From ac1d3a0ff1a914b1ef70cf66686cfa388931a5fe Mon Sep 17 00:00:00 2001 From: enochd Date: Wed, 15 Jan 2014 09:49:17 -0500 Subject: [PATCH 1/4] added installation dependencies I noticed I had to install both freetype2 and libpng-dev before matplotlib could be installed (on a 64 bit machine running linux) --- documentation/source/users/rmg/installation/linux.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/documentation/source/users/rmg/installation/linux.rst b/documentation/source/users/rmg/installation/linux.rst index ed3c94e50b..1a92d2c7f5 100644 --- a/documentation/source/users/rmg/installation/linux.rst +++ b/documentation/source/users/rmg/installation/linux.rst @@ -23,7 +23,7 @@ The instructions listed below have been confirmed on a fresh Ubuntu 12.04 instal sudo pip install numpy # install NumPy before other packages - sudo pip install scipy cython nose matplotlib quantities guppy sphinx psutil xlwt + sudo pip install scipy cython nose matplotlib quantities guppy sphinx psutil xlwt freetype2 libpng-dev cd ~ git clone git@github.com:jwallen/PyDAS.git From bf6ca105a6ed487595a112c7d9cbb81b4510c39f Mon Sep 17 00:00:00 2001 From: enochd Date: Wed, 15 Jan 2014 15:27:33 -0500 Subject: [PATCH 2/4] expanded documentation Added a couple things to output and running sections --- documentation/source/users/rmg/output.rst | 11 ++++++++++- documentation/source/users/rmg/running.rst | 9 ++++++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/documentation/source/users/rmg/output.rst b/documentation/source/users/rmg/output.rst index bd3b68a148..e0bcdd3781 100755 --- a/documentation/source/users/rmg/output.rst +++ b/documentation/source/users/rmg/output.rst @@ -3,4 +3,13 @@ ************************** Analyzing the Output Files ************************** - \ No newline at end of file + +You will see that RMG has created multiple output files and folders: :: + :file:'/chemkin input.py output.html /pdep /plot restart.pkl RMG.log /solver /species' + +The :file:'/chemkin' folder will likely have a large number of chemkin formatted files. In general, these can be disregarded, as you will be mainly interested in :file:'chem.inp', the chemkin formatted input file with a species list, thermochemical database, and a kinetic mechanism. The file :file:'chem_annotated.inp' is provided as a means to help make sense of species syntax and information sources. In addition, a species dictionary,:file:'species_dictionary.txt', is generated. Either chemkin file, in addition to the dictionary, may be used as inputs in the tools section of this website to better visualize the species and reactions: http://rmg.mit.edu/simulate/chemkin +(alternatively, you can open :file:'output.html') + +The :file:'/pdep' folder will contain files associated with the pressure-dependent reactions that RMG has generated. These files are formatted as input files for CanTherm. + +RMG currently includes a solver for isothermal batch reactors. This is in fact a critical part of the model enlargement algorithm. If you have included simulations in your input file, the solutions will be located in :file:'/solver'. You will probably only be interested in the files with the largest number tags. \ No newline at end of file diff --git a/documentation/source/users/rmg/running.rst b/documentation/source/users/rmg/running.rst index 10c3a9587b..9ebaa90c3c 100755 --- a/documentation/source/users/rmg/running.rst +++ b/documentation/source/users/rmg/running.rst @@ -3,4 +3,11 @@ ************* Running a Job ************* - \ No newline at end of file + + Submitting a job is easy :: + + python rmg.py input.py + +We recommend you make a job-specific directory for each RMG simulation. Some jobs can take quite a while to complete, so we also recommend using a job scheduler (if working in an linux environment). + + From 54362885400f9030819414df13ed57cdfd144f76 Mon Sep 17 00:00:00 2001 From: enochd Date: Wed, 5 Feb 2014 14:54:08 -0500 Subject: [PATCH 3/4] added rate rule caveat to documentation ...it might be wise to double check existing rules to ensure there are not too many instances of this --- .../source/users/rmg/database/modification.rst | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/documentation/source/users/rmg/database/modification.rst b/documentation/source/users/rmg/database/modification.rst index fa6515cfdc..149aefa856 100644 --- a/documentation/source/users/rmg/database/modification.rst +++ b/documentation/source/users/rmg/database/modification.rst @@ -264,4 +264,12 @@ Be sure to give errors whenever adding rules. If you don't know the uncertainty, why do you trust the kinetics? After you are done always check via populate reactions or the website, that your -modifications are behaving the way you expect. \ No newline at end of file +modifications are behaving the way you expect. + +Caveat regarding how rate rules are used by RMG and the rate parameters you input: because tunneling is +important for many chemical reactions, the rate of a reaction may not be easily represented by +a bi-Arrhenius fit. 3-parameter fits are more common. However, the resulting fit may report an +'activation energy' that is much different (possibly by 10+ kcals) than the the true barrier height. +When RMG is assembling pressure-dependent networks, it will use barrier heights from rate rules. This can +lead to very inaccurate rate calculations. To avoid this issue, try to ensure that your fitted arrhenius +activation energy truly does reflect the reaction barrier height. \ No newline at end of file From 265b45c1f9f3ea670d909348630c5a8914042db3 Mon Sep 17 00:00:00 2001 From: Enoch Dames Date: Wed, 5 Feb 2014 17:27:49 -0500 Subject: [PATCH 4/4] added molecular constraints to documentation This regards RMG-Py issue #174. Also made sure generatedSpeciesConstraints works properly. --- documentation/source/users/rmg/input.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/documentation/source/users/rmg/input.rst b/documentation/source/users/rmg/input.rst index 2aed83acbf..f31c50657e 100644 --- a/documentation/source/users/rmg/input.rst +++ b/documentation/source/users/rmg/input.rst @@ -337,6 +337,17 @@ Miscellaneous options:: generatePlots=False, ) + generatedSpeciesConstraints( + maximumCarbonAtoms=10, + maximumHydrogenAtoms=10, + maximumOxygenAtoms=10, + maximumNitrogenAtoms=10, + maximumSiliconAtoms=10, + maximumSulfurAtoms=10, + maximumHeavyAtoms=10, + maximumRadicalElectrons=10, + ) + Examples ========