def efield(efield=0.05, n=30):
printit('running GS calculation for {}'.format(efield))
fname = "sb_relaxed.cif"
a = read(fname)
atom = read(fname)
wire = make_supercell(atom, [[n, 0, 0], [0, 1, 0], [
0, 0, 1]], wrap=True, tol=1e-05)
wire.center(vacuum=15, axis=0)
a = wire.copy()
if not os.path.isfile('gs_{}.gpw'.format(efield)):
calc = GPAW( # mode='lcao',
mode='fd',
basis='szp(dzp)',
# eigensolver='cg',
#mixer=Mixer(beta=0.2, nmaxold=3, weight=70.0),
xc='PBE',
# poissonsolver=DipoleCorrection(PoissonSolver(relax='GS'), 2),
mixer=Mixer(beta=0.06, nmaxold=5, weight=100.0),
occupations=FermiDirac(width=0.1),
kpts={'density': 4.5},
txt='gs_output_{}.txt'.format(efield),
h=0.20,
external=ConstantElectricField(efield, [0, 0, 1]))
a.set_calculator(calc)
a.get_potential_energy()
calc.write('gs_{}.gpw'.format(efield))
calc = GPAW('gs_{}.gpw'.format(efield),
nbands=-100,
fixdensity=True,
symmetry='off',
kpts={'path': 'XGX', 'npoints': 100},
convergence={'bands': 'CBM+1'},
txt='gs_output_{}.txt'.format(efield))
calc.get_potential_energy()
bs = calc.band_structure()
bs.plot(filename='bandstructure_{}.png'.format(
efield), show=False, emax=calc.get_fermi_level()+1, emin=calc.get_fermi_level()-1)
bs.write('bs_{}.json'.format(
efield))
try:
gap, p1, p2 = get_gap(calc)
printit("{} {} {} {}".format(efield, gap, p1, p2), fname="gaps.dat")
except:
None
# 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)
from gpaw import GPAW
calc = GPAW('groundstate.rutile.gpw')
atoms = calc.get_atoms()
path = calc.bandpath(density=7)
path.write('path.rutile.json')
calc.set(kpts=path, fixdensity=True, symmetry='off')
atoms.get_potential_energy()
bs = calc.band_structure()
bs.write('bs.rutile.json')
e = atom.get_potential_energy()
calc.write('coo_gs.gpw')
parprint("total energy = {}".format(e))
calc.set(nbands='nao',
fixdensity=True,
symmetry='off',
kpts={
'path': atom.cell.bandpath().path,
'npoints': 200
},
convergence={'bands': 'all'})
calc.get_potential_energy()
calc.write('coo_bands.gpw')
bs = calc.band_structure()
with open('band_energies.pickle', 'wb') as handle:
pickle.dump(calc.band_structure().todict(),
handle,
protocol=pickle.HIGHEST_PROTOCOL)
bs.plot(filename='bandstructure.png',
show=False,
emax=8.0,
emin=-8.0,
reference=8.84354)
else:
atom = read("sqs_coo.cif")
parprint("Reading from restart file")
calc = GPAW('coo_gs.gpw',
nbands='nao',
def test_bs(self):
sb = StructureBuilder()
atoms, *_ = sb.get_structure("Si", "diamond")
# print(atoms)
base_dir = os.path.join(os.path.dirname(__file__),
"../../tmp/Si-class/")
m_calc = MaterCalc(atoms=atoms, base_dir=base_dir)
self.assertTrue(m_calc.relax(fmax=0.002)) # Very tight limit!
self.assertTrue(m_calc.ground_state())
# get the PBE BS
lattice_type = get_cellinfo(m_calc.atoms.cell).lattice
self.assertTrue(lattice_type in special_paths.keys())
kpts_bs = dict(path=special_paths[lattice_type], npoints=120)
gpw_name = os.path.join(base_dir, "gs.gpw")
self.assertTrue(os.path.exists(gpw_name))
calc_bs = GPAW(restart=gpw_name,
kpts=kpts_bs,
fixdensity=True,
symmetry='off',
txt=os.path.join(base_dir, "pbe-bs.txt"))
calc_bs.get_potential_energy()
# PBE bandgap
bg_pbe_min, *_ = bandgap(calc_bs, direct=False)
bg_pbe_dir, *_ = bandgap(calc_bs, direct=True)
calc_bs.write(os.path.join(base_dir, "pbe-bs.gpw"))
bs_pbe = calc_bs.band_structure()
bs_pbe.plot(emin=-10,
emax=10,
filename=os.path.join(base_dir, "pbe-bs.png"))
# get the gllbsc by steps
calc_ = GPAW(restart=gpw_name)
calc_gllb = GPAW(**calc_.parameters)
calc_gllb.set(xc="GLLBSC", txt=os.path.join(base_dir, "gllb-gs.txt"))
calc_gllb.atoms = calc_.atoms
del calc_
calc_gllb.get_potential_energy() # SC calculation
calc_gllb.write("gllb-gs.gpw")
calc_gllb_bs = GPAW(restart="gllb-gs.gpw",
kpts=kpts_bs,
fixdensity=True,
symmetry="off",
txt=os.path.join(base_dir, "gllb-bs.txt"))
world.barrier()
calc_gllb_bs.get_potential_energy()
homolumo = calc_gllb_bs.get_homo_lumo()
bg_gllb_ks = homolumo[1] - homolumo[0]
response = calc_gllb_bs.hamiltonian.xc.xcs["RESPONSE"]
response.calculate_delta_xc(homolumo / Ha)
EKs, Dxc = response.calculate_delta_xc_perturbation()
bg_gllb_deltaxc = EKs + Dxc
ibz_kpts = calc_gllb_bs.get_ibz_k_points()
