def __init__(self, width, orbitals):
FermiDirac.__init__(self, width)
self.orbitals = orbitals
self.norbitals = len(self.orbitals)
self.cnoe = 0.0
for orb in self.orbitals:
self.cnoe += orb[0]
def __init__(self, width, orbitals):
FermiDirac.__init__(self, width)
self.orbitals = orbitals
self.norbitals = len(self.orbitals)
self.cnoe = 0.0
for orb in self.orbitals:
self.cnoe += orb[0]
def calculate_band_energy(self, wfs):
FermiDirac.calculate_band_energy(self, wfs)
de_band = 0.0
for kpt in wfs.kpt_u:
if hasattr(kpt, 'c_on'):
for ne, c_n in zip(kpt.ne_o, kpt.c_on):
de_band += ne * np.dot(np.abs(c_n)**2, kpt.eps_n)
self.e_band += wfs.band_comm.sum(wfs.kpt_comm.sum(de_band))
def calculate_band_energy(self, wfs):
FermiDirac.calculate_band_energy(self, wfs)
de_band = 0.0
for kpt in wfs.kpt_u:
if hasattr(kpt, 'c_on'):
for ne, c_n in zip(kpt.ne_o, kpt.c_on):
de_band += ne * np.dot(np.abs(c_n)**2, kpt.eps_n)
self.e_band += wfs.bd.comm.sum(wfs.kd.comm.sum(de_band))
def get_paw():
"""Return calculator object."""
c = {'energy': 0.001, 'eigenstates': 0.001, 'density': 0.001}
return GPAW(convergence=c, eigensolver=RMMDIIS(),
xc='LCY-PBE:omega=0.83:unocc=True',
parallel={'domain': world.size}, h=0.35,
occupations=FermiDirac(width=0.0, fixmagmom=True))
def get_paw():
"""Return calculator object."""
c = {'energy': 0.05, 'eigenstates': 0.05, 'density': 0.05}
return GPAW(convergence=c, eigensolver=RMMDIIS(),
nbands=3,
xc='PBE',
# experimental={'niter_fixdensity': 2},
parallel={'domain': world.size}, h=0.35,
occupations=FermiDirac(width=0.0, fixmagmom=True))
def setup_calculator(self):
hund = (len(self.system) == 1)
self.system.set_calculator(
GPAW(xc=self.xc,
h=self.h,
hund=hund,
setups=self.setups,
txt=self.name + '.txt',
mode=self.mode,
spinpol=True,
occupations=FermiDirac(0, fixmagmom=True)))
def calculate(self, wfs):
FermiDirac.calculate(self, wfs)
# Get the expansion coefficients c_un for each dscf-orbital
# and incorporate their respective occupations into kpt.ne_o
c_oun = []
for orb in self.orbitals:
ef = self.fermilevel
if self.fixmagmom:
fermilevels = [ef + 0.5 * self.split, ef - 0.5 * self.split]
else:
fermilevels = ef
c_oun.append(orb[1].expand(fermilevels, wfs))
for u, kpt in enumerate(wfs.kpt_u):
kpt.ne_o = np.zeros(self.norbitals, dtype=float)
kpt.c_on = np.zeros((self.norbitals, len(kpt.f_n)), dtype=complex)
for o, orb in enumerate(self.orbitals):
#TODO XXX false if orb[0]<0 since abs(c_n)**2>0
#kpt.c_on[o,:] = abs(orb[0])**0.5 * c_oun[o][u]
kpt.ne_o[o] = orb[0]
kpt.c_on[o,:] = c_oun[o][u]
if wfs.nspins == 2:
assert orb[2] in range(2), 'Invalid spin index'
if orb[2] == kpt.s:
kpt.ne_o[o] *= kpt.weight
else:
kpt.ne_o[o] = 0.0
else:
kpt.ne_o[o] *= 0.5 * kpt.weight
# Correct the magnetic moment
for orb in self.orbitals:
if orb[2] == 0:
self.magmom += orb[0]
elif orb[2] == 1:
self.magmom -= orb[0]
def calculate(self, wfs):
FermiDirac.calculate(self, wfs)
