atorvi 0.1.1

Package for visualizing atomic orbitals

atorvi - ATomic ORbitals VIsualization

atorvi is a Python package for visualizing individual atomic orbitals and their various linear combinations. The library generates requested atomic orbitals on a 3D mesh and exports them, along with the inputted crystal structure (molecule or periodic crystal), into a file in XCrysDen .xsf format.

The resulting .xsf file can be opened and visualized using your favorite visualization software, such as XCrysDen, VESTA or VMD.

Installation

To install atorvi, you can use pip:

pip install atorvi

Features

• Atomic Orbitals Generation: Create atomic orbitals at a specific position in space or at a designated atom/element within a crystal structure.

• Flexible Structure Input: Input crystal structures either manually, atom-by-atom, or directly from standard file formats such as POSCAR, XSF, CIF, and more. The integration with the pymatgen package simplifies structure handling.

• Orbital Hybridization: Implement orbital hybridization by mixing different orbitals with custom coefficients, allowing for the exploration of complex bonding interactions.

• Orbital Squared Moduli: Generate squared moduli of orbitals, providing insight into their spatial distribution and probability densities.

Examples of orbitals generated with atorvi: could be found in examples folder.

Quick start

The full user manual is available in docs/atorvi_manual.md.

atorvi can be used in two modes: package mode (for scripting and notebooks) and CLI interactive mode (only basic functionality is available).

1.Package Mode

In your Python script or Jupyter notebook, you can generate and visualize atomic orbitals with the following example:

import atorvi

# Example: visualize a d_{3z^2-r^2} orbital for an Ni atom (Z = 28)
outfile = atorvi.OrbitalFile("Ni_orbital.xsf")

outfile.add_orbital("d_{3z^2-r^2}", position=[0, 0, 0], znumber=28)

outfile.write_data()

Then just open the Ni_orbital.xsf file in your favorite visualization software.

The orbitals available for generation are: $$s$$ $$p_z, p_x, p_y$$ $$d_{3z^2-r^2}, d_{xz}, d_{yz}, d_{xy}, d_{x^2-y^2} $$ $$f_{z^3}, f_{xz^2}, f_{yz^2}, f_{xyz}, f_{z(x^2-y^2)}, f_{x(x^2-3y^2)}, f_{y(3x^2-y^2)}$$

print(atorvi.supported_orbitals)

['s', 
'p_z', 'p_x', 'p_y', 
'd_{3z^2-r^2}', 'd_{xz}', 'd_{yz}', 'd_{xy}', 'd_{x^2-y^2}', 
'f_{z^3}', 'f_{xz^2}', 'f_{yz^2}', 'f_{xyz}', 'f_{z(x^2-y^2)}', 'f_{x(x^2-3y^2)}', 'f_{y(3x^2-y^2)}']

2. CLI Interactive Mode

atorvi also offers an interactive mode via the command line interface (CLI). You can simply run the script directly in a terminal:

atorvi_cli

Follow the prompts to generate orbitals and export them to XCrysDen-compatible formats.

Once the file is generated, you can open it using visualization tools like XCrysDen or VESTA.

Author

atorvi is developed and maintained by Dmitry Korotin. Contributions, suggestions, and feedback are welcome to help improve the project.

License

atorvi is released under the MIT License. You are free to use, modify, and distribute the software, provided that the original copyright and permission notice are included in all copies or substantial portions of the software.

The author kindly asks that you cite this GitHub repository github.com/dkorotin/atorvi and the related paper (link will be available soon) in any publications that use images or data generated with the atorvi package.

For more details, refer to the full MIT License.