def set_mixer(self, mixer):
if mixer is not None:
if self.nspins == 1 and isinstance(mixer, MixerSum):
raise RuntimeError('Cannot use MixerSum with nspins==1')
self.mixer = mixer
else:
if self.gd.pbc_c.any():
beta = 0.1
weight = 50.0
else:
beta = 0.25
weight = 1.0
if self.nspins == 2:
self.mixer = MixerSum(beta=beta, weight=weight)
else:
self.mixer = Mixer(beta=beta, weight=weight)
self.mixer.initialize(self)
def create_calc(name, spinpol, pbc):
# Bond lengths between H-C and C-C for ethyne (acetylene) cf.
# CRC Handbook of Chemistry and Physics, 87th ed., p. 9-28
dhc = 1.060
dcc = 1.203
atoms = Atoms([
Atom('H', (0, 0, 0)),
Atom('C', (dhc, 0, 0)),
Atom('C', (dhc + dcc, 0, 0)),
Atom('H', (2 * dhc + dcc, 0, 0))
],
pbc=pbc)
atoms.center(vacuum=2.0)
# Number of occupied and unoccupied bands to converge
nbands = int(10 / 2.0)
nextra = 3
#TODO use pbc and cell to calculate nkpts
kwargs = {}
if spinpol:
kwargs['mixer'] = MixerSum(nmaxold=5, beta=0.1, weight=100)
else:
kwargs['mixer'] = Mixer(nmaxold=5, beta=0.1, weight=100)
calc = GPAW(h=0.3,
nbands=nbands+nextra,
xc='PBE',
spinpol=spinpol,
eigensolver='cg',
convergence={'energy':1e-4/len(atoms), 'density':1e-5, \
'eigenstates': 1e-9, 'bands':-1},
txt=name+'.txt', **kwargs)
atoms.set_calculator(calc)
atoms.get_potential_energy()
calc.write(name + '.gpw', mode='all')
exx.calculate()
E0_hf = exx.get_total_energy()
calc.diagonalize_full_hamiltonian()
calc.write('CO.ralda.pbe_wfcs_CO.gpw', mode='all')
# C
C = Atoms('C')
C.set_pbc(True)
C.set_cell(CO.cell)
C.center()
calc = GPAW(mode=PW(600, force_complex_dtype=True),
parallel={'domain': 1},
xc='PBE',
mixer=MixerSum(beta=0.1, nmaxold=5, weight=50.0),
hund=True,
occupations=FermiDirac(0.01, fixmagmom=True),
txt='CO.ralda_01_C_pbe.txt',
convergence={'density': 1.e-6})
C.set_calculator(calc)
E1_pbe = C.get_potential_energy()
exx = EXX(calc, txt='CO.ralda_01_C_exx.txt')
exx.calculate()
E1_hf = exx.get_total_energy()
f = paropen('CO.ralda.PBE_HF_C.dat', 'w')
print(E1_pbe, E1_hf, file=f)
f.close()
spinpol=True,
convergence={
'energy': 100,
'density': 100,
'eigenstates': 1.0e-9,
'bands': 'occupied'
},
txt='CO_homo.txt')
calc = GPAW(nbands=80,
h=0.2,
xc='RPBE',
kpts=(8, 6, 1),
eigensolver='cg',
spinpol=True,
mixer=MixerSum(nmaxold=5, beta=0.1, weight=100),
convergence={
'energy': 100,
'density': 100,
'eigenstates': 1.0e-7,
'bands': -10
},
txt=filename + '.txt')
# Import Slab with relaxed CO
slab = fcc111('Pt', size=(1, 2, 3), orthogonal=True)
add_adsorbate(slab, 'C', 2.0, 'ontop')
add_adsorbate(slab, 'O', 3.15, 'ontop')
slab.center(axis=2, vacuum=4.0)
view(slab)
def calculate(element, h, vacuum, xc, magmom):
atom = Atoms([Atom(element, (0, 0, 0))])
if magmom > 0.0:
mms = [magmom for i in range(len(atom))]
atom.set_initial_magnetic_moments(mms)
