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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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2015-12-10 17:23:56 +00:00
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doc/compute_msd.txt
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@ -71,26 +71,25 @@ their average positions relative to the center of mass of the system
are stationary. The most common case is crystalline solids undergoing
thermal motion.
IMPORTANT NOTE: Initial coordinates are stored in "unwrapped" form, by
using the image flags associated with each atom. See the "dump
NOTE: Initial coordinates 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: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,
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-atom
NOTE: If you want the quantities calculated by this compute to be
continuous when running from a "restart file"_read_restart.html, 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-atom
quantities will also have the same ID, and thus be initialized
correctly with atom reference positions from the restart file.
When {average} is set to yes, then the atom reference positions
are restored correctly, but not the number of samples used
obtain them. As a result, the reference positions from the restart
file are combined with subsequent positions as if they were from a
single sample, instead of many, which will change the values of msd
somewhat.
correctly with atom reference positions from the restart file. When
{average} is set to yes, then the atom reference positions are
restored correctly, but not the number of samples used obtain them. As
a result, the reference positions from the restart file are combined
with subsequent positions as if they were from a single sample,
instead of many, which will change the values of msd somewhat.
[Output info:]