ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3501 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2009-12-04 00:42:15 +00:00
parent 4f5e9b3c24
commit 1453cc4864
10 changed files with 157 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files

18
doc/compute_msd.txt
View File

@ -21,8 +21,8 @@ keyword = {com} :l
[Examples:]
fix 1 all compute
fix 1 upper compute com yes :pre
compute 1 all msd
compute 1 upper msd com yes :pre
[Description:]
@ -36,8 +36,8 @@ and averaged over atoms in the group. The 4th component is the total
squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and
averaged over atoms in the group.
The slope of the mean-squared displacement versus time is proportional
to the diffusion coefficient of the diffusing atoms.
The slope of the mean-squared displacement (MSD) versus time is
proportional to the diffusion coefficient of the diffusing atoms.
The displacement of an atom is from its original position at the time
the compute command was issued. To store the original coordinates,
@ -67,11 +67,11 @@ image"_set.html command.
IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and the computed MSD will not reflect its true displacement. See the
"fix rigid"_fix_rigid.html command for details. Thus, to compute the
MSD of rigid bodies as they cross periodic boundaries, you will need
to post-process a "dump file"_dump.html containing coordinates of the
atoms in the bodies.
and its contribution to the MSD may not reflect its true contribution.
See the "fix rigid"_fix_rigid.html command for details. Thus, to
compute the MSD of rigid bodies as they cross periodic boundaries, you
will need to post-process a "dump file"_dump.html containing
coordinates of the atoms in the bodies.
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,