# Generate setup for oxygen with half a core-hole:
gen('O', name='hch1s', corehole=(1, 0, 0.5))
if 1:
a = 5.0
d = 0.9575
t = pi / 180 * 104.51
H2O = Atoms([
Atom('O', (0, 0, 0)),
Atom('H', (d, 0, 0)),
Atom('H', (d * cos(t), d * sin(t), 0))
],
cell=(a, a, a),
pbc=False)
H2O.center()
calc = GPAW(nbands=10, h=0.2, setups={'O': 'hch1s'})
H2O.set_calculator(calc)
e = H2O.get_potential_energy()
niter = calc.get_number_of_iterations()
calc.write('h2o.gpw')
else:
calc = GPAW('h2o.gpw')
calc.initialize_positions()
from gpaw.xas import RecursionMethod
if 1:
r = RecursionMethod(calc)
r.run(400)
r.write('h2o.pckl')
else:
n = size // 3 # number of cpu's per image
j = 1 + rank // n # my image number
assert 3 * n == size
images = [initial]
for i in range(3):
ranks = range(i * n, (i + 1) * n)
image = initial.copy()
if rank in ranks:
calc = GPAW(h=0.3,
kpts=(2, 2, 1),
txt='neb%d.txt' % j,
communicator=ranks)
image.set_calculator(calc)
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images, parallel=True)
neb.interpolate()
qn = BFGS(neb, logfile='qn.log')
traj = PickleTrajectory('neb%d.traj' % j,
from ase import Atoms
from ase.visualize import view
atoms = Atoms(symbols=myGpaw.symstr,
pbc=[True, True, True],
cell=myGpaw.gcell,
positions=myGpaw.pos)
# view(atoms)
kpts = {'size': (4, 4, 4), 'gamma': True}
calc = GPAW(#h=0.16,
mode=PW(360),
kpts=kpts,
xc='PBE',
txt=myGpaw.symstr+'_360.out',
occupations=FermiDirac(width=0.05),
# nbands=-2,
convergence={'energy': 0.0005, # eV / electron
'density': 1.0e-4,
'eigenstates': 4.0e-8, # eV^2 / electron
'bands': 'CBM+2.0',
'forces': float('inf')} # eV / Ang Max
)
atoms.calc = calc
e2 = atoms.get_potential_energy()
d0 = atoms.get_distance(0, 1)
fd = open('optimization.txt', 'w')
print('experimental bond length:', file=fd)
print('hydrogen molecule energy: %5.2f eV' % e2, file=fd)
print('bondlength : %5.2f Ang' % d0, file=fd)
from ase.structure import molecule
from gpaw import GPAW
atoms = molecule('C6H6')
atoms.center(vacuum=3.5)
calc = GPAW(h=.21, xc='PBE', txt='benzene.txt', nbands=18)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.set(fixdensity=True,
txt='benzene-harris.txt',
nbands=40,
eigensolver='cg',
convergence={'bands': 35})
atoms.get_potential_energy()
calc.write('benzene.gpw', mode='all')
import numpy as np
from ase.build import bulk
from ase.units import Hartree, Bohr
from gpaw import GPAW, FermiDirac
from ase.dft.kpoints import monkhorst_pack
for kpt in (3, 4):
kpts = (kpt, kpt, kpt)
bzk_kc = monkhorst_pack(kpts)
shift_c = []
for Nk in kpts:
if Nk % 2 == 0:
shift_c.append(0.5 / Nk)
else:
shift_c.append(0.)
