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40
doc/compute_displace_atom.html
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@ -13,42 +13,48 @@
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID displace/atom fix-ID
<PRE>compute ID group-ID displace/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>displace/atom = style name of this compute command
<LI>fix-ID = ID of a fix of style <A HREF = "fix_coord_original.html">coord/original</A>
<LI>displace/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all displace/atom myCoords
<PRE>compute 1 all displace/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
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.
due to atoms passing thru periodic boundaries. Four quantites per
atom are computed: the x,y,z displacements and the total displacement.
See below for details.
</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
<P>To store the original coordinates at the time this compute is issued,
the compute creates its own fix of style "coord/original", as if this
command had been issued:
</P>
<PRE>fix compute-ID_coord_original group-ID coord/original
</PRE>
<P>See the <A HREF = "fix_coord_original.html">fix coord/original</A> command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
the same as the compute group.
</P>
<P>IMPORTANT NOTE: Fix coord/original 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
(e.g. to 0) before invoking 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
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
specified compute group.
</P>
<P><B>Output info:</B>
</P>

40
doc/compute_displace_atom.txt
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@ -10,42 +10,48 @@ compute displace/atom command :h3
[Syntax:]
compute ID group-ID displace/atom fix-ID :pre
compute ID group-ID displace/atom :pre
ID, group-ID are documented in "compute"_compute.html command
displace/atom = style name of this compute command
fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul
displace/atom = style name of this compute command :ul
[Examples:]
compute 1 all displace/atom myCoords :pre
compute 1 all displace/atom :pre
[Description:]
Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects
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.
due to atoms passing thru periodic boundaries. Four quantites per
atom are computed: the x,y,z displacements and the total displacement.
See below for details.
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
To store the original coordinates at the time this compute is issued,
the compute creates its own fix of style "coord/original", as if this
command had been issued:
fix compute-ID_coord_original group-ID coord/original :pre
See the "fix coord/original"_fix_coord_original.html command for
details. Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", and the group for the new fix is
the same as the compute group.
IMPORTANT NOTE: Fix coord/original 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
(e.g. to 0) before invoking 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
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
specified compute group.
[Output info:]