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

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 edit the Makefile and change:

1. Edit the file configure.ac

And change:

PKG_CHECK_MODULES(GTK, [gtk+-3.0 >= 3.16])
dnl PKG_CHECK_MODULES(GTK, [gtk4 >= 4.60])

To:

dnl PKG_CHECK_MODULES(GTK, [gtk+-3.0 >= 3.16])
PKG_CHECK_MODULES(GTK, [gtk4 >= 4.60])

1. Edit the file src/Makefile.am

And change:

-DGTK3

To:

-DGTK4

1. Update the configure script:

rm -f aclocal.m4
rm -rf autom4te.cache 
rm -f configure~
aclocal
autoconf
automake --add-missing

1. Build Atomes

./configure
make

Here are some issues with GTK4 that cannot be sovled for the time being: 1. No way to use Pango markups in menus 2. Add widgets to menus is impossible, ex: color selections 3. Selection in tables is not working properly (see the Measures dialog: wrong lines are picked) 4. No way to moves lines in tables (curves and crystal builder)

Issues 1) and 2) are the most critical so far since Atomes menus are dynamical and cannot be created by reading a basic XML file.

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. Edit the file src/Makefile.am

And remove all:

-DOPENMP -fopenmp

1. Update the configure script:

rm -f aclocal.m4
rm -rf autom4te.cache 
rm -f configure~
aclocal
autoconf
automake --add-missing

1. Build Atomes

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