atom.center(vacuum=vacuum)
mixer = MixerSum(beta=0.4)
if element == 'O':
mixer = MixerSum(0.4, nmaxold=1, weight=100)
atom.set_positions(atom.get_positions() + [0.0, 0.0, 0.0001])
calc_atom = GPAW(h=h,
xc=_xc(data[element][xc][2]),
experimental={'niter_fixdensity': 2},
eigensolver='rmm-diis',
occupations=FermiDirac(0.0, fixmagmom=True),
mixer=mixer,
parallel=dict(augment_grids=True),
nbands=-2,
txt='%s.%s.txt' % (element, xc))
atom.set_calculator(calc_atom)
mixer = Mixer(beta=0.4, weight=100)
compound = molecule(element + '2')
if compound == 'O2':
mixer = MixerSum(beta=0.4)
mms = [1.0 for i in range(len(compound))]
compound.set_initial_magnetic_moments(mms)
calc = GPAW(h=h,
xc=_xc(data[element][xc][2]),
experimental={'niter_fixdensity': 2},
eigensolver='rmm-diis',
mixer=mixer,
parallel=dict(augment_grids=True),
txt='%s2.%s.txt' % (element, xc))
compound.set_distance(0, 1, data[element]['R_AA_B3LYP'])
compound.center(vacuum=vacuum)
compound.set_calculator(calc)
if data[element][xc][3] == 'hyb_gga': # only for hybrids
e_atom = atom.get_potential_energy()
e_compound = compound.get_potential_energy()
calc_atom.set(xc=_xc(xc))
calc.set(xc=_xc(xc))
e_atom = atom.get_potential_energy()
e_compound = compound.get_potential_energy()
dHf_0 = (e_compound - 2 * e_atom + data[element]['ZPE_AA_B3LYP'] +
2 * data[element]['dHf_0_A'])
dHf_298 = (dHf_0 + data[element]['H_298_H_0_AA_B3LYP'] -
2 * data[element]['H_298_H_0_A']) * (mol / kcal)
de = dHf_298 - data[element][xc][1]
E[element][xc] = de
if rank == 0:
print((xc, h, vacuum, dHf_298, data[element][xc][1], de,
de / data[element][xc][1]))
if element == 'H':
equal(dHf_298, data[element][xc][1], 0.25,
msg=xc + ': ') # kcal/mol
elif element == 'O':
equal(dHf_298, data[element][xc][1], 7.5,
msg=xc + ': ') # kcal/mol
else:
equal(dHf_298, data[element][xc][1], 2.15,
msg=xc + ': ') # kcal/mol
equal(de, E_ref[element][xc], 0.06, msg=xc + ': ') # kcal/mol
from ase.lattice import bulk
modes = ['gpw']
try:
import _gpaw_hdf5
modes.append('hdf5')
except ImportError:
pass
# bulk Fe with k-point, band, and domain parallelization
a = 2.87
atoms = bulk('Fe', 'bcc', a=a)
atoms.set_initial_magnetic_moments([2.2,])
calc = GPAW(h=0.20,
eigensolver=RMM_DIIS(),
mixer=MixerSum(0.1,3),
nbands=6,
kpts=(4,4,4),
parallel={'band' : 2, 'domain' : (2,1,1)},
maxiter=4)
atoms.set_calculator(calc)
try:
atoms.get_potential_energy()
except ConvergenceError:
pass
for mode in modes:
calc.write('tmp.%s' % mode, mode='all')
# Continue calculation for few iterations
for mode in modes:
atoms, calc = restart('tmp.%s' % mode,
def calculate(element, h, vacuum, xc, magmom):
atom = Atoms([Atom(element, (0, 0, 0))])
if magmom > 0.0:
mms = [magmom for i in range(len(atom))]
atom.set_initial_magnetic_moments(mms)
atom.center(vacuum=vacuum)
