Moiré Phonon Analysis

This repository contains three scripts to analyze the phonon band structure of MoS2 1D moiré patterns. The scripts are designed to work with MPI for parallel processing.

Scripts

1. 1_generate_phonopy_yaml.py

   • Generates a Phonopy YAML file with displacement information from a relaxed atomic structure.

2. 2_generate_forces.py

   • Uses MPI to generate forces for each displacement structure using Allegro or LAMMPS calculators.

3. 3_analyze_structure.py

   • Analyzes the structure to produce and plot the unfolded phonon band structure based on the forces and the Phonopy YAML file.

Setup

Prerequisites

• Python 3.x
• ASE
• Phonopy
• mpi4py
• numpy
• matplotlib

Installation

1. Clone the repository:

   git clone https://github.com/jdgeorga/phonon_unfolding.git
   cd phonon_unfolding

2. Install the required Python packages:

   pip install numpy ase phonopy mpi4py matplotlib

Files and Directories

• relaxed_structure.xyz: Relaxed supercell structure file.
• primitive_unitcell.xyz: Primitive unit cell structure file.
• intralayer_allegro.pth: Intralayer model file for Allegro calculator.
• interlayer_allegro.pth: Interlayer model file for Allegro calculator.

Usage

1. Generate Phonopy YAML File

This script generates a Phonopy YAML file with displacement information.

python 1_generate_phonopy_yaml.py

Expected Output:

• phonon_with_displacements.yaml: YAML file containing Phonopy displacement information.
• Printed displacements.

2. Generate Forces

This script uses MPI to generate forces for each displacement structure. Run it using the srun command with the desired number of processes.

srun -N 1 -n (num processes) python 2_generate_forces.py

Example:

srun -N 1 -n 4 python 2_generate_forces.py

Expected Output:

• disp_forces.npy: Numpy file containing displacement forces.

3. Analyze Structure

This script analyzes the structure to produce and plot the unfolded phonon band structure.

python 3_analyze_structure.py

Expected Output:

• folded_phonon_band_structure.png: Plot folded supercell phonon band structure.
• unfold_phonon_band_structure.png: Plot of the unfolded phonon band structure.
• Path_on_Wigner_Seitz_cells.png: Plot of the high-symmetry paths.
• Printed steps during the analysis process.

Description of Each Script

1_generate_phonopy_yaml.py

This script generates a Phonopy YAML file with displacement information from a relaxed atomic structure.

Arguments:

• input_file: Path to the input file containing the relaxed atomic structure.
• supercell_dim: List of three integers representing the supercell dimensions.

2_generate_forces.py

This script uses MPI to generate forces for each displacement structure using Allegro or LAMMPS calculators.

Arguments:

• input_file: Path to the input file containing the relaxed atomic structure.
• yaml_file: Path to the Phonopy YAML file with displacements.
• layer_symbols: List of layer symbols.
• calculator_type: Type of calculator to use (allegro or lammps).
• out_file: Path to the output file to save the forces.
• intralayer_model: Path to the intralayer model file (only for Allegro).
• interlayer_model: Path to the interlayer model file (only for Allegro).

3_analyze_structure.py

This script analyzes the structure to produce and plot the unfolded phonon band structure based on the forces and the Phonopy YAML file.

Arguments:

• input_file: Path to the input file containing the relaxed atomic structure.
• disp_forces_file: Path to the input file containing the displacement forces (numpy format).
• phonopy_yaml_file: Path to the input file containing the Phonopy YAML data.
• primitive_file: Path to the input file containing the primitive unit cell structure.
• atom_layers: List of integers indicating the layer assignment of each atom.

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