RMG-Py v2.1.2 release

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 v2.1.1**
+**RMG v2.1.2**
 [![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/source/users/rmg/database/introduction.rst

@@ -53,6 +53,34 @@ table below shows all atoms types in RMG.
 +----------+-------------------+-----------------------------------------------------+
 |Cbf       |Carbon             |Three benzene bonds (Fused aromatics)                |
 +----------+-------------------+-----------------------------------------------------+
+|N         |Nitrogen           |No requirements                                      |
++----------+-------------------+-----------------------------------------------------+
+|N1sc      |Nitrogen           |Up to one single bond, 3 lone pairs                  |
++----------+-------------------+-----------------------------------------------------+
+|N1s       |Nitrogen           |Up to one single bond, 2 lone pairs                  |
++----------+-------------------+-----------------------------------------------------+
+|N1d       |Nitrogen           |Exactly one double bond, 2 lone pairs                |
++----------+-------------------+-----------------------------------------------------+
+|N2s       |Nitrogen           |One ot Two single bonds, 2 lone pairs                |
++----------+-------------------+-----------------------------------------------------+
+|N3s       |Nitrogen           |Up to 3 single bonds, 1 lone pair                    |
++----------+-------------------+-----------------------------------------------------+
+|N3d       |Nitrogen           |Up to 1 single, exactly one double bond, 1 lone pair |
++----------+-------------------+-----------------------------------------------------+
+|N3t       |Nitrogen           |Exactly one triple bond, 1 lone pair                 |
++----------+-------------------+-----------------------------------------------------+
+|N3b       |Nitrogen           |Exactly two benzene bonds, 1 lone pair               |
++----------+-------------------+-----------------------------------------------------+
+|N5s       |Nitrogen           |Up to 5 single bonds, 0 lone pairs                   |
++----------+-------------------+-----------------------------------------------------+
+|N5d       |Nitrogen           |Up to 3 single, exacly one double bond, 0 lone pairs |
++----------+-------------------+-----------------------------------------------------+
+|N5dd      |Nitrogen           |Exactly two double bonds, 0 lone pairs               |
++----------+-------------------+-----------------------------------------------------+
+|N5t       |Nitrogen           |Up to 1 single, exactly one triple bond, 0 lone pairs|
++----------+-------------------+-----------------------------------------------------+
+|N5b       |Nitrogen           |Up to 1 single, exactly two benzene bonds, 0 lone    |
++----------+-------------------+-----------------------------------------------------+
 |O         |Oxygen             |No requirements                                      |
 +----------+-------------------+-----------------------------------------------------+
 |Os        |Oxygen             |No double bonds                                      |

documentation/source/users/rmg/input.rst

@@ -82,7 +82,10 @@ are to be used in addition to the Glarborg C3 library::
 	reactionLibraries = [('Glarborg/C3',False)],
 	 	
 The keyword False/True permits user to append all unused reactions (= kept in the edge) from this library to the chemkin file.
-True means those reactions will be appended.
+True means those reactions will be appended. Using just the string inputs would lead to
+a default value of `False`. In the previous example, this would look like::
+
+	reactionLibraries = ['Glarborg/C3'],
 
 The reaction libraries are stored in :file:`$RMG-database/input/kinetics/libraries/`
 and the `Location:` should be specified relative to this path.
@@ -513,6 +516,8 @@ plese refer to the :class:`rmgpy.kinetics.Chebyshev` documentation.
 The number of pressures and temperature coefficents should always be smaller 
 than the respective number of user-specified temperatures and pressures. 
 
+.. _miscellaneousoptions:
+
 Miscellaneous Options
 ===================== 
 

documentation/source/users/rmg/modules/diffModels.rst

@@ -24,5 +24,5 @@ Running the script without any optional flags looks like::
 Output of each comparison is printed, and the method then produces a html file (``diff.html``)
 for easy viewing of the comparison.  
 
