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PhonoMake

Easy and automated workflow for Phonopy calculations using Quantum ESPRESSO.

Workflow

Copy the /pm/ directory into your calculation folder, as well as the scf.slurm file.

We start from a relaxed, geometry optimized structure. To use the PhonoMake scripts, we need to have two keywords on the relax.in input file:

  • !END_HEADER, which goes right after K_POINTS, and before ATOMIC_SPECIES, CELL_PARAMETERS and ATOMIC_POSITIONS
  • !BEGIN_COORDINATES, which goes right after ATOMIC_SPECIES, before CELL_PARAMETERS and ATOMIC_POSITIONS
&CONTROL
&SYSTEM
...
K_POINTS
!END_HEADER
ATOMIC_SPECIES
!BEGIN_COORDINATES
CELL_PARAMETERS
ATOMIC_POSITIONS

Once relaxed, we create a scf.in file by running:

source pm/0_scf.sh

Check that the resulting scf.in file is properly configured, eg. by running the cat scf.in command.

Then, create the 2x2 supercells with

source pm/1_supercells.sh

Or if you want a different supercell, edit the shell command in the pm/1_supercells.sh file.

Next, add the headers (taken from the scf.in file) with

source pm/2_headers.sh

Cat a random supercell to check that everything is ok.

By now, you should have copied the provided scf.slurm file inside your folder. Modify it to your needs, but do not change the JOB_NAME, INPUT_FILE nor OUTPUT_FILE keywords.

To submit the calculations, run

source pm/3_slurms.sh

Finally, once the calculations are done, calculate the forces with

source pm/4_forces.sh

In addition, there are some scripts to fix common errors in the calculations:

  • pm/fix_scancel.sh
  • pm/fix_unfinished.sh
  • pm/fix_yaml.sh

The file EXCLUDE.rsync can be used to exclude files from the manual rsync command, when copying the final results to your local machine, as

rsync -av --exclude-from=EXCLUDE.rsync CLUSTER://scratch/USER/CALCULATION/ .

What are these scripts doing to my beloved files?

pm/0_scf.sh

The pm/0_scf.sh script performs the following tasks.

To create the scf.in file, it first copies the input parameters from relax.in, up to the !BEGIN_COORDINATES keyword, right after ATOMIC_SPECIES and before CELL_PARAMETERS and ATOMIC_POSITIONS.

Then, it copies the CELL_PARAMETERS and ATOMIC_POSITIONS sections from the relax.out file.

Phonopy requires a &SYSTEM celldm(1) flag to specify the lattice parameter in bohr units. Notice that the previous lattice parameter A introduced by cif2cell is in Armstrongs. We can find the proper celldm(1) value in the CELL_PARAMETERS output (alat= 16.7...). The CELL_PARAMETERS line is then left as CELL_PARAMETERS alat, such as follows:

&SYSTEM 
	!A = 8.86370  ! Old lattice parameter used to relax
	celldm(1) = 16.74996545  ! Add this line with the proper alat value
	...

!CELL_PARAMETERS (alat= 16.74996545)  ! Leave only 'alat', as follows:
CELL_PARAMETERS alat
	...

pm/1_supercells.sh

It just creates the supercells, by running the phonopy command:

phonopy --qe -d --dim="2 2 2" -c scf.in

pm/2_headers.sh

It extracts the header from scf.in up to the !END_HEADER keyword, and adds it to the new supercells. It also updates the number of atoms, and comments the old lattice parameter which is no longer needed.

pm/3_slurms.sh

It creates the slurm files for each supercell from the provided scf.slurm template, and sbatch'es the corresponding jobs. You can modify scf.slurm to your needs, just try not to change the JOB_NAME, INPUT_FILE and OUTPUT_FILE keywords.

pm/4_forces.sh

It creates the FORCE_SETS file from the QE output of the supercell calculations, and uses it to create the phonopy.yaml file, by running

phonopy -f supercell-*.out
phonopy --include-all

pm/fix_scancel.sh

Scancels all the jobs with a slurm-JOB_ID file in the folder.

pm/fix_unfinished.sh

Resubmits all unfinished supercells. It asks for a new memory value, in case the previous one was not enough.

pm/fix_yaml.sh

In case Phonopy does not recognise some of your atomic species and changes it by a random one, you can use this to fix the final phonopy.yaml file. However, this is already fixed if your custom atomic species follow a symbol+number format, so luckily you will never have to use this script.