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Can we pickle and unpickle, reconstruct from __repr__, and does the isIdenticalTo method work? (The answer to the last two is currently No)
First, the Tmin and Tmax were being printed for Pmin and Pmax, and the Pmin was being printed as the comment. Second, the uncertainty was not being reported.
This method just checks that Tmin and Tmax are equal. But if they were equal, it used to return False. Now it returns False if one or other is None, or they're different. Note, however, that because the Quantity.equals method defaults to a 1% tolerance, that's 20K difference needed at 2000K.
Fix a few bugs and add tests: KineticsModel and uncertainty handling.
The updated fingerprint approach resulted in different fingerprint depending on atom order when the molecule contained more than two elements aside from CHNOS. This fixes the issue by sorting the elements alphabetically.
Fix inconsistent molecule fingerprint generation
The default value for the `force` argument changed from False to True in matplotlib 3. However, we don't want to force the backend change if we're using an ipython notebook.
added a try/except block around the clean build directories function. This should catch the error and provide a message instead of crashing the script.
Fix two calls to Exception.message, which no longer exists
…hat do not contain charged atoms
…tiplebond_paths and find_adj_lone_pair_multiple_bond_delocalization_paths
…ultiple bond resonance pathways
Dms oxy changes
In Python 2, negative numbers were treated as a single node In Python 3, negative numbers are treated as a UnaryOp + a Num
Change shebang to point to python3 and remove encoding line Ignore __pycache__ directories Update name of Arkane.py script
Update file headers and shebangs
We check that the user is using python 3 calling code in utilities.py This file is not present though in the binary install. Thankfully, this check is also not necessary in the binary install, as conda ensures the correct python version for us. Therefore, we don't need to throw an error.
We currently don't support Windows
The class was combined long ago with rmgpy.species.Species
Also fix some docstrings in MBSampledReactor
Use autodoc_default_options instead
API documentation updates
…ments Tree generation improvements
I ran into issues related to negative predicted moments of inertia with this interpolant This commit replaces that interpolant (the 2D case) with the LinearNDInterpolator
The old scheme using nquad only worked fast because the value of the integral was below the absolute tolerance, and it wasn't very accurate after fixing the numerical issue nquad takes impractically long since the integration is over a fit to data points we don't even know the function well enough for an nquad calculation to make sense for this reason I've used simpsons rule for integration which is much faster and should be just as accurate we still fit and use function evaluations for convenience
…ments ND Hindered Rotor Improvements
No need to set python version in meta.yaml
Update conda channels used for build
Codecov Report
@@ Coverage Diff @@
## stable #1852 +/- ##
==========================================
+ Coverage 41.7% 44.25% +2.54%
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Files 176 83 -93
Lines 29341 21551 -7790
Branches 6049 5648 -401
==========================================
- Hits 12237 9537 -2700
+ Misses 16235 10944 -5291
- Partials 869 1070 +201
Continue to review full report at Codecov.
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This release represents a major milestone in RMG development and includes many backwards-incompatible changes, most notably Python 3 compatibility and major API changes. Users switching to RMG 3 will need to create new conda environments and update any scripts which access the API. We recommend using the
futurizescript from python-future for updating scripts for Python 3 and the providedrmg2to3.pyscript for updating scripts for RMG 3.Python 3 #1724
Arkane
New features and other additions
Bug fixes
Other
Thanks to all contributors: ajocher, alongd, amarkpayne, cgrambow, dranasinghe, hwpang, kspieks, goldmanm, mazeau, mjohnson541, mliu49, oscarwumit, rwest, rgillis8, sarakha, sudoursa, xiaoruiDong, yunsiechung, zjburas