Tag Archives: ovito

lammps-in-ovito

Writing molecular dynamics data to binary LAMMPS format

In this post I will explain  how to write to the binary LAMMPS file format from C++, using data stored in Armadillo vectors and matrices. After running the example in this post you should be able to open the resulting file in Ovito or any other program capable of reading binary LAMMPS files. The example should also be fairly easy to port to other data structure type, if needed.

For the impatient: You’ll find a working main.cpp file and a qmake project file on GitHub.

The result, if rendered in Ovito, is two silicon atoms (in red) and one oxygen atom:

lammps-in-ovito

About the LAMMPS format

LAMMPS is a molecular dynamics simulation package that is extremely versatile with plenty of interaction potentials and features implemented. However, you may have written some other code involving atoms and found yourself in the position of considering using a standard file format to write atom data to file. In this case, the XYZ-format has likely passed your mind, but because this is a ASCII-based text format, it is slow to read and write. This format also lacks standardized headers for information such as the system boundaries – causing visualizers like Ovito to have to guess for the right boundaries in your system.

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Getting the latest version of Ovito for Ubuntu

Ovito is a great tool to visualize atoms from molecular dynamics simulations and to perform some statistical analysis on the data. The tool is an alternative to other similar tools such as VMD and ParaView.

Ovito
The main window of Ovito in the newest version.

The current version of Ovito in the Ubuntu repositories (version 0.9.2) is sadly very outdated. Even though you of course may download the latest version from Ovito’s webpages and install it locally in your home folder, I often find it better to get a newer package version.

At the Computational Physics group’s PPA I have now uploaded the latest build of Ovito for Ubuntu in a package that will automatically replace the current Ovito version. Note that this is not a release version of Ovito, but the latest version fetched from Ovito’s sources (currently nicknamed 1.1.1.90). The reason is that Ovito’s creator, Alexander Stukowski, was kind enough to implement a suggestion we proposed to change the default input handler for the viewports to be the orbit input handler. This behavior feels so much more natural and makes the already great Ovito application even better.

To install the latest version of Ovito, all you need to do is to open up a terminal and type these lines:

sudo apt-add-repository ppa:comp-phys/stable
sudo apt-get install ovito

Note that the Computational Physics repository also contains newer versions of the Armadillo package, which will automatically be updated if you do not remove the repository after installing Ovito.