Atomes is a Free (Open Source) cross-platform toolbox developed to analyze, to visualize and to edit/create three-dimensional atomistic models. It offers a workspace that allows to have many projects opened simultaneously.

The different projects in the workspace can exchange data: analysis results, atomic coordinates ... Atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes:

• Classical MD : DLPOLY and LAMMPS
• ab-initio MD : CPMD and CP2K
• QM-MM MD : CPMD and CP2K

To prepare the input filles for these calculations is likely to be the key, and most complicated step towards MD simulations. Atomes offers a user-friendly assistant to help and guide the user step by step to achieve this crucial step. Features

• Analysis of 3D atomistic model: neutron and x-rays diffraction, rings statistics, chain statistics, bond order, MSD ...
• Visualization: measures, coordination polyhedras, advanced coloring, advanced design
• Edition: molecular library, crystal builder, cell edition, surface creation and passivation ...
• MD input preparation:
  • Classical MD: DLPOLY and LAMMPS
  • ab-initio MD: CPMD and CP2K
  • QM-MM MD: CPMD and CP2K

Atomes is developed by Dr. Sébastien Le Roux, research engineer for the CNRS

Dr. Sébastien Le Roux works at the Institut de Physique et Chimie des Matériaux de Strasbourg IPCMS

This repository contains the latest version of the .yml file to build the Flatpak, source tarball for the Atomes program ... ... and the script to build / run it !

• If required initialize a git repository:

git init

• Install the shared modules repository (required to use glu):

git submodule add https://github.com/flathub/shared-modules.git

• Build the FLATPAK

flatpak-builder atomes org.flatpak.atomes.yml --force-clean

For the time being atomes flatpak is not in the official repositories, therefore you have to install it manually:

flatpak-builder --user --install --force-clean atomes org.flatpak.atomes.yml

To run it:

flatpak run --socket=session-bus --nosocket=fallback-x11 --socket=x11 org.flatpak.atomes

The documenation is hosted on GitHub here: Atomes documentation