forked from lijiext/lammps
95 lines
3.3 KiB
Plaintext
95 lines
3.3 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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fix rigid :h3
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[Syntax:]
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fix ID group-ID rigid keyword values :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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rigid = style name of this fix command :l
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keyword = {single} or {molecule} or {group} :l
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{single} values = none
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{molecule} values = none
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{group} values = list of group IDs :pre
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:ule
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[Examples:]
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fix 1 clump rigid single
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fix 1 polychains rigid molecule
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fix 2 fluid rigid group clump1 clump2 clump3 :pre
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[Description:]
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Treat one or more sets of atoms as an independent rigid body. This
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means that each timestep the total force and torque on each rigid body
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is computed and the coordinates and velocities of the atoms in each
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body are updated so that they move as a rigid body. This can be
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useful for freezing one or more portions of a large biomolecule, or
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for simulating a system of colloidal particles.
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This fix updates the positions and velocities of the rigid atoms with
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a constant-energy time integration, so you should not update the same
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atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).
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Each body must have two or more atoms. Which atoms are in which
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bodies can be defined via several options.
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For option {single} the entire group of atoms is treated as one rigid
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body.
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For option {molecule}, each set of atoms in the group with a different
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molecule ID is treated as a rigid body.
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For option {group}, each of the listed groups is treated as a separate
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rigid body. Note that only atoms that are also in the fix group are
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included in each rigid body.
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For computational efficiency, you should also turn off pairwise and
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bond interactions within each rigid body, as they no longer contribute
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to the motion. The "neigh_modify exclude"_neigh_modify.html and
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"delete_bonds"_delete_bonds.html commands are used to do this.
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For computational efficiency, you should define one fix rigid which
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includes all the desired rigid bodies. LAMMPS will allow multiple
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rigid fixes to be defined, but it is more expensive.
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The degrees-of-freedom removed by rigid bodies are accounted for in
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temperature and pressure computations. Similary, the rigid body
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contribution to the pressure virial is also accounted for. The latter
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is only correct if forces within the bodies have been turned off, and
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there is only a single fix rigid defined.
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Note that this fix uses constant-energy integration, so you need to
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impose additional constraints to control the temperature of an
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ensemble of rigid bodies. You can use "fix
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langevin"_fix_langevin.html for this purpose to treat the system as
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effectively immersed in an implicit solvent, i.e. a Brownian dynamics
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model. Or you can thermostat the atoms of an explicit solvent
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directly.
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[Restrictions:]
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This fix performs an MPI_Allreduce each timestep that is proportional
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in length to the number of rigid bodies. Hence it will not scale well
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in parallel if large numbers of rigid bodies are simulated.
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If the atoms in a single rigid body initially straddle a periodic
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boundary, the input data file must define the image flags for each
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atom correctly, so that LAMMPS can "unwrap" the atoms into a valid
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rigid body.
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[Related commands:]
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"delete_bonds"_delete_bonds.html, "neigh_modify"_neigh_modify.html
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exclude
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[Default:] none
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