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rLAMMPS lammps
compute_com_molecule.html
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<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>compute com/molecule command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID com/molecule
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>com/molecule = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 fluid com/molecule
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the center-of-mass of individual
molecules. The calculation includes all effects due to atoms passing
thru periodic boundaries.
</P>
<P>The x,y,z coordinates of the center-of-mass for a particular molecule
are only computed if one or more of its atoms are in the specified
group. Normally all atoms in the molecule should be in the group,
however this is not required. LAMMPS will warn you if this is not the
case. Only atoms in the group contribute to the center-of-mass
calculation for the molecule.
</P>
<P>The ordering of per-molecule quantities produced by this compute is
consistent with the ordering produced by other compute commands that
generate per-molecule datums. Conceptually, them molecule IDs will be
in ascending order for any molecule with one or more of its atoms in
the specified group.
</P>
<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
molecule's center-of-mass in "unwrapped" form, by using the image
flags associated with each atom. See the <A HREF = "dump.html">dump custom</A>
command for a discussion of "unwrapped" coordinates. See the Atoms
section of the <A HREF = "read_data.html">read_data</A> command for a discussion of
image flags and how they are set for each atom. You can reset the
image flags (e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,
and its contribution to the center-of-mass may not reflect its true
contribution. See the <A HREF = "fix_rigid.html">fix rigid</A> command for details.
Thus, to compute the center-of-mass of rigid bodies as they cross
periodic boundaries, you will need to post-process a <A HREF = "dump.html">dump
file</A> containing coordinates of the atoms in the bodies.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global array where the number of rows =
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
coordinates of each molecule. These values can be accessed by any
command that uses global array values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
<P>The array values are "intensive". The array values will be in
distance <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_com.html">compute com</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
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