# Get the expansion coefficients c_un for each dscf-orbital
# and incorporate their respective occupations into kpt.ne_o
c_oun = []
for orb in self.orbitals:
ef = self.fermilevel
if self.fixmagmom:
fermilevels = [ef + 0.5 * self.split, ef - 0.5 * self.split]
else:
fermilevels = ef
c_oun.append(orb[1].expand(fermilevels, wfs, self.fixmagmom))
for u, kpt in enumerate(wfs.kpt_u):
kpt.ne_o = np.zeros(self.norbitals, dtype=float)
kpt.c_on = np.zeros((self.norbitals, len(kpt.f_n)), dtype=complex)
for o, orb in enumerate(self.orbitals):
# TODO XXX false if orb[0]<0 since abs(c_n)**2>0
#kpt.c_on[o,:] = abs(orb[0])**0.5 * c_oun[o][u]
kpt.ne_o[o] = orb[0]
kpt.c_on[o, :] = c_oun[o][u]
if wfs.nspins == 2:
assert orb[2] in range(2), 'Invalid spin index'
if orb[2] == kpt.s:
kpt.ne_o[o] *= kpt.weight
else:
kpt.ne_o[o] = 0.0
else:
kpt.ne_o[o] *= 0.5 * kpt.weight
# Correct the magnetic moment
for orb in self.orbitals:
if orb[2] == 0:
self.magmom += orb[0]
elif orb[2] == 1:
self.magmom -= orb[0]
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
def do_gs_calc(fname):
printit('running GS calculation')
a = read(fname)
calc = GPAW(mode='lcao',
basis='dzp',
xc='PBE',
occupations=FermiDirac(width=0.01),
kpts={
'size': (1, 20, 1),
'gamma': True
},
txt='gs_output.txt')
a.set_calculator(calc)
a.get_potential_energy()
calc.write('gs_' + fname + '.gpw', mode='all')
printit('GS calculation done')
def set_calculator(calc, e_km, v_knm=None, width=None):
from gpaw.occupations import FermiDirac
from ase.units import Hartree
if width is None:
width = calc.occupations.width * Hartree
calc.wfs.bd.nbands *= 2
calc.wfs.nspins = 1
for kpt in calc.wfs.kpt_u:
kpt.eps_n = e_km[kpt.k] / Hartree
kpt.f_n = np.zeros_like(kpt.eps_n)
kpt.weight /= 2
ef = calc.occupations.fermilevel
calc.occupations = FermiDirac(width)
calc.occupations.nvalence = calc.wfs.setups.nvalence - calc.density.charge
calc.occupations.fermilevel = ef
calc.occupations.calculate_occupation_numbers(calc.wfs)
for kpt in calc.wfs.kpt_u:
kpt.f_n *= 2
kpt.weight *= 2
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
def read(self, reader):
"""Read state from file."""
r = reader
version = r['version']
assert version >= 0.3
self.xc = r['XCFunctional']
self.nbands = r.dimension('nbands')
self.spinpol = (r.dimension('nspins') == 2)
bzk_kc = r.get('BZKPoints', broadcast=True)
if r.has_array('NBZKPoints'):
self.kpts = r.get('NBZKPoints', broadcast=True)
if r.has_array('MonkhorstPackOffset'):
offset_c = r.get('MonkhorstPackOffset', broadcast=True)
if offset_c.any():
self.kpts = monkhorst_pack(self.kpts) + offset_c
else:
self.kpts = bzk_kc
if version < 4:
self.symmetry = usesymm2symmetry(r['UseSymmetry'])
else:
self.symmetry = {'point_group': r['SymmetryOnSwitch'],
'symmorphic': r['SymmetrySymmorphicSwitch'],
'time_reversal': r['SymmetryTimeReversalSwitch'],
'tolerance': r['SymmetryToleranceCriterion']}
try:
self.basis = r['BasisSet']
except KeyError:
pass
if version >= 2:
try:
h = r['GridSpacing']
except KeyError: # CMR can't handle None!
