Phono3py workchains
Contents
Phono3py workchains¶
Before reading this section, it is recommended to read Phonopy workchain
and try PhonopyWorkChainbecause how to usePhono3pyWorkChainis similar to
that ofPhonopyWorkChainand it is assumed you have already
experiencedPhonopyWorkChain.
Phono3py workchain is used to calculate phonon-phonon interaction properties. There are three phono3py workchains:
Phono3pyWorkChain: Calculate supercell forces, parameters for non-analytical term correction (NAC), and optionally run the following two workchains.Phono3pyFCWorkChain: Calculate force constants from supercell forces and displacements.Phono3pyLTCWorkChain: Calculate lattice thermal conductivity from force constants and NAC parameters.
Phonon-phonon interaction calculation settings¶
Supported parameters for phonon calculation are
supercell_matrix: Dimension of supercell used by phono3py.phonon_supercell_matrix(optional): Dimension of supercell used to calculate harmonic phonon by phono3py.distance(optional): Atomic displacement distance.mesh(optional): Sampling mesh used in phonon projected DOS and thermal property calculations.fc_calculator(optional): Only “alm” is supported.
Although random displacement setting (number_of_snapshots) is not directory
supported by Phono3pyWorkChain, supercell forces and displacements calculated
using random displacement setting by PhonopyWorkChain can be used as inputs of
Phono3pyFCWorkChain.
Detailed explanations about the parameters are refereed to the phono3py documentation.
An example of settings is:
phonopy_settings = {
"mesh": 50.0,
"supercell_matrix": [2, 2, 2],
"phonon_supercell_matrix": [4, 4, 4]
"distance": 0.03,
}
The displacement information is stored in displacement_dataset. With setting
phonon_supercell_matrix, the displacement information is stored in
phonon_displacement_dataset.
Initialization¶
At the initialization step, supercells with displacements are created. Data nodes of
displacement_datasetandphonon_displacement_dataset(optional).phonon_setting_info
are created and attached to outputs port namespace. Input structure is
considered as a conventional unit cell, which can be obtained using, e.g., using
spglib. The primitive cell is found automatically and the transformation matrix
from the input structure to the primitive cell is found in
phonon_setting_info as primitive_matrix.
Calculations launched from Phono3py workchain¶
Supercell forces and NAC parameters
Similar to
PhonopyWorkChain(Calculations launched from Phonopy workchain),force_setsnac_params(optional)
are obtained. In addition,
phonon_force_sets(optional)
is obtained when
phonon_supercell_matrixis set.Force constants (when
run_fc = Bool(True))fc2:SingleFileDataoffc2.hdf5.fc3:SingleFileDataoffc3.hdf5.
Lattice thermal conductivity calculation (when
run_ltc = Bool(True))ltc:SingleFileDataofkappa-xxx.hdf5.
Usage and examples¶
The basic usage is explained as a python script shown below.
launch_phono3py_with_vasp: Run phono3py calculation using phono3py & VASP.launch_phono3py_fc: Run phono3py force constants calculation.launch_phono3py_ltc: Run phono3py lattice thermal conductivity calculation.
"""Examples to submit Phono3pyWorkChain, Phono3pyFCWorkChain, Phono3pyLTCWorkChain."""
from aiida import load_profile
from aiida.engine import submit
from aiida.orm import Bool, Code, Dict, load_group, load_node
from aiida.plugins import WorkflowFactory
from aiida_phonoxpy.utils.utils import phonopy_atoms_to_structure
from phonopy.interface.vasp import read_vasp_from_strings
load_profile()
def launch_phonop3y_fc():
"""Submit phono3py force constants calculation."""
