Models: Sqw: import from PhonoPy to be able to use PhononDB data base

[farhi]

not so easy. Requires to handle spacegroups in ASE: https://github.com/McStasMcXtrace/iFit/issues/34

[farhi]

Spacegroups are now fully supported. See https://github.com/McStasMcXtrace/iFit/commit/2d5d63b1a21cd21b4a655e1531c6e82d3fa473ac Commit https://github.com/McStasMcXtrace/iFit/commit/0a73001124e3433506315f1551a319d74c655a36 allows to use PhonoPy methods. In principle, we can then import FORCE_SET and reformat it for ASE, as done in ifit.py

[farhi]

PhonoPy/phonopy/file_IO.py: _get_set_of_force FORCE_SETS files are stored in a number of directories together with POSCAR-unitcell files. The FORCE_SETS file contains entries with [displacements, forces] which are then stored into a dataset["first_atoms"] == {"displacement","forces"}

Importing PhonoPy results then requires to:

• provide a set of directory names
• read the POSCAR-unitcell with ASE.io
• read the FORCE_SETS with phonopy.file_IO.parse_FORCE_SETS(filename)
• re-generate the PhonoPy object with set_displacement_dataset
• proceed with the ifit.phonon_run_pnonopy to convert to an ASE.Phonon object (C_N)

[farhi]

Look at https://github.com/atztogo/phonopy/blob/master/scripts/phonopy line 409- where PhonoPy reads FORCE_SET and creates a PhonoPy object. Then we can stick to the existing procedure in iFit sqw_phonons ifit.py

[farhi]

from a directory with ONLY FORCE_SETS, we can compute the DOS:

• create a mesh.conf file with:

  ATOM_NAME = <elements, e.g. Si O>
  DIM = <supercell, e.g. 3 3 2>
  MP = 8 8 8

• run phonopy -p mesh.conf (-p == 'plot')
• this creates phonopy.yaml, mesh.yaml, total_dos.dat, POSCAR

[farhi]

the above procedure calls in order: with run_mode == 'mesh'

• 146: run_mode == 'mesh':
• 345: unitcell, optional_structure_file_information = read_crystal_structure() -> Atoms(VASP)
• 409: else: # Read FORCE_SETS, FORCE_CONSTANTS, or force_constants.hdf5
• 448: force_sets = file_IO.parse_FORCE_SETS()
• 463: phonon = Phonopy(unitcell,...)
• 491: phonon.get_symmetry().get_international_table()
• 574: phonon.set_displacement_dataset(force_sets)
• 585: phonon.produce_force_constants(calculate_full_force_constants=False,
• 739: settings.get_mesh()
• phonon.set_mesh()
• 914: phonon.set_total_DOS(

[farhi]

Done with commit https://github.com/McStasMcXtrace/iFit/commit/d964ae4363cf59265d5366939503a02bd9f3819d