forked from lijiext/lammps
88 lines
3.4 KiB
Plaintext
88 lines
3.4 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 recenter command :h3
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[Syntax:]
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fix ID group-ID recenter x y z keyword value ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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recenter = style name of this fix command :l
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x,y,z = constrain center-of-mass to these coords (distance units), \
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any coord can also be NULL or INIT (see below) :l
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zero or more keyword/value pairs may be appended to the args :l
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keyword = {shift} or {units} :l
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{shift} value = group-ID
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group-ID = group of atoms whose coords are shifted
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{units} value = {box} or {lattice} or {fraction} :pre
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:ule
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[Examples:]
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fix 1 all recenter 1 1 1 0 :pre
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[Description:]
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Constrain the center-of-mass position of a group of atoms by adjusting
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the coordinates of the atoms every timestep. This is simply a small
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shift that does not alter the dynamics of the system or change the
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relative coordinates of any pair of atoms in the group. This can be
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used to insure the entire collection of atoms (or a portion of them)
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do not drift during the simulation due to random perturbations
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(e.g. "fix langevin"_fix_langevin.html thermostatting).
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Distance units for the x,y,z values are determined by the setting of
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the {units} keyword, as discussed below. One or more x,y,z values can
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also be specified as NULL, which means exclude that dimension from
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this operation. Or it can be specified as INIT which means to
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constain the center-of-mass to its initial value at the beginning of
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the run.
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The center-of-mass (COM) is computed for the group specified by the
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fix. If the current COM is different than the specified x,y,z, then a
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group of atoms has their coordinates shifted by the difference. By
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default the shifted group is also the group specified by the fix. A
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different group can be shifted by using the {shift} keyword. For
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example, the COM could be computed on a protein to keep it in the
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center of the simulation box. But the entire system (protein + water)
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could be shifted.
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If the {units} keyword is set to {box}, then the distance units of
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x,y,z are defined by the "units"_units.html command - e.g. Angstroms
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for {real} units. {Lattice} means to use lattice spacings as defined
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by the "lattice"_lattice.html command. {Fraction} means a fractional
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distance between the lo/hi box boundaries, e.g. 0.5 = middle of the
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box. The default is to use lattice units.
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Note that the "velocity"_velocity.html command can be used to create
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velocities with zero aggregate linear and/or angular momentum.
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[Restrictions:]
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This fix should not be used with an x,y,z setting that causes a large
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shift in the system on the 1st timestep, due to the requested COM
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being very different from the initial COM. This could cause atoms to
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be lost,especially in parallel. Instead, use the
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"displace_atoms"_displace_atoms.html command, which can be used
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several times in succession to move atoms a large distance.
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This fix should be specified after integration fixes ("fix
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nve"_fix_nve.html, "fix_nvt"_fix_nvt.html, "fix npt"_fix_npt.html,
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etc), because the adjustments it makes to atom coordinates should come
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after atom coordinates are changed due to time integration. LAMMPS
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will warn you if your fixes are not ordered this way.
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[Related commands:]
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"fix momentum"_fix_momentum.html, "velocity"_velocity.html
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[Default:]
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The option defaults are adjust = fix group-ID, and units = lattice.
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