RMG-Py v2.1.5 release

.travis.yml

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

Makefile

@@ -83,13 +83,31 @@ else
 	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 endif
 
-test:
+test-unittests:
 ifeq ($(OS),Windows_NT)
-	nosetests --nocapture --nologcapture --all-modules --attr '!auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
+	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 else
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
-	nosetests --nocapture --nologcapture --all-modules --attr '!auth' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
+	nosetests --nocapture --nologcapture --all-modules -A 'not functional' --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
+endif
+
+test test-unittests-non-auth:
+ifeq ($(OS),Windows_NT)
+	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
+else
+	mkdir -p testing/coverage
+	rm -rf testing/coverage/*
+	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
+endif
+
+test-functional:
+ifeq ($(OS),Windows_NT)
+	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
+else
+	mkdir -p testing/coverage
+	rm -rf testing/coverage/*
+	nosetests --nocapture --nologcapture --all-modules -A 'functional' --verbose --exe rmgpy
 endif
 
 test-database:

README.md

@@ -1,5 +1,12 @@
 # <img align="top" src="https://raw.githubusercontent.com/ReactionMechanismGenerator/RMG-Py/master/documentation/source/_static/rmg-logo-small.png"> Reaction Mechanism Generator (RMG)
 
+[![Build status](https://img.shields.io/travis/ReactionMechanismGenerator/RMG-Py/master.svg)](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py)
+[![Codecov report](https://img.shields.io/codecov/c/github/ReactionMechanismGenerator/RMG-Py/master.svg)](https://codecov.io/gh/ReactionMechanismGenerator/RMG-Py)
+[![Codacy report](https://img.shields.io/codacy/grade/c4b23c89e2e6486e981704d8d973d3e7/master.svg)](https://www.codacy.com/app/ReactionMechanismGenerator/RMG-Py/dashboard)
+[![GitHub release](https://img.shields.io/github/release/ReactionMechanismGenerator/RMG-Py.svg)](https://github.com/ReactionMechanismGenerator/RMG-Py/releases)
+[![Anconda](https://img.shields.io/conda/v/rmg/rmg.svg)](https://anaconda.org/rmg/rmg)
+[![Gitter](https://img.shields.io/gitter/room/ReactionMechanismGenerator/RMG-Py.svg)](https://gitter.im/ReactionMechanismGenerator/RMG-Py)
+[![RMG Website](https://img.shields.io/website-up-down-green-red/http/rmg.mit.edu.svg?label=rmg%20website)](http://rmg.mit.edu/)
 
 ## Description
 This repository contains the Python version of **Reaction Mechanism Generator (RMG)**,
@@ -16,14 +23,9 @@ Gaussian, MOPAC, QChem, and MOLPRO.
 - [RMG Github Repository](https://github.com/ReactionMechanismGenerator/RMG-Py): contains the latest source code for RMG
 - [RMG-database Github Repository](https://github.com/ReactionMechanismGenerator/RMG-database): contains source code for the latest version of the database
 
-## Latest Stable Release
-**RMG v2.1.4**
-[![Anaconda-Server Badge](https://anaconda.org/rmg/rmg/badges/version.svg)](https://anaconda.org/rmg/rmg)
-
-View the [Release Notes](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/releaseNotes.html).
-
 ## How to Install
-View the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page.
+You can either download the source from GitHub and compile yourself, or download the binaries from Anaconda.
+Please see the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-Py/users/rmg/installation/index.html) page for detailed instructions.
 
 ## Documentation
 - [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))
@@ -32,18 +34,14 @@ View the [Download and Install](http://reactionmechanismgenerator.github.io/RMG-
 
 Alternatively, PDF versions of all the documentation can also be found in the `documentation` folder of the source code.  
 
-## Credits
-
-- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the 
-[Massachusetts Institute of Technology](http://web.mit.edu/) 
-- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at 
-[Northeastern University](http://www.northeastern.edu/). 
+## How to Contribute
+Please see the [Contributor Guidelines](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki/RMG-Contributor-Guidelines)
+for details on how to contribute to RMG-Py or RMG-database.
 
