Aluminum Example

Here is the example of Aluminum. Aluminum has FCC lattice with a single atom per primitive unit cell. The following structure.yml file is used in this example:

structure.yml

# CrystalFTG
vec:
  [[ 0.00000000,  1.99208958,  1.99208958],
   [ 1.99208958,  0.00000000,  1.99208958],
   [ 1.99208958,  1.99208958,  0.00000000]]
atoms:
  - Al:
      [[ 0.00000000,  0.00000000,  0.00000000]]
orbitals: p
supa:
  [[ 1,  0,  0],
   [ 0,  1,  0],
   [ 0,  0,  1]]

This example can be found in the examples/compute_id/al/hsbid/order2 directory of the principia-materia-examples repository.

Compute phonon with HS-BID

1. First, we execute the symmetry analysis and create the jobs that need to be calculated with a first principle method. These jobs we be saved in the database database.db.

pm-hsbid --config config.yml --create --save-hsbid

The config.yml file is defined below:

config.yml

structure: '../../data/structure.yml'
supa: |
  4 0 0
  0 4 0
  0 0 4
pg: 'Oh'
order:  2
full_symmetry: True
delta: [ 0.02, 0.03, 0.04]
fdtype: 'c'
root_directory: '.'
database: 'database.db'
db_type: 'sqlite'
db_table: 'bid_phonon'

2. In this example, we use VASP to perform first principle calculations. This we need to create the input files for VASP calculations.

pm-jobs --config config.yml --create --engine vasp --save-config jobs_config.yml \
  --job-config-path ../../data/dft_files --root-directory jobs-to-run

Where ../../data/dft_files stores the template input files including INCAR, POTCAR and KPOINTS. After the input files are generated, we can execute VASP inside the directories of the individual jobs.

3. When the first principle calculations are finished. The following command can parse out the results of the calculations and store them into the database we created.

pm-jobs --config jobs_config.yml --retrieve

The jobs_config.yml file is generated from the previous step.

4. Finally, we run the post-processing step to solve for the irreducible derivatives and compute dynamic tensors and real space force constant tensors.

pm-hsbid --load-hsbid hsbid.hdf5 --config config.yml \
    --post --save-fi --save-ids --save-dts

Plot phonon band structure and DOS

1. First we prepare the configuration file phonon_config.yml to compute phonon band structure and DOS:

phonon_config.yml

band:
  - 0 0 0; 1/2 1/2 0
  - -1/2 1/2 0; 0 0 0
  - 0 0 0; 1/2 0 0
band_label:
  - $\Gamma$
  - X
  - $\Gamma$
  - L
mesh: 20 20 20

2. Then we compute phonon band structure and DOS with pm-phonon-band-dos command.

pm-phonon-band-dos --load-fi fourier_interpolation.hdf5 --config phonon_config.yml \
  --save-band --save-grid --save-dos --save-plot --units THz

3. Finally we can plot the phonon band structure and DOS of Al with the following to get Fig. 15.

pm-plot-band --show band_plot_config.yml

Fig. 15 Phonon band structure and DOS of Al.

Working with Quantum-ESPRESSO

1. If in this case we are working with Quantum-ESPRESSO (QE) instead of VASP, first we will need to create a template QE input file.

   NaCl.scf.in

    &control
       calculation = 'scf'
       tprnfor = .true.
       tstress = .true.
       pseudo_dir = 'pseudo/'
       restart_mode='from_scratch',
       outdir='tmp'
    /
    &system
       ibrav = 0
       nat = 1
       ntyp = 1
       ecutwfc = 60.0
    /
    &electrons
       diagonalization = 'david'
       conv_thr = 1.0d-8
    /
   ATOMIC_SPECIES
    Al  26.981539 Al.pbe-n-kjpaw_psl.1.0.0.UPF
   ATOMIC_POSITIONS crystal
    Al   0.0000000000000000  0.0000000000000000  0.0000000000000000
   CELL_PARAMETERS angstrom
     0.00000000   1.99208958   1.99208958
     1.99208958   0.00000000   1.99208958
     1.99208958   1.99208958   0.00000000
   K_POINTS automatic
     20 20 20 0 0 0
   

2. Then we create the input files for QE calculations. In the case of QE the option --job-config-path expects the path to the above template QE input file (The data in nat, ATOMIC_POSITIONS, CELL_PARAMETERS and K_POINTS of the template file will be replaced with the configurations of the jobs).

pm-jobs --config config.yml --create --engine qe --save-config jobs_config.yml \
  --job-config-path NaCl.scf.in --root-directory jobs-to-run

After the input files are created the static QE calculations can be executed and the remaining steps are the same as before.