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LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend.



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Related Projects is a collection of Python tools that perform pre- and post-processing for the LAMMPS molecular dynamics package (or other simulators). Software wrapped by, so it can be invoked from Python, includes GnuPlot, MatLab, Raster3d, and RasMol

Pymsi2lmp - Python scripts for converting INSIGHT2 files to LAMMPS input files.

pymsi2lmp - convert *.car and *.mdl files into a LAMMPS input data file. compass-fit - used to calibrate forcefield parameters to a trajectory file.

Virtual Photonics

The Virtual Photonics Technology Initiative was established by the Laser Microbeam and Medical Program (LAMMP), an NIH/NIBIB Biotechnology Resource Center at the Beckman Laser Institute and Medical Clinic ( in April 2008.

Ase-atomistic-potential-tests - basic tests of atomistic potentials, implemented using ASE

These are Python routines utilizing Atomistic Simulation Environment (ASE) and LAMMPS to perform basic tests of atomistic potentials. ASE is used to create atomic configurations for LAMMPS, to write input scripts for LAMMPS, and to read results from LAMMPS output files, as advocated in the NIST workshop presentation. Evaluated properties are: formation energies and volumes of point defects (vacancies, substitutions, and interstitials), formation energies of basic surfaces, heats of formation of

Neblammps - Module that enables LAMMPS to be run with NEB method

With this module, users can use LAMMPS MD simulations with NEB method.

Gosam - generator of simple atomistic models

gosam is a bunch of Python scripts that can: create monocrystal in PBC box (atomistic model), create bicrystals with coincidence site lattice (CSL) boundaries in PBC box, create crystalline grains of given shape, with vacancies, thermal vibrations, etc. read/write several file formats (AtomEye cfg, VASP POSCAR, LAMMPS, DL_POLY, XMOL XYZ). Dependencies: Python and numpy. also requires the qhull program. Installation: Just download the content of,

Ibi-coarse-graining - A set of python scripts to perform Iterative Boltzmann Inversion with LAMMPS.

A set of scripts that automate the calibration of coarse-grain potentials to fit the structural distributions of an all-atom model. Uses the LAMMPS molecular dynamics code.

Mdanalysis - A python library to analyze and manipulate molecular dynamics trajectories

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively fast framework for complex analysis tasks. In addition, CHARMM-style atom selection commands are implemented. Trajectories can also be manipulated (for instance, fit to a reference structure) and written o

Fix-phonon - FixPhonon: An extension to LAMMPS for the evaluation of phonons

This project presents an implementation of the method to evaluate the phonon dispersion directly from molecular dynamics simulations. The basic algorithm is to construct the dynamical matrices by observing the displacement fluctuations. For details, check the documents of the project. The implemented method enables one to evaluate the phonon dispersion under finite temperature/pressures without turning to the usual quasi-harmonic procedure. The code presented here needs to work along with LAMMPS

Mango-selm - (MA)thematical and (N)umerical (G)raphical (O)rchestrator for the (S)tochastic (E)uleri

Provides software for setting up mathematical models and numerical simulations. MANGO provides a graphical user interface and scripting language for the specification of models and numerical simulations. SELM provides a collection of numerical methods integrated with the LAMMPS-MD package for simulations of fluid-structure interactions when subject to thermal fluctuations. This website serves as the main repository for information concerning the code development of MANGO-SELM. For more informati

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