jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3450 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-11-30 15:48:33 +00:00
parent 5e6ab952f7
commit d7e5ba757e
4 changed files with 40 additions and 22 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

17
doc/compute_displace_atom.html
View File

@ -31,10 +31,19 @@ due to atoms passing thru periodic boundaries. The original
coordinates are stored by a <A HREF = "fix_coord_original.html">fix
coord/original</A> command, whose ID must be
specified with this compute. They are the coordinates at the time the
fix command was issued. The displacement can be output directly via
the <A HREF = "dump.html">dump custom</A> command. It could also be used to
calculate a diffusion coefficient for a group of atoms, as is done by
the <A HREF = "fix_msd.html">fix msd</A> command.
fix command was issued.
</P>
<P>IMPORTANT NOTE: The fix coord/original command stores the initial
coordinates in "unwrapped" form, by using the image flags associated
with each atom. See the <A HREF = "dump.html">dump custom</A> command for a
discussion of "unwrapped" coordinates. See the Atoms section of the
<A HREF = "read_data.html">read_data</A> 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 the fix and this compute by using the <A HREF = "set.html">set
image</A> command.
</P>
<P>The displacements can be output directly via the <A HREF = "dump.html">dump
custom</A> command.
</P>
<P>The value of the displacement will be 0.0 for atoms not in the
specified compute group. Note that the fix defines its own group and

17
doc/compute_displace_atom.txt
View File

@ -28,10 +28,19 @@ due to atoms passing thru periodic boundaries. The original
coordinates are stored by a "fix
coord/original"_fix_coord_original.html command, whose ID must be
specified with this compute. They are the coordinates at the time the
fix command was issued. The displacement can be output directly via
the "dump custom"_dump.html command. It could also be used to
calculate a diffusion coefficient for a group of atoms, as is done by
the "fix msd"_fix_msd.html command.
fix command was issued.
IMPORTANT NOTE: The fix coord/original command stores the initial
coordinates 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 the fix and this compute by using the "set
image"_set.html command.
The displacements can be output directly via the "dump
custom"_dump.html command.
The value of the displacement will be 0.0 for atoms not in the
specified compute group. Note that the fix defines its own group and

14
doc/fix_coord_original.html
View File

@ -32,13 +32,13 @@ coordinates can be accessed by other <A HREF = "Section_howto.html#4_15">output
commands</A> that use per-atom quantities such as
the <A HREF = "dump.html">dump custom</A> command.
</P>
<P>IMPORTANT NOTE: To enable displacements to be calculated which include
the effects of atoms passing through periodic boundaries, the original
coordinates are stored in "unwrapped" form, by using the image flags
associated with each atom. See the <A HREF = "dump.html">dump custom</A> command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the <A HREF = "read_data.html">read_data</A> command for a discussion of image flags
and how they are set for each atom.
<P>IMPORTANT NOTE: The original coordinates are stored in "unwrapped"
form, by using the image flags associated with each atom. See the
<A HREF = "dump.html">dump custom</A> command for a discussion of "unwrapped"
coordinates. See the Atoms section of the <A HREF = "read_data.html">read_data</A>
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
fix by using the <A HREF = "set.html">set image</A> command.
</P>
<P>IMPORTANT NOTE: If an atom is part of a rigid body (see the <A HREF = "fix_rigid.html">fix
rigid</A> command), it's periodic image flags are altered,

14
doc/fix_coord_original.txt
View File

@ -29,13 +29,13 @@ coordinates can be accessed by other "output
commands"_Section_howto.html#4_15 that use per-atom quantities such as
the "dump custom"_dump.html command.
IMPORTANT NOTE: To enable displacements to be calculated which include
the effects of atoms passing through periodic boundaries, the original
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.
IMPORTANT NOTE: The original 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
fix by using the "set 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,