Skip to content

Commit

Permalink
RMG-Py v2.1.6 release
Browse files Browse the repository at this point in the history
  • Loading branch information
mliu49 committed May 2, 2018
2 parents 57d0c53 + ffbaa08 commit 9b2c66d
Show file tree
Hide file tree
Showing 65 changed files with 2,084 additions and 1,416 deletions.
23 changes: 8 additions & 15 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,6 @@ language: python
sudo: false
python:
- "2.7"
virtualenv:
system_site_packages: true
env:
global:
- secure: "L2ja+ZnV83w4qG3E8FwTjm0D6IWNOnj5wuFOjYTwbzQP4OAgLAWBzCMtxzWy5sMxFLtRgkswBH1d5f5kg8Ab7GIyAMFgQwe8UFqMJ+N05QNszE1mJkAvJtv2XN7669XXQhTt5EXfHrCcGZaODVnI2CEA8GB5DxiHO2Lcqf/xvgE="
Expand All @@ -12,29 +10,24 @@ env:
- secure: "cfosGf5hvUhIlPoGJu0d/HFddrMwIFU7FfLwd8yRrMGkYv0ePOwAW9kmhFSxUYvuXkxzgD75cIICMFY2fSm6VXBXXzfPQD7vwzoApXf7a8vi0C64XhinXhdEyUYb5/v8fswa0zheUENYhUS1tOqDXT/h8EPNZT5wKizaA3O2Wa8="
- secure: "QXuqKYuwCocqsTMePBc5OugBbQC4/t+335TYLdkletiateP/rF/eDsVRG792/BVq5gKRZgz3NH9ipTNm5pZoCbAEPt9+eDpfts8WeAbxmjdcEjfBxxwZ69wUTPAVrezTGn2k7W2UBdFrWeUNKPAVCKIkoviXqOHFitqJEC+c6JY="
- secure: "jIyBEzR10l5SWvY5ouEYzA8YzPHIZNMXMBdcXwuwte8NCU8GBYUqhHA1L67nTaBdLhWbrZ2NireVKPQWJp3ctcI0IB6xZzaYlVpgN/udGPO+1MZd9Xhp9TWuJWrGZ9EoWGB9L5H+O7RYwcDMVH5CUrCIBdsSJuyE8aDpky1/IVE="
addons:
apt:
packages:
- git

before_install:
# Set up anaconda
- wget http://repo.continuum.io/miniconda/Miniconda2-4.0.5-Linux-x86_64.sh -O miniconda.sh
- chmod +x miniconda.sh
- ./miniconda.sh -b -p $HOME/miniconda
- cd ..
# Install miniconda
- wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH=$HOME/miniconda/bin:$PATH
- export PYTHONPATH=$TRAVIS_BUILD_DIR/RMG-Py:$PYTHONPATH
# Update conda itself
- conda update --yes conda
- cd ..
- conda info -a
# Clone RMG-database
- git clone https://github.com/ReactionMechanismGenerator/RMG-database.git
- cd RMG-Py

install:
- conda env create -f environment_linux.yml
- conda env create -q -f environment_linux.yml
- source activate rmg_env
- conda install -y -c conda-forge codecov
- conda list
- pip install codecov
- yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
- make

Expand Down
218 changes: 123 additions & 95 deletions documentation/source/users/rmg/database/kinetics.rst

Large diffs are not rendered by default.

41 changes: 41 additions & 0 deletions documentation/source/users/rmg/releaseNotes.rst
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,47 @@
Release Notes
*************

RMG-Py Version 2.1.6
====================
Date: December 21, 2017

- Model resurrection:
- Automatically attempts to save simulation after encountering a DASPK error
- Adds species and reactions in order to modify model dynamics and fix the error

- New features:
- Add functionality to read RCCSD(T)-F12 energies from MolPro log files
- Add liquidReactor support to flux diagram generation

- Other changes:
- Removed rmgpy.rmg.model.Species class and merged functionality into main rmgpy.species.Species class
- Refactored parsing of RMG-generated kinetics comments from Chemkin files and fixed related issues
- Refactored framework for generating reactions to reduce code duplication
- Resonance methods renamed from generateResonanceIsomers to generate_resonance_structures across all modules
- Raise CpInf to Cphigh for entropy calculations to prevent invalid results

- Fixes:
- Update sensitivity analysis to use ModelSettings and SimulatorSettings classes introduced in v2.1.5
- Fixed generate_reactions methods in KineticsDatabase to be directly usable again
- Fixed issues with aromaticity perception and generation of aromatic resonance structures

RMG-database Version 2.1.6
==========================
Date: December 21, 2017

- Additions:
- New training reactions added for [NH2] related H_Abstractions
- 14 new kinetics libraries related to aromatics formation (see RMG-database #222 for details)

- Other changes:
- Removed some global forbidden groups which are no longer needed
- Forbid CO and CS biradicals
- Updated lone_electron_pair_bond family and removed from recommended list

- Fixes:
- Fixed unit errors in some H_Abstraction and R_Addition_MultipleBond depositories


RMG-Py Version 2.1.5
====================
Date: October 18, 2017
Expand Down
Loading

0 comments on commit 9b2c66d

Please sign in to comment.