Quasi-Harmonic Approximation (QHA) workflow

Overview

This guide outlines the steps required to estimate temperature-dependent mechanical properties of periodic systems using the Quasi-Harmonic Approximation (QHA) method. The workflow involves structure relaxation, deformation, force constant extraction, and processing of thermal properties.

Prerequisites

• You have to have VASP license.
• Required packages
  • conda environment - call it phonon.
  • Install phonopy from Atsushi Togo.
  • Pymatgen, ASE and Pandas
• Install and activate the phonon environment:

  conda activate phonon

• Ensure VASP is installed and properly configured with mpirun.
• Set the curresponding paths and libraries in sh files with VASP run.
• Python scripts (preprocess.py, postprocess.py, QHA_phonopy_process.py, QHA_manual_process.py, QHA_elastic_constants.py) should be in the working directory.

Workflow

Step 1: Relax Input Structure

relax input structure under vasp_input/GO/
cp vasp_input/GO/CONTCAR POSCAR_unitcell

Step 2: Generate Deformed Structures

python preprocess.py

• Creates bi-axial deformation structures.
• Deformation magnitude and direction can be controlled in preprocess.py.

Step 3: Static Calculations

sh exec_vasp_run_for_static.sh

• Creates deformed_structures/static_run/ and runs static calculations.

Step 4: DFPT Calculations for Vibrational Energy

sh exec_vasp_run_for_DFPT.sh

• Creates a DFPT supercell and runs DFPT calculations in VASP.

Step 5: Extract Force Constants

sh post_process_DFPT.sh

• Collects force constants from vasprun.xml.
• Generates thermal_properties.yaml.

Step 6: Generate Energy-Volume Data

python postprocess.py

• Creates QHA_phonpy_process/e-v.dat.

Step 7: Process Thermal Properties from phonopy

python QHA_phonopy_process.py

• Generates thermal output files under QHA_phonopy_results/.

Step 8: Compute temperature dependant Lattice Parameter

python QHA_manual_process.py

• Computes lattice constant's variations with temperature.

Step 9: Compute temperature dependant Elastic constants

python QHA_elastic_constants.py

• Computes elastic constant's variations with temperature.

Output Files

• thermal_properties.yaml: Contains extracted force constants.
• QHA_phonopy_results/: Stores processed thermal properties output from Phonopy.
• QHA_manual_results/: Stores processed thermal properties output such as strain-volume, elastic constants, lattice parameters etc..
• QHA_phonpy_process/e-v.dat: Energy-volume relationship data.
• Computed lattice and elastic property variations.

Notes

• Modify preprocess.py to control deformation parameters.
• Ensure VASP is configured correctly for DFPT calculations.

License

This guide is intended for research purposes. Use at your own discretion.