Python Phonopy.set_mesh方法代碼示例

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
def get_phonopy_qha(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos,
                      pressure=0):
    """
    Return phonopy QHA interface.

    Args:
        energies (list):
        volumes (list):
        force_constants (list):
        structure (Structure):
        t_min (float): min temperature
        t_step (float): temperature step
        t_max (float): max temperature
        mesh (list/tuple): reciprocal space density
        eos (str): equation of state used for fitting the energies and the volumes.
            options supported by phonopy: vinet, murnaghan, birch_murnaghan
        pressure (float): in GPa, optional.

    Returns:
        PhonopyQHA
    """
    from phonopy import Phonopy
    from phonopy.structure.atoms import Atoms as PhonopyAtoms
    from phonopy import PhonopyQHA
    from phonopy.units import EVAngstromToGPa

    phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
                              scaled_positions=structure.frac_coords,
                              cell=structure.lattice.matrix)
    scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
    phonon = Phonopy(phon_atoms, scell)
    # compute the required phonon thermal properties
    temperatures = []
    free_energy = []
    entropy = []
    cv = []
    for f in force_constants:
        phonon.set_force_constants(-np.array(f))
        phonon.set_mesh(list(mesh))
        phonon.set_thermal_properties(t_step=t_step, t_min=t_min, t_max=t_max)
        t, g, e, c = phonon.get_thermal_properties()
        temperatures.append(t)
        free_energy.append(g)
        entropy.append(e)
        cv.append(c)

    # add pressure contribution
    energies = np.array(energies) + np.array(volumes) * pressure / EVAngstromToGPa
    # quasi-harmonic approx
    return PhonopyQHA(volumes, energies, eos=eos, temperatures=temperatures[0],
                      free_energy=np.array(free_energy).T, cv=np.array(cv).T,
                      entropy=np.array(entropy).T, t_max=np.max(temperatures[0]))

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
phonon.set_nac_params(nac_params)

# BAND = 0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q, d, freq in zip(q_points, distances, frequencies):
    print q, d, freq
phonon.plot_band_structure().show()

# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
                              t_max=1000,
                              t_min=0)

# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
    print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()

# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
    print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
phonon.plot_thermal_properties().show()

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
#!/usr/bin/env python

from cogue.task.phonon_relax import get_unstable_modulations
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import numpy as np

cutoff_eigenvalue = -0.02
supercell_dimension = [2, 2, 2]
cell = read_vasp("POSCAR-unitcell")
phonon = Phonopy(cell, np.diag(supercell_dimension))
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonon.set_mesh(supercell_dimension, is_gamma_center=True)

get_unstable_modulations(
    phonon, supercell_dimension, cutoff_eigenvalue=cutoff_eigenvalue, symmetry_tolerance=0.1, max_displacement=0.11
)

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
import phonopy.interface.vasp as vasp
import numpy as np
import lxml.etree as etree
from phonopy import Phonopy
from phonopy.structure.atoms import Atoms as PhonopyAtoms


vasprun = etree.iterparse('vasprun.xml', tag='varray')
fc = vasp.get_force_constants_vasprun_xml(vasprun)

primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
superc =  vasp.get_atoms_from_poscar(open('POSCAR'),'W')

print superc.get_scaled_positions()

a = 5.404
bulk = PhonopyAtoms(symbols=['W'] * 216,
                    positions=superc.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,[[1,0,0],[0,1,0],[0,0,1]],primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]])

phonon.set_force_constants(fc)

mesh = [3, 3, 3]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()


phonon.set_total_DOS()
phonon.plot_total_DOS().show()

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
                       'dielectric': epsilon})

# BAND = 0.0 0.0 0.0  0.5 0.0 0.0  0.5 0.5 0.0  0.0 0.0 0.0  0.5 0.5 0.5
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon.set_band_structure(bands)
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
for q, d, freq in zip(q_points, distances, frequencies):
    print q, d, freq
phonon.plot_band_structure().show()

# Mesh sampling 20x20x20
phonon.set_mesh([20, 20, 20])
phonon.set_thermal_properties(t_step=10,
                              t_max=1000,
                              t_min=0)

# DOS
phonon.set_total_DOS(sigma=0.1)
for omega, dos in np.array(phonon.get_total_DOS()).T:
    print "%15.7f%15.7f" % (omega, dos)
phonon.plot_total_DOS().show()

# Thermal properties
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
    print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
phonon.plot_thermal_properties().show()

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
 def __init__(self, numbatom=125, supercell=5):
     
     #species = 'WRe_0.25_conv'
     species = 'WRe_0.00'
     #species = 'Re'
     ###read force constants from vasprun.xml###
     vasprun = etree.iterparse('vasprun.xml', tag='varray')
     #fc = vasp.get_force_constants_vasprun_xml(vasprun,1) #pass xml input and species atomic weight.
     ###########################################
     
     ########### read positionsl ###############
     primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
     superc =  vasp.get_atoms_from_poscar(open('POSCAR'),'W')
     ###########################################
     numbatom =  superc.get_number_of_atoms()
     #print primitive.get_cell()
     #print primitive.get_scaled_positions()
     #print superc.get_scaled_positions()
     
     print numbatom, species, os.getcwd()
     if species=='W':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,64)
         s = 4.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
         
     elif species=='W_conv_2x2x2':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
         s = 2.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W','W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
     
     elif species=='W_conv':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
         s = 4.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W','W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
#.........這裏部分代碼省略.........

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
print "%12s %15s%15s%15s" % ('T [K]',
                              'F [kJ/mol]',
                              'S [J/K/mol]',
                              'C_v [J/K/mol]')

# get_thermal_properties returns numpy array of
#
# [[ temperature, free energy, entropy, heat capacity ],
#  [ temperature, free energy, entropy, heat capacity ],...,]
#
# Frequency has to be given in THz internally. Therefore unit
# conversion factor may be specified when calling Phonon class. The
# unit of frequency in a calculator is square root of the unit of
# dynamical matrix, i.e.,
#
# /      [energy]       \^(1/2)
# | ------------------- |
# \ [mass] [distance]^2 /
#
# THz is the value above divided by 2pi*1e12 (2pi comes from the
# factor between angular frequency and ordinary frequency). See
# units.py in the phonopy directory.
phonon.set_mesh( mesh, shift )
phonon.set_thermal_properties( t_step=10,
                               t_max=1000,
                               t_min=0 )
for t, free_energy, entropy, cv in phonon.get_thermal_properties():
    print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )

phonon.plot_thermal_properties().show()

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_mesh [as 別名]
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS, parse_BORN
import matplotlib.pyplot as plt

unitcell = read_vasp("POSCAR")
phonon = Phonopy(unitcell,
                 [[2, 0, 0],
                  [0, 2, 0],
                  [0, 0, 2]],
                 primitive_matrix=[[0, 0.5, 0.5],
                                   [0.5, 0, 0.5],
                                   [0.5, 0.5, 0]])

force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
primitive = phonon.get_primitive()
nac_params = parse_BORN(primitive, filename="BORN")
phonon.set_nac_params(nac_params)
phonon.set_group_velocity()
phonon.set_mesh([31, 31, 31])
qpoints, weights, frequencies, _ = phonon.get_mesh()
group_velocity = phonon.get_group_velocity()
gv_norm = np.sqrt((group_velocity ** 2).sum(axis=2))
for i, (f, g) in enumerate(zip(frequencies.T, gv_norm.T)):
    plt.plot(f, g, 'o', label=('band%d' % (i + 1)))
plt.legend()
plt.xlabel("Frequency (THz)")
plt.ylabel("|group-velocity| (THz.A)")
plt.show()