2006-09-22 00:22:34 +08:00
|
|
|
<HTML>
|
|
|
|
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H3>displace_atoms command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>displace_atoms group-ID style args keyword value ...
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>group-ID = ID of group of atoms to displace
|
|
|
|
|
|
2007-06-20 20:56:17 +08:00
|
|
|
<LI>style = <I>move</I> or <I>ramp</I> or <I>random</I>
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
<PRE> <I>move</I> args = delx dely delz
|
|
|
|
|
delx,dely,delz = distance to displace in each dimension (distance units)
|
|
|
|
|
<I>ramp</I> args = ddim dlo dhi dim clo chi
|
|
|
|
|
ddim = <I>x</I> or <I>y</I> or <I>z</I>
|
|
|
|
|
dlo,dhi = displacement distance between dlo and dhi (distance units)
|
|
|
|
|
dim = <I>x</I> or <I>y</I> or <I>z</I>
|
2007-06-20 20:56:17 +08:00
|
|
|
clo,chi = lower and upper bound of domain to displace (distance units)
|
|
|
|
|
<I>random</I> args = dx dy dz seed
|
|
|
|
|
dx,dy,dz = random displacement magnitude in each dimension (distance units)
|
2007-10-10 07:40:45 +08:00
|
|
|
seed = random # seed (positive integer)
|
2006-09-22 00:22:34 +08:00
|
|
|
</PRE>
|
2007-07-03 04:04:44 +08:00
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
<PRE> keyword = <I>units</I>
|
|
|
|
|
value = <I>box</I> or <I>lattice</I>
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>displace_atoms top move 0 -5 0 units box
|
|
|
|
|
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
2007-03-21 04:14:06 +08:00
|
|
|
<P>Displace a group of atoms. This can be used to move atoms a large
|
2007-06-20 20:56:17 +08:00
|
|
|
distance before beginning a simulation or to randomize atoms initially
|
|
|
|
|
on a lattice. For example, in a shear simulation, an initial strain
|
|
|
|
|
can be imposed on the system. Or two groups of atoms can be brought
|
|
|
|
|
into closer proximity.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The <I>move</I> style displaces the group of atoms by the specified 3d
|
2007-06-20 20:56:17 +08:00
|
|
|
distance.
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>ramp</I> style displaces atoms a variable amount in one dimension
|
|
|
|
|
depending on the atom's coordinate in a (possibly) different
|
2006-09-22 00:22:34 +08:00
|
|
|
dimension. For example, the second example command displaces atoms in
|
|
|
|
|
the x-direction an amount between 0.0 and 5.0 distance units. Each
|
|
|
|
|
atom's displacement depends on the fractional distance its y
|
|
|
|
|
coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
|
|
|
|
|
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
|
|
|
|
|
</P>
|
2007-06-20 20:56:17 +08:00
|
|
|
<P>The <I>random</I> style independently moves each atom in the group by a
|
|
|
|
|
random displacement, uniformly sampled from a value between -dx and
|
|
|
|
|
+dx in the x dimension, and similarly for y and z. Random numbers are
|
|
|
|
|
used in such a way that the displacement of a particular atom is the
|
|
|
|
|
same, regardless of how many processors are being used.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Distance units for displacement are determined by the setting of <I>box</I>
|
|
|
|
|
or <I>lattice</I> for the <I>units</I> keyword. <I>Box</I> means distance units as
|
|
|
|
|
defined by the <A HREF = "units.html">units</A> command - e.g. Angstroms for <I>real</I>
|
|
|
|
|
units. <I>Lattice</I> means distance units are in lattice spacings. The
|
|
|
|
|
<A HREF = "lattice.html">lattice</A> command must have been previously used to
|
|
|
|
|
define the lattice spacing.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-06-28 00:47:01 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>Care should be taken not to move atoms on top of other atoms. After
|
2007-04-21 07:59:34 +08:00
|
|
|
the move, atoms are remapped into the periodic simulation box if
|
|
|
|
|
needed.
|
|
|
|
|
</P>
|
2007-06-28 00:47:01 +08:00
|
|
|
<P>Atoms can be moved arbitrarily long distances by this command. If the
|
|
|
|
|
simulation box is non-periodic, this can change its size or shape.
|
|
|
|
|
This is not a problem, except that the mapping of processors to the
|
|
|
|
|
simulation box is not changed by this command from its initial 3d
|
|
|
|
|
configuration; see the <A HREF = "processors.html">processors</A> command. Thus, if
|
|
|
|
|
the box size or shape changes dramatically, the simulation may not be
|
|
|
|
|
as well load-balanced (atoms per processor) as the initial mapping
|
|
|
|
|
tried to achieve.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This command requires inter-processor communication to migrate atoms
|
|
|
|
|
once they have been displaced. This means that your system must be
|
|
|
|
|
ready to perform a simulation before using this command (force fields
|
2007-03-21 04:14:06 +08:00
|
|
|
are setup, atom masses are set, etc).
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2006-11-14 06:18:34 +08:00
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "lattice.html">lattice</A>
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The option defaults are units = lattice.
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
