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RMG-Py v2.1.5 release
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‎.travis.yml‎

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@@ -33,12 +33,14 @@ before_install:
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install:
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- conda env create -f environment_linux.yml
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- source activate rmg_env
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- conda list
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- pip install codecov
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- yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
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- make
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script:
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- make test-all
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- make test-unittests
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- make test-functional
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- make test-database
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after_success:

‎Makefile‎

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nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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endif
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test:
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test-unittests:
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ifeq ($(OS),Windows_NT)
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nosetests --nocapture --nologcapture --all-modules --attr '!auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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else
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mkdir -p testing/coverage
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rm -rf testing/coverage/*
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nosetests --nocapture --nologcapture --all-modules --attr '!auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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endif
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test test-unittests-non-auth:
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ifeq ($(OS),Windows_NT)
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nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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else
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mkdir -p testing/coverage
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rm -rf testing/coverage/*
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nosetests --nocapture --nologcapture --all-modules -A 'not functional and not auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
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endif
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test-functional:
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ifeq ($(OS),Windows_NT)
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nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
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else
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mkdir -p testing/coverage
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rm -rf testing/coverage/*
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nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
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endif
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test-database:

‎README.md‎

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# <img align="top" src="https://raw.githubusercontent.com/ReactionMechanismGenerator/RMG-Py/master/documentation/source/_static/rmg-logo-small.png"> Reaction Mechanism Generator (RMG)
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[![Build status](https://img.shields.io/travis/ReactionMechanismGenerator/RMG-Py/master.svg)](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py)
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[![Codecov report](https://img.shields.io/codecov/c/github/ReactionMechanismGenerator/RMG-Py/master.svg)](https://codecov.io/gh/ReactionMechanismGenerator/RMG-Py)
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[![Codacy report](https://img.shields.io/codacy/grade/c4b23c89e2e6486e981704d8d973d3e7/master.svg)](https://www.codacy.com/app/ReactionMechanismGenerator/RMG-Py/dashboard)
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[![GitHub release](https://img.shields.io/github/release/ReactionMechanismGenerator/RMG-Py.svg)](https://github.com/ReactionMechanismGenerator/RMG-Py/releases)
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[![Anconda](https://img.shields.io/conda/v/rmg/rmg.svg)](https://anaconda.org/rmg/rmg)
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[![Gitter](https://img.shields.io/gitter/room/ReactionMechanismGenerator/RMG-Py.svg)](https://gitter.im/ReactionMechanismGenerator/RMG-Py)
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[![RMG Website](https://img.shields.io/website-up-down-green-red/http/rmg.mit.edu.svg?label=rmg%20website)](http://rmg.mit.edu/)
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## Description
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This repository contains the Python version of **Reaction Mechanism Generator (RMG)**,
@@ -16,14 +23,9 @@ Gaussian, MOPAC, QChem, and MOLPRO.
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- [RMG Github Repository](https://github.com/ReactionMechanismGenerator/RMG-Py): contains the latest source code for RMG
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- [RMG-database Github Repository](https://github.com/ReactionMechanismGenerator/RMG-database): contains source code for the latest version of the database
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## Latest Stable Release
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**RMG v2.1.4**
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[![Anaconda-Server Badge](https://anaconda.org/rmg/rmg/badges/version.svg)](https://anaconda.org/rmg/rmg)
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View the [Release Notes](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/releaseNotes.html).
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## How to Install
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View the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page.
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You can either download the source from GitHub and compile yourself, or download the binaries from Anaconda.
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Please see the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
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## Documentation
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- [RMG Documentation](http://ReactionMechanismGenerator.github.io/RMG-Py/) ([PDF version](https://github.com/ReactionMechanismGenerator/RMG-Py/raw/master/documentation/RMG-Py_and_CanTherm_Documentation.pdf))
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Alternatively, PDF versions of all the documentation can also be found in the `documentation` folder of the source code.
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## Credits
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- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the
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[Massachusetts Institute of Technology](http://web.mit.edu/)
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- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at
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[Northeastern University](http://www.northeastern.edu/).
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## How to Contribute
38+
Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/RMG-Contributor-Guidelines)
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for details on how to contribute to RMG-Py or RMG-database.
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## How to Give Feedback
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Please post any issues you may have to the [issues page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/)
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or drop in to the [chat room](https://gitter.im/ReactionMechanismGenerator/RMG-Py) or email [rmg_dev@mit.edu](mailto:rmg_dev@mit.edu) if you have questions.
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[![Join the chat at https://gitter.im/ReactionMechanismGenerator/RMG-Py](https://badges.gitter.im/ReactionMechanismGenerator/RMG-Py.svg)](https://gitter.im/ReactionMechanismGenerator/RMG-Py?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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## Useful Links
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- [Wiki](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki): a wiki for developer notes
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- [Issues Page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/): view current issues and feature requests
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## Credits
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## Continuous Integration
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We have a continuous integration build test suite
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which you can access at https://travis-ci.org/ReactionMechanismGenerator/RMG-Py
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The current build status is
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[![Build Status](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py.svg?branch=master)](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py)
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- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the
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[Massachusetts Institute of Technology](http://web.mit.edu/)
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- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at
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[Northeastern University](http://www.northeastern.edu/).

