9. 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.

9.1. 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 Keir is no longer there and cannot support these tools which are out-of-date with respect to the current LAMMPS version (and maybe with respect to AMBER as well).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.

9.2. 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.

9.3. 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 a PDB file with associated CHARMM info, including CHARMM force field data, 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.

9.4. 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.

9.5. colvars tools

The colvars directory contains a collection of tools for postprocessing data produced by the colvars collective variable library. To compile the tools, edit the makefile for your system and run “make”.

Please report problems and issues the colvars library and its tools at: https://github.com/colvars/colvars/issues

abf_integrate:

MC-based integration of multidimensional free energy gradient Version 20110511

Syntax: ./abf_integrate < filename > [-n < nsteps >] [-t < temp >] [-m [0|1] (metadynamics)] [-h < hill_height >] [-f < variable_hill_factor >]

The LAMMPS interface to the colvars collective variable library, as well as these tools, were created by Axel Kohlmeyer (akohlmey at gmail.com) at ICTP, Italy.

9.6. createatoms tool

The tools/createatoms directory contains a Fortran program called createAtoms.f which can generate a variety of interesting crystal structures and geometries and output the resulting list of atom coordinates in LAMMPS or other formats.

See the included Manual.pdf for details.

The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.

9.7. 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.

9.8. eam database tool

The tools/eam_database directory contains a Fortran program that will generate EAM alloy setfl potential files for any combination of 16 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, Zr. The files can then be used with the pair_style eam/alloy command.

The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov, and is based on his paper:

X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69, 144113 (2004).

9.9. 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, and can be used with the pair_style eam/alloy command.

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

9.10. eff tool

The tools/eff directory contains various scripts for generating structures and post-processing output for simulations using the electron force field (eFF).

These tools were provided by Andres Jaramillo-Botero at CalTech (ajaramil at wag.caltech.edu).

9.11. emacs tool

The tools/emacs directory contains a Lips add-on file for Emacs that enables a lammps-mode for editing of input scripts when using Emacs, with various highlighting options setup.

These tools were provided by Aidan Thompson at Sandia (athomps at sandia.gov).

9.12. fep tool

The tools/fep directory contains Python scripts useful for post-processing results from performing free-energy perturbation simulations using the USER-FEP package.

The scripts were contributed by Agilio Padua (Universite Blaise Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.

See README file in the tools/fep directory.

9.13. i-pi tool

The tools/i-pi directory contains a version of the i-PI package, with all the LAMMPS-unrelated files removed. It is provided so that it can be used with the fix ipi command to perform path-integral molecular dynamics (PIMD).

The i-PI package was created and is maintained by Michele Ceriotti, michele.ceriotti at gmail.com, to interface to a variety of molecular dynamics codes.

See the tools/i-pi/manual.pdf file for an overview of i-PI, and the fix ipi doc page for further details on running PIMD calculations with LAMMPS.

9.14. ipp tool

The tools/ipp directory contains a Perl script ipp which can be used to facilitate the creation of a complicated file (say, a lammps input script or tools/createatoms input file) using a template file.

ipp was created and is maintained by Reese Jones (Sandia), rjones at sandia.gov.

See two examples in the tools/ipp directory. One of them is for the tools/createatoms tool’s input file.

9.15. kate tool

The file in the tools/kate directory is an add-on to the Kate editor in the KDE suite that allow syntax highlighting of LAMMPS input scripts. See the README.txt file for details.

The file was provided by Alessandro Luigi Sellerio (alessandro.sellerio at ieni.cnr.it).

9.16. 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).

9.17. 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).

9.18. lmp2vmd tool

The lmp2vmd sub-directory contains a README.txt file that describes details of scripts and plugin support within the VMD package for visualizing LAMMPS dump files.

The VMD plugins and other supporting scripts were written by Axel Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.

9.19. 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 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).

9.20. 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.

9.21. moltemplate tool

The moltemplate sub-directory contains a Python-based tool for building molecular systems based on a text-file description, and creating LAMMPS data files that encode their molecular topology as lists of bonds, angles, dihedrals, etc. See the README.TXT file for more information.

This tool was written by Andrew Jewett (jewett.aij at gmail.com), who supports it. It has its own WWW page at http://moltemplate.org.

9.22. 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.

9.23. phonon tool

The phonon sub-directory contains a post-processing tool useful for analyzing the output of the fix phonon command in the USER-PHONON package.

See the README file for instruction on building the tool and what library it needs. And see the examples/USER/phonon directory for example problems that can be post-processed with this tool.

This tool was written by Ling-Ti Kong at Shanghai Jiao Tong University.

9.24. polymer bonding tool

The polybond sub-directory contains a Python-based tool useful for performing “programmable polymer bonding”. The Python file lmpsdata.py provides a “Lmpsdata” class with various methods which can be invoked by a user-written Python script to create data files with complex bonding topologies.

See the Manual.pdf for details and example scripts.

This tool was written by Zachary Kraus at Georgia Tech.

9.25. 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 or its open source variant.

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.

9.26. python tool

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

  • 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 multiple NEB dump files into one dump file for viz
  • 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.

9.27. reax tool

The reax sub-directory contains stand-alond codes that can post-process the output of the fix reax/bonds command from a LAMMPS simulation using ReaxFF. See the README.txt file for more info.

These tools were written by Aidan Thompson at Sandia.

9.28. restart2data tool

Note

This tool is now obsolete and is not included in the current LAMMPS distribution. This is becaues there is now a write_data command, which can create a data file from within an input script. Running LAMMPS with the “-r” command-line switch as follows:

lmp_g++ -r restartfile datafile

is the same as running a 2-line input script:

read_restart restartfile write_data datafile

which will produce the same data file that the restart2data tool used to create. The following information is included in case you have an older version of LAMMPS which still includes the 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.

9.29. 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)

9.30. xmgrace tool

The files in the tools/xmgrace directory can be used to plot the thermodynamic data in LAMMPS log files via the xmgrace plotting package. There are several tools in the directory that can be used in post-processing mode. The lammpsplot.cpp file can be compiled and used to create plots from the current state of a running LAMMPS simulation.

See the README file for details.

These files were provided by Vikas Varshney (vv0210 at gmail.com)

9.31. 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!