h = None
if h is not None:
self.h = Bohr * h
if r.has_array('GridPoints'):
self.gpts = r.get('GridPoints')
else:
if version >= 0.9:
h = r['GridSpacing']
else:
h = None
gpts = ((r.dimension('ngptsx') + 1) // 2 * 2,
(r.dimension('ngptsy') + 1) // 2 * 2,
(r.dimension('ngptsz') + 1) // 2 * 2)
if h is None:
self.gpts = gpts
else:
self.h = Bohr * h
self.lmax = r['MaximumAngularMomentum']
self.setups = r['SetupTypes']
self.fixdensity = r['FixDensity']
if version <= 0.4:
# Old version: XXX
print(('# Warning: Reading old version 0.3/0.4 restart files ' +
'will be disabled some day in the future!'))
self.convergence['eigenstates'] = r['Tolerance']
else:
nbtc = r['NumberOfBandsToConverge']
if not isinstance(nbtc, (int, str)):
# The string 'all' was eval'ed to the all() function!
nbtc = 'all'
if version < 5:
force_crit = None
else:
force_crit = r['ForcesConvergenceCriterion']
if force_crit is not None:
force_crit *= (Hartree / Bohr)
self.convergence = {'density': r['DensityConvergenceCriterion'],
'energy':
r['EnergyConvergenceCriterion'] * Hartree,
'eigenstates':
r['EigenstatesConvergenceCriterion'],
'bands': nbtc,
'forces': force_crit}
if version < 1:
# Volume per grid-point:
dv = (abs(np.linalg.det(r.get('UnitCell'))) /
(gpts[0] * gpts[1] * gpts[2]))
self.convergence['eigenstates'] *= Hartree**2 * dv
if version <= 0.6:
mixer = 'Mixer'
weight = r['MixMetric']
elif version <= 0.7:
mixer = r['MixClass']
weight = r['MixWeight']
metric = r['MixMetric']
if metric is None:
weight = 1.0
else:
mixer = r['MixClass']
weight = r['MixWeight']
if mixer == 'Mixer':
from gpaw.mixer import Mixer
elif mixer == 'MixerSum':
from gpaw.mixer import MixerSum as Mixer
elif mixer == 'MixerSum2':
from gpaw.mixer import MixerSum2 as Mixer
elif mixer == 'MixerDif':
from gpaw.mixer import MixerDif as Mixer
elif mixer == 'DummyMixer':
from gpaw.mixer import DummyMixer as Mixer
else:
Mixer = None
if Mixer is None:
self.mixer = None
else:
self.mixer = Mixer(r['MixBeta'], r['MixOld'], weight)
if version == 0.3:
# Old version: XXX
print(('# Warning: Reading old version 0.3 restart files is ' +
'dangerous and will be disabled some day in the future!'))
self.stencils = (2, 3)
self.charge = 0.0
fixmom = False
else:
self.stencils = (r['KohnShamStencil'],
r['InterpolationStencil'])
if r['PoissonStencil'] == 999:
self.poissonsolver = FFTPoissonSolver()
else:
self.poissonsolver = PoissonSolver(nn=r['PoissonStencil'])
self.charge = r['Charge']
fixmom = r['FixMagneticMoment']
self.occupations = FermiDirac(r['FermiWidth'] * Hartree,
fixmagmom=fixmom)
try:
self.mode = r['Mode']
except KeyError:
self.mode = 'fd'
if self.mode == 'pw':
self.mode = PW(ecut=r['PlaneWaveCutoff'] * Hartree)
if len(bzk_kc) == 1 and not bzk_kc[0].any():
# Gamma point only:
if r['DataType'] == 'Complex':
self.dtype = complex
atoms = Atoms('N2', positions=[(0, 0, 0), (0, 0, d_bond + d_disp)])
atoms.set_pbc(False)
atoms.center(vacuum=6.0)
cell_c = np.sum(atoms.get_cell()**2, axis=1)**0.5
N_c = 8 * np.round(cell_c / (0.2 * 8))
calc = GPAW(gpts=N_c, nbands=5, basis='dzp', # TODO xc='PBE'
txt=name + '_gs.txt', parallel={'band': 1})
atoms.set_calculator(calc)
# QuasiNewton relaxation before we increase the number of bands
qn = BFGS(atoms, logfile=name + '_gs.log',
