Phonopy workchainΒΆ
Phonopy workchain is used to calculate force constants. Phonons and some phonon derived properties can be optionally calculated. The workchain I/O design is not sophisticated and can be changed in the future.
The current usage is explained using python scripts found in the
examples directory. The first script is used to launch an
aiida-phonopy calculation of rocksalt NaCl.
from phonopy.interface.vasp import read_vasp_from_strings
from aiida.plugins import DataFactory, WorkflowFactory
from aiida.engine import submit
from aiida_phonopy.common.utils import phonopy_atoms_to_structure
from aiida.orm import Float, Bool, Str
from aiida import load_profile
load_profile()
def launch_aiida():
Dict = DataFactory('dict')
unitcell_str = """ Na Cl
1.00000000000000
5.6903014761756712 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.6903014761756712 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6903014761756712
4 4
Direct
0.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.5000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000"""
cell = read_vasp_from_strings(unitcell_str)
structure = phonopy_atoms_to_structure(cell)
base_incar_dict = {
'PREC': 'Accurate',
'IBRION': -1,
'EDIFF': 1e-8,
'NELMIN': 5,
'NELM': 100,
'ENCUT': 520,
'IALGO': 38,
'ISMEAR': 0,
'SIGMA': 0.01,
'LREAL': False,
'lcharg': False,
'lwave': False,
}
base_config = {'code_string': 'vasp544mpi@nancy',
'kpoints_density': 0.5, # k-point density,
'potential_family': 'PBE.54',
'potential_mapping': {'Na': 'Na_pv', 'Cl': 'Cl'},
'options': {'resources': {'num_machines': 1,
'parallel_env': 'mpi*',
'tot_num_mpiprocs': 24},
'max_wallclock_seconds': 3600 * 10}}
base_parser_settings = {'add_energies': True,
'add_forces': True,
'add_stress': True}
forces_config = base_config.copy()
forces_config.update({'parser_settings': base_parser_settings,
'parameters': base_incar_dict})
nac_config = base_config.copy()
nac_parser_settings = {'add_born_charges': True,
'add_dielectrics': True}
nac_parser_settings.update(base_parser_settings)
nac_incar_dict = {'lepsilon': True}
nac_incar_dict.update(base_incar_dict)
nac_config.update({'parser_settings': nac_parser_settings,
'parameters': nac_incar_dict})
PhononPhonopy = WorkflowFactory('phonopy.phonopy')
builder = PhononPhonopy.get_builder()
builder.structure = structure
builder.calculator_settings = Dict(dict={'forces': forces_config,
'nac': nac_config})
builder.run_phonopy = Bool(True)
builder.remote_phonopy = Bool(True)
builder.code_string = Str('phonopy@nancy')
builder.phonon_settings = Dict(
dict={'mesh': 50.0,
'supercell_matrix': [2, 2, 2],
'distance': 0.01,
'is_nac': True})
builder.symmetry_tolerance = Float(1e-5)
builder.options = Dict(dict=base_config['options'])
builder.metadata.label = "NaCl 2x2x2 phonon example"
builder.metadata.description = "NaCl 2x2x2 phonon example"
future = submit(builder)
print(future)
print('Running workchain with pk={}'.format(future.pk))
if __name__ == '__main__':
launch_aiida()
The following is the script to extract data necessary to run phonopy and dump the data in the phonopy.yaml format.
import sys
from phonopy import Phonopy
from aiida_phonopy.common.utils import phonopy_atoms_from_structure
from aiida.orm import load_node
from aiida import load_profile
load_profile()
def dump_phonopy(pk):
n = load_node(pk)
unitcell = phonopy_atoms_from_structure(n.inputs.structure)
smat = n.outputs.phonon_setting_info['supercell_matrix']
ph = Phonopy(unitcell, smat, primitive_matrix='auto')
force_sets = n.outputs.force_sets.get_array('force_sets')
dataset = n.outputs.phonon_setting_info['displacement_dataset']
ph.dataset = dataset
ph.forces = force_sets
if 'nac_params' in n.outputs:
borns = n.outputs.nac_params.get_array('born_charges')
epsilon = n.outputs.nac_params.get_array('epsilon')
nac_params = {'born': borns,
'factor': 14.399652,
'dielectric': epsilon}
ph.nac_params = nac_params
# phonopy-params.yaml is written out.
ph.save()
print("phonopy_params.yaml was made for PK=%d" % pk)
if __name__ == '__main__':
# PK as the first argument
dump_phonopy(int(sys.argv[1]))