‎documentation/source/users/rmg/database/kinetics.rst‎

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+---------------------------------------+------------------------------------------------------------------------------------------+
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|BurkeH2O2inN2 |Comprehensive H2/O2 kinetic model in N2 atmosphere |
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+---------------------------------------+------------------------------------------------------------------------------------------+
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|C2H4+O_Klipp2017 |C2H4 + O intersystem crossing reactions, probably important for all C/H/O combustion |
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+---------------------------------------+------------------------------------------------------------------------------------------+
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|C10H11 |Cyclopentadiene pyrolysis in the presence of ethene |
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+---------------------------------------+------------------------------------------------------------------------------------------+
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|C3 |Cyclopentadiene pyrolysis in the presence of ethene |

‎documentation/source/users/rmg/releaseNotes.rst‎

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Release Notes
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*************
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RMG-Py Version 2.1.5
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====================
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Date: October 18, 2017
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- New bicyclic formula:
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- Estimates polycyclic corrections for unsaturated bicyclics by adjusting the correction for the saturated version
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- Can provide a decent estimate in many cases where there is not an exact match
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- Other changes:
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- Refactored simulation algorithm to properly add multiple objects per iteration
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- Print equilibrium constant and reverse rate coefficient values when using Cantherm to calculate kinetics
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- Speed up degeneracy calculation by reducing unnecessary operations
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- Fixes:
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- Loosen tolerance for bond order identification to account for floating point error
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- Fixed uncertainty analysis to allow floats as bond orders
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- Fixed some comment parsing issues in uncertainty analysis
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- Added product structure atom relabeling for families added in RMG-database v2.1.5
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- Fixed issue with automatic debugging of kinetics errors due to forbidden structures
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RMG-database Version 2.1.5
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==========================
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Date: October 18, 2017
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- Additions:
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- New thermo groups added for species relevant in cyclopentadiene and natural gas pyrolysis
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- Added C2H4+O_Klipp2017 kinetics library
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- Fixes:
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- Prevent charged carbenes from reacting in Singlet_Carbene_Intra_Disproportionation
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- Updated H_Abstraction rates in ethylamine library and corresponding training reactions
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RMG-Py Version 2.1.4
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====================
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Date: September 08, 2017

‎environment_linux.yml‎

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- libgcc # [unix]
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- python
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- numpy >=1.10.0
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- cantera >=2.2
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- cantera >=2.3.0a3
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- coolprop
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- cython >=0.25.2
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- matplotlib >=1.5

‎environment_mac.yml‎

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- libgcc # [unix]
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- python
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- numpy >=1.10.0
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- cantera >=2.2
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- cantera >=2.3.0a3
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- coolprop
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- cython >=0.25.2
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- matplotlib >=1.5

‎environment_windows.yml‎

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- mingwpy
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- python
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- numpy >=1.10.0
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- cantera >=2.2
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- cantera >=2.3.0a3
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- coolprop
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- cython >=0.25.2
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- matplotlib >=1.5

‎examples/rmg/minimal_multisurf/input.py‎

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# Data sources
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database(
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thermoLibraries = ['primaryThermoLibrary'],
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reactionLibraries = [],
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seedMechanisms = [],
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kineticsDepositories = ['training'],
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kineticsFamilies = 'default',
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kineticsEstimator = 'rate rules',
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)
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# List of species
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species(
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label='ethane',
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reactive=True,
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structure=SMILES("CC"),
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)
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# Reaction systems
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simpleReactor(
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temperature=(1350,'K'),
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pressure=(1.0,'bar'),
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initialMoleFractions={
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"ethane": 1.0,
24+
},
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terminationConversion={
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'ethane': 0.9,
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},
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terminationTime=(1e6,'s'),
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)
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simpleReactor(
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temperature=(1000,'K'),
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pressure=(1.0,'bar'),
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initialMoleFractions={
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"ethane": 1.0,
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},
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terminationConversion={
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'ethane': 0.9,
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},
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terminationTime=(1e6,'s'),
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)
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simulator(
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atol=1e-16,
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rtol=1e-8,
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)
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model(
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toleranceKeepInEdge=0.0,
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toleranceMoveToCore=100,
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toleranceInterruptSimulation=100,
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maximumEdgeSpecies=100000,
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toleranceMoveEdgeReactionToSurface=2.0,
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toleranceMoveSurfaceReactionToCore=100,
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toleranceMoveSurfaceSpeciesToCore=1e-6,
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maxNumObjsPerIter=0,
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)
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options(
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units='si',
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saveRestartPeriod=None,
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generateOutputHTML=False,
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generatePlots=False,
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saveEdgeSpecies=True,
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saveSimulationProfiles=True,
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)

‎examples/rmg/minimal_staged/input.py‎

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model( #second stage
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toleranceKeepInEdge=0.0,
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toleranceMoveToCore=0.1,
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toleranceInterruptSimulation=0.1,
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toleranceInterruptSimulation=1.0,
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maximumEdgeSpecies=100000,
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maxNumObjsPerIter=2,
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maxNumObjsPerIter=3,
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maxNumSpecies = 100,
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)
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