RMG-Py v2.4.1 release #1664
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RMG-Py v2.4.1 release #1664
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Require newer version of RDKit and add rdkit channel Alphabetize dependencies Remove libgcc and libgfortran (they are included implicitly) Remove scoop
RDKit now generates different SMILES strings for some molecules
Update environment files, including RDKit and Cantera versions
The 1.014 factor represents the relationship between the harmonic frequencies scaling factor and the zero point energy scaling factor, see https://pubs.acs.org/doi/10.1021/ct100326h Section 3.1.3.
Previously we used E0 for the electronic energy, and E0_withZPE for the corrected energy. The updated terminology is E0 = e_electronic + ZPE (E0 includes the ZPE)
- Corrected scaling factors which were for ZPE instead of freq - Organized the references - Removed commented out levels - Added some more levels (one of which calculated by Duminda, as noted)
v2.4.0 release changes
Merge stable branch into master
Reaction Mechanism Simulator YAML File Generation
Previously, NASA.as_dict would throw an error if attributes like Tmin, Tmax, E0 were unset. These variables, however, are optional, so Arkane should not crash if they are unset. This commit fixes the as_dict method to not throw an error for optional attributes
This commit adds two test methods for NASA.as_dict and two tests to load species from nasa polynomials in Arkane. squash! Add tests to load species from NASA polynomials
…as_dict Bugfix nasa as dict
…a_dependencies Fix Travis builds by adding in missing miniconda dependencies
Modified the Arkane ScanLog documentation
Make new encorr package which handles all energy corrections. Store all correction parameters in a dedicated data file. Handle bond additivity corrections in its own module, so that new types of bond additivity corrections can easily be implemented in the future.
Instead of correcting the electronic energy using explicitly defined bond types, Anantharaman and Melius (JPCA, 2005) only use three fitted parameters per atom type to correct the energy. Implement the framework for this type of correction in the encorr package.
bondCorrectionType can be set to 'p' to use conventional bond additivity corrections or to 'm' to use the newly implemented Melius-type corrections.
Otherwise when trying to make a sample molecule with an F groupAtom, it fails (and crashes with a segfault)
This list should cover all elements used in atomTypes.
…xamples Fix frequencyScaleFactor in Arkane examples
Motivation: - processNewReactions requires a newSpecies argument which was not being properly identified after multiprocessing changes in #1459 Background: - The newSpecies argument is retained from early RMG when reactions were generated right after adding a new species to the core. - Hence, newSpecies referred to the newly added core species which was used to generate the new reactions. - The overall model generation algorithm has since changed, so identifying newSpecies is not as straightforward. - The multiprocessing PR changed newSpecies to be any core species, missing the original purpose of identifying the species from which the reaction was generated. Changes: - Use the species tuples created during reaction generation to keep track of which species were used to generate the reaction - Update unit tests which are affected by the changes in return values from react and react_all
Also rename the spc_tuples arg in the react method to spc_fam_tuples to reflect updated usage.
Sort alphabetically and also remove relative imports
This reverts commit d59da68. Lesson to be learned: If a unit test fails, make sure you understand why before changing the correct answer...
With tests for pdep network generation
Fix pressure dependent network generation in RMG jobs
For now only tests the element_count_from_conformer() method, should be expanded.
THe Species.props['element_counts'] is only used in Arkane. renamed elementCounts to element_counts to be consistent with prior changes
…t_from_conf Element count from conformer
Silence numpy warnings and use new default behavior From numpy documentation: Changed in version 1.14.0: If not set, a FutureWarning is given. The previous default of -1 will use the machine precision as rcond parameter, the new default will use the machine precision times max(M, N). To silence the warning and use the new default, use rcond=None, to keep using the old behavior, use rcond=-1.
…_multi Support reversing PDepArrhenius objects containing MultiArrhenius rates
Codecov Report
@@ Coverage Diff @@
## stable #1664 +/- ##
=========================================
+ Coverage 41.52% 41.7% +0.18%
=========================================
Files 176 176
Lines 29314 29341 +27
Branches 6035 6049 +14
=========================================
+ Hits 12172 12237 +65
+ Misses 16289 16235 -54
- Partials 853 869 +16
Continue to review full report at Codecov.
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