RMG-Py v2.1.3 release

ReactionMechanismGenerator · May 2, 2018 · 3f4b028 · 3f4b028
2 parents bd5fcca + 1cebdf6
commit 3f4b028
Show file tree

Hide file tree

Showing 303 changed files with 131,445 additions and 6,465 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -8,6 +8,10 @@ env:
   global:
     - secure: "L2ja+ZnV83w4qG3E8FwTjm0D6IWNOnj5wuFOjYTwbzQP4OAgLAWBzCMtxzWy5sMxFLtRgkswBH1d5f5kg8Ab7GIyAMFgQwe8UFqMJ+N05QNszE1mJkAvJtv2XN7669XXQhTt5EXfHrCcGZaODVnI2CEA8GB5DxiHO2Lcqf/xvgE="
     - secure: "Fa/qcHKKkTzgNanhgz+XWXg5K+uae5Ukxd0hfzYaiOI4+ldFbyMrYbPpxxoYVXw1SSO0psSupLfPfXzHwyJpFOyc46P+fo+R3YgNTJwr2VfdvSC0bp9K01nlRJ/z62IpMwmDwR2UH5xnfTeB9nhtzviFNKZoDZ/GR7F1Wqd/nnU="
+    - secure: "dkhvrkbNEHv55q3NU+lNJ0SqaNG0/vPMsG3X2eQvYjFsq/e8EliILtEtjrugSgeFohxqms0F+sSyDpw46mtn+jukYejdywLVL7w8o9pxlkHv8uEqYhNiwCD8RjNyRPQAS9jL+sAJiqdqUWR6AzjwaLproCe6rFzzGe7Io5oDLMg="
+    - secure: "cfosGf5hvUhIlPoGJu0d/HFddrMwIFU7FfLwd8yRrMGkYv0ePOwAW9kmhFSxUYvuXkxzgD75cIICMFY2fSm6VXBXXzfPQD7vwzoApXf7a8vi0C64XhinXhdEyUYb5/v8fswa0zheUENYhUS1tOqDXT/h8EPNZT5wKizaA3O2Wa8="
+    - secure: "QXuqKYuwCocqsTMePBc5OugBbQC4/t+335TYLdkletiateP/rF/eDsVRG792/BVq5gKRZgz3NH9ipTNm5pZoCbAEPt9+eDpfts8WeAbxmjdcEjfBxxwZ69wUTPAVrezTGn2k7W2UBdFrWeUNKPAVCKIkoviXqOHFitqJEC+c6JY="
+    - secure: "jIyBEzR10l5SWvY5ouEYzA8YzPHIZNMXMBdcXwuwte8NCU8GBYUqhHA1L67nTaBdLhWbrZ2NireVKPQWJp3ctcI0IB6xZzaYlVpgN/udGPO+1MZd9Xhp9TWuJWrGZ9EoWGB9L5H+O7RYwcDMVH5CUrCIBdsSJuyE8aDpky1/IVE="
 addons:
   apt:
     packages:
@@ -33,7 +37,7 @@ install:
   - make
 
 script: 
-  - make test
+  - make test-all
   - make test-database
 
 after_success:

diff --git a/COPYING.txt → LICENSE.txt b/COPYING.txt → LICENSE.txt
diff --git a/Makefile b/Makefile
@@ -74,17 +74,32 @@ decython:
 	find . -name *.so ! \( -name _statmech.so -o -name quantity.so -o -regex '.*rmgpy/solver/.*' \) -exec rm -f '{}' \;
 	find . -name *.pyc -exec rm -f '{}' \;
 
-test:
+test-all:
 ifeq ($(OS),Windows_NT)
 	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 else
 	mkdir -p testing/coverage
 	rm -rf testing/coverage/*
 	nosetests --nocapture --nologcapture --all-modules --verbose --with-coverage --cover-inclusive --cover-package=rmgpy --cover-erase --cover-html --cover-html-dir=testing/coverage --exe rmgpy
 endif
+
+test:
+ifeq ($(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
+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
+endif
+
 test-database:
 	nosetests -v -d testing/databaseTest.py	
-
+eg0: noQM
+	mkdir -p testing/eg0
+	rm -rf testing/eg0/*
+	cp examples/rmg/superminimal/input.py testing/eg0/input.py
+	@ echo "Running eg0: superminimal (H2 oxidation) example"
+	python rmg.py testing/eg0/input.py
 eg1: noQM
 	mkdir -p testing/eg1
 	rm -rf testing/eg1/*

diff --git a/README.md b/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 v2.1.2**
+**RMG v2.1.3**
 [![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).

