mliu49
commented
4 years ago RMG-Py v3.0.0 Release Notes (draft)
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 futurize script from python-future for updating scripts for Python 3 and the provided rmg2to3.py script for updating scripts for RMG 3.
Python 3 #1724
- RMG is now compatible with Python 3.7 and newer
- RMG v2.x versions will no longer be supported
- API changes
- Method, function, and argument names have been standardized to use snake_case across RMG and Arkane
- Input file related code was not changed, in order to continue support for existing syntax
- Conversion script has been provided to aid transition (scripts/rmg2to3.py)
- Standardized submodule names in the rmgpy.tools module #1794
- Accompanying changes
- Reduction and scoop_framework modules have been removed
- New/updated hash and comparison methods for Species/Molecule/Atom/Bond classes
- DDE thermochemistry estimator has been replaced by chemprop
- Update example IPython notebooks #1735
- Update global uncertainty module to work with MUQ 2 and Python 3 #1738
- Miscellaneous clean up and bug fixes following transition #1741, #1744, #1752, #1759, #1785, #1802, #1798, #1799, #1808
Arkane
- Improvements and refactoring of job output file creation and content #1607
- Fix kinetics fitting bug #1672
- Improvements to automatic network exploration tool #1647
- Support for ND classical and semi-classical rotor calculations #1640, #1849
- Support for 2D quantum mechanical rotor calculations using Q2DTor #1640
- Support for providing absolute file paths #1685
- Output RMG-style libraries #1769
- Check for error termination in Gaussian log files #1766
- Support for parsing Orca log files #1749
- Support for parsing MP2, double hybrid DFT, CCSD, and CCSD(T) energies from Gaussian log files #1815
- Support for TeraChem log files #1788
- Miscellaneous bug fixes #1810
New features and other additions
- Additional options for heterocycles in MLEstimator #1621
- Automatic tree generation algorithm implementation completed #1486, #1675, #1848
- New simulation restart approach using seed mechanisms (old pickle-based method removed) #1641
- Added new MBSampledReactor type for simulating molecular beam experiments (does not support model generation) #1669
- Improvements to group additivity thermo estimates for aromatics and sulfur species #1731, #1751
- Improvements to solvation correction determination with multiple resonance structures #1832
- Add support for reading and writing extended element syntax in Chemkin NASA polynomials #1636
- Add support for fitting negative Arrhenius rates (found in MultiArrhenius data) #1834
Bug fixes
- Fix numpy rcond usage to restore support for older numpy versions #1670
- Fix bug with duplicate library reactions when using RMG generated seed mechanisms #1676
- Move parse_command_line_arguments to facilitate importing in binary package #1717
- Fix issues with is_identical_to methods of kinetics models #1705
- Fix cython issue with make_object definitions #1817
- Fix issue with estimating solvation corrections for radicals #1773
- Fix parsing of certain types of RMG generated reaction comments #1842
- Fix identifier generation for surface species using OpenBabel #1842
- Fix mole fraction normalization for SimpleReactor #1809
- Fix permissions error when writing seed mechanisms in WSL #1796
- Fix issue with restarting from job without reaction filters #1847
Other
- Improvements to mergeModels.py script #1649
- Miscellaneous performance improvements #1677, #1765,
- Raise errors when NaN is encountered in solver #1679
- Allow sulfur species to have valence 12 in resonance algorithm #1751
- Add support for maxproc argument to generate_reactions module #1780
- Display atom index when drawing groups #1758
- Update sensitivity example #1805
- Update commented input file #1806
- Generate reverse reaction recipes in reverse order of the forward recipe #1829
- Add iodine to Chemkin elements list #1825
- Remove unnecessary duplicate checking for seed mechanisms #1824
- Organize examples for running RMG scripts #1840
- Increase RDKit version requirement to avoid memory leak #1851
- Logging changes #1721, #1755
- Documentation updates #1680, #1709, #1767, #1781, #1784, #1807, #1845
Thanks to all contributors: ajocher, alongd, amarkpayne, cgrambow, dranasinghe, hwpang, kspieks, goldmanm, mazeau, mjohnson541, mliu49, oscarwumit, rwest, rgillis8, sarakha, sudoursa, xiaoruiDong, yunsiechung, zjburas
goldmanm
It's time to start preparing for the RMG v3.0.0 release. This is a major release, with the biggest changes being Python 3 support and API naming style changes.
There will be an accompanying paper highlighting some of the major changes since RMG v1.0, and I assume that the ongoing Arkane paper will most likely be updated to reference this release as well.
There are still a number of PR's which need to be merged, which are tagged with For Next Release.
This issue is for any release related discussion. Draft release notes will also be prepared here.