trajectory=name + '_gs.traj')
qn.run(0.01, steps=100)
# Converge enough unoccupied bands for dSCF expansion
calc.set(nbands=10, spinpol=True, occupations=FermiDirac(0.1),
convergence={'bands': -2, 'eigenstates': 1.0e-9})
atoms.get_potential_energy()
calc.write(name + '_gs.gpw', mode='all')
del qn, calc, atoms
time.sleep(10)
while not os.path.isfile(name + '_gs.gpw'):
print('Node %d waiting for %s...' % (world.rank, name + '_gs.gpw'))
time.sleep(10)
world.barrier()
if not os.path.isfile(name + '_es.gpw'):
# Resume ground state calculator and use as basis for excited state
calc = GPAW(name + '_gs.gpw',
txt=name + '_es.txt',
L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na9', pbc=(0, 0, 1), cell=[L, L, 9 * a])
atoms.positions[:9, 2] = [i * a for i in range(9)]
atoms.positions[:, :2] = L / 2.
atoms.center()
pl_atoms1 = range(4)
pl_atoms2 = range(5, 9)
pl_cell1 = (L, L, 4 * a)
pl_cell2 = pl_cell1
t = Transport(h=0.3,
xc='LDA',
basis={'Na': basis},
kpts=(1, 1, 1),
occupations=FermiDirac(0.1),
mode='lcao',
poissonsolver=PoissonSolver(nn=2, relax='GS'),
txt='Na_lcao.txt',
mixer=Mixer(0.1, 5, weight=100.0),
pl_atoms=[pl_atoms1, pl_atoms2],
pl_cells=[pl_cell1, pl_cell2],
pl_kpts=(1, 1, 5),
edge_atoms=[[0, 3], [0, 8]],
mol_atoms=[4],
guess_steps=1,
fixed_boundary=False)
atoms.set_calculator(t)
t.calculate_iv(0.5, 2)
from gpaw.elf import ELF
# Graphene nanoribbon
ribbon = graphene_nanoribbon(5, 6, type='armchair', saturated=True, vacuum=3.5)
# Gold adsorbate
pos = (ribbon[35].position + ribbon[60].position) / 2.0
pos[1] += 2.2
adsorbate = Atoms('Au', (pos, ))
ribbon += adsorbate
ribbon.center(axis=1, vacuum=3.5)
txt = 'output_p_{}.txt'.format(size)
ribbon.calc = GPAW(
h=0.22,
xc='PBE',
txt=txt,
occupations=FermiDirac(0.2),
eigensolver=RMMDIIS(),
)
ribbon.get_potential_energy()
# Calculate electron localization function
elf = ELF(ribbon.calc)
elf.update()
elf_g = elf.get_electronic_localization_function(gridrefinement=2)
if rank == 0:
write('elf_ribbon.cube', ribbon, data=elf_g)
yukawa_gamma=0.83, gpernode=149)
h = 0.35
be = Cluster(Atoms('Be', positions=[[0, 0, 0]]))
be.minimal_box(3.0, h=h)
c = {'energy': 0.05, 'eigenstates': 0.05, 'density': 0.05}
IP = 8.79
xc = HybridXC('LCY-PBE', omega=0.83)
fname = 'Be_rsf.gpw'
calc = GPAW(txt='Be.txt', xc=xc, convergence=c,
eigensolver=RMMDIIS(), h=h,
occupations=FermiDirac(width=0.0), spinpol=False)
be.set_calculator(calc)
# energy = na2.get_potential_energy()
# calc.set(xc=xc)
energy_083 = be.get_potential_energy()
(eps_homo, eps_lumo) = calc.get_homo_lumo()
equal(eps_homo, -IP, 0.15)
xc2 = 'LCY-PBE'
energy_075 = calc.get_xc_difference(HybridXC(xc2))
equal(energy_083 - energy_075, 21.13, 0.2, 'wrong energy difference')
calc.write(fname)
calc2 = GPAW(fname)
func = calc2.get_xc_functional()
assert func['name'] == 'LCY-PBE', 'wrong name for functional'
assert func['omega'] == 0.83, 'wrong value for RSF omega'
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
def dscf_collapse_orbitals(paw, nbands_max='occupied', f_tol=1e-4,
verify_density=True, nt_tol=1e-5, D_tol=1e-3):
bd, gd, kd = paw.wfs.bd, paw.wfs.gd, paw.wfs.kd
if bd.comm.size != 1:
raise NotImplementedError('Undefined action for band parallelization.')
