Nookiin

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Primitive cell & commensurate supercell generation for multilayer 2D heterostructures

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1. Description

Nookiin is a Python-based software designed to construct primitive and commensurate cells for multilayer 2D heterostructures, with support for arbitrary relative orientations and Bravais lattices.

Main Features

• Primitive Cell Calculation: Identifies the smallest primitive cells for multilayer two-dimensional structures.
  
• Reciprocal Space: Generates reciprocal space representations and theoretical diffraction patterns for the analyzed systems.
  
• Compatibility and Flexibility: Designed to work with complex geometrical configurations in multilayer systems with different Bravais lattices, lattice constants, orientations, and number of layers. Results are compatible with crystallography software that supports POSCAR format files.
  

Key Features

• Supports n-layer twisted or non-twisted structures
  
• Geometrical and symmetry-based algorithms with strain control
  
• Reciprocal space representation and primitive cell reduction
  
• POSCAR export, pattern diffraction module, and reproducibility options

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2. Installation

To get started with Nookiin, follow these instructions:

Importing the software in Python

To use Nookiin in a Python script, import all components from the Nook-iin/src/System.py file.

If you are creating your Python script in the root directory of the Nookiin project, you should use the following line:

python from src.System import * This will load all essential modules needed to construct and analyze 2D multilayer systems.

Detailed Usage Guides

For a complete technical overview and usage instructions, refer to the following files included in this repository: - NookiinOverview.pdf Provides detailed technical documentation and methodology. - Interface_Guide.md Offers a step-by-step explanation of the console-guided interface.

These documents provide in-depth guidance on software functionalities and best practices.

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3. Examples

Explore the examples/ folder for interactive Jupyter Notebooks illustrating Nookiins capabilities: - Full Workflow Example: Step-by-step guide through a typical Nookiin workflow from system definition to reciprocal space visualization and diffraction pattern generation. Ideal as an introduction. - Twisted Bilayer Graphene:Generation of primitive cells for bilayer graphene with incommensurate twist angles: 2.54, 5.63, 14.21, 16.18, and 23.85. - Multilayer Heterostructures: Construction of primitive cells for theoretical multilayer systems (e.g., -GeSe, CdS, hBN, WS, WSe, black phosphorene), with strain constraints and diffraction pattern analysis. - Angular Interval Search: Search for commensurate primitive cells across a range of twist angles in a bilayer system, with controlled strain. Useful for studying moir physics, band modulation, and angle-dependent properties. - Difraction Map: This example demonstrates the capability of Nookiin to generate diffraction maps for multilayer systems. Unlike traditional diffraction patterns that only indicate the location of Bragg peaks, diffraction maps represent the continuous intensity distribution across reciprocal space.

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4. Requirements

• Python 3.6
  
• Required: numpy, matplotlib

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5. Citing Nookiin

If you use Nookiin in your research, please cite it appropriately to support ongoing development and ensure reproducibility.

Recommended citation:

bibtex @software{Nookiin2025, author = {Aguilar-Spndola Ossiel and SnchezOchoa Francisco}, title = {{Nookiin}: Software for the construction and analysis of Van der Waals heterostructures and homostructures in 2D multilayer systems}, version = {v1.9.0}, date = {2025-07-14}, doi = {10.5281/zenodo.14257396}, url = {https://github.com/OssielAg/Nook-iin}, } Suggested sentence for citation in publications: The commensurate primitive cell was generated using the Nookiin code.

For further citation metadata, see the CITATION file.

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6. Contributing

We welcome your contributions!
1. Open an issue or discussion.
2. Fork the repository and create a feature branch.
3. Submit a pull request with clear explanations.

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7. License

This software is distributed under the GNU General Public License (GNU GPL), allowing use, modification, and distribution under the same licensing terms. For more information, see the LICENSE file in this repository.

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8. Publications

This section lists the scientific articles and conference papers directly related to the development, implementation, and capabilities of Nookiin.

• [1] Aguilar-Spindola O., SnchezOchoa F. Nookiin: Software para la construccin de heteroestructuras 3D multicapa, (in preparation).
• [2] AguilarSpndola O., RubioPonce A., LpezUras F., SnchezOchoa F. Electronic and optical properties in helical trilayer graphene under compression, Phys. Chem. Chem. Phys. 27, 1154111550 (2025). DOI:10.1039/D5CP00337G

9. Publications Utilizing Nookiin

Below are peer-reviewed works, theses, or preprints from independent research groups that use Nookiin as part of their methodology. If you used Nookiin in your work, feel free to submit a pull request or contact the authors to have your work listed here.

- [1] AguilarSpndola O., RubioPonce A., LpezUras F., SnchezOchoa F. Electronic and optical properties in helical trilayer graphene under compression, Phys. Chem. Chem. Phys. 27, 1154111550 (2025). DOI:10.1039/D5CP00337G

Contact

Nookiin was created by Ossiel Aguilar-Spndola.
- Contact email: OssielAE@ciencias.unam.mx

- ORCID: 0009-0002-8229-8543

Acknowledgments

• Developed under supervision of Francisco Snchez
  
• Inspired by tools like BandUP, CellMatch, and SuperCell
  

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Espaol

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1. Descripcin

Nookiin es un software en Python para la construccin de celdas primitivas y superceldas conmensurables en heteroestructuras 2D multicapa, permitiendo orientaciones relativas y tipos de red de Bravais arbitrarios.

