Dear all,
I want to simulate hydrodynamic effects on diffusion of a janus particle (whose surface has a special property because of which it has self propulsion velocity whose magnitude is fixed and direction varies randomly) under confinement. I am trying to find out whether it is doable with LAMMPS. If anybody have any experience of simulating such particles, please share it.
Thank you all.
Regards,
CMB
You’ll have to be more specific about what you want to do,
in MD language. I don’t know what self-propulsion means
in a fundamental physics sense. E.g. Newtons 3rd law.
You can write a fix in LAMMPS to do whatever you want
with particle velocities. Even violate Newton’s laws.
Steve
You'll have to be more specific about what you want to do,
in MD language. I don't know what self-propulsion means
in a fundamental physics sense. E.g. Newtons 3rd law.
Some questions:
1) How do you want to simulate the Janus particle? Is it point-like,
or are willing to represent it multiple particles? (In the later
case, standard Langevin dynamics equations would be enough to change
its direction randomly.)
2) Do you need to use an implicit solvent or are you content using an
explicit (perhaps coarse-grained) solvent?
3) Hydrodynamics:
  Most LAMMPS simulations I've seen use some kind of explicit solvent.
   LAMMPS does support Lattice-Boltzmann fluids, DPD and SRD:
http://lammps.sandia.gov/doc/fix_lb_fluid.html
http://lammps.sandia.gov/doc/pair_dpd.html
http://lammps.sandia.gov/doc/fix_srd.html
  Unfortunatley, what has not been done yet (too my knowledge) is
implement hydrodynamics in the limit of high Schmidt number.
(Typically this is done using an Oseen or Rotne-Prager-Yamakawa
tensor.) LAMMPS does not have support this yet. If you want to
implement this, we can point you in the right direction to get
started.
3) If you really want the particle to move with true constant speed
(random direction), and if you have multiple such particles, then I
think this would require editing the LAMMPS code. If you only have
one such particle, you might be able to get away with using fix
temp/rescale. (But that's not the way it was intended to be used.)
    But why do you need constant speed? (And how do you plan to
reconcile this with your desire to reproduce accurate hydrodynamics?)
Is this some kind of Brownian-ratchet?
4) Approximatley how many particles do you intend to have in your simulations?
   Keep in mind (the spatial decomposition) algorithms used in LAMMPS
were originally optimized for simulating systems with a large number
of particles, and (approximately) uniform density. However you don't
have to use it that way. (However I recall that GPU-enabled versions
of LAMMPS use a different decomposition algorithm. LAMMPS also has a
fix balance feature to help with non-uniform density simulations.)
You can write a fix in LAMMPS to do whatever you want
with particle velocities. Even violate Newton's laws.
You can even violate conservation of particle number (create and
destroy particles, although, again you may need to write your own fix
code).
Cheers
Andrew
First of all, thank you very much for your detailed reply. I will answer your questions one by one.
The Janus particle is an ellipsoid and there is only one Janus particle. I want to study the hydrodynamic effect on diffusion of a Janus particle within a cavity. In addition to the random collision with the solvent particles, the janus particle should have a self propulsion velocity with fix magnitude and randomly varying direction. I want to determine several properties as a function of the shape of the cavity and the particle itself.
To see the hydrodynamic effect I wanted to introduce the solvent implicitly.
However, fix_srd seems to do exactly what I want.
Yes, I want to study Self-Propelled Janus Particles in a Ratchet. Numerical simulations are done (Please ignore them if not interested)
For the self propulsion velocity, if an appropriate force (fix_addforce) is added each time-step to the particle, will that be okay?
Regards,
CMB
Note that atom_style ellipsoid has support for ellipsoidal particles. It
also works with fix srd.
For the self propulsion velocity, if an appropriate force (fix_addforce) is added each time-step to the particle, will that be >okay?
That’s up to you. You can use fix addforce (on a single-particle group) to
add a constant vector force. Or if you use its variable option
the added force could be defined by a time-varying variable. That
variable could use a random number. See the variable doc page for details.
Steve