forked from lijiext/lammps
135 lines
5.1 KiB
Plaintext
135 lines
5.1 KiB
Plaintext
.. index:: compute msd/chunk
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compute msd/chunk command
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=========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID msd/chunk chunkID
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* msd/chunk = style name of this compute command
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* chunkID = ID of :doc:`compute chunk/atom <compute_chunk_atom>` command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all msd/chunk molchunk
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Description
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"""""""""""
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Define a computation that calculates the mean-squared displacement
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(MSD) for multiple chunks of atoms.
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In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom <compute_chunk_atom>` doc page and ":ref:`Section_howto 23 <howto_23>` for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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Four quantites are calculated by this compute for each chunk. The
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first 3 quantities are the squared dx,dy,dz displacements of the
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center-of-mass. The 4th component is the total squared displacement,
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i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
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calculations include all effects due to atoms passing thru periodic
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boundaries.
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Note that only atoms in the specified group contribute to the
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calculation. The :doc:`compute chunk/atom <compute_chunk_atom>` command
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defines its own group; atoms will have a chunk ID = 0 if they are not
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
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"all" group for this command if you simply want to include atoms with
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non-zero chunk IDs.
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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 chunks.
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The displacement of the center-of-mass of the chunk is from its
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original center-of-mass position, calculated on the timestep this
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compute command was first invoked.
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.. note::
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The number of chunks *Nchunk* calculated by the :doc:`compute chunk/atom <compute_chunk_atom>` command must remain constant each
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time this compute is invoked, so that the displacement for each chunk
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from its original position can be computed consistently. If *Nchunk*
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does not remain constant, an error will be generated. If needed, you
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can enforce a constant *Nchunk* by using the *nchunk once* or *ids
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once* options when specifying the :doc:`compute chunk/atom <compute_chunk_atom>` command.
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.. note::
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This compute stores the original position (of the
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center-of-mass) of each chunk. When a displacement is calculated on a
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later timestep, it is assumed that the same atoms are assigned to the
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same chunk ID. However LAMMPS has no simple way to insure this is the
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case, though you can use the *ids once* option when specifying the
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:doc:`compute chunk/atom <compute_chunk_atom>` command. Note that if
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this is not the case, the MSD calculation does not have a sensible
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meaning.
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.. note::
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The initial coordinates of the atoms in each chunk are stored in
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"unwrapped" form, by using the image flags associated with each atom.
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See the :doc:`dump custom <dump>` command for a discussion of
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"unwrapped" coordinates. See the Atoms section of the
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:doc:`read_data <read_data>` 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 :doc:`set image <set>` command.
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.. note::
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If you want the quantities calculated by this compute to be
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continuous when running from a :doc:`restart file <read_restart>`, then
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you should use the same ID for this compute, as in the original run.
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This is so that the fix this compute creates to store per-chunk
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quantities will also have the same ID, and thus be initialized
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correctly with chunk reference positions from the restart file.
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The simplest way to output the results of the compute com/msd
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calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>`
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command, for example:
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.. parsed-literal::
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compute cc1 all chunk/atom molecule
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compute myChunk all com/msd cc1
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fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
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**Output info:**
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This compute calculates a global array where the number of rows = the
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number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The number of columns =
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4 for dx,dy,dz and the total displacement. These values can be
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accessed by any command that uses global array values from a compute
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as input. See :ref:`this section <howto_15>` for an
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overview of LAMMPS output options.
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The array values are "intensive". The array values will be in
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distance^2 :doc:`units <units>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute msd <compute_msd>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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