In order to determine the nucleation rate J, using MD simulations by following the mean first passage time (MFPT) technique, it is necessary to determine the size of the largest cluster of atoms formed (n) over the time period of the simulation (Tn). The mean first-passage time for each size (n) is simply obtained by averaging (Tin) over several repetitions of the simulations with different initial configurations.
Could anyone kindly highlight or provide insight on how this can be achieved in LAMMPS or in general in any MD software package? Thanks.
For LAMMPS:
This should work:
compute clusters all cluster/atom [cutoff] # you know what cutoff you need in your system
compute chunks all chunk/atom c_clusters compress yes # compression to discard empty clusters, although I'm not 100 % sure this is needed in this case
compute counts all property/chunk chunks count
variable largest equal max(c_counts)
thermo_style custom step temp press etotal pe vol v_largest
Jyri Kimari : Thank you so much for the detailed response!!
I will evaluate these methods and apply the best suited technique to the problem.
I think the compute chunk/atom option will most likely do the job in this problem as I can then call the "c_clusters" variable in the thermo output as well to do the forward flux sampling !!
Abhay Vincent Note that you will need all of those in sequence to get the output of the largest cluster size during simulation, each needs the output of the previous as the input.
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