RMG-Py v2.1.4 release

Author: mliu49

.travis.yml

@@ -33,6 +33,7 @@ before_install:
 install:
   - conda env create -f environment_linux.yml
   - source activate rmg_env
+  - pip install codecov
   - yes 'Yes' | $HOME/miniconda/envs/rmg_env/bin/mopac $MOPACKEY > /dev/null
   - make
 
@@ -41,4 +42,5 @@ script:
   - make test-database
 
 after_success:
+  - codecov
   - bash ./deploy.sh

CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# RMG Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at rmg_dev@mit.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct/
+
+[homepage]: https://www.contributor-covenant.org
+

README.md

@@ -17,7 +17,7 @@ Gaussian, MOPAC, QChem, and MOLPRO.
 - [RMG-database Github Repository](https://github.com/ReactionMechanismGenerator/RMG-database): contains source code for the latest version of the database
 
 ## Latest Stable Release
-**RMG v2.1.3**
+**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).

documentation/Makefile

@@ -39,8 +39,7 @@ setup_github_pages:
 # Turn the build/html directory into a git repository linked to github ready to push to gh-pages branch!
 # Should only need to be run once.
 	rm -rf $(BUILDDIR)/html
-	mkdir -p $(BUILDDIR)/html
-	git clone --shared --branch gh-pages --config remote.official.url=git@github.com:ReactionMechanismGenerator/RMG-Py.git --config remote.official.fetch=+refs/heads/*:refs/remotes/official/* --config branch.gh-pages.remote=official --config branch.gh-pages.merge=refs/heads/gh-pages ../.git $(BUILDDIR)/html
+	git clone --single-branch --branch gh-pages --origin official git@github.com:ReactionMechanismGenerator/RMG-Py.git build/html
 
 publish: $(BUILDDIR)/html/.git
 # Commit changes to gh-pages and push to github, to publish the results!

documentation/source/conf.py

@@ -43,7 +43,7 @@
 
 # General information about the project.
 project = u'RMG Py'
-copyright = u'2002-2015, William H. Green, Richard H. West, and the RMG Team'
+copyright = u'2002-2017, William H. Green, Richard H. West, and the RMG Team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

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

@@ -101,6 +101,8 @@ Below is a list of pre-packaged kinetics library reactions in RMG:
 +---------------------------------------+------------------------------------------------------------------------------------------+
 |JetSurF2.0                             |Jet Surrogate Fuel model up tp C12 (excited species removed)                              |
 +---------------------------------------+------------------------------------------------------------------------------------------+
+|Klippenstein_Glarborg2016              |Methane oxidation at high pressures and intermediate temperatures                         |
++---------------------------------------+------------------------------------------------------------------------------------------+
 |Mebel_C6H5_C2H2                        |Pathways from benzene to naphthalene                                                      |
 +---------------------------------------+------------------------------------------------------------------------------------------+
 |Mebel_Naphthyl                         |Reactions of naphthyl-1 and naphthyl-2                                                    |

documentation/source/users/rmg/input.rst

@@ -365,6 +365,24 @@ Because the ODE simulation is always interrupted, no pruning is performed.
 
 Please find more details about the theory behind pruning at :ref:`Pruning Theory <prune>`.
 
+Advanced Setting: Taking Multiple Species At A Time
+----------------------------------------------------
+Taking multiple objects (species, reactions or pdepNetworks) during a given simulation can often decrease your overall model generation time
+over only taking one.  For this purpose there is a maxNumObjsPerIter parameter that allows RMG to take
+that many species, reactions or pdepNetworks from a given simulation. This is done in the order they trigger their respective criteria.   
+
+For example ::
+
+	model(
+		toleranceKeepInEdge=0.0,
+		toleranceMoveToCore=0.1,
+		toleranceInterruptSimulation=0.1,
+		maxNumObjsPerIter=2,
+	)
+
+Note that this can also result in larger models, however, sometimes these larger models (from taking more than one
+object at a time) pick up chemistry that would otherwise have been missed.  
+
 .. _ontheflyquantumcalculations:
 
 On the fly Quantum Calculations
@@ -522,6 +540,9 @@ Miscellaneous Options
 Miscellaneous options:: 
 
     options(
+        name='Seed',
+        generateSeedEachIteration=True,
+        saveSeedToDatabase=True,
         units='si',
         saveRestartPeriod=(1,'hour'),
         generateOutputHTML=True,
@@ -531,6 +552,12 @@ Miscellaneous options::
         saveEdgeSpecies=True,
     )
 
+The ``name`` field is the name of any generated seed mechanisms
+
+Setting ``generateSeedEachIteration`` to ``True`` tells RMG to save and update a seed mechanism and thermo library during the current run
+
+Setting ``saveSeedToDatabase`` to ``True`` tells RMG (if generating a seed) to also save that seed mechanism and thermo library directly into the database
+
 The ``units`` field is set to ``si``.  Currently there are no other unit options.
 
