AKMC Tutorial#
You can find a sample setup for the AKMC method in the examples/akmc-pt directory of your copy of eon. The system is a Pt heptamer island on a Pt(111) surface:
The Pt heptamer island on a Pt(111) surface.#
After following the installation instructions:
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ python -m eon.server
Eon version 1d9860cf
State list path does not exist; Creating: .//states/
Registering results
Processed 0 results
Queue contains 0 searches
Making 2 process searches
Job finished: .//jobs/scratch/0_0
Job finished: .//jobs/scratch/0_1
Created 2 searches
Currently in state 0 with confidence 0.000000
Each time you run EON, the server registers results from the previous execution.
The first time the EON server is run, there are no results to register. Two
saddle searches are executed, but their results will only be registered on the
next execution of EON. You can see this by looking at the search_results.txt
file in your states directory.
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ cat states/0/search_results.txt
wuid type barrier max-dist sad-fcs mins-fcs pref-fcs result
-------------------------------------------------------------------------------------
It’s empty. We can register the results of the first execution of EON by running the server again
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ python -m eon.server
Eon version 1d9860cf
Registering results
Found new lowest barrier 0.987074 for state 0 (type: random)
Found new barrier 0.987074 for state 0 (type: random)
Found new barrier 1.196473 for state 0 (type: random)
Processed 2 results
Queue contains 0 searches
Making 2 process searches
Job finished: .//jobs/scratch/0_2
Job finished: .//jobs/scratch/0_3
Created 2 searches
Currently in state 0 with confidence 0.000000
Now some results should be present in the table (these will vary):
EONgit/examples/akmc-pt on main via 🅒 eongit took 10s
➜ cat states/0/search_results.txt
wuid type barrier max-dist sad-fcs mins-fcs pref-fcs result
-------------------------------------------------------------------------------------
0 random 0.98707 0.00000 282 339 1044 good-0
1 random 1.19647 0.00000 630 375 1287 good-1
The search_results.txt file provides information about how a particular job
went. The data collected is contained in the processtable file in the state
directory:
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ cat states/0/processtable
proc # saddle energy prefactor product product energy product prefactor barrier rate repeats
0 -1774.80409 7.32913e+12 -1 -1775.00608 2.64735e+12 0.98707 1.91855e-04 0
1 -1774.59469 1.48200e+13 -1 -1775.09375 4.55267e+12 1.19647 1.17764e-07 0
You can find the files relevant to a process in the procdata directory of a
given state:
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ ls states/0/procdata
mode_0.dat product_0.con reactant_0.con results_0.dat saddle_0.con stdout_0.dat
mode_1.dat product_1.con reactant_1.con results_1.dat saddle_1.con stdout_1.dat
The data relevant to process 0 is in the process table. The figures below show the reactant, saddle, and product configurations for this process:
Left to right, reactant, saddle and product configurations.#
Subsequent runs of EON will show an increasing confidence as the event table (in the specified energy window) becomes complete:
currently in state 0 with confidence 0.313698
...
currently in state 0 with confidence 0.641981
...
currently in state 0 with confidence 0.675757
We need to explore a larger part of the phase space until a KMC step can be
taken. To iterate over states quickly, consider a for loop in bash:
EONgit/examples/akmc-pt on main via 🅒 eongit took 7s
➜ for i in {0..60}; do python -m eon.server; done
Eventually, the simulation will reach the required confidence and take a KMC step to the next state:
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ python -m eon.server
Registering results
Processed 4 results
Cancelled 0 workunits from state 0
register_process: new product state
register_process: into eq rate test
Meantime for Step 1: 0.0003931769704500849
KMC step from state 0 through process 2 to state 1
currently in state 1 with confidence 0.000000
This will then be reflected in the dynamics.txt file of the simulation directory:
EONgit/examples/akmc-pt on main via 🅒 eongit
➜ cat dynamics.txt
step-number reactant-id process-id product-id step-time total-time barrier rate energy
-----------------------------------------------------------------------------------------------------------------------------
0 0 2 1 1.531416e-03 1.531416e-03 0.601060 9.861450e+02 -1775.791160