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Phonopy workchain

Phonopy workchain is used to calculate harmonic phonon properties.

Phonon calculation settings

Supported parameters for phonon calculation are

• supercell_matrix: Dimension of supercell used by phonopy.

• 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.

• number_of_snapshots (optional): Random displacements.

• random_seed (optional): Random seed used to generate displacements.

Detailed explanations about the parameters are refereed to the phonopy documentation.

An example of settings is:

phonopy_settings = {
    "mesh": 50.0,
    "supercell_matrix": [2, 2, 2],
    "distance": 0.03,
}

Without setting number_of_snapshots, systematic atomic displacements considering crystal symmetry are introduced to perfect supercells. The displacement information is stored in displacement_dataset. With setting number_of_snapshots, all atomics are randomly displaced in direction at a fixed displacement distance. In this case, the displacement information is stored in displacements.

Initialization

At the initialization step, supercells with displacements are created. Data nodes of

• displacement_dataset or displacements

• 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 Phonopy workchain

Specific calculations are launched from the phonopy workchain to obtain data necessary for phonon calculations, which are intermediate data calculated by external calculator, supercell forces and parameters for non-analytical term correction (NAC). Using these intermediate data, phonon properties are calculated. The former calculations are the computationally demanding part. Therefore for the practical purpose, those data are stored in data nodes and attached to outputs port namespace. With these data, phonon properties are calculated and stored in data nodes and attached to outputs port namespace. Since the later phonon calculation is much less computational demanding, it is not performed as default.

• force_sets: Sets of supercell forces

• nac_params (optional): Parameters for non-analytical term correction. This is calculated when calculator_inputs.nac is set.

• force_constants, thermal_properties, band_structure, projected_dos (optional): Phonon properties calculated when run_phonopy = Bool(True).

Usage and examples

The basic usage is explained as a python script shown below.

• launch_phonopy_with_vasp: Run phonon calculation using phonopy & VASP.

• launch_phonopy_with_qe: Run phonon calculation using phonopy & QE.

• launch_phonopy_with_precalculated_dataset: Run phonon calculation using outputs of previous PhonopyWorkChain calculation without running supercell force and NAC calculations.

"""Examples to submit PhonopyWorkChain."""
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_phonopy_with_precalculated_dataset():
    """Submit phonopy calculation with pre-calculated force_sets."""
    n = load_node(226097)  # PhonopyWorkchain by launch_phonopy_with_vasp.
    supercell_matrix = n.outputs.phonon_setting_info["supercell_matrix"]

    #
    # Settings for phonopy calculation
    #
    phonopy_settings = {
        "mesh": 100.0,
        "supercell_matrix": supercell_matrix,
    }
    phonopy_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
    phonopy_metadata = {
        "options": {
            "resources": phonopy_resources,
            "max_wallclock_seconds": 3600 * 10,
        },
    }

    #
    # PhonopyWorkChain inputs
    #
    PhonopyWorkChain = WorkflowFactory("phonoxpy.phonopy")
    label = f"NaCl phonopy calculation after PhonopyWorkChain (pk={n.pk})"
    inputs = {
        "code": Code.get_from_string("phonopy@nancy"),
        "structure": n.inputs.structure,
        "settings": Dict(dict=phonopy_settings),
        "force_sets": n.outputs.force_sets,
        "nac_params": n.outputs.nac_params,
        "displacement_dataset": n.outputs.displacement_dataset,
        "run_phonopy": Bool(True),
        "metadata": {
            "label": label,
            "description": label,
        },
        "phonopy": {"metadata": phonopy_metadata},
    }

    g = load_group("phonopy-example")
    node = submit(PhonopyWorkChain, **inputs)
    print(node)
    g.add_nodes(node)


def launch_phonopy_with_vasp():
    """Run PhonopyWorkChain 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 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
    #
    phonopy_settings = {
        "mesh": 50.0,
        "supercell_matrix": supercell_matrix,
        "distance": 0.03,
    }
    phonopy_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
    phonopy_metadata = {
        "options": {
            "resources": phonopy_resources,
            "max_wallclock_seconds": 3600 * 10,
        },
    }

