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### 7. Additional tools

LAMMPS is designed to be a computational kernel for performing molecular dynamics computations. Additional pre- and post-processing steps are often necessary to setup and analyze a simulation. A few additional tools are provided with the LAMMPS distribution and are described in this section.

Our group has also written and released a separate toolkit called Pizza.py which provides tools for doing setup, analysis, plotting, and visualization for LAMMPS simulations. Pizza.py is written in Python and is available for download from the Pizza.py WWW site.

Note that many users write their own setup or analysis tools or use other existing codes and convert their output to a LAMMPS input format or vice versa. The tools listed here are included in the LAMMPS distribution as examples of auxiliary tools. Some of them are not actively supported by Sandia, as they were contributed by LAMMPS users. If you have problems using them, we can direct you to the authors.

The source code for each of these codes is in the tools sub-directory of the LAMMPS distribution. There is a Makefile (which you may need to edit for your platform) which will build several of the tools which reside in that directory. Some of them are larger packages in their own sub-directories with their own Makefiles.

- amber2lmp
- binary2txt
- ch2lmp
- chain
- data2xmovie
- eam generate
- lmp2arc
- lmp2cfg
- lmp2traj
- lmp2vmd
- matlab
- micelle2d
- msi2lmp
- pymol_asphere
- python
- restart2data
- thermo_extract
- vim
- xmovie

#### amber2lmp tool

The amber2lmp sub-directory contains two Python scripts for converting files back-and-forth between the AMBER MD code and LAMMPS. See the README file in amber2lmp for more information.

These tools were written by Keir Novik while he was at Queen Mary University of London. Keir is no longer there and cannot support these tools which are out-of-date with respect to the current LAMMPS version (and maybe with respect to AMBER as well). Since we don't use these tools at Sandia, you'll need to experiment with them and make necessary modifications yourself.

#### binary2txt tool

The file binary2txt.cpp converts one or more binary LAMMPS dump file into ASCII text files. The syntax for running the tool is

    binary2txt file1 file2 ...

which creates file1.txt, file2.txt, etc. This tool must be compiled on a platform that can read the binary file created by a LAMMPS run, since binary files are not compatible across all platforms.

#### ch2lmp tool

The ch2lmp sub-directory contains tools for converting files back-and-forth between the CHARMM MD code and LAMMPS.

They are intended to make it easy to use CHARMM as a builder and as a post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an ensemble built in CHARMM into its LAMMPS equivalent. Using lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.

See the README file in the ch2lmp sub-directory for more information.

These tools were created by Pieter in't Veld (pjintve at sandia.gov) and Paul Crozier (pscrozi at sandia.gov) at Sandia.

#### chain tool

The file chain.f creates a LAMMPS data file containing bead-spring polymer chains and/or monomer solvent atoms. It uses a text file containing chain definition parameters as an input. The created chains and solvent atoms can strongly overlap, so LAMMPS needs to run the system initially with a "soft" pair potential to un-overlap it. The syntax for running the tool is

    chain < def.chain > data.file

See the def.chain or def.chain.ab files in the tools directory for examples of definition files. This tool was used to create the system for the chain benchmark.

#### data2xmovie tool

The file data2xmovie.c converts a LAMMPS data file into a snapshot suitable for visualizing with the xmovie tool, as if it had been output with a dump command from LAMMPS itself. The syntax for running the tool is

    data2xmovie options < infile > outfile

See the top of the data2xmovie.c file for a discussion of the options.

#### eam generate tool

The tools/eam_generate directory contains several one-file C programs that convert an analytic formula into a tabulated embedded atom method (EAM) setfl potential file. The potentials they produce are in the potentials directory.

The source files and potentials were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com).

#### lmp2arc tool

The lmp2arc sub-directory contains a tool for converting LAMMPS output files to the format for Accelrys' Insight MD code (formerly MSI/Biosym and its Discover MD code). See the README file for more information.

This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic (jec at mayo.edu), but still fields questions about the tool.

This tool was updated for the current LAMMPS C++ version by Jeff Greathouse at Sandia (jagreat at sandia.gov).

#### lmp2cfg tool

The lmp2cfg sub-directory contains a tool for converting LAMMPS output files into a series of *.cfg files which can be read into the AtomEye visualizer. See the README file for more information.

This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).

#### lmp2traj tool

The lmp2traj sub-directory contains a tool for converting LAMMPS output files into 3 analysis files. One file can be used to create contour maps of the atom positions over the course of the simulation. The other two files provide density profiles and dipole moments. See the README file for more information.

This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).

#### lmp2vmd tool

The lmp2vmd sub-directory contains some scripts for converting LAMMPS files into formats suitable for visualizing with the VMD package.

