forked from lijiext/lammps
105 lines
3.7 KiB
Plaintext
105 lines
3.7 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 msd command :h3
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[Syntax:]
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compute ID group-ID msd keyword values ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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msd = style name of this compute command :l
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zero or more keyword/value pairs may be appended :l
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keyword = {com} :l
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{com} value = {yes} or {no} :pre
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:ule
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[Examples:]
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compute 1 all msd
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compute 1 upper msd com yes :pre
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[Description:]
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Define a computation that calculates the mean-squared displacement
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(MSD) of the group of atoms, including all effects due to atoms
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passing thru periodic boundaries.
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A vector of four quantites is calculated by this compute. The first 3
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elements of the vector are the squared dx,dy,dz displacements, summed
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and averaged over atoms in the group. The 4th component is the total
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squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
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averaged over atoms in the group.
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The slope of the mean-squared displacement (MSD) versus time is
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proportional to the diffusion coefficient of the diffusing atoms.
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The displacement of an atom is from its original position at the time
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the compute command was issued. To store the original coordinates,
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the compute creates its own fix of style "store/state", as if this
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command had been issued:
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fix compute-ID_store_state group-ID store/state xu yu zu :pre
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See the "fix store/state"_fix_store_state.html command for details.
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Note that the ID of the new fix is the compute-ID + underscore +
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"store_state", and the group for the new fix is the same as the
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compute group.
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If the {com} option is set to {yes} then the effect of any drift in
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the center-of-mass of the group of atoms is subtracted out before the
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displacment of each atom is calcluated. The {com} option is also
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passed to the created fix store/state.
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IMPORTANT NOTE: Fix store/state stores the initial coordinates 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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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 MSD may not reflect its true contribution.
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See the "fix rigid"_fix_rigid.html command for details. Thus, to
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compute the MSD of rigid bodies as they cross periodic boundaries, you
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will need to post-process a "dump file"_dump.html containing
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coordinates of the atoms in the bodies.
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IMPORTANT NOTE: If you want the quantities calculated by this compute
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to be continuous when running from a "restart file"_read_restart.html,
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then you should use the same ID for this compute, as in the original
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run. This is so that the created fix will also have the same ID, and
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thus be initialized correctly with atom coordinates from the restart
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file.
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[Output info:]
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This compute calculates a global vector of length 4, which can be
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accessed by indices 1-4 by any command that uses global vector values
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from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The vector values are "intensive". The vector values will be in
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distance^2 "units"_units.html.
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[Restrictions:] none
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[Related commands:]
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"compute displace_atom"_compute_displace_atom.html, "fix
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store/state"_fix_store_state.html, "compute
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msd/molecule"_compute_msd_molecule.html
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[Default:]
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The option default is com = no.
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