e_kn = numpy.array([calc_gllb_bs.get_eigenvalues(kpt=k) \
for k in range(len(ibz_kpts))])
efermi = calc_gllb_bs.get_fermi_level()
e_kn[e_kn > efermi] += Dxc
bg_gllb_min, *_ = bandgap(eigenvalues=e_kn,
efermi=efermi,
direct=False)
bg_gllb_dir, *_ = bandgap(eigenvalues=e_kn, efermi=efermi, direct=True)
parprint("PBE: E_min \t E_dir")
parprint("{:.3f}\t{:.3f}".format(bg_pbe_min, bg_pbe_dir))
parprint("Gllb: EKS \t E_deltaxc")
parprint("{:.3f}\t{:.3f}".format(bg_gllb_ks, bg_gllb_deltaxc))
parprint("Gllb: E_min \t E_dir")
parprint("{:.3f}\t{:.3f}".format(bg_gllb_min, bg_gllb_dir))
bs_gllb = calc_gllb_bs.band_structure()
bs_gllb.energies[bs_gllb.energies > bs_gllb.reference] += Dxc
bs_gllb.plot(emin=-10,
emax=10,
filename=os.path.join(base_dir, "gllb-bs.png"))
calc_gllb_bs.write(os.path.join(base_dir, "gllb-bs.gpw"))
def _main():
si = make_Si_cell()
# First step: find the ground-state charge density.
# Use plane-wave basis with 200 eV wavefunction cutoff energy.
# Cutoff energy should be chosen such that the error introduced by the incompleteness
# of the basis is not too high.
# The appropriate energy is different for each atom.
# See here: https://wiki.fysik.dtu.dk/gpaw/setups/Si.html
calc = GPAW(
mode=PW(200),
# PBE exchange-correlation functional
xc='PBE',
# Sample the Brillouin zone with 8 k-points in each reciprocal lattice direction
kpts=(8, 8, 8),
# Smear step functions appearing in Brillouin zone integrals using Fermi-Dirac
# distribution at temperature k_B T = 0.01 eV.
occupations=FermiDirac(0.01),
# Start calculation using random wavefunctions.
# We have a physically-reasonable initial value for the charge density based
# on the atomic positions.
# The Hamiltonian is diagonalized iteratively, so we also need an initial guess for
# the wavefunctions. Random starting wavefunctions generally work well.
random=True,
# Set the log file for the ground-state DFT calculation.
txt="Si_gs.txt")
si.calc = calc
# To make GPAW perform the DFT calculation, we need to ask it for something
# that it needs to perform the calculation to know.
si.get_potential_energy()
# Save the result for the ground state so we can load it later.
ground_state_file = "Si_gs.gpw"
calc.write(ground_state_file)
# Second step: using the converged ground-state charge density, calculate the
# wavefunctions along a high-symmetry path in the Brilllouin zone.
# The energies along this path give the band structure diagram.
calc = GPAW(
ground_state_file,
# Include the 16 lowest-energy valence bands in the calculation.
nbands=16,
# Keep the charge density constant, using our converged ground-state density.
fixdensity=True,
# Don't consider symmetry in the k-point distribution: we want to use exactly
# the k-points we specify.
# (In the ground-state calculation, many k-points can be eliminated due to
# being redundant by symmetry.)
symmetry='off',
# Use a high-symmetry k-point path.
# High-symmetry paths following the [SC10] convention for band structure are
# built-in (can use these if our unit cell also follows the [SC10] convention).
# Use 300 k-points total.
kpts={
'path': special_paths['fcc'],
'npoints': 300
},
# Require that the energies of the lowest 8 bands are well-converged.
convergence={'bands': 8},
# Set the log file for the band-structure calculation.
txt="Si_bands.txt")
# Make GPAW perform the band-structure calculation.
calc.get_potential_energy()
# Plot the band structure.
# Since we used kpoints={'path': ...}, we can use an ASE convenience function for this.
bs = calc.band_structure()
bs.plot(filename="Si_bands.png")
from gpaw import GPAW
# Restart from ground state and fix potential:
calc = GPAW("Si_gs.gpw",
nbands=16,
fixdensity=True,
symmetry="off",
kpts={"path": "GXWKL", "npoints": 60},
convergence={"bands": 8},
txt="LOG_Si_bands.txt")
calc.get_potential_energy()
bs = calc.band_structure() # band structure info, such as energies, path, etc
bs.plot(filename="bandstructure.png", emax=10.0)
calc.write("Si_bands.gpw")
def bandgap(self, method="GLLB", save=True, skip=False):
# Check method input
method = method.strip().lower()
if method not in ("pbe", "gllb", "hse", "gw"):
raise ValueError("Method for bandgap calculation not known!")
