forked from lijiext/lammps
105 lines
3.8 KiB
HTML
105 lines
3.8 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 keyword value ...
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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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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>tensor</I>
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<PRE> <I>tensor</I> value = none
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</PRE>
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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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compute 2 molecule gyration/molecule tensor
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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 as the
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square root of the Rg^2 value in this 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>If the <I>tensor</I> keyword is specified, then the scalar Rg value is not
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calculated, but a 6-element Rg^2 tensor is instead calculated for each
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molecule. The formula for the components of the tensor is the same as
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the above formula, except that (Ri - Rcm)^2 is replaced by (Rix -
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Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 components of
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the tensor are ordered xx, yy, zz, xy, xz, yz. Note
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that unlike the scalar Rg, each of the 6 values of the tensor is
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effectively a "squared" value, since the cross-terms may be negative
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and taking a sqrt() would be invalid.
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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>The ordering of per-molecule quantities produced by this compute is
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consistent with the ordering produced by other compute commands that
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generate per-molecule datums. Conceptually, the molecule IDs will be
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in ascending order for any molecule with one or more of its atoms in
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the specified group.
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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 if the <I>tensor</I> keyword is not
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specified and a global array if it is. The length of the vector or
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number of rows in the array is the number of molecules. If the
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<I>tensor</I> keyword is specified, the global array has 6 columns. The
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vector or array can be accessed by any command that uses global values
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from a compute as input. See <A HREF = "Section_howto.html#howto_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>All the vector or array values calculated by this compute are
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"intensive". The vector and aray values will be in distance and
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distance^2 <A HREF = "units.html">units</A> respectively.
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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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</HTML>
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