How to run AutoTST

[AH9316]

Hello, developers. I have created AutoTST environment on my Mac, but there is no guide to tell us how to run or activate AutoTST simulation.

Because the AutoTST is based on RMG, my guess is that once we activate AutoTST environment (tst_env), we can run AutoTST as same as run RMG, for example, type " rmg.py input.py" in the terminal (it actually works).

Here are my questions, 1st, do we need to modify input file to tell RMG we need to activate AutoTST; 2nd, what and where is the output of AutoTST simulation, for example, when we finish RMG simulation, we can get a mechanism(chem.inp), for AutoTST what kind of files we are looking for?

Regard to the 2nd question, I run 2 RMG simulations under rmg_env environment and tst_env environment with the same input, respectively. After finishing these 2 simulations, I found that they have exactly the same output files, so I wonder if I activate AutoTST under the tst_env environment.

Below is my simple input file, just for the test.
input.txt

Looking forward to your response, thanks!!

[nateharms]

Hi there! Thank you for reaching out! At its present set up, AutoTST does not have an input file method similar to RMG's inputs. We are working to make this and have it as a ToDo (see #65). This is one of the issues that we hope to resolve soon (and now will move this to the top of our priority list!).

To specifically answer your questions:

1. The input file to RMG will not run AutoTST. There is no input format for AutoTST in its present form but we will work on making that. This might explain why when you run your 2 RMG simulations with the rmg_env and the tst_env you get the same results.

2. The output of AutoTST will be in the form of files that end with .kinetics that would have contents as follows:

method = "m062x"
reaction = Reaction(reactants=[Molecule(smiles="[CH2]CCCO")], products=[Molecule(smiles="CCC[CH]O")], kinetics=Arrhenius(A=(0.978755,'s^-1'), n=3.40625, Ea=(56.5596,'kJ/mol'), T0=(1,'K'), Tmin=(303.03,'K'), Tmax=(2500,'K'), comment="""Fitted to 59 data points; dA = *|/ 6.2754, dn = +|- 0.241042, dEa = +|- 1.32597 kJ/mol"""))

These files can be parsed out by AutoTST and used with RMG.

I'm sorry that the code isn't doing what you need at the moment. Are you trying to calculate all reaction rates from an RMG-created model and parse that out into mechanism file?

[AH9316]

Hi, @nateharms. Thank you for your response! And, yes, we are trying to use RMG to generate some aromatic combustion mechanisms and hope AutoTST can calculate and improve all reaction rates from those RMG mechanisms and then parse those rates out into the final mechanism.

[sthakris]

Adding up to this issue. Some queries, AutoTST requires Gaussian package to be installed in computer? How to submit a job for AutoTST after activating autotst environment. How does the input structure looks like. Are there any pdf documentation for using AutoTST, so the one can follow it. For. e.g, I would like to know how any give molecule can decompose in different ways.