forked from lijiext/lammps
90 lines
3.1 KiB
Plaintext
90 lines
3.1 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 displace/atom command :h3
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[Syntax:]
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compute ID group-ID displace/atom :pre
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ID, group-ID are documented in "compute"_compute.html command
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displace/atom = style name of this compute command :ul
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[Examples:]
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compute 1 all displace/atom :pre
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[Description:]
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Define a computation that calculates the current displacement of each
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atom in the group from its original coordinates, including all effects
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due to atoms passing thru periodic boundaries.
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A vector of four quantites per atom is calculated by this compute.
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The first 3 elements of the vector are the dx,dy,dz displacements.
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The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
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dz*dz).
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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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The value of the displacement will be 0.0 for atoms not in the
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specified compute group.
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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 the computed displacement may not reflect its true displacement.
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See the "fix rigid"_fix_rigid.html command for details. Thus, to
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compute the displacement of rigid bodies as they cross periodic
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boundaries, you will need to post-process a "dump file"_dump.html
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containing 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 per-atom array with 4 columns, which can be
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accessed by indices 1-4 by any command that uses per-atom values from
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a compute as input. See "Section_howto
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15"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The per-atom array values will be in distance "units"_units.html.
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[Restrictions:] none
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[Related commands:]
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"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
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store/state"_fix_store_state.html
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[Default:] none
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