def calc_elast_dipole_dft(input_file, vasp_calc=True):
"""Reads OUTCAR file in the same directory with one shot forces
induced by removal of defect. Reads defect position
from .xyz file (which contains the defect) defined by `input_file`
calculates and returns the elastic dipole tensor of the defect.
Args:
input_file(str): name of input .xyz file containing defect cell.
Returns:
Elastic Dipole Tensor 3x3 numpy array.
"""
elastic = ElasticDipole()
ats_def = Atoms(input_file)
defect = find_h_atom(ats_def)
if vasp_calc:
import ase.io.vasp as vasp
ats_pos = vasp.read_vasp()
ats = vasp.read_vasp_out()
ats = Atoms(ats)
else:
pass
print 'Defect index', defect.index, 'Position', defect.position, 'Type: ', defect.number
f = ats.get_forces()
ats.add_property('force', f.T)
ats.write('force.xyz')
return elastic.compute_vacancy_dipole(defect,
ats_pos.copy(),
forces=ats.get_forces())
block=block,
corner=corner,
shape=shape,
exe = vasp,
ediffg = -0.05,
nelmin = 6,
nelmdl = -15,
kpar = 32,
parmode='cobalt',
xc='PBE',
lreal=False, ibrion=13, nsw=40,
algo='VeryFast', npar=8,
lplane=False, lwave=False, lcharg=False, nsim=1,
voskown=1, ismear=1, sigma=0.01, iwavpr=11, isym=2, nelm=100)
sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True)
bulk.set_calculator(sock_calc)
opt = LBFGS(bulk)
opt.run(fmax=0.05, steps=100)
sock_e = bulk.get_potential_energy()
sock_f = bulk.get_forces()
sock_s = bulk.get_stress()
print 'energy', sock_e
print 'forces', sock_f
print 'stress', sock_s
sock_calc.shutdown()
ibrion=13,
nsw=40,
algo='VeryFast',
npar=8,
lplane=False,
lwave=False,
lcharg=False,
nsim=1,
voskown=1,
ismear=1,
sigma=0.01,
iwavpr=11,
isym=2,
nelm=100)
sock_calc = SocketCalculator(vasp_client, ip=ip, bgq=True)
bulk.set_calculator(sock_calc)
opt = LBFGS(bulk)
opt.run(fmax=0.05, steps=100)
sock_e = bulk.get_potential_energy()
sock_f = bulk.get_forces()
sock_s = bulk.get_stress()
print 'energy', sock_e
print 'forces', sock_f
print 'stress', sock_s
sock_calc.shutdown()
THZ_to_mev = 4.135665538536
unit_cell = PhonopyAtoms(symbols=symbols, cell=cell, scaled_positions=scaled_positions)
phonon = Phonopy(unit_cell, [[n_sup_x,0,0],[0,n_sup_y,0],[0,0,n_sup_z]])
phonon.generate_displacements(distance=0.05)
supercells = phonon.get_supercells_with_displacements()
#We need to get the forces on these atoms...
forces = []
print 'There are', len(supercells), 'displacement patterns'
for sc in supercells:
cell = aseAtoms(symbols=sc.get_chemical_symbols(), scaled_positions=sc.get_scaled_positions(),
cell=sc.get_cell(), pbc=(1,1,1))
cell = Atoms(cell)
cell.set_calculator(pot)
forces.append(cell.get_forces())
phonon.set_forces(forces)
phonon.produce_force_constants()
mesh = [nqx, nqy, nqz]
phonon.set_mesh(mesh, is_eigenvectors=True)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
#SHOW DOS STRUCTURE
phonon.set_total_DOS(freq_min=0.0, freq_max=12.0, tetrahedron_method=False)
phonon.get_total_DOS()
phonon.write_total_DOS()
phonon.plot_total_DOS().show()
#BAND STRUCTURE