# Supercell force calculations with random displacements.
n222 = load_node(220964) # PhonopyWorkchain with 2x2x2 supercell (200 supercells)
n444 = load_node(220888) # PhonopyWorkchain with 4x4x4 supercell (4 supercells)
#
# Settings for phono3py calculation
#
phono3py_settings = {
"supercell_matrix": n222.outputs.phonon_setting_info["supercell_matrix"],
"phonon_supercell_matrix": n444.outputs.phonon_setting_info["supercell_matrix"],
}
phono3py_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
phono3py_metadata = {
"options": {
"resources": phono3py_resources,
"max_wallclock_seconds": 3600 * 10,
},
}
#
# Phono3pyFCWorkChain inputs
#
label = "NaCl phono3py force constants calculation (222-444)"
inputs = {
"code": Code.get_from_string("phono3py@nancy"),
"structure": n222.inputs.structure,
"settings": Dict(dict=phono3py_settings),
"force_sets": n222.outputs.force_sets,
"displacements": n222.outputs.displacements,
"phonon_force_sets": n444.outputs.force_sets,
"phonon_displacements": n444.outputs.displacements,
"metadata": {
"label": label,
"description": label,
},
"phono3py": {"metadata": phono3py_metadata},
}
g = load_group("NaCl-222-444")
Phono3pyFCWorkChain = WorkflowFactory("phonoxpy.phono3py_fc")
node = submit(Phono3pyFCWorkChain, **inputs)
print(node)
g.add_nodes(node)
def launch_phonop3y_ltc():
"""Submit phono3py force constants calculation."""
n_fc = load_node(257252) # Phono3pyFCWorkchain
n_nac = load_node(255135) # NacParamsWorkChain
#
# Settings for phono3py calculation
#
phono3py_settings = {
"supercell_matrix": n_fc.outputs.phonon_setting_info["supercell_matrix"],
"phonon_supercell_matrix": n_fc.outputs.phonon_setting_info[
"phonon_supercell_matrix"
],
"mesh": 100,
}
phono3py_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
phono3py_metadata = {
"options": {
"resources": phono3py_resources,
"max_wallclock_seconds": 3600 * 10,
},
}
#
# Phono3pyFCWorkChain inputs
#
label = "NaCl phono3py lattice thermal conductivity calculation (222-444)"
inputs = {
"code": Code.get_from_string("phono3py@nancy"),
"structure": n_fc.inputs.structure,
"settings": Dict(dict=phono3py_settings),
"fc2": n_fc.outputs.fc2,
"fc3": n_fc.outputs.fc3,
"nac_params": n_nac.outputs.nac_params,
"metadata": {
"label": label,
"description": label,
},
"phono3py": {"metadata": phono3py_metadata},
}
g = load_group("NaCl-222-444")
Phono3pyLTCWorkChain = WorkflowFactory("phonoxpy.phono3py_ltc")
node = submit(Phono3pyLTCWorkChain, **inputs)
print(node)
g.add_nodes(node)
def launch_phono3py_with_vasp():
"""Run Phono3pyWorkChain using aiida-vasp."""
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)
cutoff_energy = 350
#
# Settings for supercell forces
#
supercell_matrix = [2, 2, 2]
force_kpoints_mesh = [2, 2, 2]
force_incar_dict = {
"PREC": "Accurate",
"IBRION": -1,
"EDIFF": 1e-8,
"NELMIN": 5,
"NELM": 100,
"ENCUT": cutoff_energy,
"IALGO": 38,
"ISMEAR": 0,
"SIGMA": 0.01,
"LREAL": False,
"lcharg": False,
"lwave": False,
"NPAR": 4,
}
force_code = Code.get_from_string("vasp621mpi@nancy")
force_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
force_parser_settings = {
"add_energies": True,
"add_forces": True,
"add_stress": True,
}
force_config = {
"code": force_code,
"kpoints_mesh": force_kpoints_mesh,
"kpoints_offset": [0.5, 0.5, 0.5],
"potential_family": "PBE.54",