One script extracts bond topology info from a LAMMPS data file. A second script attached amino acid (residue) information to what is extracted from a data file. See the README file for more information.

These scripts were written by Axel Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.

#### matlab tool

The matlab sub-directory contains several MATLAB scripts for post-processing LAMMPS output. The scripts include readers for log and dump files, a reader for radial distribution output from the fix rdf command, a reader for EAM potential files, and a converter that reads LAMMPS dump files and produces CFG files that can be visualized with the AtomEye visualizer.

See the README.pdf file for more information.

These scripts were written by Arun Subramaniyan at Purdue Univ (asubrama at purdue.edu).

#### micelle2d tool

The file micelle2d.f creates a LAMMPS data file containing short lipid chains in a monomer solution. It uses a text file containing lipid definition parameters as an input. The created molecules and solvent atoms can strongly overlap, so LAMMPS needs to run the system initially with a "soft" pair potential to un-overlap it. The syntax for running the tool is

    micelle2d < def.micelle2d > data.file

See the def.micelle2d file in the tools directory for an example of a definition file. This tool was used to create the system for the micelle example.

#### msi2lmp tool

The msi2lmp sub-directory contains a tool for creating LAMMPS input data files from Accelrys' Insight MD code (formerly MSI/Biosym and its Discover MD code). See the README file for more information.

This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic (jec at mayo.edu), but still fields questions about the tool.

This tool may be out-of-date with respect to the current LAMMPS and Insight versions. Since we don't use it at Sandia, you'll need to experiment with it yourself.

#### pymol_asphere tool

The pymol_asphere sub-directory contains a tool for converting a LAMMPS dump file that contains orientation info for ellipsoidal particles into an input file for the PyMol visualization package.

Specifically, the tool triangulates the ellipsoids so they can be viewed as true ellipsoidal particles within PyMol. See the README and examples directory within pymol_asphere for more information.

This tool was written by Mike Brown at Sandia.

#### python tool

The python sub-directory contains several Python scripts that perform common LAMMPS post-processing tasks, like

- extract thermodynamic info from a log file as columns of numbers
- plot two columns of thermodynamic info from a log file using GnuPlot
- sort the snapshots in a dump file by atom ID
- convert dump files into XYZ, CFG, or PDB format for viz by other packages

These are simple scripts built on Pizza.py modules. See the README for more info on Pizza.py and how to use these scripts.

#### restart2data tool

The file restart2data.cpp converts a binary LAMMPS restart file into an ASCII data file. The syntax for running the tool is

    restart2data restart-file data-file (input-file)

Input-file is optional and if specified will contain LAMMPS input commands for the masses and force field parameters, instead of putting those in the data-file. Only a few force field styles currently support this option.

This tool must be compiled on a platform that can read the binary file created by a LAMMPS run, since binary files are not compatible across all platforms.

Note that a text data file has less precision than a binary restart file. Hence, continuing a run from a converted data file will typically not conform as closely to a previous run as will restarting from a binary restart file.

If a "%" appears in the specified restart-file, the tool expects a set of multiple files to exist. See the restart and write_restart commands for info on how such sets of files are written by LAMMPS, and how the files are named.

#### thermo_extract tool

The thermo_extract tool reads one of more LAMMPS log files and extracts a thermodynamic value (e.g. Temp, Press). It spits out the time,value as 2 columns of numbers so the tool can be used as a quick way to plot some quantity of interest. See the header of the thermo_extract.c file for the syntax of how to run it and other details.

This tool was written by Vikas Varshney at Wright Patterson AFB (vikas.varshney at gmail.com).

#### vim tool

The files in the tools/vim directory are add-ons to the VIM editor that allow easier editing of LAMMPS input scripts. See the README.txt file for details.

These files were provided by Gerolf Ziegenhain (gerolf at ziegenhain.com)

#### xmovie tool

The xmovie tool is an X-based visualization package that can read LAMMPS dump files and animate them. It is in its own sub-directory with the tools directory. You may need to modify its Makefile so that it can find the appropriate X libraries to link against.

The syntax for running xmovie is

    xmovie options dump.file1 dump.file2 ...

If you just type "xmovie" you will see a list of options. Note that by default, LAMMPS dump files are in scaled coordinates, so you typically need to use the -scale option with xmovie. When xmovie runs it opens a visualization window and a control window. The control options are straightforward to use.

Xmovie was mostly written by Mike Uttormark (U Wisconsin) while he spent a summer at Sandia. It displays 2d projections of a 3d domain. While simple in design, it is an amazingly fast program that can render large numbers of atoms very quickly. It's a useful tool for debugging LAMMPS input and output and making sure your simulation is doing what you think it should. The animations on the Examples page of the LAMMPS WWW site were created with xmovie.

I've lost contact with Mike, so I hope he's comfortable with us distributing his great tool!