Atom Architect

Purpose

Atom Architect is a VASP visualization and structure building tool. Its unique feature is that atom placement is conducted in a relative fashion, i.e. with respect to the existing atomic structure. This is especially useful for catalysis purposes where atoms are typically placed at e.g. bridge, threefold or fourfold sites.

Downloads

Latest installer for Window: here

Compilation

Windows

Compilation for Windows is most easily done by installing Qt Creator and loading the project file atom-architect.pro.

Linux Debian / Ubuntu

Please note that Atom Architect is only tested for Debian 12 and Ubuntu 22.04. For other distributions, you are on your own.

Qt6

Start by installing all the required dependencies

sudo apt update && sudo apt install -y \
qt6-tools-dev \
qt6-base-dev \
libqt6charts6-dev \
libqt6widgets6 \
libqt6gui6 \
libqt6opengl6-dev \
libgl1-mesa-dev \
build-essential \
cmake

After having cloned this repository and starting at its root folder, execute

mkdir build
cd build
cmake ../
make -j

This will generate the compilation scripts and compile Atom Architect. You can use Atom Architect by running ./atom_architect in your build folder. If you wish to install Atom Architect on your system, you can run in your build folder the following command.

sudo cp -v ./atom_architect /usr/local/bin/atom_architect

Qt5

Start by installing all the required dependencies

sudo apt update && sudo apt install -y \
qtbase5-dev \
libqt5charts5-dev \
libgl1-mesa-dev \
build-essential \
cmake

After having cloned this repository and starting at its root folder, run a patch file to change from Qt6 to Qt5.

patch -p1 CMakeLists.txt < qt5.patch

Create a new build folder, go to this folder, create the compilation and start the compilation.

mkdir build
cd build
cmake ../
make -j

This will generate the compilation scripts and compile Atom Architect. You can use Atom Architect by running ./atom_architect in your build folder. If you wish to install Atom Architect on your system, you can run in your build folder the following command.

sudo cp -v ./atom_architect /usr/local/bin/atom_architect

Snellius

To compile for the Snellius infrastructure, it is recommended to use the Qt5 toolchain.

module load 2023 Qt5/5.15.10-GCCcore-12.3.0

and apply the patch

patch -p1 CMakeLists.txt < qt5.patch

Next, compilation is fairly straightforward.

mkdir build
cd build
cmake ../
make -j

Dependencies

Atom Architect depends on GLM and Eigen3. Both are header-only C++ libraries and are for convenience purposes added to this repository. This implies that compilation of Atom Architect will not use your system-installed version of GLM and Eigen3, but use the one provided in this repository.

Common problems

I have troubles running Atom Architect remotely via MobaXterm.

Try to enable direct rendering by setting the following environmental variable:

export LIBGL_ALWAYS_INDIRECT=0