Are there any plans to any minimization options to lammps (steepest
descent, conkigate gradient, etc)? Thanks.
Naven Michaud-Agrawal
Oops, sorry for the typo. I meant conjugate gradient.
Yes, we are still planning to implement a CG minimizer … it just
hasn’t gotten to the top of the (growing) to-do list …
Steve
Is there any possibility of adding a write_data command to lammps,
which could be used to output the current coordinate set?
Naveen
Naveen,
I'd recommend trying Pizza.py on this task. It is
actually very easy to use for this kind of thing and
you'll find other nice features there for building
LAMMPS input files:
http://www.cs.sandia.gov/~sjplimp/pizza.html
Specifically, try using the "newxyz" function and then
the "write" function in data.py.
Paul
The reason I was asking was that I've implemented a rough Steepest Descent
algorithm (using the basic run_style framework and verlet.cpp as an
example) and I would like to be able to write out a new starting data file
for my dynamics input file. Or the other option would be to change the
boundary options after they've already been defined (from shrink-wrapped
during minimization to periodic during dynamics runs.) Is there any reason
for not allowing this (it gives me an error if I have two boundary calls
in the input file)?
Another option is to use “write_restart” within LAMMPS, then
use the tools/restart2data tool to convert it to a data file.
You will tend to get atom overlaps if you convert a shrink-wrapped
boundary into a periodic one.
Steve
Does lammps have anything like charmm's restraining potentials? Either
planar or spherical? Thanks.
Naveen
Hello,
Are the molecule ids used for anything besides the group command? For
example do they affect any calculations? Thanks.
Naveen
Naveen,
No, molecule IDs do not affect the calculations. I
can't think of anywhere besides the group command
where they are used.
Paul