Hello Sir,
I have a system of Active Brownian particles. I want to calculate the rotational diffusion constant for the persistent time of ABPs( persistent time=1/rotational diffusion constant). Which commands ll be helpful to calculate Dr.
fix 1 all nve/sphere
fix 4 mobile langevin 1.0 1.0
1.0 437624 omega yes scale 1 3.3
fix fric all viscous 1.0
fix active1 mobile propel/self velocity 0.5
in.code.txt (916 Bytes)
There is no suitable functionality in LAMMPS that I know of.
For example you would need to compute the ASD instead of the MSD for translational displacement. So you would need to program such a compute style (and debug/test it).
Of course you can also program this as an external post-processing tool (or look for some MD analysis software package that has it) which you would feed a suitable custom trajectory dump file.
1 Like
Thank you sir.
sir can you tell me a how i can calculate orientational autocorelation function as mensioned in this answer…
Error in fix langevin? - LAMMPS / LAMMPS Mailing List Mirror - Materials Science Community Discourse (matsci.org)
Hi Steve!
Sorry for being so slow, but I finally had time to have a look at the Langevin issue! It seems your analysis is correct, apart from that gamma1 and gamma2 should be increased rather than decreased. More explicitly, I’ve replaced the gamma1 and gamma2 definitions in the omega part of fix_langevin.cpp with
gamma1 = -(10.0/3.0)inertiaone / t_period / ftm2v;
gamma2 = sqrt(inertiaone) * sqrt(80.0boltz/t_period/dt/mvv2e) / ftm2v;
As you said, the change does not affect the rotational temperature, but only the rotational diffusion. I attach a plot of the orientational autocorrelation function for a system of spherical particles in 2D simulated using the new and the old codes; with the parameters used (t_period = 0.01, temp = 1.0, mass = 1.0, diameter = 1.0) the expected rotational diffusion constant is 0.03, which fits well with the data. The rotational temperature is reproduced correctly (fluctuating around 1.0) in both cases, although the timestep needs to be decreased slightly in the new code for the rotational motion not to blow up.
As with any other computation of a property to be extracted in post-processing from a simulation, you have to search the corresponding text books or published articles or other locations that describe how this specific property is computed. Since LAMMPS does not provide this functionality, this is not really a LAMMPS question.