2009-12-22 01:27:08 +08:00
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<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>
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<HR>
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<H3>compute com/molecule command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID com/molecule
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>com/molecule = style name of this compute command
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute 1 fluid com/molecule
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the center-of-mass of individual
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molecules. The calculation includes all effects due to atoms passing
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thru periodic boundaries.
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</P>
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2009-12-22 01:34:52 +08:00
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<P>The x,y,z coordinates of the center-of-mass for a particular molecule
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are only computed if one or more of its atoms are in the specified
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group. Normally all atoms in the molecule should be in the group,
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however this is not required. LAMMPS will warn you if this is not the
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case. Only atoms in the group contribute to the center-of-mass
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calculation for the molecule.
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</P>
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<P>Let Nmolecules be the number of molecules for which the center-of-mass
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is calculated. If not all molecules have atoms in the group, then the
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molecule with the lowest ID is the first of the Nmolecules. The next
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lowest ID is the second, etc, up to Nmolecules.
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</P>
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<P>IMPORTANT NOTE: The coordinates of an atom contribute to the
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molecule's center-of-mass in "unwrapped" form, by using the image
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flags associated with each atom. See the <A HREF = "dump.html">dump custom</A>
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command for a discussion of "unwrapped" coordinates. See the Atoms
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section of the <A HREF = "read_data.html">read_data</A> command for a discussion of
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image flags and how they are set for each atom. You can reset the
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image flags (e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
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image</A> command.
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</P>
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<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
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rigid</A> command), it's periodic image flags are altered,
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and its contribution to the center-of-mass may not reflect its true
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contribution. See the <A HREF = "fix_rigid.html">fix rigid</A> command for details.
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Thus, to compute the center-of-mass of rigid bodies as they cross
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periodic boundaries, you will need to post-process a <A HREF = "dump.html">dump
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file</A> containing coordinates of the atoms in the bodies.
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</P>
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<P><B>Output info:</B>
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</P>
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<P>This compute calculates a global array where the number of rows =
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Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
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coordinates of each molecule. These values can be accessed by any
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command that uses global array values from a compute as input. See
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<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
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output options.
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</P>
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<P>The array values are "intensive", meaning they are independent of the
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number of atoms in the simulation.
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</P>
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2010-01-24 07:20:05 +08:00
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<P>The array values will be in distance <A HREF = "units.html">units</A>.
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</P>
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2009-12-22 01:27:08 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_com.html">compute com</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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