bzk_kc += shift_c
atoms = bulk('Si', 'diamond', a=5.431)
calc = GPAW(h=0.2, kpts=bzk_kc)
atoms.set_calculator(calc)
atoms.get_potential_energy()
kd = calc.wfs.kd
bzq_qc = kd.get_bz_q_points()
ibzq_qc = kd.get_ibz_q_points(bzq_qc, calc.wfs.kd.symmetry.op_scc)[0]
assert np.abs(bzq_qc - kd.bzk_kc).sum() < 1e-8
assert np.abs(ibzq_qc - kd.ibzk_kc).sum() < 1e-8
nk = 12
kpts = monkhorst_pack((nk, nk, nk)) + 0.5 / nk
c = ase.db.connect('gaps.db')
for name in ['Si', 'C', 'GaAs', 'MgO', 'NaCl', 'Ar']:
id = c.reserve(name=name)
if id is None:
continue
x, a = bfb[name][:2]
atoms = bulk(name, x, a=a)
atoms.calc = GPAW(xc='PBE',
mode=PW(500),
parallel=dict(band=1),
nbands=-8,
convergence=dict(bands=-7),
kpts=kpts,
txt='%s.txt' % name)
if name in ['MgO', 'NaCl']:
atoms.calc.set(eigensolver='dav')
atoms.get_potential_energy()
atoms.calc.write(name, mode='all')
ibzk_kc = atoms.calc.get_ibz_k_points()
n = int(atoms.calc.get_number_of_electrons()) // 2
ibzk = []
eps_kn = []
###############GROUND STATE CALCULATION####################
a = 3.57 # Lattice constant for diamond in angstrom
# Create diamond structure
diamond = bulk('C', 'diamond', a)
# Set up calculator
# Mode is plane wave with cut off 200 eV
# Exchange-correlation functional is Perdew, Burke, Ernzerhof
# Brilloin-zone will be sampled with a regular grid of 8x8x8 k-points
# Use random numbers for wave function initialization
# Occupation numbers follow Fermi-Dirac statistics with a width of 0.01 eV
# Text output sent to Di_gs.txt
calc = GPAW(mode=PW(200),
xc='PBE',
kpts=(8, 8, 8),
random=True,
occupations=FermiDirac(0.01),
txt='Di_gs.txt')
diamond.set_calculator(calc)
diamond.get_potential_energy()
# Save the ground state to a gpaw file
calc.write('Di_gs.gpw')
efermi = calc.get_fermi_level()
###############GENERATING K-POINTS#########################
# Number of lowest bands to converge
nbands = 11
# Restart the ground state calculator and fix potential
# Include 16 electronic bands for each spin calculation
h = 0.3
# No energies - simpley convergence test, esp. for 3d TM
# for atom in ['F', 'Cl', 'Br', 'Cu', 'Ag']:
for atom in ['Ti']:
gen(atom, xcname='PBE', scalarrel=False, exx=True)
work_atom = Cluster(Atoms(atom, [(0, 0, 0)]))
work_atom.minimal_box(4, h=h)
work_atom.translate([0.01, 0.02, 0.03])
work_atom.set_initial_magnetic_moments([2.0])
calculator = GPAW(convergence={
'energy': 0.01,
'eigenstates': 3,
'density': 3
},
eigensolver=RMMDIIS(),
poissonsolver=PoissonSolver(use_charge_center=True),
occupations=FermiDirac(width=0.0, fixmagmom=True),
h=h,
maxiter=35) # Up to 24 are needed by now
calculator.set(xc=HybridXC('PBE0'))
calculator.set(txt=atom + '-PBE0.txt')
work_atom.set_calculator(calculator)
try:
work_atom.get_potential_energy()
except KohnShamConvergenceError:
pass
assert calculator.scf.converged, 'Calculation not converged'
txt = '-'
txt = None
load = True
load = False
R = 0.7 # approx. experimental bond length
a = 4.0
c = 5.0
H2 = Atoms([
Atom('H', (a / 2, a / 2, (c - R) / 2)),
Atom('H', (a / 2, a / 2, (c + R) / 2))
],
cell=(a, a, c))
calc = GPAW(xc='PBE', nbands=2, spinpol=False, txt=txt)
H2.set_calculator(calc)
H2.get_potential_energy()
calc.write('H2saved_wfs.gpw', 'all')
calc.write('H2saved.gpw')
wfs_error = calc.wfs.eigensolver.error
xc = 'LDA'
#print "-> starting directly after a gs calculation"
lr = LrTDDFT(calc, xc=xc, txt='-')
lr.diagonalize()
#print "-> reading gs with wfs"
gs = GPAW('H2saved_wfs.gpw', txt=txt)
