forked from lijiext/lammps
125 lines
5.0 KiB
Plaintext
125 lines
5.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
fix rigid :h3
|
|
|
|
[Syntax:]
|
|
|
|
fix ID group-ID rigid keyword values :pre
|
|
|
|
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
|
rigid = style name of this fix command :l
|
|
keyword = {single} or {molecule} or {group} :l
|
|
{single} values = none
|
|
{molecule} values = none
|
|
{group} values = list of group IDs :pre
|
|
:ule
|
|
|
|
[Examples:]
|
|
|
|
fix 1 clump rigid single
|
|
fix 1 polychains rigid molecule
|
|
fix 2 fluid rigid group clump1 clump2 clump3 :pre
|
|
|
|
[Description:]
|
|
|
|
Treat one or more sets of atoms as an independent rigid body. This
|
|
means that each timestep the total force and torque on each rigid body
|
|
is computed and the coordinates and velocities of the atoms in each
|
|
body are updated so that they move as a rigid body. This can be
|
|
useful for freezing one or more portions of a large biomolecule, or
|
|
for simulating a system of colloidal particles.
|
|
|
|
This fix updates the positions and velocities of the rigid atoms with
|
|
a constant-energy time integration, so you should not update the same
|
|
atoms via other fixes (e.g. nve, nvt, npt).
|
|
|
|
Each body must have two or more atoms. Which atoms are in which
|
|
bodies can be defined via several options.
|
|
|
|
For option {single} the entire group of atoms is treated as one rigid
|
|
body.
|
|
|
|
For option {molecule}, each set of atoms in the group with a different
|
|
molecule ID is treated as a rigid body.
|
|
|
|
For option {group}, each of the listed groups is treated as a separate
|
|
rigid body. Note that only atoms that are also in the fix group are
|
|
included in each rigid body.
|
|
|
|
For computational efficiency, you should also turn off pairwise and
|
|
bond interactions within each rigid body, as they no longer contribute
|
|
to the motion. The "neigh_modify exclude"_neigh_modify.html and
|
|
"delete_bonds"_delete_bonds.html commands are used to do this.
|
|
|
|
For computational efficiency, you should define one fix rigid which
|
|
includes all the desired rigid bodies. LAMMPS will allow multiple
|
|
rigid fixes to be defined, but it is more expensive.
|
|
|
|
This fix uses constant-energy integration, so you may need to impose
|
|
additional constraints to control the temperature of an ensemble of
|
|
rigid bodies. You can use "fix langevin"_fix_langevin.html for this
|
|
purpose to treat the system as effectively immersed in an implicit
|
|
solvent, i.e. a Brownian dynamics model. Or you can thermostat
|
|
additional atoms of an explicit solvent directly.
|
|
|
|
The degrees-of-freedom removed by rigid bodies are accounted for in
|
|
temperature and pressure computations. Similarly, the rigid body
|
|
contribution to the pressure of the system (virial) is also accounted
|
|
for. For linear rigid bodies of three or more atoms, one additional
|
|
degree-of-freedom must be subtracted manually using the
|
|
"compute_modify"_compute_modify.html command. E.g. for a simulation
|
|
of 10 such rigid bodies, use "compute_modify thermo_temp extra 13",
|
|
after the thermo_style command, where 3 is the default setting and an
|
|
additional 10 degrees-of-freedom are subtracted.
|
|
|
|
IMPORTANT NOTE: The periodic image flags of atoms in rigid bodies are
|
|
modified when the center-of-mass of the rigid body moves across a
|
|
periodic boundary. They are not incremented/decremented as they would
|
|
be for non-rigid atoms. This change does not affect dynamics, but
|
|
means that any diagnostic computation based on the atomic image flag
|
|
values must be adjusted accordingly. For example, the "fix
|
|
msd"_fix_msd.html will not compute the expected mean-squared
|
|
displacement for such atoms, and the image flag values written to a
|
|
"dump file"_dump.html will be different than they would be if the
|
|
atoms were not in a rigid body.
|
|
|
|
[Restart, fix_modify, output, run start/stop, minimize info:]
|
|
|
|
No information about this fix is written to "binary restart
|
|
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
|
are relevant to this fix. No global scalar or vector or per-atom
|
|
quantities are stored by this fix for access by various "output
|
|
commands"_Section_howto.html#4_15. No parameter of this fix can be
|
|
used with the {start/stop} keywords of the "run"_run.html command.
|
|
This fix is not invoked during "energy minimization"_minimize.html.
|
|
|
|
[Restrictions:]
|
|
|
|
This fix performs an MPI_Allreduce each timestep that is proportional
|
|
in length to the number of rigid bodies. Hence it will not scale well
|
|
in parallel if large numbers of rigid bodies are simulated.
|
|
|
|
If the atoms in a single rigid body initially straddle a periodic
|
|
boundary, the input data file must define the image flags for each
|
|
atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
|
|
rigid body.
|
|
|
|
You should not use this fix if you just want to hold group of atoms
|
|
stationary. A better way to do this is to not include those atoms in
|
|
your time integration fix. E.g. use "fix 1 mobile nve" instead of
|
|
"fix 1 all nve", where "mobile" is the group of atoms that you want to
|
|
move.
|
|
|
|
[Related commands:]
|
|
|
|
"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html
|
|
exclude
|
|
|
|
[Default:] none
|