 ## How to Give Feedback
 
 Please post any issues you may have to the [issues page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/)
 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.  
-[![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)
 
 ## Useful Links
 
@@ -52,10 +50,9 @@ perform thermodynamics and kinetics searches
 - [Wiki](https://github.com/ReactionMechanismGenerator/RMG-Py/wiki): a wiki for developer notes
 - [Issues Page](https://github.com/ReactionMechanismGenerator/RMG-Py/issues/): view current issues and feature requests
 
+## Credits
 
-## Continuous Integration
-
-We have a continuous integration build test suite 
-which you can access at https://travis-ci.org/ReactionMechanismGenerator/RMG-Py
-The current build status is
-[![Build Status](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py.svg?branch=master)](https://travis-ci.org/ReactionMechanismGenerator/RMG-Py)
+- [Professor William H. Green's research group](http://cheme.scripts.mit.edu/green-group/) at the 
+[Massachusetts Institute of Technology](http://web.mit.edu/) 
+- [Professor Richard H. West's research group](http://www.northeastern.edu/comocheng/) at 
+[Northeastern University](http://www.northeastern.edu/). 

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

@@ -71,6 +71,8 @@ Below is a list of pre-packaged kinetics library reactions in RMG:
 +---------------------------------------+------------------------------------------------------------------------------------------+
 |BurkeH2O2inN2                          |Comprehensive H2/O2 kinetic model in N2 atmosphere                                        |
 +---------------------------------------+------------------------------------------------------------------------------------------+
+|C2H4+O_Klipp2017                       |C2H4 + O intersystem crossing reactions, probably important for all C/H/O combustion      |
++---------------------------------------+------------------------------------------------------------------------------------------+
 |C10H11                                 |Cyclopentadiene pyrolysis in the presence of ethene                                       |
 +---------------------------------------+------------------------------------------------------------------------------------------+
 |C3                                     |Cyclopentadiene pyrolysis in the presence of ethene                                       |

documentation/source/users/rmg/releaseNotes.rst

@@ -4,6 +4,39 @@
 Release Notes
 *************
 
+RMG-Py Version 2.1.5
+====================
+Date: October 18, 2017
+
+- New bicyclic formula:
+    - Estimates polycyclic corrections for unsaturated bicyclics by adjusting the correction for the saturated version
+    - Can provide a decent estimate in many cases where there is not an exact match
+
+- Other changes:
+    - Refactored simulation algorithm to properly add multiple objects per iteration
+    - Print equilibrium constant and reverse rate coefficient values when using Cantherm to calculate kinetics
+    - Speed up degeneracy calculation by reducing unnecessary operations
+
+- Fixes:
+    - Loosen tolerance for bond order identification to account for floating point error
+    - Fixed uncertainty analysis to allow floats as bond orders
+    - Fixed some comment parsing issues in uncertainty analysis
+    - Added product structure atom relabeling for families added in RMG-database v2.1.5
+    - Fixed issue with automatic debugging of kinetics errors due to forbidden structures
+
+RMG-database Version 2.1.5
+==========================
+Date: October 18, 2017
+
+- Additions:
+    - New thermo groups added for species relevant in cyclopentadiene and natural gas pyrolysis
+    - Added C2H4+O_Klipp2017 kinetics library
+
+- Fixes:
+    - Prevent charged carbenes from reacting in Singlet_Carbene_Intra_Disproportionation
+    - Updated H_Abstraction rates in ethylamine library and corresponding training reactions
+
+
 RMG-Py Version 2.1.4
 ====================
 Date: September 08, 2017

environment_linux.yml

@@ -6,7 +6,7 @@ dependencies:
   - libgcc # [unix]
   - python
   - numpy >=1.10.0
-  - cantera >=2.2
+  - cantera >=2.3.0a3
   - coolprop
   - cython >=0.25.2
   - matplotlib >=1.5

environment_mac.yml

@@ -6,7 +6,7 @@ dependencies:
   - libgcc # [unix]
   - python
   - numpy >=1.10.0
-  - cantera >=2.2
+  - cantera >=2.3.0a3
   - coolprop
   - cython >=0.25.2
   - matplotlib >=1.5

environment_windows.yml

@@ -6,7 +6,7 @@ dependencies:
   - mingwpy
   - python
   - numpy >=1.10.0
-  - cantera >=2.2
+  - cantera >=2.3.0a3
   - coolprop
   - cython >=0.25.2
   - matplotlib >=1.5

examples/rmg/minimal_multisurf/input.py

@@ -0,0 +1,68 @@
+# Data sources
+database(
+    thermoLibraries = ['primaryThermoLibrary'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = 'default',
+    kineticsEstimator = 'rate rules',
+)
+
+# List of species
+species(
+    label='ethane',
+    reactive=True,
+    structure=SMILES("CC"),
+)
+
+# Reaction systems
+simpleReactor(
+    temperature=(1350,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        "ethane": 1.0,
+    },
+    terminationConversion={
+        'ethane': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+simpleReactor(
+    temperature=(1000,'K'),
+    pressure=(1.0,'bar'),
+    initialMoleFractions={
+        "ethane": 1.0,
+    },
+    terminationConversion={
+        'ethane': 0.9,
+    },
+    terminationTime=(1e6,'s'),
+)
+
+
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=0.0,
+    toleranceMoveToCore=100,
+    toleranceInterruptSimulation=100,
+    maximumEdgeSpecies=100000,
+    toleranceMoveEdgeReactionToSurface=2.0,
+    toleranceMoveSurfaceReactionToCore=100,
+    toleranceMoveSurfaceSpeciesToCore=1e-6,
+    maxNumObjsPerIter=0,
+)
+
+options(
+    units='si',
+    saveRestartPeriod=None,
+    generateOutputHTML=False,
+    generatePlots=False,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=True,
+)

