forked from lijiext/lammps
75 lines
2.4 KiB
Plaintext
75 lines
2.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute gyration/molecule command :h3
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[Syntax:]
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compute ID group-ID gyration/molecule :pre
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ID, group-ID are documented in "compute"_compute.html command
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gyration/molecule = style name of this compute command :ul
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[Examples:]
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compute 1 molecule gyration/molecule :pre
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[Description:]
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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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Rg is a measure of the size of a molecule, and is computed by this
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formula
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:c,image(Eqs/compute_gyration.jpg)
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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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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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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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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 "dump custom"_dump.html command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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"read_data"_read_data.html 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 "set
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image"_set.html command.
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[Output info:]
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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 "this
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section"_Section_howto.html#4_15 for an overview of LAMMPS output
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options.
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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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[Restrictions:] none
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[Related commands:] none
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"compute gyration"_compute_gyration.html
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[Default:] none
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