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doc/compute_displace_atom.html
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</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>compute ID group-ID displace/atom fix-ID <PRE>compute ID group-ID displace/atom
</PRE> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command <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>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>
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>compute 1 all displace/atom myCoords <PRE>compute 1 all displace/atom
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Define a computation that calculates the current displacement of each <P>Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries. The original due to atoms passing thru periodic boundaries. Four quantites per
coordinates are stored by a <A HREF = "fix_coord_original.html">fix atom are computed: the x,y,z displacements and the total displacement.
coord/original</A> command, whose ID must be See below for details.
specified with this compute. They are the coordinates at the time the
fix command was issued.
</P> </P>
<P>IMPORTANT NOTE: The fix coord/original command stores the initial <P>To store the original coordinates at the time this compute is issued,
coordinates in "unwrapped" form, by using the image flags associated the compute creates its own fix of style "coord/original", as if this
with each atom. See the <A HREF = "dump.html">dump custom</A> command for a command had been issued:
discussion of "unwrapped" coordinates. See the Atoms section of the </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 <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 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. image</A> command.
</P> </P>
<P>The displacements can be output directly via the <A HREF = "dump.html">dump <P>The displacements can be output directly via the <A HREF = "dump.html">dump
custom</A> command. custom</A> command.
</P> </P>
<P>The value of the displacement will be 0.0 for atoms not in the <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 specified compute group.
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
</P> </P>
<P><B>Output info:</B> <P><B>Output info:</B>
</P> </P>

40
doc/compute_displace_atom.txt
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@ -10,42 +10,48 @@ compute displace/atom command :h3
[Syntax:] [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 ID, group-ID are documented in "compute"_compute.html command
displace/atom = style name of this compute command displace/atom = style name of this compute command :ul
fix-ID = ID of a fix of style "coord/original"_fix_coord_original.html :ul
[Examples:] [Examples:]
compute 1 all displace/atom myCoords :pre compute 1 all displace/atom :pre
[Description:] [Description:]
Define a computation that calculates the current displacement of each Define a computation that calculates the current displacement of each
atom in the group from its original coordinates, including all effects atom in the group from its original coordinates, including all effects
due to atoms passing thru periodic boundaries. The original due to atoms passing thru periodic boundaries. Four quantites per
coordinates are stored by a "fix atom are computed: the x,y,z displacements and the total displacement.
coord/original"_fix_coord_original.html command, whose ID must be See below for details.
specified with this compute. They are the coordinates at the time the
fix command was issued.
IMPORTANT NOTE: The fix coord/original command stores the initial To store the original coordinates at the time this compute is issued,
coordinates in "unwrapped" form, by using the image flags associated the compute creates its own fix of style "coord/original", as if this
with each atom. See the "dump custom"_dump.html command for a command had been issued:
discussion of "unwrapped" coordinates. See the Atoms section of the
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 "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 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. image"_set.html command.
The displacements can be output directly via the "dump The displacements can be output directly via the "dump
custom"_dump.html command. custom"_dump.html command.
The value of the displacement will be 0.0 for atoms not in the 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 specified compute group.
stores (0.0,0.0,0.0) for the original coordinates of any atom not in
the fix group.
[Output info:] [Output info:]