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RMG-Py v2.4.1 release #1664
RMG-Py v2.4.1 release #1664
Commits on Jun 14, 2019
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Increase RDKit version requirement and reformat environment files
Require newer version of RDKit and add rdkit channel Alphabetize dependencies Remove libgcc and libgfortran (they are included implicitly) Remove scoop
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Update Kekule SMILES tests following RDKit changes
RDKit now generates different SMILES strings for some molecules
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Commits on Jun 15, 2019
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Merge pull request #1623 from ReactionMechanismGenerator/update_env
Update environment files, including RDKit and Cantera versions
Colin Grambow authoredJun 15, 2019 Configuration menu - View commit details
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Commits on Jun 16, 2019
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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.
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Corrected the energy (e_elect, zpe, and E0) terminology in Arkane
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)
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Updated the frequency scale factor assignemt
- 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)
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Commits on Jun 17, 2019
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Merge pull request #1619 from ReactionMechanismGenerator/scaling_zpe
Scaling zpe
Colin Grambow authoredJun 17, 2019 Configuration menu - View commit details
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Merge pull request #1628 from ReactionMechanismGenerator/v2.4.0
v2.4.0 release changes
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Merge pull request #1631 from ReactionMechanismGenerator/stable
Merge stable branch into master
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Commits on Jun 24, 2019
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Merge pull request #1629 from ReactionMechanismGenerator/rmsyaml
Reaction Mechanism Simulator YAML File Generation
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Commits on Jun 25, 2019
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Get NASA.as_dict to ignore unset variables
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
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Add tests to load species from NASA polynomials
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
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Merge pull request #1630 from ReactionMechanismGenerator/bugfix_nasa_…
…as_dict Bugfix nasa as dict
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Commits on Jun 27, 2019
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Commits on Jun 28, 2019
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Merge pull request #1644 from ReactionMechanismGenerator/add_minicond…
…a_dependencies Fix Travis builds by adding in missing miniconda dependencies
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Commits on Jul 2, 2019
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Commits on Jul 12, 2019
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Merge pull request #1650 from ReactionMechanismGenerator/arkane_scan_doc
Modified the Arkane ScanLog documentation
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Refactor energy corrections in Arkane
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.
Colin Grambow committedJul 12, 2019 Configuration menu - View commit details
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Implement Melius-type bond additivity corrections in Arkane
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.
Colin Grambow committedJul 12, 2019 Configuration menu - View commit details
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Add bondCorrectionType option to Arkane
bondCorrectionType can be set to 'p' to use conventional bond additivity corrections or to 'm' to use the newly implemented Melius-type corrections.
Colin Grambow committedJul 12, 2019 Configuration menu - View commit details
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Update Arkane documentation to reflect Melius-type bond additivity co…
…rrections
Colin Grambow committedJul 12, 2019 Configuration menu - View commit details
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Merge pull request #1605 from ReactionMechanismGenerator/new_bacs
Refactor energy corrections in Arkane and implement new bond additivity correction type
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Commits on Jul 16, 2019
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Added frequency scaling factors to Arkane
Calculated using Truhlar's method
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Merge pull request #1653 from ReactionMechanismGenerator/freq_scale
Added two frequency scaling factors to Arkane
Colin Grambow authoredJul 16, 2019 Configuration menu - View commit details
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Commits on Jul 17, 2019
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Refactor code for making objects so that it works recursively
Should work no matter how many objects or dictionaries or lists are nested in each other. Most objects that inherits from RMGObject should work by default without having to overwrite the make_object method
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Commits on Jul 18, 2019
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Merge pull request #1643 from ReactionMechanismGenerator/recursive_as…
…_dictionary Recursive as dictionary
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F needs to be in element list.
Otherwise when trying to make a sample molecule with an F groupAtom, it fails (and crashes with a segfault)
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Also consider I atoms when making sample molecules.
This list should cover all elements used in atomTypes.
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Merge pull request #1656 from ReactionMechanismGenerator/fluorinefixes
Fluorine fixes
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Commits on Jul 20, 2019
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Merge pull request #1657 from ReactionMechanismGenerator/fix_arkane_e…
…xamples Fix frequencyScaleFactor in Arkane examples
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Refactor reaction generation and processing for reactEdge phase
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
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Update docstrings in rmgpy.rmg.react module
Also rename the spc_tuples arg in the react method to spc_fam_tuples to reflect updated usage.
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Reorganize imports in rmgpy.rmg.model
Sort alphabetically and also remove relative imports
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Revert "Update arkane/explorerTest.py."
This reverts commit d59da68. Lesson to be learned: If a unit test fails, make sure you understand why before changing the correct answer...
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Add test class for CoreEdgeReactionModel.enlarge
With tests for pdep network generation
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Commits on Jul 21, 2019
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Merge pull request #1658 from ReactionMechanismGenerator/pdep_fix
Fix pressure dependent network generation in RMG jobs
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Tests: Added Arkane thermoTest
For now only tests the element_count_from_conformer() method, should be expanded.
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Renamed elementCounts as element_counts
THe Species.props['element_counts'] is only used in Arkane. renamed elementCounts to element_counts to be consistent with prior changes
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Commits on Jul 23, 2019
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Merge pull request #1651 from ReactionMechanismGenerator/element_coun…
…t_from_conf Element count from conformer
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Pass
rcond=None
tonumpy.linalg.lstsq
to silence warningSilence 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.
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Merge pull request #1659 from ReactionMechanismGenerator/reverse_pdep…
…_multi Support reversing PDepArrhenius objects containing MultiArrhenius rates
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