"potential_mapping": {"Na": "Na_pv", "Cl": "Cl"},
"options": {
"resources": force_resources,
"max_wallclock_seconds": 3600 * 10,
},
}
force_config.update(
{
"settings": {"parser_settings": force_parser_settings},
"parameters": {"incar": force_incar_dict},
}
)
#
# Settings for phonon supercell forces
#
phonon_supercell_matrix = [4, 4, 4]
phonon_force_kpoints_mesh = [1, 1, 1]
phonon_force_incar_dict = {
"PREC": "Accurate",
"IBRION": -1,
"EDIFF": 1e-8,
"NELMIN": 5,
"NELM": 100,
"ENCUT": cutoff_energy,
"IALGO": 48,
"ISMEAR": 0,
"SIGMA": 0.01,
"LREAL": False,
"lcharg": False,
"lwave": False,
"NPAR": 8,
}
phonon_force_code = Code.get_from_string("vasp621mpi@asahi")
phonon_force_resources = {"num_machines": 2, "tot_num_mpiprocs": 96}
phonon_force_parser_settings = {
"add_energies": True,
"add_forces": True,
"add_stress": True,
}
phonon_force_config = {
"code": phonon_force_code,
"kpoints_mesh": phonon_force_kpoints_mesh,
"kpoints_offset": [0.5, 0.5, 0.5],
"potential_family": "PBE.54",
"potential_mapping": {"Na": "Na_pv", "Cl": "Cl"},
"options": {
# "queue_name": "qM048",
"resources": phonon_force_resources,
"max_wallclock_seconds": 3600 * 10,
},
}
phonon_force_config.update(
{
"settings": {"parser_settings": phonon_force_parser_settings},
"parameters": {"incar": phonon_force_incar_dict},
}
)
#
# Settings for Born effective charges and dielectric constant.
#
nac_code = Code.get_from_string("vasp621mpi@nancy")
nac_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
nac_config = {
"code": nac_code,
"kpoints_mesh": [8, 8, 8],
"kpoints_offset": [0, 0, 0],
"potential_family": "PBE.54",
"potential_mapping": {"Na": "Na_pv", "Cl": "Cl"},
"options": {"resources": nac_resources, "max_wallclock_seconds": 3600 * 10},
}
nac_parser_settings = {
"add_energies": True,
"add_forces": True,
"add_stress": True,
"add_born_charges": True,
"add_dielectrics": True,
}
nac_incar_dict = {
"PREC": "Accurate",
"IBRION": -1,
"EDIFF": 1e-8,
"NELMIN": 5,
"NELM": 100,
"ENCUT": cutoff_energy,
"IALGO": 38,
"ISMEAR": 0,
"SIGMA": 0.01,
"LREAL": False,
"lcharg": False,
"lwave": False,
"lepsilon": True,
}
nac_config.update(
{
"settings": {"parser_settings": nac_parser_settings},
"parameters": {"incar": nac_incar_dict},
}
)
#
# Settings for phonopy calculation
#
phono3py_settings = {
"mesh": 50.0,
"supercell_matrix": supercell_matrix,
"phonon_supercell_matrix": phonon_supercell_matrix,
"distance": 0.03,
}
phono3py_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
phono3py_metadata = {
"options": {
"resources": phono3py_resources,
"max_wallclock_seconds": 3600 * 10,
},
}
#
# Phono3pyWorkChain inputs
#
label = "NaCl phonopy %dx%dx%d kpt %dx%dx%d PBE %d eV (distance :%4.2f)" % (
tuple(supercell_matrix)
+ tuple(force_kpoints_mesh)
+ (
cutoff_energy,
phono3py_settings["distance"],
)
)
inputs = {
"structure": structure,
"calculator_inputs": {
"force": force_config,
"nac": nac_config,
"phonon_force": phonon_force_config,
},
"run_fc": Bool(True),
"run_ltc": Bool(True),
"code": Code.get_from_string("phono3py@nancy"),
"settings": Dict(dict=phono3py_settings),
"metadata": {
"label": label,
"description": label,
},
"phono3py": {"metadata": phono3py_metadata},
}
g = load_group("phono3py-example")
Phono3pyWorkChain = WorkflowFactory("phonoxpy.phono3py")
node = submit(Phono3pyWorkChain, **inputs)
print(node)
g.add_nodes(node)