Author Topic: list of configurational moves in .def file  (Read 21 times)

ae213

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list of configurational moves in .def file
« on: June 21, 2022, 08:40:19 PM »
Dear Prof. Dubbeldam and RASPA community,

I am simulating adsorption in MOFs of an adsorbate with large molecules which shows zero adsorption in UiO-66 (although it is quite significant in other MOFs of similar pore size). I nevertheless suspect it is due to insertion issues.
I am therefore trying to run configurational-bias Monte Carlo, which is, in my understanding, requires a list of configurational moves in .def file, for example, as it is listed in dimethylpropane.def file:

# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
433.75
3196300.0
0.197
# number of atoms
5
# atomic types
0 CH3_sp3
1 C_sp3
2 CH3_sp3
3 CH3_sp3
4 CH3_sp3
...
...
...
# Number of config moves
4
# nr fixed, list
2 0 1
2 1 4
2 1 2
2 1 3


Could you please give me some details on how this list is constructed?

David Dubbeldam

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Re: list of configurational moves in .def file
« Reply #1 on: June 22, 2022, 10:13:44 PM »
This for the PartialReinsertionProbability move, where only a few atoms are regrown and the others are left fixed.
So, in this case there are 4 config move defined (and you see 5 lines). For each line you have the number of fixed atoms, and the the list of the fixed atom ids.
The other atoms are regrown using CBMC. This move has high efficiency, because the molecule is already present and is only partially regrown.
Note that in CBMC all branches need to be grown at the same time, so you can not keep more than one branch fixed (in a branched molecule).

ae213

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Re: list of configurational moves in .def file
« Reply #2 on: June 23, 2022, 06:17:44 PM »
Got it! Thank you so much for your time and clear explanation