-This method is also available to use with a web browser from the RMG website: `Model Comparison Tool <http://rmg.mit.edu/simulate/compare>`_.
+This method is also available to use with a web browser from the RMG website: `Model Comparison Tool <http://rmg.mit.edu/tools/compare>`_.
 

documentation/source/users/rmg/modules/generateChemkinHTML.rst

@@ -0,0 +1,34 @@
+.. _generateChemkinHTML:
+
+*******************
+HTML Chemkin Output
+*******************
+
+The script, ``generateChemkinHTML.py``, will create a formatted HTML page displaying
+all of the species and reactions in a given Chemkin file. Thermo and kinetics parameters
+are also displayed, along with any comments if the Chemkin file was generated by RMG.
+
+This script gives the same output as turning on ``generateOutputHTML`` in the :ref:`options <miscellaneousoptions>`
+section of the RMG input file. However, having using that setting can increase the
+memory usage and computation time for large jobs, so this script provides an option
+for generating the HTML file after job completion.
+
+To use this script, you need a Chemkin input file and an RMG species dictionary.
+The syntax is as follows::
+
+    python importChemkinLibrary.py [-h, -f] CHEMKIN DICTIONARY [OUTPUT]
+
+Positional arguments::
+
+    CHEMKIN        The path to the Chemkin file
+    DICTIONARY     The path to the RMG dictionary file
+    OUTPUT         Location to save the output files, defaults to the current directory
+
+Optional arguments::
+
+    -h, --help     Show help message and exit
+    -f, --foreign  Not an RMG generated Chemkin file
+
+
+This method is also available to use with a web browser from the RMG website: `Convert Chemkin File <http://rmg.mit.edu/tools/chemkin>`_.
+

documentation/source/users/rmg/modules/generateFluxDiagram.rst

@@ -14,5 +14,5 @@ To use this method, you just need a completed RMG run.  THe syntax is as follows
 where ``input.py`` is the input file for the completed RMG run.  The program will use the automatically
 generated file structure to find the other necessary files to create the movie.
 
-This method is also available to use with a web browser from the RMG website: `Generate Flux Diagram <http://rmg.mit.edu/simulate/flux>`_.
+This method is also available to use with a web browser from the RMG website: `Generate Flux Diagram <http://rmg.mit.edu/tools/flux>`_.
 

documentation/source/users/rmg/modules/generateReactions.rst

@@ -17,5 +17,5 @@ for RMG to generate reactions between.  An example file is placed in ``$RMGPy/ex
 This method will produce an ``output.html`` file in the directory of ``input.py`` which contains the all the reactions produced between the species.  
 
 
-This method is also available to use with a web browser from the RMG website: `Populate Reactions <http://rmg.mit.edu/simulate/populate_reactions>`_.
+This method is also available to use with a web browser from the RMG website: `Populate Reactions <http://rmg.mit.edu/tools/populate_reactions>`_.
 

documentation/source/users/rmg/modules/index.rst

@@ -11,6 +11,7 @@ otherwise.
 .. toctree::
     :maxdepth: 1
 
+    generateChemkinHTML
     diffModels
     mergeModels
     generateReactions

documentation/source/users/rmg/modules/mergeModels.rst

@@ -20,5 +20,5 @@ Running this method will create a new species dictionary (species_dictionary.txt
 and chemkin input file (chem.inp) in the parent directory of the terminal.
 
 
-This method is also available to use with a web browser from the RMG website: `Model Merge Tool <http://rmg.mit.edu/simulate/merge_models>`_.
+This method is also available to use with a web browser from the RMG website: `Model Merge Tool <http://rmg.mit.edu/tools/merge_models>`_.
 

