def dfpt(self):
'''
'''
atoms = self.atoms
self.log('-'*60)
self.log('Submit job {0}'.format(job))
self.log.print_atoms(atoms)
calc = Espresso(
label = os.path.join(self.label, job),
**self.calculator,
)
calc.parameters['input_data']['prefix'] = job
atoms.calc = calc
energy = atoms.get_potential_energy()
# dos
calc.post(queue = queue,
package = 'ph',
tr2_ph = 1e-14,
ldisp = True,
nq1 = 4,
nq2 = 4,
nq3 = 3,
)
calc.post(queue = queue,
fildyn = 'matdyn',
package = 'q2r',
zasr = 'simple',
flfrc = '%s.fc'%job,
)
calc.post(queue = queue,
package = 'matdyn',
asr = 'simple',
dos = True,
flfrc = '%s.fc'%job,
fldos = '%s.phdos'%job,
nk1 = 40,
nk2 = 40,
nk3 = 30,
)
calc.plot_phdos(fldos = '%s'%job,
output = 'images/%s-phdos.png'%job)
pass
label='scf/al',
ecutwfc=40,
occupations='smearing',
degauss=0.01,
kpts=(4, 4, 1))
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
e = calc.results['energy']
fermi = calc.get_fermi_level()
print('Energy: {0:1.3f}'.format(e))
#===============================================================
# post calculation
calc.post(package='pp',
plot_num=5,
sample_bias=0.0735,
iflag=3,
output_format=6,
fileout='stm1_1eV.cube')
# ========================
# Creates: 2d.png, 2d_I.png, line.png, dIdV.png
from ase.dft.stm import STM
from ase.io.cube import read_cube_data
import pickle
ldos, atoms = read_cube_data('scf/al/stm1_1eV.cube')
with open('scf/al/datas.pickle', 'wb') as f:
pickle.dump([ldos, 1.0, atoms.cell], f)
stm = STM('scf/al/datas.pickle')
z = 8.0
bias = 1.0
c = stm.get_averaged_current(bias, z)
x, y, h = stm.scan(bias, c, repeat=(3, 5))
}
pseudopotentials = {
'Fe': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
'Fe1': 'Fe.pbe-spn-rrkjus_psl.1.0.0.UPF',
}
calc = Espresso(pseudopotentials=pseudopotentials,
label='scf/fe-afm',
input_data=input_data,
kpts=(6, 6, 6))
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
e = calc.results['energy']
print('Energy {0:1.3f}'.format(e))
parameters_hp = {
'nq1': 1,
'nq2': 1,
'nq3': 1,
'equiv_type': 0,
'conv_thr_chi': 1e-5,
'perturb_only_atom': {
'1': True
} # key(i)
}
calc.post(package='hp', **parameters_hp)
'''
Energy -6737.122
'''
calc = Espresso(
label='scf/co',
pseudopotentials=pseudopotentials,
ecutwfc=30,
occupations='smearing',
degauss=0.03,
kpts=(1, 1, 1),
debug=True,
)
atoms.calc = calc
e = atoms.get_potential_energy()
print('Energy = {0:1.3f} eV'.format(e))
#===============================================================
# start nscf calculation
fe = calc.get_fermi_level()
print('fermi level: ', fe)
calc.nscf(occupations='tetrahedra', kpts=(3, 3, 3))
calc.nscf_calculate()
# dos, projwfc
calc.post(package='dos', Emin=fe - 30, Emax=fe + 30, DeltaE=0.01)
calc.post(package='projwfc', Emin=fe - 30, Emax=fe + 30, DeltaE=0.01)
# DOS analysis
dos = DOS(label='scf/co', prefix='co')
dos.read_dos()
dos.plot_dos(Emin=-10, Emax=10, smearing=[0.02, 0.01])
plt.savefig('images/co-dos.png')
dos.read_pdos()
dos.plot_pdos(Emin=-10, Emax=10, smearing=[0.02, 0.01], legend=True)
plt.savefig('images/co-pdos.png')
print('energy: ', e)
# Phonon calculations at gamma
input = {
'tr2_ph':1.0e-14,
'epsil':True,
}
#
# phonon calculation on a (444) uniform grid of q-points
input = {
'tr2_ph':1.0e-12,
'ldisp':True,
'nq1':4,
'nq2':4,
'nq3':4,
}
calc.post(queue = queue, package = 'ph', parallel = '-nk 4', **input)
#
input = {
'asr':'simple',
'dos': True,
'nk1':12,
'nk2':12,
'nk3':12,
}
calc.post(queue = queue, package = 'matdyn', **input)
# oer = Phonon(atoms,
# label = 'ZnO',
# calculator = calc,
# view = True,
# )
# oer.run()
import matplotlib.pyplot as plt
atoms = molecule('CO')
atoms.center(5)
atoms.pbc = [True, True, True]
pseudopotentials = {
'O': 'O.pbe-n-rrkjus_psl.1.0.0.UPF',
'C': 'C.pbe-n-rrkjus_psl.1.0.0.UPF'
}
calc = Espresso(
label='scf/co',
pseudopotentials=pseudopotentials,
ecutwfc=30,
kpts=(1, 1, 1),
)
atoms.calc = calc
e = atoms.get_potential_energy()
calc.read_results()
print('Energy = {0:1.3f} eV'.format(e))
#===============================================================
# start nscf calculation, and dos, projwfc
calc.read_results()
fermi = calc.get_fermi_level()
calc.nscf(kpts=(1, 1, 1))
calc.nscf_calculate()
calc.post(package='dos', Emin=fermi - 20, Emax=fermi + 10, DeltaE=0.1)
# DOS analysis
dos = DOS(calc)
dos.read_dos()
dos.plot_dos()
plt.savefig('images/co-dos.png')