forked from lijiext/lammps
79 lines
2.8 KiB
HTML
79 lines
2.8 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 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
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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 = 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
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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 the
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group of atoms, including all effects due to atoms passing thru
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periodic boundaries.
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</P>
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<P>Rg is a measure of the size of the group of atoms, and is computed as
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the 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 group, Rcm is the center-of-mass
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position of the group, and the sum is over all atoms in the group.
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</P>
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<P>A Rg^2 tensor, stored as a 6-element vector, is also calculated by
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this compute. The formula for the components of the tensor is the
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same as the above formula, except that (Ri - Rcm)^2 is replaced by
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(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
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components of the vector 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>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 scalar (Rg) and a global vector of
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length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
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values can be used by any command that uses a global scalar value or
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vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">Section_howto
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15</A> for an overview of LAMMPS output
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options.
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</P>
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<P>The scalar and vector values calculated by this compute are
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"intensive". The scalar and vector 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>
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</P>
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<P><A HREF = "compute_gyration_chunk.html">compute gyration/chunk</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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