atomes

atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. Atoms 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 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

RPM building

This repository contains the latest version of the .spec file, source tarball and source RPM for the atomes program ... ... and the script to build it !

You will find 2 folders:

• 'Fedora' : contains the spec file, and RPMs, with directives specific to the Fedora Linux distribution

This package uses the following libs distributed along with Fedora:

- libavcodec-free(-devel)
- libavformat-free(-devel)
- libavutil-free(-devel)
- libswscale-free(-devel)

In that case the encoding of videos using proprietary codecs is disabled:

- MP4
- H264
- Flash

It is possible to get it back by installing the ffmpeg-libs package from RPM Fusion

• 'RPM-fusion' : contains the spec file, and RPMS, with more general directives

This package uses the following libs distributed by RPM Fusion

- ffmpeg-devel (to build atomes)
- ffmpeg-libs (at runtime)

Build instructions

To build atomes:

./configure

Followed by:

make

Build options

Building the GTK4 version of atomes

atomes uses the GTK lib for the GUI, by default GTK3 is used, however it is possible to build the GTK4 version (beta).

To do that:

1. Configure using the --with-gtk= flag:

./configure --with-gtk=4

Note the default flag is: --with-gtk=3

2. Build atomes

make

Here are some issues with GTK4 that cannot be sovled for the time being:

1. No way to attach widget to menu items not in the top level of the menu (https://gitlab.gnome.org/GNOME/gtk/-/issues/5955)

Building the serial version of atomes

By default atomes uses OpenMP to parallelize several calculations over the CPU cores. It is possible to turn this off, and to build a serial version of atomes, to do that:

1. Configure using the --disable-openmp flag:

./configure --disable-openmp

2. Build atomes

make

Install atomes

make install

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

Documentation

The documenation is hosted on GitHub here: atomes documentation

Tutorials

Tutorial are regrouped and hosted on GitHub here: atomes tutorials