f_skn = np.empty((kd.nspins, kd.nibzkpts, bd.nbands), dtype=float)
for s, f_kn in enumerate(f_skn):
for k, f_n in enumerate(f_kn):
kpt_rank, myu = kd.get_rank_and_index(s, k)
if kd.comm.rank == kpt_rank:
f_n[:] = paw.wfs.kpt_u[myu].f_n
kd.comm.broadcast(f_n, kpt_rank)
# Find smallest band index, from which all bands have negligeble occupations
n0 = np.argmax(f_skn<f_tol, axis=-1).max()
assert np.all(f_skn[...,n0:]<f_tol) # XXX use f_skn[...,n0:].sum()<f_tol
# Read the number of Delta-SCF orbitals
norbitals = paw.occupations.norbitals
if debug: mpi_debug('n0=%d, norbitals=%d, bd:%d, gd:%d, kd:%d' % (n0,norbitals,bd.comm.size,gd.comm.size,kd.comm.size))
if nbands_max < 0:
nbands_max = n0 + norbitals - nbands_max
elif nbands_max == 'occupied':
nbands_max = n0 + norbitals
assert nbands_max >= n0 + norbitals, 'Too few bands to include occupations.'
ncut = nbands_max-norbitals
if debug: mpi_debug('nbands_max=%d' % nbands_max)
paw.wfs.initialize_wave_functions_from_restart_file() # hurts memmory
for kpt in paw.wfs.kpt_u:
mol = kpt.P_ani.keys() # XXX stupid
(f_o, eps_o, wf_oG, P_aoi,) = dscf_reconstruct_orbitals_k_point(paw, norbitals, mol, kpt)
assert np.abs(f_o-1).max() < 1e-9, 'Orbitals must be properly normalized.'
f_o = kpt.ne_o # actual ocupatiion numbers
# Crop band-data and inject data for Delta-SCF orbitals
kpt.f_n = np.hstack((kpt.f_n[:n0], f_o, kpt.f_n[n0:ncut]))
kpt.eps_n = np.hstack((kpt.eps_n[:n0], eps_o, kpt.eps_n[n0:ncut]))
for a, P_ni in kpt.P_ani.items():
kpt.P_ani[a] = np.vstack((P_ni[:n0], P_aoi[a], P_ni[n0:ncut]))
old_psit_nG = kpt.psit_nG
kpt.psit_nG = gd.empty(nbands_max, dtype=old_psit_nG.dtype)
if isinstance(old_psit_nG, FileReference):
assert old_psit_nG.shape[-3:] == wf_oG.shape[-3:], 'Shape mismatch!'
# Read band-by-band to save memory as full psit_nG may be large
for n,psit_G in enumerate(kpt.psit_nG):
if n < n0:
full_psit_G = old_psit_nG[n]
elif n in range(n0,n0+norbitals):
full_psit_G = wf_oG[n-n0]
else:
full_psit_G = old_psit_nG[n-norbitals]
gd.distribute(full_psit_G, psit_G)
else:
kpt.psit_nG[:n0] = old_psit_nG[:n0]
kpt.psit_nG[n0:n0+norbitals] = wf_oG
kpt.psit_nG[n0+norbitals:] = old_psit_nG[n0:ncut]
del kpt.ne_o, kpt.c_on, old_psit_nG
del paw.occupations.norbitals
# Change various parameters related to new number of bands
paw.wfs.bd = BandDescriptor(nbands_max, bd.comm, bd.strided)
if paw.wfs.eigensolver:
paw.wfs.eigensolver.initialized = False
del bd
# Crop convergence criteria nbands_converge to new number of bands
par = paw.input_parameters
if 'convergence' in par:
cc = par['convergence']
if 'bands' in cc:
cc['bands'] = min(nbands_max, cc['bands'])
