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lammps/doc/src/fix_recenter.txt
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fix_recenter.txt
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"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 recenter command :h3
[Syntax:]
fix ID group-ID recenter x y z keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
recenter = style name of this fix command :l
x,y,z = constrain center-of-mass to these coords (distance units), \
any coord can also be NULL or INIT (see below) :l
zero or more keyword/value pairs may be appended :l
keyword = {shift} or {units} :l
{shift} value = group-ID
group-ID = group of atoms whose coords are shifted
{units} value = {box} or {lattice} or {fraction} :pre
:ule
[Examples:]
fix 1 all recenter 0.0 0.5 0.0
fix 1 all recenter INIT INIT NULL
fix 1 all recenter INIT 0.0 0.0 units box :pre
[Description:]
Constrain the center-of-mass position of a group of atoms by adjusting
the coordinates of the atoms every timestep. This is simply a small
shift that does not alter the dynamics of the system or change the
relative coordinates of any pair of atoms in the group. This can be
used to insure the entire collection of atoms (or a portion of them)
do not drift during the simulation due to random perturbations
(e.g. "fix langevin"_fix_langevin.html thermostatting).
Distance units for the x,y,z values are determined by the setting of
the {units} keyword, as discussed below. One or more x,y,z values can
also be specified as NULL, which means exclude that dimension from
this operation. Or it can be specified as INIT which means to
constrain the center-of-mass to its initial value at the beginning of
the run.
The center-of-mass (COM) is computed for the group specified by the
fix. If the current COM is different than the specified x,y,z, then a
group of atoms has their coordinates shifted by the difference. By
default the shifted group is also the group specified by the fix. A
different group can be shifted by using the {shift} keyword. For
example, the COM could be computed on a protein to keep it in the
center of the simulation box. But the entire system (protein + water)
could be shifted.
If the {units} keyword is set to {box}, then the distance units of
x,y,z are defined by the "units"_units.html command - e.g. Angstroms
for {real} units. A {lattice} value means the distance units are in
lattice spacings. The "lattice"_lattice.html command must have been
previously used to define the lattice spacing. A {fraction} value
means a fractional distance between the lo/hi box boundaries, e.g. 0.5
= middle of the box. The default is to use lattice units.
Note that the "velocity"_velocity.html command can be used to create
velocities with zero aggregate linear and/or angular momentum.
NOTE: This fix performs its operations at the same point in the
timestep as other time integration fixes, such as "fix
nve"_fix_nve.html, "fix nvt"_fix_nh.html, or "fix npt"_fix_nh.html.
Thus fix recenter should normally be the last such fix specified in
the input script, since the adjustments it makes to atom coordinates
should come after the changes made by time integration. LAMMPS will
warn you if your fixes are not ordered this way.
NOTE: If you use this fix on a small group of atoms (e.g. a molecule
in solvent) without using the {shift} keyword to adjust the positions
of all atoms in the system, then the results can be unpredictable.
For example, if the molecule is pushed consistently in one direction
by a flowing solvent, its velocity will increase. But its coordinates
will be recentered, meaning it is moved back towards the force. Thus
over time, the velocity and effective temperature of the molecule
could become very large, though it won't actually be moving due to the
recentering. If you are thermostatting the entire system, then the
solvent would be cooled to compensate. A better solution for this
simulation scenario is to use the "fix spring"_fix_spring.html command
to tether the molecule in place.
[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.
This fix computes a global scalar which can be accessed by various
"output commands"_Section_howto.html#howto_15. The scalar is the
distance the group is moved by fix recenter.
This fix also computes global 3-vector which can be accessed by
various "output commands"_Section_howto.html#howto_15. The 3
quantities in the vector are xyz components of displacement applied to
the group of atoms by the fix.
The scalar and vector values calculated by this fix are "extensive".
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 should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost, especially in parallel. Instead, use the
"displace_atoms"_displace_atoms.html command, which can be used to
move atoms a large distance.
[Related commands:]
"fix momentum"_fix_momentum.html, "velocity"_velocity.html
[Default:]
The option defaults are shift = fix group-ID, and units = lattice.
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