diff --git a/deploy.sh b/deploy.sh
@@ -75,4 +75,7 @@ git checkout $RMGTESTSBRANCH
 git commit --allow-empty -m rmgpy-$REV
 
 # push to the branch to the RMG/RMG-tests repo:
-git push -f $REPO $RMGTESTSBRANCH > /dev/null
+git push -f $REPO $RMGTESTSBRANCH > /dev/null
+
+# kill ssh-agent if neccessary
+ssh-agent -k
diff --git a/documentation/source/users/cantherm/acetyl+O2.jpg b/documentation/source/users/cantherm/acetyl+O2.jpg
diff --git a/documentation/source/users/cantherm/input.rst b/documentation/source/users/cantherm/input.rst
diff --git a/documentation/source/users/cantherm/input_pdep.rst b/documentation/source/users/cantherm/input_pdep.rst
diff --git a/documentation/source/users/cantherm/installation.rst b/documentation/source/users/cantherm/installation.rst
@@ -2,61 +2,15 @@
 Installation
 ************
 
-Dependencies
-============
-
-Python versions 2.6+ are recommended for CanTherm.  Currently Python 3.x versions
-are incompatible with CanTherm.
-
-CanTherm relies on a number of Python packages for certain functionality. The
-following lists the required Python packages that are not part of the Python
-standard library:
-
-* `NumPy <http://www.numpy.org>`_. Provides efficient array and matrix 
-  operations.
-
-* `SciPy <http://www.scipy.org>`_. Provides efficient linear algebra functions
-  and special functions.
-
-* `Cython v0.19+ <http://www.cython.org>`_. C-extensions for Python
-
-* `RDKit <http://www.rdkit.org>`_. Cheminformatics libraries and functions
-
-* `Cairo <http://cairographics.org/>`_. Cairo graphics rendering for Python for drawing reaction networks
-
-* Quantities. For converting between different scientific units
-
-* Argparse. For parsing input arguments when running scripts
-
-You can install these dependencies on Linux in the following fashion. ::
-
-	sudo apt-get install python-numpy python-scipy python-cairo
-	sudo pip install cython>=0.19 quantities argparse
-
-It is recommended that RDKit be installed manually with InChI capabilities on.
-
-
 Installing CanTherm
 ===================
 
-Once you have obtained the required dependencies, CanTherm can be installed by 
-first obtaining the RMG-Py source code by either downloading into a directory using git::
-
-	git clone git@github.com:ReactionMechanismGenerator/RMG-Py.git
-	
-or by downloading the zip file of the current RMG-Py master source code found 
-`here <https://github.com/ReactionMechanismGenerator/RMG-Py/archive/master.zip>`_ and unzipping into
-the appropriate directory.
-
-Inside the root package directory for ``RMG-Py``, execute the following make command::
-
-	make cantherm
-	
-The appropriate cythonization and compilation steps will now begin.  When they are completed,
-you can run a test example by going into the examples folder to run a sample Cantherm job 
-to verify the installation::
+CanTherm can be obtained by installing the `RMG-Py <http://rmg.mit.edu/>`_ software, which
+includes all neccesary dependancies.
 
-	cd examples/cantherm/networks/acetyl+O2
-	python ../../../../cantherm.py input.py
+Instructions to install RMG-Py can be found at the :ref:`RMG-Py Installation page <installation>`.
 
