atoms = ase.io.read("./primCIFs/Cd.cif")
#atoms = bulk(element,struct,a=La,b=Lb,c=Lc,alpha=Lalpha)
# sc,fcc,bcc,tetragonal,bct,hcp,rhmbohedral,orthorhombic
# mlc, diamond,zincblende,rocksalt,cesiumchloride, fluorite, wurtzite
atoms.set_calculator(calc)
atoms.get_potential_energy()
# Get the valence band maximum
efermi = calc.get_fermi_level()
Nk = len(calc.get_ibz_k_points())
Ns = calc.get_number_of_spins()
eigval = np.array([[calc.get_eigenvalues(kpt=k, spin=s)
for k in range(Nk)] for s in range(Ns)])
evbm = np.max(eigval[eigval < efermi])
# Next, a band structure calculation
calc.set(nbands=nbnd, # 4 occupied and 4 unoccupied bands
fixdensity=True,
eigensolver=CG(niter=5),
symmetry='off',
kpts={'path': spath, 'npoints': 50},
convergence={'bands': 'all'},
)
calc.get_potential_energy()
bs_gpaw = calc.band_structure()
#bs_gpaw.reference = evbm
bs_gpaw_reference = evbm
bs_gpaw.plot(filename='bs_gpaw_data.png', show=False, emax=evbm + 5., emin=evbm - 15.)
write_json('bs_gpaw.json', bs_gpaw)
tprnfor=True, # kwargs added to parameters
input_data=input_data)
atoms.calc = calc
atoms.get_potential_energy()
# Get the valence band maximum
efermi = calc.get_fermi_level()
Nk = len(calc.get_ibz_k_points())
Ns = calc.get_number_of_spins()
eigval = np.array([[calc.get_eigenvalues(kpt=k, spin=s) for k in range(Nk)]
for s in range(Ns)])
evbm = np.max(eigval[eigval < efermi])
# Next, a band structure calculation
input_data['control'].update({
'calculation': 'bands',
'restart_mode': 'restart',
'verbosity': 'high'
})
calc.set(kpts={'path': spath, 'npoints': 50}, input_data=input_data)
calc.calculate(atoms)
bs_qe = calc.band_structure()
bs_qe.reference = evbm
bs_qe.plot(filename='bs_qe_data.png',
show=False,
emax=evbm + 5.,
emin=evbm - 15.)
write_json('bs_qe.json', bs_qe)
def write(self, filename):
"""Write local density of states to JSON file."""
write_json(filename, (self.ldos, self.bias, self.cell))
def dump(self, data):
if world.rank == 0 and self.restart is not None:
with open(self.restart, 'w') as fd:
write_json(fd, data)
from datetime import datetime
import numpy as np
import io
from ase.io.jsonio import encode, decode, read_json, write_json
assert decode(encode(np.int64(42))) == 42
c = np.array([0.1j])
assert (decode(encode(c)) == c).all()
fd = io.StringIO()
obj1 = {'hello': 'world'}
write_json(fd, obj1)
fd.seek(0)
obj2 = read_json(fd)
print(obj1)
print(obj2)
for obj in [0.5 + 1.5j, datetime.now()]:
s = encode(obj)
o = decode(s)
print(obj)
print(s)
print(obj)
assert obj == o, (obj, o, s)
def write_file():
f_ = open("tmp.traj","a")
f_.write("{}".format(spositions))
return 0
if __name__ == '__main__':
#write_file()
jsonio.write_json("tmp.traj",positions)
sys.exit()