Caractersticas principales

• Compatible con sistemas multicapa con o sin torsin
  
• Algoritmos geomtricos con control de deformacin
  
• Representacin en espacio recproco y reduccin estructural
  
• Exportacin a POSCAR, clculo de patrones de difraccin y seguimiento reproducible

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2. Instalacin

Para comenzar a utilizar Nookiin, sigue estas instrucciones:

Importar el software en Python

Para utilizar Nookiin en un script de Python, importa todos los componentes desde el archivo Nook-iin/src/System.py. Si ests creando el script de Python en la raz del proyecto Nookiin, debes escribir la siguiente lnea:

python from src.System import * Esto cargar todos los mdulos esenciales para la construccin y anlisis de sistemas multicapa 2D.

Guas de uso detalladas.

Para obtener una explicacin ms completa sobre la metodologa y el funcionamiento del software, consulta los siguientes documentos incluidos en este repositorio: - NookiinOverview.pdf Contiene documentacin tcnica detallada y metodologa. - Guiadeinterfaz.md Explica paso a paso el uso de la interfaz guiada por consola.

Estos documentos proporcionan orientacin detallada sobre las funcionalidades del software y mejores prcticas de uso.

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3. Ejemplos

Consulta la carpeta examples/ para encontrar notebooks interactivos que muestran las capacidades de Nookiin: - Ejemplo Completo de Uso: Gua paso a paso que cubre el flujo completo de trabajo: desde la definicin del sistema hasta la visualizacin del espacio recproco y el patrn de difraccin. Ideal como introduccin. - Grafeno Bicapas Retorcidas: Clculo de celdas primitivas para grafeno bicapa con ngulos de rotacin incomensurables: 2.54, 5.63, 14.21, 16.18 y 23.85. - Heteroestructuras Multicapa: Construccin de celdas primitivas para sistemas tericos multicapa (ej. -GeSe, CdS, hBN, WS, WSe, fosforeno), respetando lmites de deformacin y mostrando el patrn de difraccin. - Bsqueda en Intervalo Angular: Exploracin de celdas primitivas compatibles para un sistema bicapa dentro de un intervalo de ngulos, manteniendo la deformacin bajo un umbral. til en el estudio de moir, diseo de bandas y propiedades angulares. - Mapas de difraccin: Este ejemplo muestra la capacidad de Nookiin para generar mapas de difraccin para sistemas multicapa. A diferencia de los patrones de difraccin tradicionales que solo marcan la posicin de los picos de Bragg, los mapas de difraccin representan la distribucin continua de intensidad en el espacio recproco.

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4. Requisitos

• Python 3.6
  
• Requiere: numpy, matplotlib

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5. Citando a Nookiin

Si utilizas Nookiin en tu trabajo de investigacin, por favor ctalo adecuadamente para apoyar su desarrollo continuo y garantizar la reproducibilidad.

Citacin recomendada:

bibtex @software{Nookiin2025, author = {Aguilar-Spndola Ossiel and SnchezOchoa Francisco}, title = {{Nookiin}: Software for the construction and analysis of Van der Waals heterostructures and homostructures in 2D multilayer systems}, version = {v1.9.0}, date = {2025-07-14}, doi = {10.5281/zenodo.14257396}, url = {https://github.com/OssielAg/Nook-iin}, } Frase sugerida para incluir en publicaciones: La celda primitiva conmensurable fue generada utilizando el cdigo Nookiin.

Para ms informacin sobre la citacin, consulta el archivo CITATION.

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6. Contribucin

Tu participacin es bienvenida:
1. Abre un issue o discusin.
2. Crea una rama en tu fork.
3. Enva un pull request con una descripcin clara.

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7. Licencia

Este software es distribuido bajo la Licencia Pblica General GNU (GNU GPL), lo que permite su uso, modificacin y distribucin bajo las mismas condiciones de licencia. Para ms informacin, consulta el archivo LICENSE en este repositorio.

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8. Publicaciones

Esta seccin enumera los artculos cientficos y contribuciones que presentan el desarrollo, las funcionalidades y las aplicaciones principales de Nookiin.

• [1] Aguilar-Spindola O., SnchezOchoa F. Nookiin: Software para la construccin de heteroestructuras 3D multicapa, (en preparacin).
• [2] AguilarSpndola O., RubioPonce A., LpezUras F., SnchezOchoa F. Electronic and optical properties in helical trilayer graphene under compression, Phys. Chem. Chem. Phys. 27, 1154111550 (2025). DOI:10.1039/D5CP00337G

9. Publicaciones que utilizan Nookiin

A continuacin se enlistan trabajos de investigacin, tesis o preprints revisados por pares que han empleado Nookiin como parte de su metodologa. Si usaste Nookiin en tu trabajo, puedes enviar un pull request o contactar a los autores para agregar tu publicacin a esta seccin.

- [1] AguilarSpndola O., RubioPonce A., LpezUras F., SnchezOchoa F. Electronic and optical properties in helical trilayer graphene under compression, Phys. Chem. Chem. Phys. 27, 1154111550 (2025). DOI:10.1039/D5CP00337G

Contacto

Nookiin fue creado por Ossiel Aguilar-Spndola.
- Correo de contacto: OssielAE@ciencias.unam.mx
- ORCID: 0009-0002-8229-8543

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Crditos

• Desarrollado bajo la supervisin de Francisco Snchez
  
• Inspirado por herramientas como BandUP, CellMatch y SuperCell