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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14349 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-12-10 17:23:56 +00:00
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32
doc/compute_msd_chunk.txt
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@ -57,16 +57,16 @@ The displacement of the center-of-mass of the chunk is from its
original center-of-mass position, calculated on the timestep this
compute command was first invoked.
IMPORTANT NOTE: The number of chunks {Nchunk} calculated by the
"compute chunk/atom"_compute_chunk_atom.html 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 {Nchunk} does not remain constant, an error will be
generated. If needed, you can enforce a constant {Nchunk} by using
the {nchunk once} or {ids once} options when specifying the "compute
NOTE: The number of chunks {Nchunk} calculated by the "compute
chunk/atom"_compute_chunk_atom.html 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 {Nchunk}
does not remain constant, an error will be generated. If needed, you
can enforce a constant {Nchunk} by using the {nchunk once} or {ids
once} options when specifying the "compute
chunk/atom"_compute_chunk_atom.html command.
IMPORTANT NOTE: This compute stores the original position (of the
NOTE: This compute stores the original position (of the
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
@ -75,19 +75,19 @@ case, though you can use the {ids once} option when specifying the
this is not the case, the MSD calculation does not have a sensible
meaning.
IMPORTANT NOTE: 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 "dump custom"_dump.html command for a discussion
of "unwrapped" coordinates. See the Atoms section of the
NOTE: 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 "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
"read_data"_read_data.html command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the "set
image"_set.html command.
IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command,
this compute does not store the initial center-of-mass coorindates of
its molecules in a restart file. Thus you cannot continue the MSD per
chunk calculation of this compute when running from a "restart
NOTE: Unlike the "compute msd"_compute_msd.html command, this compute
does not store the initial center-of-mass coorindates of its molecules
in a restart file. Thus you cannot continue the MSD per chunk
calculation of this compute when running from a "restart
file"_read_restart.html.
The simplest way to output the results of the compute com/msd