documentation/source/users/rmg/releaseNotes.rst

@@ -4,6 +4,41 @@
 Release Notes
 *************
 
+RMG-Py Version 2.1.2
+====================
+Date: May 18, 2017
+
+- Improvements:
+    - New nitrogen atom types
+    - Kinetics libraries can now be specified as a list of strings in the input file
+    - New script to generate output HTML locally: generateChemkinHTML.py
+    - New kekulization module replaces RDKit for generating Kekule structures
+    - Benzene bonds can now be reacted in reaction families
+    - Removed cantherm.geometry module due to redundancy with statmech.conformer
+
+- Fixes:
+    - Reaction direction is now more deterministic after accounting for floating point error
+    - Multiple bugs with resonance structure generation for aromatics have been addressed
+
+
+RMG-database Version 2.1.2
+==========================
+Date: May 18, 2017
+
+- Nitrogen improvements:
+    - Added ethylamine kinetics library
+    - Updated group additivity values for nitrogen species
+    - Added rate rules and training reactions for nitrogen species
+
+- Additions:
+    - New CO_Disproportionation family
+    - Added CurranPentane kinetics and thermo libraries
+
+- Fixes:
+    - Corrected some rates in FFCM1(-) to use MultiArrhenius kinetics
+    - Corrected a few adjlists in FFCM1(-)
+
+
 RMG-Py Version 2.1.1
 ====================
 Date: April 07, 2017

examples/generateReactions/input.py

@@ -1,6 +1,6 @@
 # Data sources for kinetics
 database(
-    thermoLibraries = ['KlippensteinH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
+    thermoLibraries = ['BurkeH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
     reactionLibraries = [],  
     seedMechanisms = [],
     kineticsDepositories = 'default', 

examples/rmg/ch3no2/input.py

@@ -1,6 +1,6 @@
 # Data sources
 database(
-    thermoLibraries = ['KlippensteinH2O2', 'primaryThermoLibrary','DFT_QCI_thermo','CH','CHN','CHO','CHON','CN','NISTThermoLibrary','thermo_DFT_CCSDTF12_BAC','GRI-Mech3.0-N'],
+    thermoLibraries = ['BurkeH2O2', 'primaryThermoLibrary','DFT_QCI_thermo','CH','CHN','CHO','CHON','CN','NISTThermoLibrary','thermo_DFT_CCSDTF12_BAC','GRI-Mech3.0-N'],
     reactionLibraries = [('Nitrogen_Dean_and_Bozzelli',False)], 
     seedMechanisms = ['ERC-FoundationFuelv0.9'],
     kineticsDepositories = ['training'],

examples/rmg/commented/input.py

@@ -4,17 +4,20 @@
 	#libraries found at http://rmg.mit.edu/database/thermo/libraries/
 	#if species exist in multiple libraries, the earlier libraries overwrite the 
 	#previous values
-    thermoLibraries = ['KlippensteinH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
+    thermoLibraries = ['BurkeH2O2','primaryThermoLibrary','DFT_QCI_thermo','CBS_QB3_1dHR'],
 	#overrides RMG kinetics estimation if needed in the core of RMG. 
 	#list of libraries found at http://rmg.mit.edu/database/kinetics/libraries/
-	#input each library as a ('library_name',True/False) where a True means that all 
-	#unused reactions will be automatically added to the chemkin file
-    reactionLibraries = [],
+	#libraries can be input as either a string or tuple of form ('library_name',True/False) 
+     #where a `True` indicates that all unused reactions will be automatically added 
+	#to the chemkin file at the end of the simulation. Placing just string values
+     #defaults the tuple to `False`. The string input is sufficient in almost
+     #all situations
+    reactionLibraries = [('C3', False)],
 	#seed mechanisms are reactionLibraries that are forced into the initial mechanism 
 	#in addition to species listed in this input file.  
 	#This is helpful for reducing run time for species you know will appear in 
 	#the mechanism.  
-    seedMechanisms = ['KlippensteinH2O2','ERC-FoundationFuelv0.9'],
+    seedMechanisms = ['BurkeH2O2inN2','ERC-FoundationFuelv0.9'],
 	#this is normally not changed in general RMG runs.  Usually used for testing with 
 	#outside kinetics databases
     kineticsDepositories = 'default',