    #
    # PhonopyWorkChain inputs
    #
    PhonopyWorkChain = WorkflowFactory("phonoxpy.phonopy")
    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,
            phonopy_settings["distance"],
        )
    )
    inputs = {
        "structure": structure,
        "calculator_inputs": {"force": force_config, "nac": nac_config},
        "run_phonopy": Bool(True),
        "code": Code.get_from_string("phonopy@nancy"),
        "settings": Dict(dict=phonopy_settings),
        "metadata": {
            "label": label,
            "description": label,
        },
        "phonopy": {"metadata": phonopy_metadata},
    }

    g = load_group("phonopy-example")
    node = submit(PhonopyWorkChain, **inputs)
    print(node)
    g.add_nodes(node)


def launch_phonopy_with_qe():
    """Run PhonopyWorkChain using aiida-quantumespresso."""
    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)

    #
    # Settings for supercell forces
    #
    supercell_matrix = [2, 2, 2]
    force_kpoints_mesh = [2, 2, 2]
    force_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
    force_options = {"resources": force_resources, "max_wallclock_seconds": 3600 * 10}
    force_parameters = {
        "CONTROL": {
            "calculation": "scf",
            "restart_mode": "from_scratch",
            "tprnfor": True,
        },
        "SYSTEM": {
            "occupations": "fixed",
            "ecutwfc": 30.0,
            "ecutrho": 240.0,
        },
        "ELECTRONS": {
            "conv_thr": 1.0e-6,
        },
    }
    force_config = {
        "kpoints_mesh": force_kpoints_mesh,
        "kpoints_offset": [0.5, 0.5, 0.5],
        "pw": {
            "code": Code.get_from_string("qe-pw-6.8@nancy"),
            "metadata": {"options": force_options},
            "pseudo_family_string": "SSSP/1.1/PBE/efficiency",
            "parameters": force_parameters,
        },
    }

    #
    # Settings for Born effective charges and dielectric constant.
    #
    nac_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
    nac_options = {"resources": nac_resources, "max_wallclock_seconds": 3600 * 10}
    nac_pw_parameters = {
        "CONTROL": {
            "calculation": "scf",
            "restart_mode": "from_scratch",
            "tprnfor": True,
        },
        "SYSTEM": {
            "occupations": "fixed",
            "ecutwfc": 30.0,
            "ecutrho": 240.0,
        },
        "ELECTRONS": {
            "conv_thr": 1.0e-6,
        },
    }
    nac_ph_parameters = {
        "INPUTPH": {
            "tr2_ph": 1.0e-8,
            "epsil": True,
        }
    }
    nac_config = {
        "steps": [
            {
                "kpoints_mesh": [8, 8, 8],
                "kpoints_offset": [0, 0, 0],
                "pw": {
                    Code.get_from_string("qe-pw-6.8@nancy"),
                    "metadata": {"options": nac_options},
                    "pseudo_family_string": "SSSP/1.1/PBE/efficiency",
                    "parameters": nac_pw_parameters,
                },
            },
            {
                "ph": {
                    Code.get_from_string("qe-ph-6.8@nancy"),
                    "metadata": {"options": nac_options},
                    "parameters": nac_ph_parameters,
                }
            },
        ],
    }

    #
    # Settings for phonopy calculation
    #
    phonopy_settings = {
        "mesh": 50.0,
        "supercell_matrix": supercell_matrix,
        "distance": 0.03,
    }
    phonopy_resources = {"parallel_env": "mpi*", "tot_num_mpiprocs": 24}
    phonopy_metadata = {
        "options": {
            "resources": phonopy_resources,
            "max_wallclock_seconds": 3600 * 10,
        },
    }

    #
    # PhonopyWorkChain inputs
    #
    PhonopyWorkChain = WorkflowFactory("phonoxpy.phonopy")
    label = "NaCl qe-phonopy %dx%dx%d kpt %dx%dx%d PBE" "(distance :%4.2f)" % (
        tuple(supercell_matrix)
        + tuple(force_kpoints_mesh)
        + (phonopy_settings["distance"],)
    )
    inputs = {
        "structure": structure,
        "calculator_inputs": {"force": force_config, "nac": nac_config},
        "run_phonopy": Bool(True),
        "code": Code.get_from_string("phonopy@nancy"),
        "settings": Dict(dict=phonopy_settings),
        "metadata": {
            "label": label,
            "description": label,
        },
        "phonopy": {"metadata": phonopy_metadata},
    }

    g = load_group("phonopy-example")
    node = submit(PhonopyWorkChain, **inputs)
    print(node)
    g.add_nodes(node)

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