d3ad4a [Thermo] add read_hdf and update docstrings 2019-10-02 22:16:55 -04:00
Ingmar Schoegl
213612bd33 [Thermo] recreation of SolutionArray objects from stored data 
This commit implements new methods for SolutionArray:
* `restore_data` can restore data previously exported by `collect_data`
* `read_csv` restores data previously saved by `write_csv`
* unit tests are added for SolutionArray's based on ThermoPhase and PureFluid
 2019-10-02 22:16:55 -04:00