Some useful scripts for preparing, running and postprocessing Phonopy calculations using Quantum ESPRESSO on a cluster running Slurm.

Get FORCE_SETS

Inputs for this part are given in get_FORCE_SETS.

First create a header.in file from pwscf.in. Then:

# Create displaced structures (modify command below as needed)
phonopy --qe -d --dim="1 1 1" -c pwscf.in

# Prepare and run SCF calculations
bash run_scfs.sh

# Get FORCE_SETS
python make_fs_command.py > fs_command.sh
bash fs_command.sh

Create modulations along eigenvectors

Inputs for this part are given in modulations.

Eigenvectors at q = (0, 0, 0) may be printed to qpoints.yaml using

phonopy qpoints.conf

Modulations of the original structure along phonon eigenvectors may be created using:

phonopy modulation.conf

as decribed in the Phonopy documentation. To calculate the amplitudes of modulations, such that the average displacement of the atoms in a modulation is equal to avg_displacement (in Bohr), use

python calculate_amplitudes.py <avg_displacement> <band indices>

The unit cell vectors in the resulting MPOSCAR-* files have incorrect units (Phonopy v2.21.2). This is fixed by:

python fix_MPOSCAR.py

The average displacement in MPOSCAR-* files may be checked by (requires ASE):

python check_displacements.py

The same calculation of the modulation amplitudes as described above may be also performed disregarding hydrogen atoms by using calculate_amplitudes_noH.py and check_displacements_noH.py.

Create QE calculations

Inputs for this part are given in calculate_qe.

To create a k-point path for pw.x using SeeK-path from an ASE readable structure, use

python get_pw_kpath.py <structure_filename>

The results will be stored in kpoints.dat, path.pkl and explicit_labels.pkl. To create the ATOMIC COORDINATES and CELL PARAMETERS cards for pw.x from an ASE readable structure, use

python get_pw_structure.py <structure_filename>

The results will be stored in structure_pw.dat.

The previous two scripts are used to create all inputs for an electronic band structure and PDOS calculations at once:

bash create_qe_inputs.sh <structure_filename>

which requires a header_pw.in file.

create_qe_inputs.sh can be run in batch (for multiple structures) using:

bash create_batch_qe_inputs.sh

The structure filenames are searched for using the structure_names variable defined in create_batch_qe_inputs.sh. Inputs for the calculations are created in batch_$structure_filename directories.

A batch of calculations may be run using:

bash batch_sub.sh <submission_script_filename>

batch_sub.sh will enter each subdirectory of current directory named batch_* and run sbatch <submission_script_filename>.

Postprocess QE calculations

Inputs for this part are given in postprocess_qe and calculate_qe.

To plot a band structure, use:

python plot_bands.py

The data required for plotting will be parsed from pwscf.out, pp_bands.out, explicit_labels.pkl and the *dat.gnu band structure file generated by QE. The image will be saved to bands.png and all the data required for replotting will be saved to bands.pkl.

A batch of Python calculations may be run using:

bash batch_python.sh <python_script_filename>

batch_python.sh will enter each subdirectory of current directory named batch_* and run python <python_script_filename>.

The projected density of states (PDOS) for each of the atomic species defined in the ATOMIC_SPECIES card in pwscf.in may be calculated using:

source sumpdos.sh

which may also be run in batch using

source batch_bash.sh <bash_script_filename>