LAMMPS and OVITO

In this training, LAMMPS will be used for performing molecular dynamics simulations and OVITO to
visualize the result of the simulation. The visualization software OVITO and the simulation software
LAMMPS should be installed on your computer in order to do the exercise.

1. LAMMPS (http://lammps.sandia.gov/)

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular
Massively Parallel Simulator.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter
(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms
or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-
decomposition of the simulation domain. Many of its models have versions that provide accelerated
performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend
with new functionality.

LAMMPS is distributed as an open source code under the terms of the GPL.

In this training, we assume you will use Window based LAMMPS. Pre-compiled Windows installers
which install LAMMPS executables on a Windows system can be downloaded from this site:
http://rpm.lammps.org/windows.html. Follow the instructions there to install LAMMPS on your
computer.

LAMMPS user documentation can be found here: http://lammps.sandia.gov/doc/Manual.html

In order to run LAMMPS on Windows, you need to use the command line environment. This can be
done, for example, by choosing "Command prompt" in “Windows system” from the Start menu. On
the command prompt window, you can go to the folder where LAMMPS is installed using standard
DOS commands. For example, if you installed LAMMPS in a folder named "LAMMPS" in your c: drive,
you type “cd c:\LAMMPS” to go to that folder.

The input file you want to run should be put in the same folder containing LAMMPS. If you want to
run an input file, for example with the name "in.example", you type:

lmp_serial < in.example

in the command prompt window, and the simulation should start. This requires that you have been
already in the folder where "lmp_serial" is located. If you want to cancel/stop a simulation before it is
finished, just press "CTRL+c" at any time.

In order to run a simulation using LAMMPS, an input script must be provided. For all documentation
of the commands used in the input file, please see the LAMMPS homepage, where all commands are
thoroughly described in the section: http://lammps.sandia.gov/doc/Section_commands.html. In the
exercise, an example script will be provided.
2. OVITO (https://ovito.org/)

OVITO is a scientific visualization and analysis software for atomistic and particle simulation data. It
helps scientists gain better insights into materials phenomena and physical processes.

OVITO is being developed by Alexander Stukowski at Darmstadt University of Technology, Germany.

The program is Open Source and freely available for all major platforms.

OVITO can be downloaded here: https://ovito.org/index.php/download

OVITO user manual can be found here: https://ovito.org/manual/