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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8160 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2012-05-23 15:52:08 +00:00
parent 144f2f2fd6
commit 123a9b569d
4 changed files with 50 additions and 20 deletions
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9
doc/dump.html
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@ -279,7 +279,14 @@ box. Note that these coordinates may thus be far outside the box size
stored with the snapshot.
</P>
<P>The <I>xyz</I> style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
coordinate format that many codes can read. Specifically it has
a line with the number of atoms, then a comment line that is
usually ignored followed by one line per atom with the atom type
and the x-, y-, and z-coordinate of that atom. You can use the
<A HREF = "dump_modify.html">dump_modify element</A> option to change the output
from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
bonds and colors.
</P>
<P>Note that DCD, XTC, and XYZ formatted files can be read directly by
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing

9
doc/dump.txt
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@ -268,7 +268,14 @@ box. Note that these coordinates may thus be far outside the box size
stored with the snapshot.
The {xyz} style writes XYZ files, which is a simple text-based
coordinate format that many codes can read.
coordinate format that many codes can read. Specifically it has
a line with the number of atoms, then a comment line that is
usually ignored followed by one line per atom with the atom type
and the x-, y-, and z-coordinate of that atom. You can use the
"dump_modify element"_dump_modify.html option to change the output
from using the (numerical) atom type to an element name (or some
other label). This will help many visualization programs to guess
bonds and colors.
Note that DCD, XTC, and XYZ formatted files can be read directly by
"VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing

26
doc/dump_modify.html
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@ -335,15 +335,23 @@ pre-defined color names with new RBG values.
</P>
<HR>
<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I> and <I>image</I>
styles. It associates element names (e.g. H, C, Fe) with LAMMPS atom
types. See the list of element names at the bottom of this page. In
the case of dump <I>cfg</I>, it allows the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> visualization
package to read the dump file and render atoms with the appropriate
size and color. In the case of dump <I>image</I>, the output images will
follow the same <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> convention. An element name is
specified for each atom type (1 to Ntype) in the simulation. The same
element name can be given to multiple atom types.
<P>The <I>element</I> keyword applies only to the the dump <I>cfg</I>, <I>xyz</I>, and
<I>image</I> styles. It associates element names (e.g. H, C, Fe) with
LAMMPS atom types. See the list of element names at the bottom of
this page.
</P>
<P>In the case of dump <I>cfg</I>, this allows the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
visualization package to read the dump file and render atoms with the
appropriate size and color.
</P>
<P>In the case of dump <I>image</I>, the output images will follow the same
<A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A> convention. An element name is specified for each
atom type (1 to Ntype) in the simulation. The same element name can
be given to multiple atom types.
</P>
<P>In the case of <I>xyz</I> format dumps, there are no restrictions to what
label can be used as an element name. Any whitespace separated text
will be accepted.
</P>

26
doc/dump_modify.txt
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@ -328,15 +328,23 @@ pre-defined color names with new RBG values.
:line
The {element} keyword applies only to the the dump {cfg} and {image}
styles. It associates element names (e.g. H, C, Fe) with LAMMPS atom
types. See the list of element names at the bottom of this page. In
the case of dump {cfg}, it allows the "AtomEye"_atomeye visualization
package to read the dump file and render atoms with the appropriate
size and color. In the case of dump {image}, the output images will
follow the same "AtomEye"_atomeye convention. An element name is
specified for each atom type (1 to Ntype) in the simulation. The same
element name can be given to multiple atom types.
The {element} keyword applies only to the the dump {cfg}, {xyz}, and
{image} styles. It associates element names (e.g. H, C, Fe) with
LAMMPS atom types. See the list of element names at the bottom of
this page.
In the case of dump {cfg}, this allows the "AtomEye"_atomeye
visualization package to read the dump file and render atoms with the
appropriate size and color.
In the case of dump {image}, the output images will follow the same
"AtomEye"_atomeye convention. An element name is specified for each
atom type (1 to Ntype) in the simulation. The same element name can
be given to multiple atom types.
In the case of {xyz} format dumps, there are no restrictions to what
label can be used as an element name. Any whitespace separated text
will be accepted.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)