-This will allow you to use the cantherm.py as a Python script anytime you point to it. 
+Note that you'll need to choose between the Basic User or Developer installation instructions
+that are specific to your operating system. Modifying cantherm source code will 
+require Developer installation. If you are only looking to run the code, the 
+Basic User installation will work.
diff --git a/documentation/source/users/cantherm/introduction.rst b/documentation/source/users/cantherm/introduction.rst
@@ -17,14 +17,16 @@ one-dimensional master equation, then apply one of several available model
 reduction methods of varying accuracy, speed, and robustness to simplify the 
 detailed model into a set of phenomenological rate coefficients. The result 
 is a set of :math:`k(T,P)` functions suitable for use in chemical reaction
-mechanisms.
+mechanisms. More information is available at `Allen et al. <http://dx.doi.org/10.1039/c1cp22765c>`_.
 
-
-About CanTherm
-==============
+CanTherm is developed and distributed as part of `RMG-Py <http://rmg.mit.edu/>`_, but can be used as a stand-alone
+application for Thermochemistry, Transition State Theory, and Master Equation chemical kinetics calculations. 
 
 CanTherm is written in the `Python <http://www.python.org/>`_ programming
-language to facilitate ease of development, installation, and use. 
+language to facilitate ease of development, installation, and use.
+
+Additional theoretical background can be found at `RMG's Theory Guide <http://reactionmechanismgenerator.github.io/RMG-Py/theory/index.html>`_
+and `CanTherm's Manual <manual.pdf>`_ as well as the `manual's supplement information <manual_supplement-Solving1DSchrodingerEquation.pdf>`_.
 
 License
 =======
@@ -35,4 +37,4 @@ full, official license is reproduced below
 
 
 
-.. literalinclude:: ../../../../COPYING.txt
+.. literalinclude:: ../../../../LICENSE.txt
diff --git a/documentation/source/users/cantherm/output.rst b/documentation/source/users/cantherm/output.rst
@@ -19,15 +19,31 @@ The output file contains the entire contents of the input file. In
 addition, the output file contains a block of ``pdepreaction()`` calls. The 
 parameters of each ``pdepreaction()`` block match those of the ``reaction()`` 
 block from the input file, except that no transition state data is given and 
-the ``kinetics`` are by definition pressure-dependent. 
-
-A ``pdepreaction()`` item is printed for the forward and reverse direction of 
-every reaction involving isomers and reactant channels only. For reactions 
-involving a product channel, there is only a ``pdepreaction()`` item for the 
-direction in which the product channel is the product of the reaction. To use
-this output, you must either keep all of the reactions and treat them as
-irreversible, or discard the duplicate reverse directions and treat the
-remaining reactions as reversible. This decision is left to the end user.
+the ``kinetics`` are by definition pressure-dependent.
+
+A ``pdepreaction()`` item is printed for each reaction pathway possible in the
+network. Each reaction is reversible. Reactions in the opposite direction are
+provided as commented out, so a user can choose to use them if she/he desires.
+
+
+Chemkin Output File
+===================
+
+In addition to the ``output.py`` which contains the thermodynamic,
+kinetic, and pressure dependent results from a cantherm run, a Chemkin 
+input file, ``chem.inp`` is also returned. This file contains species and their 
+thermodynamic parameters for each species that has the ``thermo()`` in the 
+input file. The file also contains kinetics, both pressure dependent and high 
+pressure limit, which have the ``kinetics()`` or ``pressureDependence()`` module 
+called.
+
+For the output file to function, all the names of species should be in valid
+chemkin format. The butanol and ethyl examples both show how to obtain a valid 
+chemkin file.
+
+The ``chem.inp`` file can be used in Chemkin software package or converted to 
+a Cantera input file for use in Cantera software.
+
 
 Log File
 ========

diff --git a/documentation/source/users/cantherm/running.rst b/documentation/source/users/cantherm/running.rst
@@ -4,7 +4,9 @@ Running CanTherm
 
 To execute a CanTherm job, invoke the command ::
 
-    $ python cantherm.py FILE
+    $ python cantherm.py INPUTFILE
+
+The absolute or relative paths to the cantherm.py file as well as to the input file must be given.
 
 The job will run and the results will be saved to ``output.py`` in the same
 directory as the input file. If you wish to save the output elsewhere, use