def read_force_constant_vasprun_xml( filename ):
import sys
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
sys.exit(1)
vasprun = etree.iterparse( vasp.VasprunWrapper( filename ) )
return vasp.get_force_constants_vasprun_xml( vasprun )
def read_force_constant_vasprun_xml(filename):
import sys
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
sys.exit(1)
vasprun = etree.iterparse(vasp.VasprunWrapper(filename))
return vasp.get_force_constants_vasprun_xml(vasprun)
def read_force_constant_vasprun_xml(filename):
if vasp.is_version528(filename):
vasprun = iterparse(vasp.VasprunWrapper(filename))
else:
vasprun = iterparse(filename)
return vasp.get_force_constants_vasprun_xml(vasprun)
import sys
sys.path.pop(1)
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()
def read_force_constant_vasprun_xml(filename):
if vasp.is_version528(filename):
vasprun = iterparse(vasp.VasprunWrapper(filename))
else:
vasprun = iterparse(filename)
return vasp.get_force_constants_vasprun_xml(vasprun)
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)
elif species=='WRe_0.25_conv':
#Tungsten
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,2,64)
s = 4.
a = superc.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
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 == 'WRe_B2':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,1)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['W','Re'] * 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 == 'WRe_0.00':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,numbatom)
s = supercell
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 = [200, 200, 200]
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 == 'WRe_0.03':
fc = vasp.get_force_constants_vasprun_xml(vasprun,2,0)
s = 2.
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 == 'WRe_0.06':
fc = vasp.get_force_constants_vasprun_xml(vasprun,3,0)
s = 2.
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 == 'WRe_0.09':
fc = vasp.get_force_constants_vasprun_xml(vasprun,4,0)
s = 2.
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 == 'WRe_0.12':
fc = vasp.get_force_constants_vasprun_xml(vasprun,5,0)
s = 2.
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 == 'WRe_0.18':
fc = vasp.get_force_constants_vasprun_xml(vasprun,6,0)
s = 2.
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 == 'WRe_0.25':
fc = vasp.get_force_constants_vasprun_xml(vasprun,7,0)
s = 2.
a = primitive.get_cell()[0][0]*2.
print a, primitive.get_scaled_positions()
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_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'WRe_0.50':
fc = vasp.get_force_constants_vasprun_xml(vasprun,8,0)
s = 2.
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_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=3700,
t_min=0)
elif species == 'Au':
fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0)
#Gold
s = 5.
a = superc.get_cell()[0][0]
bulk = PhonopyAtoms(symbols=['Au'] * 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, 0.0],[0.0, 0.5, 0.5],[0.5, 0.0, 0.5]],
distance=0.01, factor=15.633302)
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_partial_DOS()
phonon.set_thermal_properties(t_step=10,
t_max=1300,
t_min=0)
elif species == 'Mo':
fc = vasp.get_force_constants_vasprun_xml(vasprun,10,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Mo'] * 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=2500,
t_min=0)
elif species == 'Re':
fc = vasp.get_force_constants_vasprun_xml(vasprun,9,0)
s = 5.
a = superc.get_cell()[0][0]*2.
print a
bulk = PhonopyAtoms(symbols=['Re'] * 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=2500,
t_min=0)
f = open('F_TV','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
#print t, cv
#print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
f.write(("%12.3f " + "%15.7f" + "\n") % ( t, free_energy))
f.close()
fc = open('thermal_properties','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
fc.write(("%12.3f " + "%15.7f" *3 + "\n") % ( t, free_energy, entropy, cv ))
fc.close()
#phonon.plot_thermal_properties().show()
#phonon.plot_total_DOS().show()
phonon.write_total_DOS()
#phonon.write_partial_DOS()
phonon.write_yaml_thermal_properties()
bands = []
#### PRIMITIVE
q_start = np.array([0.0, 0.0, 0.0])
#q_start = np.array([0.5, 0.5, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
#q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
band = []
q_start = np.array([-0.5, 0.5, 0.5])
#q_start = np.array([0., 0., 0.])
q_end = np.array([0.25, 0.25, 0.25])
#q_end = np.array([1., 0., 0.])
for i in range(101):
#band.append([-0.5+3*1/400*i, 0.5-1/400*i, 0.5-1/400*i])
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#print band
q_start = np.array([0.25, 0.25, 0.25])
q_end = np.array([0., 0., 0.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0., 0., 0.])
q_end = np.array([0.0, 0., 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
#q_start = np.array([0.0, 0.0, 0.0])
#q_end = np.array([0.5, 0.5, 0.5])
#band = []
#for i in range(101):
# band.append(q_start + (q_end - q_start) / 100 * i)
#bands.append(band)
"""
###### CONVENTIONAL CELL ######
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([-0.5, 0.5, 0.5])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([-0.5, 0.5, 0.5])
q_end = np.array([1./4., 1./4., 1./4.])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([1./4., 1./4., 1./4.])
q_end = np.array([0.0, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
q_start = np.array([0.0, 0.0, 0.0])
q_end = np.array([0.5, 0.0, 0.0])
band = []
for i in range(101):
band.append(q_start + (q_end - q_start) / 100 * i)
bands.append(band)
"""
phonon.set_band_structure(bands)
#phonon.plot_band_structure().show()
q_points, distances, frequencies, eigvecs = phonon.get_band_structure()
disp = {'q':q_points, 'distances':distances, 'frequencies':frequencies, 'eigvecs':eigvecs}
f = open('ph_dispersion.pkl','w')
pickle.dump(disp, f)
f.close()