# Replace occupations class with a fixed variant (gets the magmom right) XXX?!?
fermilevel, magmom = paw.occupations.fermilevel, paw.occupations.magmom
paw.occupations = FermiDirac(paw.occupations.width * Hartree, paw.occupations.fixmagmom)
paw.occupations.fermilevel = fermilevel
paw.occupations.magmom = magmom
del fermilevel, magmom
# For good measure, self-consistency information should be destroyed
paw.scf.reset()
if verify_density:
paw.initialize_positions()
# Re-calculate pseudo density and watch for changes
old_nt_sG = paw.density.nt_sG.copy()
paw.density.calculate_pseudo_density(paw.wfs)
if debug: mpi_debug('delta-density: %g' % np.abs(old_nt_sG-paw.density.nt_sG).max())
assert np.abs(paw.density.nt_sG-old_nt_sG).max() < nt_tol, 'Density changed!'
# Re-calculate atomic density matrices and watch for changes
old_D_asp = {}
for a,D_sp in paw.density.D_asp.items():
old_D_asp[a] = D_sp.copy()
paw.wfs.calculate_atomic_density_matrices(paw.density.D_asp)
if debug: mpi_debug('delta-D_asp: %g' % max([0]+[np.abs(D_sp-old_D_asp[a]).max() for a,D_sp in paw.density.D_asp.items()]))
for a,D_sp in paw.density.D_asp.items():
assert np.abs(D_sp-old_D_asp[a]).max() < D_tol, 'Atom %d changed!' % a
# IP for CO using LCY-PBE with gamma=0.81 after
# dx.doi.org/10.1021/acs.jctc.8b00238
IP = 14.31
if setup_paths[0] != '.':
setup_paths.insert(0, '.')
for atom in ['C', 'O']:
gen(atom, xcname='PBE', scalarrel=True, exx=True, yukawa_gamma=0.81)
h = 0.30
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, 1.15)])
co.minimal_box(5)
# c = {'energy': 0.005, 'eigenstates': 1e-4} # Usable values
c = {'energy': 0.1, 'eigenstates': 3, 'density': 3} # Values for test
calc = GPAW(txt='CO.txt',
xc='LCY-PBE:omega=0.81',
convergence=c,
eigensolver=RMMDIIS(),
h=h,
poissonsolver=PoissonSolver(use_charge_center=True),
occupations=FermiDirac(width=0.0),
spinpol=False)
co.set_calculator(calc)
co.get_potential_energy()
(eps_homo, eps_lumo) = calc.get_homo_lumo()
equal(eps_homo, -IP, 0.15)
def __init__(self, width, *args, **kwargs):
raise NotImplementedError
FermiDirac.__init__(self, width, fermi)
self.set_fermi_level(epsF)
self.niter = 0
def wrap_old_gpw_reader(filename):
warnings.warn('You are reading an old-style gpw-file. Please check '
'the results carefully!')
