Dear All users
I am newcomer in LAMMPS,
In your opinion, Can i construct an hydrate structure as a initial configuration then warm to my desired temperature? Is it possibles?
Sincerely
Ali Alizadeh
Dear All users
I am newcomer in LAMMPS,
In your opinion, Can i construct an hydrate structure as a initial
configuration then warm to my desired temperature? Is it possibles?
why should it not be possible??
what LAMMPS can and cannot do is described
in the documentation. mind you, this only describes
the "mechanical" parts of a simulation (i.e. it describes
which 'tools' the 'toolbox' contains) not, what is the best
way how to simulate a particular system. that is you
task to find out.
LAMMPS doesn't contain any internal tool to set up
initial coordinates and topology information for systems
except for the simple atomic crystals. the rest is done
via external tools.
(also "a hydrate structure" is a *far* too vague description
to make any recommendation in the first place).
axel.
Dear Axel
Thank you for your reply,
That's right, "a hydrate structure" is a *far* too vague description
How can i have a ice structure as a initial configuration?
Sincerely
Ali Alizadeh
Dear Axel
Thank you for your reply,
That's right, "a hydrate structure" is a *far* too vague description
How can i have a ice structure as a initial configuration?
you need to generate the coordinates for a (conventional)
unit cell of your desired structure. then you need to decide
which potential/model you want to use and construct a
data file for it. see the documentation for "read_data" for
a description of the format.
there are some tools available that can help with that
process or you may choose to write your own tool.
http://lammps.sandia.gov/build.html
axel.
You can build ice water using moltemplate or topotools.
However finding good coordinates for (ordinary "Ih" phase) ice using
google is a pain. To help with this problem, I've attached some PDB
files which I built by hand with a text editor. The geometry of the
water molecules should match the measured geometry for ice water at
265K in this paper: Rottger K., Endriss A., and Ihringer J., Acta
Cryst, B50, 644-648 (1994)
I attached 3 PDB files containing 8, 16, and 32 water molecules.
The larger PDB files are preferable because their hydrogen bonds tend
to be more balanced. In the smaller PDB files, the hydrogen bonds are
all pointing in the same direction, which is not very realistic.
(Rectangular) periodic boundary conditions are included, so you can
stack these together to fill large rectangular 3D volumes.
If I get around to converting these PDB files into a moltemplate .LT)
format, I'll post another message here.
Cheers
Andrew
ice_wat8.pdb (2.11 KB)
ice_wat16.pdb (4.11 KB)
ice_wat32.pdb (6.25 KB)