From 123a9b569d8bc9cc0def99d93d836cfcfdf59846 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 23 May 2012 15:52:08 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8160 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/dump.html | 9 ++++++++- doc/dump.txt | 9 ++++++++- doc/dump_modify.html | 26 +++++++++++++++++--------- doc/dump_modify.txt | 26 +++++++++++++++++--------- 4 files changed, 50 insertions(+), 20 deletions(-) diff --git a/doc/dump.html b/doc/dump.html index 8feec33ead..1500d4f41b 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -279,7 +279,14 @@ 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 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 (a popular molecular viewing diff --git a/doc/dump.txt b/doc/dump.txt index 904055d9d3..6d660de29b 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -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 diff --git a/doc/dump_modify.html b/doc/dump_modify.html index cfe26eeea8..c280591581 100644 --- a/doc/dump_modify.html +++ b/doc/dump_modify.html @@ -335,15 +335,23 @@ pre-defined color names with new RBG values.

-

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 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 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 +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 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.

diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt index d37169a110..2ab4ca707f 100644 --- a/doc/dump_modify.txt +++ b/doc/dump_modify.txt @@ -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)