 The ``saveRestartPeriod`` indictes how frequently you wish to save restart files. For very large/long RMG jobs, this process can take a significant amount of time. In such cases, the user may wish to increase the time period for saving these restart files.
@@ -559,13 +586,15 @@ all of RMG's reaction families. ::
     generatedSpeciesConstraints(
         allowed=['input species','seed mechanisms','reaction libraries'],
         maximumCarbonAtoms=10,
-        maximumHydrogenAtoms=10,
-        maximumOxygenAtoms=10,
-        maximumNitrogenAtoms=10,
-        maximumSiliconAtoms=10,
-        maximumSulfurAtoms=10,
+        maximumOxygenAtoms=2,
+        maximumNitrogenAtoms=2,
+        maximumSiliconAtoms=2,
+        maximumSulfurAtoms=2,
         maximumHeavyAtoms=10,
-        maximumRadicalElectrons=10,
+        maximumRadicalElectrons=2,
+        maximumSingletCarbenes=1,
+        maximumCarbeneRadicals=0,
+        maximumIsotopicAtoms=2,
         allowSingletO2 = False,
     )
 
@@ -581,3 +610,22 @@ forbidden groups.
 By default, the ``allowSingletO2`` flag is set to ``False``.  See :ref:`representing_oxygen` for more information.  
 
 
+Staging
+========
+
+It is now possible to concatenate different model and simulator blocks into the same run in stages.  Any given stage will terminate when the RMG run terminates and then the current group of model and simulator parameters will be switched out with the next group and the run will continue until that stage terminates.  Once the last stage terminates the run ends normally.  This is currently enabled only for the model and simulator blocks.  
+
+There must be the same number of each of these blocks (although only having one simulator block and many model blocks is enabled as well) and RMG will enter each stage these define in the order they were put in the input file. 
+
+To enable easier manipulation of staging a new parameter in the model block was developed maxNumSpecies that is the number of core species at which that stage (or if it is the last stage the entire model generation process) will terminate.  
+
+For example ::
+
+	model(
+		toleranceKeepInEdge=0.0,
+		toleranceMoveToCore=0.1,
+		toleranceInterruptSimulation=0.1,
+		maximumEdgeSpecies=100000,
+		maxNumSpecies=100
+	)
+

documentation/source/users/rmg/releaseNotes.rst

@@ -4,6 +4,61 @@
 Release Notes
 *************
 
+RMG-Py Version 2.1.4
+====================
+Date: September 08, 2017
+
+- Accelerator tools:
+    - Dynamics criterion provides another method to expand the mechanism by adding reactions to the core
+    - Surface algorithm enables better control of species movement to the core when using the dynamics criterion
+    - Multiple sets of model parameters can now be specified in a input file to allow different stages of model generation
+    - A species number termination criterion can now be set to limit model size
+    - Multiple items can now be added per iteration to speed up model construction
+    - New ModelSettings and SimulatorSettings classes for storing input parameters
+
+- New features:
+    - Kinetics libraries can now be automatically generated during RMG runs to be used as seeds for subsequent runs
+    - Loading automatically generated seed mechanisms recreates the original template reaction objects to allow restarting runs from the seed mechanism
+    - Carbene constraints can now be set in the species constraint block using maxSingletCarbenes and maxCarbeneRadicals
+    - Chirality is now considered for determining symmetry numbers
+    - Thermodynamic pruning has been added to allow removal of edge species with unfavorable free energy (beta)
+
+- Other changes:
+    - RMG-Py exception classes have been consolidated in the rmgpy.exceptions module
+    - Species labels will now inherit the label from a matched thermo library entry
+    - Sensitivity analysis is now available for LiquidReactor
+
+- Fixes:
+    - Fixed sensitivity analysis following changes to the simulate method
+    - Add memory handling when generating collision matrix for pressure dependence
+    - Improved error checking for MOPAC
+    - Prevent infinite loops when retrieving thermo groups
+
+- Known issues:
+    - Seed mechanisms cannot be loaded if the database settings are different from the original ones used to generate the seed
+
+RMG-database Version 2.1.4
+==========================
+Date: September 08, 2017
+
+- New kinetics families for propargyl recombination route to benzene:
+    - Singlet_Carbene_Intra_Disproportionation
+    - Intra_5_membered_conjugated_C=C_C=C_addition
+    - Intra_Diels_alder_monocyclic
+    - Concerted_Intra_Diels_alder_monocyclic_1,2_shift
+    - Intra_2+2_cycloaddition_Cd
+    - Cyclopentadiene_scission
+    - 6_membered_central_C-C_shift
+
+- Renamed kinetics families:
+    - Intra_Diels_Alder --> Intra_Retro_Diels_alder_bicyclic
+    - H_shift_cyclopentadiene --> Intra_ene_reaction
+
+- Other additions:
+    - Klippenstein_Glarborg2016 kinetics and thermo libraries
+    - Group additivity values added for singlet carbenes, which are no longer forbidden
+
+
 RMG-Py Version 2.1.3
 ====================
 Date: July 27, 2017

documentation/source/users/rmg/thermo.rst

@@ -266,6 +266,14 @@ Chiral molecules belong to point groups that lack a superposable mirror image
 (i.e. point groups lacking :math:`\sigma_h`, :math:`\sigma_d`, :math:`\sigma_v`, and :math:`S_n`
 symmetry elements).
 
+In RMG, chirality is incorportated into the symmetry attribute by dividing the symmetry by
+two which will increase entropy by :math:`+R * ln(2)`. RMG currently checks for each chiral
+center, defined by 4 different groups attached to a carbon, and halves the symmetry 
+for each chiral center.
+
+The effect of cis-trans isomers is currently not accounted for in RMG.
+
+
 References
 ==========
 
@@ -283,4 +291,4 @@ References
 
 .. [RDKit] Landrum, G. (2012). RDKit, http://rdkit.org.
 
-.. [Benson] Benson, S.W. (1965), https://en.wikipedia.org/wiki/Benson_group_increment_theory
+.. [Benson] Benson, S.W. (1965), https://en.wikipedia.org/wiki/Benson_group_increment_theory