Follow the repo for pictures of printed structure, many to come !

CrystalPrint is a Python package that converts CIF (Crystallographic Information File) structures into printable 3D objects. It generates a mesh that accurately represents atoms and bonds, ensuring a single manifold without holes or discontinuities. In contrast, software like VESTA often produces output files that may not guarantee this level of integrity.

Gallery

Project & Team

This repository is part of a project led by Prof. Miguel Marques at Ruhr University Bochum, with contributions from Haichen Wang, Théo Cavignon, Antoine Loew and Pierre-Paul De Breuck. The project focuses on showcasing a variety of structures, which can be explored in the Gallery above or imgs/ directory.

Features

The tool converts an XYZ file into an STL file, generating a 3D model with the following features:

Spheres are placed at atomic coordinates to represent atoms. Cylinders are generated as bonds between atoms that are within the distance specified by the --cutoff parameter. A CIF file can also be provided, which will be automatically converted using the unit cell as representation.

In progress

This package is an early start, much to come:

• Adaptive atomic radii on elements
• fixing scale (2A=1cm)
• Adding color information
• Better bond detection

Installation

From PyPI (coming soon)

Once CrystalPrint is available on PyPI, you can install it with:

pip install crystalprint

From Source

You can also install the package directly from the source by following these steps:

1. Clone the repository:

   git clone https://github.com/ppdebreuck/crystalprint.git
   cd crystalprint

2. Install the package with:

   pip install .

Requirements

• Python 3.x
• numpy
• trimesh
• pymatgen
• pyglet (version < 2)

These dependencies will be automatically installed when you install the package.

Usage

After installation, you can use CrystalPrint directly from the command line to generate 3D meshes from XYZ or CIF files.

Command Line Arguments

usage: crystalprint [-h] [--cutoff BOND_CUTOFF] [--atom_radius ATOM_RADIUS]
                    [--cylinder_diam CYLINDER_DIAM] [--out_dir OUT_DIR]
                    file_path

Arguments:

• file_path: Path to the input XYZ or CIF file.
• --bond_cutoff: Bond cutoff distance (default: 2.9 A).
• --atom_radius: Radius of atoms (default: 0.65 A).
• --cylinder_diam: Diameter of the bond cylinder (default: 0.3 A).
• --out_dir: Directory to save the output STL files (default: current directory).

Example

To generate a 3D object from a CIF file:

python -m crystalprint Fe.cif

or from XYZ:

python -m crystalprint C60.xyz

or if you want to tune the parameters:

python -m crystalprint your_structure.cif --cutoff 2.8 --atom_radius 0.6 --cylinder_diam 0.4 --out_dir ./output

This will generate three STL files:

• your_structure.stl: Basic mesh with atoms and bonds.
• your_structure_repeated_2d.stl: 2D repeated mesh.
• your_structure_repeated_3d.stl: 3D repeated mesh.

You can adjust the bond cutoff, atom radius, and cylinder diameter to match your needs.

Example Output

Mesh generated from the conventional Fe CIF file:

Contributing

This is ongoing work, and any contribution is welcome ! So feel free to fork the repository and submit a pull request, even small ones !

Issues

If you encounter any issues or have suggestions for improvements, please open an issue in the GitHub repository.

License

CrystalPrint is licensed under the MIT License. See the LICENSE file for more details.

Author

CrystalPrint is developed by Pierre-Paul De Breuck. You can reach me at [email protected].