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< title > compute msd/chunk command — LAMMPS documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
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< li > compute msd/chunk command< / li >
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< div class = "section" id = "compute-msd-chunk-command" >
< span id = "index-0" > < / span > < h1 > compute msd/chunk command< a class = "headerlink" href = "#compute-msd-chunk-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute ID group-ID msd/chunk chunkID
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > msd/chunk = style name of this compute command< / li >
< li > chunkID = ID of < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all msd/chunk molchunk
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Define a computation that calculates the mean-squared displacement
(MSD) for multiple chunks of atoms.< / p >
< p > In LAMMPS, chunks are collections of atoms defined by a < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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 < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > doc page and “ < a class = "reference internal" href = "Section_howto.html#howto-23" > < span > Section_howto 23< / span > < / a > 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.< / p >
< p > 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
center-of-mass. The 4th component is the total squared displacement,
i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
calculations include all effects due to atoms passing thru periodic
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boundaries.< / p >
< p > Note that only atoms in the specified group contribute to the
calculation. The < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command
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defines its own group; atoms will have a chunk ID = 0 if they are not
in that group, signifying they are not assigned to a chunk, and will
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
non-zero chunk IDs.< / p >
< p > The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing chunks.< / p >
< p > 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.< / p >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > The number of chunks < em > Nchunk< / em > calculated by the < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command must remain constant each
time this compute is invoked, so that the displacement for each chunk
from its original position can be computed consistently. If < em > Nchunk< / em >
does not remain constant, an error will be generated. If needed, you
can enforce a constant < em > Nchunk< / em > by using the < em > nchunk once< / em > or < em > ids
once< / em > options when specifying the < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command.< / p >
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< / div >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
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< p class = "last" > 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
later timestep, it is assumed that the same atoms are assigned to the
same chunk ID. However LAMMPS has no simple way to insure this is the
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case, though you can use the < em > ids once< / em > option when specifying the
< a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > 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.< / p >
< / div >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > The initial coordinates of the atoms in each chunk are stored in
“ unwrapped” form, by using the image flags associated with each atom.
See the < a class = "reference internal" href = "dump.html" > < em > dump custom< / em > < / a > command for a discussion of
“ unwrapped” coordinates. See the Atoms section of the
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > 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 < a class = "reference internal" href = "set.html" > < em > set image< / em > < / a > command.< / p >
< / div >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
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< p class = "last" > If you want the quantities calculated by this compute to be
continuous when running from a < a class = "reference internal" href = "read_restart.html" > < em > restart file< / em > < / a > , then
you should use the same ID for this compute, as in the original run.
This is so that the fix this compute creates to store per-chunk
quantities will also have the same ID, and thus be initialized
correctly with chunk reference positions from the restart file.< / p >
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< / div >
< p > The simplest way to output the results of the compute com/msd
calculation to a file is to use the < a class = "reference internal" href = "fix_ave_time.html" > < em > fix ave/time< / em > < / a >
command, for example:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > 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
< / pre > < / div >
< / div >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a global array where the number of rows = the
number of chunks < em > Nchunk< / em > as calculated by the specified < a class = "reference internal" href = "compute_chunk_atom.html" > < em > compute chunk/atom< / em > < / a > command. The number of columns =
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4 for dx,dy,dz and the total displacement. These values can be
accessed by any command that uses global array values from a compute
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as input. See < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > this section< / span > < / a > for an
overview of LAMMPS output options.< / p >
< p > The array values are “ intensive” . The array values will be in
distance^2 < a class = "reference internal" href = "units.html" > < em > units< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "compute_msd.html" > < em > compute msd< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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