r = Reader(filename)
data = {
'version': -1,
'gpaw_version': '1.0',
'ha': Ha,
'bohr': Bohr,
'scf.': {
'converged': True
},
'atoms.': {},
'wave_functions.': {}
}
class DictBackend:
def write(self, **kwargs):
data['atoms.'].update(kwargs)
write_atoms(DictBackend(), read_atoms(r))
e_total_extrapolated = r.get('PotentialEnergy').item() * Ha
magmom_a = r.get('MagneticMoments')
data['results.'] = {
'energy': e_total_extrapolated,
'magmoms': magmom_a,
'magmom': magmom_a.sum()
}
if r.has_array('CartesianForces'):
data['results.']['forces'] = r.get('CartesianForces') * Ha / Bohr
p = data['parameters.'] = {}
p['xc'] = r['XCFunctional']
p['nbands'] = r.dimension('nbands')
p['spinpol'] = (r.dimension('nspins') == 2)
bzk_kc = r.get('BZKPoints', broadcast=True)
if r.has_array('NBZKPoints'):
p['kpts'] = r.get('NBZKPoints', broadcast=True)
if r.has_array('MonkhorstPackOffset'):
offset_c = r.get('MonkhorstPackOffset', broadcast=True)
if offset_c.any():
p['kpts'] = monkhorst_pack(p['kpts']) + offset_c
else:
p['kpts'] = bzk_kc
if r['version'] < 4:
usesymm = r['UseSymmetry']
if usesymm is None:
p['symmetry'] = {'time_reversal': False, 'point_group': False}
elif usesymm:
p['symmetry'] = {'time_reversal': True, 'point_group': True}
else:
p['symmetry'] = {'time_reversal': True, 'point_group': False}
else:
p['symmetry'] = {
'point_group': r['SymmetryOnSwitch'],
'symmorphic': r['SymmetrySymmorphicSwitch'],
'time_reversal': r['SymmetryTimeReversalSwitch'],
'tolerance': r['SymmetryToleranceCriterion']
}
p['basis'] = r['BasisSet']
try:
h = r['GridSpacing']
except KeyError: # CMR can't handle None!
h = None
if h is not None:
p['h'] = Bohr * h
if r.has_array('GridPoints'):
p['gpts'] = r.get('GridPoints')
p['lmax'] = r['MaximumAngularMomentum']
p['setups'] = r['SetupTypes']
p['fixdensity'] = r['FixDensity']
nbtc = r['NumberOfBandsToConverge']
if not isinstance(nbtc, (int, str)):
# The string 'all' was eval'ed to the all() function!
nbtc = 'all'
p['convergence'] = {
'density': r['DensityConvergenceCriterion'],
'energy': r['EnergyConvergenceCriterion'] * Ha,
'eigenstates': r['EigenstatesConvergenceCriterion'],
'bands': nbtc
}
mixer = r['MixClass']
weight = r['MixWeight']
for key in ['basis', 'setups']:
dct = p[key]
if isinstance(dct, dict) and None in dct:
dct['default'] = dct.pop(None)
if mixer == 'Mixer':
from gpaw.mixer import Mixer
elif mixer == 'MixerSum':
from gpaw.mixer import MixerSum as Mixer
elif mixer == 'MixerSum2':
from gpaw.mixer import MixerSum2 as Mixer
elif mixer == 'MixerDif':
from gpaw.mixer import MixerDif as Mixer
elif mixer == 'DummyMixer':
from gpaw.mixer import DummyMixer as Mixer
else:
Mixer = None
if Mixer is None:
p['mixer'] = None
else:
p['mixer'] = Mixer(r['MixBeta'], r['MixOld'], weight)
p['stencils'] = (r['KohnShamStencil'], r['InterpolationStencil'])
vt_sG = r.get('PseudoPotential') * Ha
ps = r['PoissonStencil']
if isinstance(ps, int) or ps == 'M':
poisson = {'name': 'fd'}
poisson['nn'] = ps
if data['atoms.']['pbc'] == [1, 1, 0]:
v1, v2 = vt_sG[0, :, :, [0, -1]].mean(axis=(1, 2))
if abs(v1 - v2) > 0.01:
warnings.warn('I am guessing that this calculation was done '
'with a dipole-layer correction?')
