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Fixed error in average option 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14281 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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athomps 2015-12-04 19:29:27 +00:00
parent 28e3ebfd10
commit 050a1367a0
1 changed files with 17 additions and 2 deletions
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19
doc/compute_msd.txt
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@ -53,8 +53,23 @@ the center-of-mass of the group of atoms is subtracted out before the
displacment of each atom is calculated.
If the {average} option is set to {yes} then the reference position of
an atom is a running average of the atom position over all the calls
to the msd calculation since the compute was invoked.
an atom is based on the average position of that atom,
corrected for center-of-mass motion if requested.
The average position
is a running average over all previous calls to the compute, including the
current call. So on the first call
it is current position, on the second call it is the arithmetic average of the
current position and the position on the first call, and so on.
Note that when using this option, the precise value of the mean square
displacement will depend on the number of times the compute is
called. So, for example, changing the frequency of thermo output may
change the computed displacement. Also, the precise values will be
changed if a single simulation is broken up into two parts, using
either multiple run commands or a restart file. It only makes
sense to use this option if the atoms are not diffusing, so that
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