atomes

atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. atomes is a toolbox developed to analyze, to visualize and to create/edit 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 models: neutrons and x-rays diffraction, ring 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

Who's behind atomes

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

APPIMAGE

Building the Appimage

• Download the latest version of atomes sources

VERSION="1.3.1"
wget https://github.com/Slookeur/atomes-GNU/archive/refs/tags/v$VERSION.tar.gz

• Install the appimage-builder tool

https://appimage-builder.readthedocs.io/en/latest/intro/install.html

• Build atomes using the sources:

tar -jxf v*.tar.bz2
cd ./atomes-*
./configure --prefix=/usr

• Create an AppDir directory

mkdir AppDir

• Install the newly built atomes package in the new AppDir directory

make install DESTDIR=$PWD"/AppDir"

• Download the recipies to build atomes appimage:

wget https://github.com/Slookeur/atomes-appimage-build/blob/main/atomes-AppImageBuilder.yml

• Finally build the appimage using the appimage-builder tool

appimage-builder --recipe ./atomes-AppImageBuilder.yml

Running the Appimage

Simply double click on the appimage

Documentation

The documentation is hosted on GitHub here: atomes documentation

Developer contribution guidelines are hosted on GitHub here: atomes developer guidelines

Developer documentation is hosted on GitHub here: atomes developer documenation

Tutorials

Tutorial are regrouped and hosted on GitHub here: atomes tutorials