Detailed usage for the Neper container

This section explains how to use the Neper image. For more details about Apptainer commands, please look at this tutorial.

Introduction

Neper is a software for modeling and simulating polycrystalline materials, generating and analyzing 2D/3D grain microstructures via Voronoi tessellations and experimental data meshing. It’s a robust, efficient tool widely used by materials scientists for grain boundary, texture, and finite element analysis of polycrystals.

The main executable in the image is neper. The software version embedded in the container image can be displayed with the following command:

apptainer exec neper.sif neper --version

The code license can be found under the following path: /share/doc/neper-xx.xx.xx/COPYING where xx.xx.xx is the software version. It can be accessed from outside the container as follows:

neper_version=$(apptainer exec neper.sif neper --version)
apptainer exec neper.sif cat /share/doc/neper-$neper_version/COPYING

The image also contains other useful executables, such as gmsh for mesh generation, or povray and asy for image generation.

Using the Neper container to generate and mesh a simple tessellation

The Neper executable within the neper.sif container image can be interacted with by simply adding the apptainer exec neper.sif command before a neper command. To illustrate this, let us consider the following tutorial from the official documentation. A simple 100-cell tessellation can be generated as follows:

apptainer exec neper.sif neper -T -n 100

This tessellation can be visualized through the following command that generates a PNG file named img1.png that should look like the image represented in the tutorial:

apptainer exec neper.sif neper -V n100-id1.tess -print img1

It can be meshed with the following command:

apptainer exec neper.sif neper -M n100-id1.tess

The mesh can be visualized through the following command that generates a PNG file named img2.png that, again, should look like the meshed image represented in the tutorial:

apptainer exec neper.sif neper -V n100-id1.tess,n100-id1.msh -print img2

The rest of the commands exposed in the tutorial can be similarly extrapolated from these examples.