2009-12-22 01:27:08 +08:00
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"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 com/molecule command :h3
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[Syntax:]
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compute ID group-ID com/molecule :pre
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ID, group-ID are documented in "compute"_compute.html command
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com/molecule = style name of this compute command :ul
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[Examples:]
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compute 1 fluid com/molecule :pre
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[Description:]
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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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2009-12-22 01:34:52 +08:00
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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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2009-12-22 01:27:08 +08:00
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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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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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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 "dump custom"_dump.html
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command for a discussion of "unwrapped" coordinates. See the Atoms
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section of the "read_data"_read_data.html 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 "set
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image"_set.html command.
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IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
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rigid"_fix_rigid.html 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 "fix rigid"_fix_rigid.html 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 "dump
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file"_dump.html containing coordinates of the atoms in the bodies.
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[Output info:]
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2009-12-22 01:34:52 +08:00
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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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"this section"_Section_howto.html#4_15 for an overview of LAMMPS
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output options.
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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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[Restrictions:] none
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[Related commands:]
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"compute com"_compute_com.html
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[Default:] none
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