Strained lattice vectors generator for SIESTA - Uniaxial strain in 2D materials - Set Up and Post-Processing

This dataset contains a Python script (Strained_Vec_Generator_uniax.py) and an example demonstrating its use for applying uniaxial strain in both the x and y directions to a graphene structure (a 2D material in the xy-plane). Use the siesta.STRUCT_OUT file to see how the script works.

It also includes a Python script for post-processing the data generated by this procedure (you will need to run the 0% strain case beforehand to obtain the .STRUCT_OUT file from SIESTA, which is provided here as an example). You can use the post-processing script with the X and Y folders provided in the Post-processing.zip file as an example, used for a BCN material.

To quickly see how the Python script works, place siesta.STRUCT_OUT and Strained_Vec_Generator_uniax.py in the same folder and run the following command in the linux terminal (for Python 3): $ python3 Strained_Vec_Generator_uniax.py
This will generate strained siesta.fdf files with strained lattice vectors (1-30%) for X and Y directions.
Use the copy.tcl script to copy the run.fdf and C.psf files inside X or Y. Modify the run.fdf in the %block GeometryConstraints before using the copy script. More details in steps to reproduce and in the readme.txt file.

Note: If the material of interest has a non-rectangular unit cell, you can extend the original structure and extract an appropriate rectangular supercell from it. Then, follow the same procedure described in steps to reproduce. Non-rectangular cells don't have the orthogonal X and Y directions as assumed here, and for them it is not trivial to clearly define something like X and Y directions for strain.

This approach is ideal if the structure is stored in a separate .fdf file. In the example, the SIESTA run parameters are in the file run.fdf, while the structure information is in siesta.fdf (generated after you run the Strained_Vec_Generator_uniax.py script), which is included in run.fdf via
%include siesta.fdf. You may rename these files as desired (e.g., parameters.fdf and structure.fdf), provided that you update the system_label in the script.

For the post-processing part, a script named 2Strain_post_processing.py is provided. After you run all the calculations, use it to output the results automatically. You can extract the .zip file and run $ python3 2Strain_post_processing.py .

This methodology greatly simplifies the investigation of mechanical properties of 2D materials using SIESTA.
See the readme.txt file for more details.

Associated PhD Thesis available at https://repositorio.ufrn.br/home.
Tittle: Structural, optical, electronic and mechanical properties of two-dimensional BxCyNz based materials.