examples/rmg/minimal_staged/input.py

@@ -50,9 +50,9 @@
 model( #second stage
     toleranceKeepInEdge=0.0,
     toleranceMoveToCore=0.1,
-    toleranceInterruptSimulation=0.1,
+    toleranceInterruptSimulation=1.0,
     maximumEdgeSpecies=100000,
-    maxNumObjsPerIter=2,
+    maxNumObjsPerIter=3,
     maxNumSpecies = 100,
 )
 

meta.yaml

@@ -75,7 +75,7 @@ requirements:
     - pyzmq
     - quantities
     - rdkit >=2015.09.2
-    - rmgdatabase >=2.1.4
+    - rmgdatabase >=2.1.5
     - scipy
     - scoop
     - symmetry

rmgpy/cantherm/kinetics.py

@@ -157,6 +157,8 @@ def generateKinetics(self,Tlist=None):
         order = len(self.reaction.reactants)
         klist *= 1e6 ** (order-1)
         self.kunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[order]
+        self.Kequnits = {2:'mol^2/cm^6', 1:'mol/cm^3', 0:'       ', -1:'cm^3/mol', -2:'cm^6/mol^2'}[len(self.reaction.products)-len(self.reaction.reactants)]
+        self.krunits = {1: 's^-1', 2: 'cm^3/(mol*s)', 3: 'cm^6/(mol^2*s)'}[len(self.reaction.products)]
         self.reaction.kinetics = Arrhenius().fitToData(Tlist, klist, kunits=self.kunits)
 
     def save(self, outputFile):
@@ -166,6 +168,11 @@ def save(self, outputFile):
         """
         reaction = self.reaction
 
+        ks = []
+        k0s = []
+        k0revs = []
+        krevs = []
+
         logging.info('Saving kinetics for {0}...'.format(reaction))
 
         order = len(self.reaction.reactants)
@@ -190,9 +197,36 @@ def save(self, outputFile):
             k = reaction.calculateTSTRateCoefficient(T) * factor
             tunneling = reaction.transitionState.tunneling
             kappa = k / k0
+            ks.append(k)
+            k0s.append(k0)
             f.write('#    {0:4g} K {1:11.3e} {2:11g} {3:11.3e} {4}\n'.format(T, k0, kappa, k, self.kunits))
         f.write('#   ======= =========== =========== =========== ===============\n')
+        f.write('\n\n')
+
+        f.write('#   ======= ============ =========== ============ ============= =========\n')
+        f.write('#   Temp.    Kc (eq)        Units     krev (TST)   krev (TST+T)   Units\n')
+        f.write('#   ======= ============ =========== ============ ============= =========\n')
 
+        for n,T in enumerate(Tlist):
+            k = ks[n]
+            k0 = k0s[n]
+            Keq = reaction.getEquilibriumConstant(T)
+            k0rev = k0/Keq
+            krev =  k/Keq
+            k0revs.append(k0rev)
+            krevs.append(krev)
+            f.write('#    {0:4g} K {1:11.3e}   {2}  {3:11.3e}   {4:11.3e}      {5}\n'.format(T, Keq, self.Kequnits, k0rev, krev, self.krunits))
+
+
+        f.write('#   ======= ============ =========== ============ ============= =========\n')
+        f.write('\n\n')
+
+        kinetics0rev = Arrhenius().fitToData(Tlist, numpy.array(k0revs), kunits=self.krunits)
+        kineticsrev = Arrhenius().fitToData(Tlist, numpy.array(krevs), kunits=self.krunits)
+
+        f.write('# krev (TST) = {0} \n'.format(kinetics0rev))
+        f.write('# krev (TST+T) = {0} \n\n'.format(kineticsrev))
+
         # Reaction path degeneracy is INCLUDED in the kinetics itself!
         string = 'kinetics(label={0!r}, kinetics={1!r})'.format(reaction.label, reaction.kinetics)
         f.write('{0}\n\n'.format(prettify(string)))