# Check ground state
if not os.path.exists(self.__gs_file):
raise FileNotFoundError("Ground state not calculated!")
# Check bandgap?
self.__bg_file = self.__bg_file_template.format(method)
if os.path.exists(self.__bg_file):
parprint(
"Bandgap for method {} is already calculated!".format(method))
data = numpy.load(self.__bg_file)
return data["Eg_min"], data["Eg_dir"], None
# Real calculation now
if method == "pbe":
# Use band_structure or simple sampling kpts?
calc = GPAW(restart=self.__gs_file)
try:
lattice_type = get_cellinfo(calc.atoms.cell).lattice
use_bs = lattice_type in special_paths.keys()
except (ValueError, AssertionError): # Monolithic cell?
use_bs = False
parprint("Use bandpath?", use_bs)
if use_bs:
kpts = dict(path=special_paths[lattice_type],
npoints=self.params["gap"][method]["npoints"])
calc.set(kpts=kpts, fixdensity=True, symmetry="off",
txt=None) # non-SC
calc.get_potential_energy(
) # Otherwise the wavefunction not known?
bg_min, *_ = bg(calc, direct=False)
bg_dir, *_ = bg(calc, direct=True)
# Possibly no gap
if bg_min is None:
bg_min = 0
if bg_dir is None:
bg_dir = 0
if use_bs:
bs = calc.band_structure()
xcoords, label_xcoords, labels = bs.get_labels()
res_bs = bs.todict()
res_bs.update(xcoords=xcoords,
label_xcoords=label_xcoords,
labels=labels)
else:
res_bs = {} # no result
if save:
if rank == 0:
numpy.savez(self.__bg_file,
Eg_min=bg_min,
Eg_dir=bg_dir,
**res_bs)
print("Bandgap saved!")
world.barrier()
return bg_min, bg_dir, res_bs
elif method == "gllb":
# Need to restart the SC calculation
if not os.path.exists(self.__gs_gllb_file):
if not os.path.exists(self.__relaxed_gllb_traj):
self.relax(fmax=0.002, steps=200, xc="gllb", skip=skip)
world.barrier()
atoms = read(self.__relaxed_gllb_traj)
calc = GPAW(**self.params["gs"],
txt=os.path.join(self.__base_dir, "gs_gllb.txt"))
atoms.set_calculator(calc)
calc.set(xc="GLLBSC")
atoms.get_potential_energy() # Recalculate GS
calc.write(self.__gs_gllb_file, mode="all")
#TODO: merge with PBE method
calc_bs = GPAW(restart=self.__gs_gllb_file)
try:
lattice_type = get_cellinfo(calc_bs.atoms.cell).lattice
use_bs = lattice_type in special_paths.keys()
except (ValueError, AssertionError): # Monolithic cell?
use_bs = False
if use_bs:
kpts = dict(path=special_paths[lattice_type],
npoints=self.params["gap"][method]["npoints"])
calc_bs.set(kpts=kpts, fixdensity=True, symmetry="off")
calc_bs.get_potential_energy()
homolumo = calc_bs.get_homo_lumo()
response = calc_bs.hamiltonian.xc.xcs["RESPONSE"]
response.calculate_delta_xc(homolumo / Ha)
EKs, Dxc = response.calculate_delta_xc_perturbation()
ns = calc_bs.get_number_of_spins()
nk = len(calc_bs.get_ibz_k_points())
e_kn = numpy.array([[calc_bs.get_eigenvalues(kpt=k, spin=s) \
for k in range(nk)] for s in range(ns)])
efermi = calc_bs.get_fermi_level()
e_kn[e_kn > efermi] += Dxc
bg_gllb_min, *_ = bg(eigenvalues=e_kn, efermi=efermi, direct=False)
bg_gllb_dir, *_ = bg(eigenvalues=e_kn, efermi=efermi, direct=True)
if bg_gllb_min is None:
bg_gllb_min = 0
if bg_gllb_dir is None:
bg_gllb_dir = 0
if use_bs:
bs = calc_bs.band_structure()
bs.energies[bs.energies >
bs.reference] += Dxc # Shift gllbsc discontinuous
res_bs = bs.todict()
xcoords, label_xcoords, labels = bs.get_labels()
res_bs.update(xcoords=xcoords,
label_xcoords=label_xcoords,
labels=labels)
else:
res_bs = {}
if save:
if rank == 0:
numpy.savez(self.__bg_file,
Eg_min=bg_gllb_min,
Eg_dir=bg_gllb_dir,
**res_bs)
print("Bandgap saved!")
world.barrier()
return bg_gllb_min, bg_gllb_dir, res_bs
else:
raise NotImplementedError("Method not implemented yet")