mixer = MixerSum(beta=0.2)
if element == 'O':
mixer = MixerSum(nmaxold=1, weight=100)
atom.set_positions(atom.get_positions() + [0.0, 0.0, 0.0001])
calc_atom = GPAW(h=h,
xc=data[element][xc][2],
occupations=FermiDirac(0.0, fixmagmom=True),
mixer=mixer,
nbands=-2,
txt='%s.%s.txt' % (element, xc))
atom.set_calculator(calc_atom)
mixer = Mixer(beta=0.2, weight=100)
compound = molecule(element + '2')
if compound == 'O2':
mixer = MixerSum(beta=0.2)
mms = [1.0 for i in range(len(compound))]
compound.set_initial_magnetic_moments(mms)
calc = GPAW(h=h,
xc=data[element][xc][2],
mixer=mixer,
txt='%s2.%s.txt' % (element, xc))
compound.set_distance(0, 1, data[element]['R_AA_B3LYP'])
compound.center(vacuum=vacuum)
compound.set_calculator(calc)
if data[element][xc][3] == 'hyb_gga': # only for hybrids
e_atom = atom.get_potential_energy()
e_compound = compound.get_potential_energy()
calc_atom.set(xc=xc)
calc.set(xc=xc)
if 0:
qn = QuasiNewton(compound)
qn.attach(
PickleTrajectory(element + '2' + '_' + xc + '.traj', 'w',
compound).write)
qn.run(fmax=0.02)
e_atom = atom.get_potential_energy()
e_compound = compound.get_potential_energy()
dHf_0 = (e_compound - 2 * e_atom + data[element]['ZPE_AA_B3LYP'] +
2 * data[element]['dHf_0_A'])
dHf_298 = (dHf_0 + data[element]['H_298_H_0_AA_B3LYP'] -
2 * data[element]['H_298_H_0_A']) * (mol / kcal)
dist_compound = compound.get_distance(0, 1)
de = dHf_298 - data[element][xc][1]
E[element][xc] = de
if rank == 0:
print(xc, h, vacuum, dHf_298, data[element][xc][1], de,
de / data[element][xc][1])
if element == 'H':
equal(dHf_298, data[element][xc][1], 0.25,
msg=xc + ': ') # kcal/mol
elif element == 'O':
equal(dHf_298, data[element][xc][1], 7.5,
msg=xc + ': ') # kcal/mol
else:
equal(dHf_298, data[element][xc][1], 2.15,
msg=xc + ': ') # kcal/mol
equal(de, E_ref[element][xc], 0.06, msg=xc + ': ') # kcal/mol
try:
m.get_potential_energy()
except ConvergenceError:
pass
assert not calc.scf.converged
del calc
# converges (fortuitously)
# C2 really needs broken spin-symmetry to converge
calc = GPAW(h=0.18,
xc='PBE',
basis='dzp',
maxiter=550,
mixer=MixerSum(0.02, 3),
eigensolver='cg',
spinpol=True,
txt='C2_conv1.txt')
m.set_calculator(calc)
try:
e1 = m.get_potential_energy()
except ConvergenceError:
e1 = None
pass
del calc
# or with broken symmetry magnetic moments, to a different solution
m.set_initial_magnetic_moments([-0.5, 0.5])
from ase import Atoms
from gpaw import GPAW
from gpaw.mixer import MixerSum
a = 2.87
m = 2.2
bulk = Atoms('Fe2',
positions=[(0, 0, 0), (a / 2, a / 2, a / 2)],
magmoms=[m, -m],
cell=(a, a, a),
pbc=True)
calc = GPAW(kpts=(6, 6, 6),
h=0.20,
nbands=18,
mixer=MixerSum(beta=0.2, nmaxold=5),
eigensolver='dav',
txt='anti.txt')
bulk.set_calculator(calc)
print bulk.get_potential_energy()
calc.write('anti.gpw')