forked from lijiext/lammps
80 lines
2.7 KiB
HTML
80 lines
2.7 KiB
HTML
<HTML>
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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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<H3>compute gyration/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 gyration/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>gyration/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 molecule gyration/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 radius of gyration Rg of
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individual molecules. The calculation includes all effects due to
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atoms passing thru periodic boundaries.
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</P>
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<P>Rg is a measure of the size of a molecule, and is computed by this
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formula
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</P>
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<CENTER><IMG SRC = "Eqs/compute_gyration.jpg">
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</CENTER>
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<P>where M is the total mass of the molecule, Rcm is the center-of-mass
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position of the molecule, and the sum is over all atoms in the
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molecule and in the group.
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</P>
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<P>Rg for a particular molecule is only computed if one or more of its
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atoms are in the specified group. Normally all atoms in the molecule
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should be in the group, however this is not required. LAMMPS will
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warn you if this is not the case. Only atoms in the group contribute
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to the Rg calculation for the molecule.
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</P>
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<P>Let Nmolecules be the number of molecules for which Rg is calculated.
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If not all molecules have atoms in the group, then the molecule with
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the lowest ID is the first of the Nmolecules. The next lowest ID is
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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 Rg in
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"unwrapped" form, by using the image flags associated with each atom.
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See the <A HREF = "dump.html">dump custom</A> command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
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how they are set for each atom. You can reset the image flags
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(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><B>Output info:</B>
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</P>
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<P>This compute calculates a global vector of Rg values where the length
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of the vector = Nmolecules. These values can be used by any command
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that uses global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
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section</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The vector values calculated by this compute are "intensive", meaning
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it is independent of the number of atoms in the simulation.
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</P>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><A HREF = "compute_gyration.html">compute gyration</A>
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</P>
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<P><B>Default:</B> none
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</P>
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