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 list of such tools can be found on the LAMMPS home page at http://lammps.sandia.gov/prepost.html
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. Most of them are larger packages in their own sub-directories with their own Makefiles and/or README files.
amber2lmp binary2txt ch2lmp chain colvars createatoms doxygen drude eam database eam generate eff emacs fep i-pi ipp kate lmp2arc lmp2cfg matlab micelle2d moltemplate msi2lmp phonon polybond pymol_asphere python reax smd vim xmgrace
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 Keir is no longer there and cannot support these tools which are out-of-date with respect to the current LAMMPS version (and maybe with respect to AMBER as well).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. Support for the CMAP correction of CHARMM22 and later is available as an option. This tool can also add solvent water molecules and Na+ or Cl- ions to the system. 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.
CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and Tigran Abramyan, (Clemson University) and Chris Lorenz (chris.lorenz at kcl.ac.uk), King’s College London.
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
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. doxygen tool
The tools/doxygen directory contains a shell script called doxygen.sh which can generate a call graph and API lists using the Doxygen software.
See the included README file for details.
The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
9.8. drude tool
The tools/drude directory contains a Python script called polarizer.py which can add Drude oscillators to a LAMMPS data file in the required format.
See the header of the polarizer.py file for details.
The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
9.9. 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).
9.10. 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).
9.11. 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).
9.12. 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).
9.13. 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.
9.14. 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.
9.15. 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.
9.16. 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).
9.17. 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).
9.18. 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).
9.19. 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 template input and data files from BIOVIA’s Materias Studio files (formerly Accelrys’ Insight MD code, formerly MSI/Biosym and its Discover MD code).
This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS.
This tool has several known limitations and is no longer under active development, so there are no changes except for the occasional bugfix.
See the README file in the tools/msi2lmp folder for more information.
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. polybond 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
These tools were written by Aidan Thompson at Sandia.
9.28. smd tool
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and Makefile which can be compiled and used to convert triangle output files created by the Smooth-Mach Dynamics (USER-SMD) package into a VTK-compatible unstructured grid file. It could then be read in and visualized by VTK.
See the header of dump2vtk.cpp for more details.
This tool was written by the USER-SMD package author, Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
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)