128 lines
4.9 KiB
ReStructuredText
128 lines
4.9 KiB
ReStructuredText
.. index:: compute msd
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compute msd command
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===================
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Syntax
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""""""
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.. code-block:: LAMMPS
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compute ID group-ID msd keyword values ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* msd = style name of this compute command
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* zero or more keyword/value pairs may be appended
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* keyword = *com* or *average*
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.. parsed-literal::
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*com* value = *yes* or *no*
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*average* value = *yes* or *no*
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all msd
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compute 1 upper msd com yes average yes
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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) of the group of atoms, including all effects due to atoms
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passing through periodic boundaries. For computation of the non-Gaussian
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parameter of mean-squared displacement, see the
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:doc:`compute msd/nongauss <compute_msd_nongauss>` command.
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A vector of four quantities is calculated by this compute. The first three
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elements of the vector are the squared *dx*, *dy*, and *dz* displacements,
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summed and averaged over atoms in the group. The fourth element is the total
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squared displacement (i.e., :math:`dx^2 + dy^2 + dz^2`), 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 reference position. This is
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normally the original position at the time
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the compute command was issued, unless the *average* keyword is set to *yes*\ .
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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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displacement of each atom is calculated.
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If the *average* option is set to *yes* then the reference position of
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an atom is based on the average position of that atom, corrected for
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center-of-mass motion if requested. The average position is a running
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average over all previous calls to the compute, including the current
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call. So on the first call it is current position, on the second call
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it is the arithmetic average of the current position and the position
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on the first call, and so on. Note that when using this option, the
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precise value of the mean square displacement will depend on the
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number of times the compute is called. So, for example, changing the
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frequency of thermo output may change the computed displacement. Also,
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the precise values will be changed if a single simulation is broken up
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into two parts, using either multiple run commands or a restart
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file. It only makes sense to use this option if the atoms are not
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diffusing, so that their average positions relative to the center of
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mass of the system are stationary. The most common case is crystalline
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solids undergoing thermal motion.
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.. note::
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Initial coordinates are stored in "unwrapped" form, by using the
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image flags associated with each atom. See the :doc:`dump custom
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<dump>` command for a discussion of "unwrapped" coordinates. See the
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Atoms section of the :doc:`read_data <read_data>` command for a
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discussion of image flags and how they are set for each atom. You
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can reset the image flags (e.g. to 0) before invoking this compute by
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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-atom
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quantities will also have the same ID, and thus be initialized
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correctly with atom reference positions from the restart file. When
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*average* is set to yes, then the atom reference positions are
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restored correctly, but not the number of samples used obtain them. As
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a result, the reference positions from the restart file are combined
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with subsequent positions as if they were from a single sample,
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instead of many, which will change the values of msd somewhat.
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Output info
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"""""""""""
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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 the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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The vector values are "intensive". The vector values will be in
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distance\ :math:`^2` :doc:`units <units>`.
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Restrictions
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""""""""""""
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Compute *msd* cannot be used with a dynamic group and the number of
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atoms in the compute group must not be changed by some fixes like,
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for example, :doc:`fix deposit <fix_deposit>` or
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:doc:`fix evaporate <fix_evaporate>`.
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Related commands
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""""""""""""""""
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:doc:`compute msd/nongauss <compute_msd_nongauss>`,
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:doc:`compute displace_atom <compute_displace_atom>`, :doc:`fix store/state <fix_store_state>`,
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:doc:`compute msd/chunk <compute_msd_chunk>`
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Default
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"""""""
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The option default are com = no, average = no.
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