How to Visualize EON output

eOn code for long time scale dynamics

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Ali04
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Joined: Tue Oct 13, 2020 4:16 pm

How to Visualize EON output

Post by Ali04 »

Hi,

I am new with EON and running AKMC simulations. I have an output with several states, I can visualize the individual file in ase-gui but I'm wondering 'how to visualize whole akmc movie'. If I am not wrong, I have obtained "dynamics.txt' file for the whole akmc simulation. Does anyone comment how to visualize this file, Is there any visualization program or any way to convert this 'dynamics.txt' file into other format like 'dynamics.con' file and then visualize it? or any other scripts I need to use for this visualization?.

Thanks,

Abid
graeme
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Re: How to Visualize EON output

Post by graeme »

Hi Abid,

Yes, for sure, this is critical, and I think we have very limited documentation about visualization.

First, there are a few scripts in the eon/tools directory which might help visualize the processes available from a particularly state, eon-prmov.sh, but the primary tool for making movies is through the eon script itself. If you run eon -h, you will see the options (below). Check out the -m tag which allows you to make different types of movie files. Using the statenumber option will give give you a movie moving through the states. The dynamics option will follow each state according to the calculated dynamics. We have added a few less-intuitive but often very useful types of movies. The fastestpath option, for example, will follow the dynamics but leave out any repeated states. In many dynamics trajectories there can be a lot of revisiting states, which will be skipped with this option. A minor variant of this is the fastestfullpath, which does the same but will make sure to visit all the states in the dynamics at least once. There are other options; if you have any further questions, please post again. This should also motivate us to add documentation about this.

---------
eon -h
Usage: eon [options] config.ini

Options:
-h, --help show this help message and exit
-C, --continuous don't quit
-R, --reset reset the aKMC simulation, discarding all data
-f, --force force a reset, no questions asked
-r, --restart restart the aKMC simulations from a clean dynamics.txt
file
-s, --status print the status of the simulation and currently
running jobs
-q, --quiet only write to the log file
-m MOVIE_TYPE, --movie=MOVIE_TYPE
Specify the type of movie to make [dynamics, states,
fastestpath, fastestfullpath, graph, processes].
Process movies are specified like so: --movie
processes,statenumber,processlimit. Where processes is
the string processes, statenumber is the number of the
state that you want to view, and process limit is the
maximum number of processes you would like in the
movie. The returned processes are reverse sorted by
rate such that the fastest processes is the first in
the movie.
-M, --separate-movie-files
Do not write the movie into a single file but use a
separate POSCAR for every state. These are created in
the "movies" directory. Only useful in conjunction
with --movie.
-n, --no-submit don't submit searches; only register finished results
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