forked from lijiext/lammps
135 lines
5.6 KiB
Plaintext
135 lines
5.6 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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displace_atoms command :h3
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[Syntax:]
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displace_atoms group-ID style args keyword value ... :pre
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group-ID = ID of group of atoms to displace :ulb,l
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style = {move} or {ramp} or {random} or {rotate} :l
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{move} args = delx dely delz
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delx,dely,delz = distance to displace in each dimension (distance units)
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any of delx,dely,delz can be a variable (see below)
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{ramp} args = ddim dlo dhi dim clo chi
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ddim = {x} or {y} or {z}
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dlo,dhi = displacement distance between dlo and dhi (distance units)
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dim = {x} or {y} or {z}
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clo,chi = lower and upper bound of domain to displace (distance units)
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{random} args = dx dy dz seed
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dx,dy,dz = random displacement magnitude in each dimension (distance units)
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seed = random # seed (positive integer)
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{rotate} args = Px Py Pz Rx Ry Rz theta
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Px,Py,Pz = origin point of axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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theta = angle of rotation (degrees) :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {units}
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value = {box} or {lattice} :pre
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:ule
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[Examples:]
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displace_atoms top move 0 -5 0 units box
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displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 :pre
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[Description:]
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Displace a group of atoms. This can be used to move atoms a large
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distance before beginning a simulation or to randomize atoms initially
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on a lattice. For example, in a shear simulation, an initial strain
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can be imposed on the system. Or two groups of atoms can be brought
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into closer proximity.
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The {move} style displaces the group of atoms by the specified 3d
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displacement vector. Any of the 3 quantities defining the vector
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components can be specified as an equal-style or atom-style
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"variable"_variable.html. If the value is a variable, it should be
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specified as v_name, where name is the variable name. In this case,
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the variable will be evaluated, and its value(s) used for the
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displacement(s). The scale factor implied by the {units} keyword will
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also be applied to the variable result.
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Equal-style variables can specify formulas with various mathematical
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functions, and include "thermo_style"_thermo_style.html command
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keywords for the simulation box parameters and timestep and elapsed
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time. Atom-style variables can specify the same formulas as
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equal-style variables but can also include per-atom values, such as
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atom coordinates or per-atom values read from a file. Note that if
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the variable references other "compute"_compute.html or "fix"_fix.html
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commands, those values must be up-to-date for the current timestep.
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See the "Variable Accuracy" section of the "variable"_variable.html
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doc page for more details.
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The {ramp} style displaces atoms a variable amount in one dimension
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depending on the atom's coordinate in a (possibly) different
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dimension. For example, the second example command displaces atoms in
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the x-direction an amount between 0.0 and 5.0 distance units. Each
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atom's displacement depends on the fractional distance its y
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coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
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those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
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The {random} style independently moves each atom in the group by a
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random displacement, uniformly sampled from a value between -dx and
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+dx in the x dimension, and similarly for y and z. Random numbers are
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used in such a way that the displacement of a particular atom is the
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same, regardless of how many processors are being used.
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The {rotate} style rotates each atom in the group by the angle {theta}
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around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
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(Px,Py,Pz). The direction of rotation for the atoms around the
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rotation axis is consistent with the right-hand rule: if your
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right-hand's thumb points along {R}, then your fingers wrap around the
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axis in the direction of positive theta.
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Distance units for displacements and the origin point of the {rotate}
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style are determined by the setting of {box} or {lattice} for the
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{units} keyword. {Box} means distance units as defined by the
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"units"_units.html command - e.g. Angstroms for {real} units.
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{Lattice} means distance units are in lattice spacings. The
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"lattice"_lattice.html command must have been previously used to
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define the lattice spacing.
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:line
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IMPORTANT NOTE: Care should be taken not to move atoms on top of other
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atoms. After the move, atoms are remapped into the periodic
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simulation box if needed, and any shrink-wrap boundary conditions (see
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the "boundary"_boundary.html command) are enforced which may change
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the box size. Other than this effect, this command does not change
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the size or shape of the simulation box. See the
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"change_box"_change_box.html command if that effect is desired.
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IMPORTANT NOTE: Atoms can be moved arbitrarily long distances by this
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command. If the simulation box is non-periodic and shrink-wrapped
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(see the "boundary"_boundary.html command), this can change its size
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or shape. This is not a problem, except that the mapping of
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processors to the simulation box is not changed by this command from
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its initial 3d configuration; see the "processors"_processors.html
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command. Thus, if the box size/shape changes dramatically, the
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mapping of processors to the simulation box may not end up as optimal
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as the initial mapping attempted to be.
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:line
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[Restrictions:]
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You cannot rotate around any rotation vector except the z-axis for a
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2d simulation.
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[Related commands:]
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"lattice"_lattice.html, "change_box"_change_box.html,
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"fix_move"_fix_move.html
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[Default:]
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The option defaults are units = lattice.
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