link changes for new Tools.html

coefficients is done in the input data file via the

"read_data"_read_data.html command or in the input script with

commands like "pair_coeff"_pair_coeff.html or

"bond_coeff"_bond_coeff.html.  See "Section 9"_Section_tools.html

for additional tools that can use CHARMM or AMBER to assign force

field coefficients and convert their output into LAMMPS input.

"bond_coeff"_bond_coeff.html.  See the "Tools"_Tools.html doc page for

additional tools that can use CHARMM or AMBER to assign force field

coefficients and convert their output into LAMMPS input.

See "(MacKerell)"_#howto-MacKerell for a description of the CHARMM force

field.  See "(Cornell)"_#howto-Cornell for a description of the AMBER force

LAMMPS snapshots are created by the "dump"_dump.html command which can

create files in several formats. The native LAMMPS dump format is a

text file (see "dump atom" or "dump custom") which can be visualized

by several popular visualization tools. The "dump image"_dump_image.html

and "dump movie"_dump_image.html styles can output internally rendered

images and convert a sequence of them to a movie during the MD run.

Several programs included with LAMMPS as auxiliary tools can convert

between LAMMPS format files and other formats.

See the "Section 9"_Section_tools.html doc page for details.

by several popular visualization tools. The "dump

image"_dump_image.html and "dump movie"_dump_image.html styles can

output internally rendered images and convert a sequence of them to a

movie during the MD run.  Several programs included with LAMMPS as

auxiliary tools can convert between LAMMPS format files and other

formats.  See the "Tools"_Tools.html doc page for details.

A Python-based toolkit distributed by our group can read native LAMMPS

dump files, including custom dump files with additional columns of

Pre- and post-processing :h4

Various pre- and post-processing serial tools are packaged

with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l

Various pre- and post-processing serial tools are packaged with

LAMMPS; see the "Tools"_Tools.html doc page for details. :ulb,l

Our group has also written and released a separate toolkit called

"Pizza.py"_pizza which provides tools for doing setup, analysis,

plot your output data :ul

A few tools for pre- and post-processing tasks are provided as part of

the LAMMPS package; they are described in "this

section"_Section_tools.html.  However, many people use other codes or

write their own tools for these tasks.

the LAMMPS package; they are described on the "Tools"_Tools.html doc

page.  However, many people use other codes or write their own tools

for these tasks.

As noted above, our group has also written and released a separate

toolkit called "Pizza.py"_pizza which addresses some of the listed

typically be specified.  We suggest you use a program like

"CHARMM"_charmm or "AMBER"_amber or other molecular builders to setup

such problems and dump its information to a file.  You can then

reformat the file as LAMMPS input.  Some of the tools in "this

section"_Section_tools.html can assist in this process.

reformat the file as LAMMPS input.  Some of the tools described on the

"Tools"_Tools.html doc page can assist in this process.

Similarly, LAMMPS creates output files in a simple format.  Most users

post-process these files with their own analysis tools or re-format

The tools sub-directory of the LAMMPS distribution has various

stand-alone codes for pre- and post-processing of LAMMPS data.  More

details are given in "Section 9"_Section_tools.html.  If you write

a new tool that users will find useful, it can be added to the LAMMPS

details are given on the "Tools"_Tools.html doc page.  If you write a

new tool that users will find useful, it can be added to the LAMMPS

distribution. :l

LAMMPS is designed to be easy to extend with new code for features

 "Previous Section"_Section_tools.html - "LAMMPS WWW Site"_lws -

"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next

 "Previous Section"_Tools.html - "LAMMPS WWW Site"_lws - "LAMMPS

Documentation"_ld - "LAMMPS Commands"_lc - "Next

Section"_Section_python.html :c

:link(lws,http://lammps.sandia.gov)

"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_tools.html :c

"Previous Section"_Section_example.html - "LAMMPS WWW Site"_lws -

"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next

Section"_Tools.html :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

individual values and the file itself.

The {atom}, {local}, and {custom} styles create files in a simple text

format that is self-explanatory when viewing a dump file.  Many of the

LAMMPS "post-processing tools"_Section_tools.html, including

"Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html, work with this

format, as does the "rerun"_rerun.html command.

format that is self-explanatory when viewing a dump file.  Some of the

LAMMPS post-processing tools described on the "Tools"_Tools.html doc

page, including "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html,

work with this format, as does the "rerun"_rerun.html command.

For post-processing purposes the {atom}, {local}, and {custom} text

files are self-describing in the following sense.

will be about the same size as a text version, but will typically

write out much faster.  Of course, when post-processing, you will need

to convert it back to text format (see the "binary2txt

tool"_Section_tools.html#binary) or write your own code to read the

binary file.  The format of the binary file can be understood by

looking at the tools/binary2txt.cpp file.  This option is only

available for the {atom} and {custom} styles.

tool"_Tools.html#binary) or write your own code to read the binary

file.  The format of the binary file can be understood by looking at

the tools/binary2txt.cpp file.  This option is only available for the

{atom} and {custom} styles.

If the filename ends with ".gz", the dump file (or files, if "*" or "%"

is also used) is written in gzipped format.  A gzipped dump file will