Calculate phonons from MD

[jan-janssen]

from ase.atoms import Atoms
from atomistics.calculators import (
    calc_molecular_dynamics_phonons_with_lammps,
    evaluate_with_lammps, 
    get_potential_by_name,
)
from atomistics.workflows import PhonopyWorkflow
from dynaphopy import Quasiparticle
import pandas
from phonopy.units import VaspToTHz

cell = [[5.4500000000, 0.0, 0.0], [0.0, 5.4500000000, 0.0], [0.0, 0.0, 5.4500000000]]
positions = [
    [4.7687500000, 4.7687500000, 4.7687500000],
    [4.7687500000, 2.0437500000, 2.0437500000],
    [2.0437500000, 4.7687500000, 2.0437500000],
    [2.0437500000, 2.0437500000, 4.7687500000],
    [0.6812500000, 0.6812500000, 0.6812500000],
    [0.6812500000, 3.4062500000, 3.4062500000],
    [3.4062500000, 0.6812500000, 3.4062500000],
    [3.4062500000, 3.4062500000, 0.6812500000],
]
symbols = ["Si"] * len(positions)
structure_ase = Atoms(symbols=symbols, positions=positions, cell=cell, pbc=True)

potential_dataframe = pandas.DataFrame({
    "Config": [[
        "pair_style tersoff",
        "pair_coeff * * SiCGe.tersoff Si(C)"
    ]],
    "Filename": [[]],
    "Model": ["Tersoff"],
    "Name": ["Tersoff"],
    "Species": [["Si"]],
})

workflow = PhonopyWorkflow(
    structure=structure_ase,
    interaction_range=10,
    factor=VaspToTHz,
    displacement=0.01,
    dos_mesh=20,
    primitive_matrix=[[0.0, 0.5, 0.5], [0.5, 0.0, 0.5], [0.5, 0.5, 0.0]],
    number_of_snapshots=None,
)
task_dict = workflow.generate_structures()
result_dict = evaluate_with_lammps(
    task_dict=task_dict,
    potential_dataframe=potential_dataframe,
)
mesh_dict, dos_dict = workflow.analyse_structures(output_dict=result_dict)

trajectory = calc_molecular_dynamics_phonons_with_lammps(
    structure_ase=structure_ase,
    potential_dataframe=potential_dataframe,
    force_constants=workflow.phonopy.get_force_constants(), 
    phonopy_unitcell=workflow.phonopy.get_unitcell(),
    phonopy_primitive_matrix=workflow.phonopy.get_primitive_matrix(),
    phonopy_supercell_matrix=workflow.phonopy.get_supercell_matrix(),
    total_time=20,      # ps
    time_step=0.001,    # ps
    relaxation_time=5,  # ps
    silent=True,
    supercell=[2, 2, 2],
    memmap=False,
    velocity_only=True,
    temperature=300,
)

# set dynaphopy calculation
calculation = Quasiparticle(trajectory)
calculation.select_power_spectra_algorithm(2)  # select FFT algorithm
calculation.get_renormalized_phonon_dispersion_bands()
renormalized_force_constants = calculation.get_renormalized_force_constants()

# Print phonon band structure
calculation.plot_renormalized_phonon_dispersion_bands()

Waiting for pyiron/pylammpsmpi#166

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