poisson['dipolelayer'] = 'xy'
p['poissonsolver'] = poisson
p['charge'] = r['Charge']
fixmom = r['FixMagneticMoment']
p['occupations'] = FermiDirac(r['FermiWidth'] * Ha, fixmagmom=fixmom)
p['mode'] = r['Mode']
if p['mode'] == 'pw':
p['mode'] = PW(ecut=r['PlaneWaveCutoff'] * Ha)
if len(bzk_kc) == 1 and not bzk_kc[0].any():
# Gamma point only:
if r['DataType'] == 'Complex':
p['dtype'] = complex
data['occupations.'] = {
'fermilevel': r['FermiLevel'] * Ha,
'split': r.parameters.get('FermiSplit', 0) * Ha,
'h**o': np.nan,
'lumo': np.nan
}
data['density.'] = {
'density': r.get('PseudoElectronDensity') * Bohr**-3,
'atomic_density_matrices': r.get('AtomicDensityMatrices')
}
data['hamiltonian.'] = {
'e_coulomb': r['Epot'] * Ha,
'e_entropy': -r['S'] * Ha,
'e_external': r['Eext'] * Ha,
'e_kinetic': r['Ekin'] * Ha,
'e_total_extrapolated': e_total_extrapolated,
'e_xc': r['Exc'] * Ha,
'e_zero': r['Ebar'] * Ha,
'potential': vt_sG,
'atomic_hamiltonian_matrices': r.get('NonLocalPartOfHamiltonian') * Ha
}
data['hamiltonian.']['e_total_free'] = (sum(
data['hamiltonian.'][e] for e in [
'e_coulomb', 'e_entropy', 'e_external', 'e_kinetic', 'e_xc',
'e_zero'
]))
if r.has_array('GLLBPseudoResponsePotential'):
data['hamiltonian.']['xc.'] = {
'gllb_pseudo_response_potential':
r.get('GLLBPseudoResponsePotential') * Ha,
'gllb_dxc_pseudo_response_potential':
r.get('GLLBDxcPseudoResponsePotential') * Ha / Bohr,
'gllb_atomic_density_matrices':
r.get('GLLBAtomicDensityMatrices'),
'gllb_atomic_response_matrices':
r.get('GLLBAtomicResponseMatrices'),
'gllb_dxc_atomic_density_matrices':
r.get('GLLBDxcAtomicDensityMatrices'),
'gllb_dxc_atomic_response_matrices':
r.get('GLLBDxcAtomicResponseMatrices')
}
special = [('eigenvalues', 'Eigenvalues'),
('occupations', 'OccupationNumbers'),
('projections', 'Projections')]
if r['Mode'] == 'pw':
special.append(('coefficients', 'PseudoWaveFunctions'))
try:
data['wave_functions.']['indices'] = r.get('PlaneWaveIndices')
except KeyError:
pass
elif r['Mode'] == 'fd':
special.append(('values', 'PseudoWaveFunctions'))
else:
special.append(('coefficients', 'WaveFunctionCoefficients'))
for name, old in special:
try:
fd, shape, size, dtype = r.get_file_object(old, ())
except KeyError:
continue
offset = fd
data['wave_functions.'][name + '.'] = {
'ndarray': (shape, dtype.name, offset)
}
new = ulm.Reader(devnull,
data=data,
little_endian=r.byteswap ^ np.little_endian)
for ref in new._data['wave_functions']._data.values():
try:
ref.fd = ref.offset
except AttributeError:
continue
ref.offset = 0
return new
xc = 'PBE'
fit = (5, 0.02)
w = 0.06
ecut = 1200
kd = 8.0
tag = 'dcdft_%s_gpaw_pw' % xc.lower()
task = Task(
calcfactory=Factory(
xc=xc,
mode=PW(ecut),
occupations=FermiDirac(w),
maxiter=250,
kptdensity=kd,
),
tag=tag,
fit=fit,
use_lock_files=True,
)
if __name__ == '__main__':
if element is None:
keys = set(parameters.keys()).intersection(set(task.collection.names))
for s in elements_slow:
keys.remove(s) # those are slow, run separately
else:
keys = [element]
def read(self, reader):
"""Read state from file."""
if isinstance(reader, str):
reader = gpaw.io.open(reader, 'r')
r = reader
version = r['version']
assert version >= 0.3
self.xc = r['XCFunctional']
self.nbands = r.dimension('nbands')
self.spinpol = (r.dimension('nspins') == 2)
if r.has_array('NBZKPoints'):
self.kpts = r.get('NBZKPoints')
else:
self.kpts = r.get('BZKPoints')
self.usesymm = r['UseSymmetry']
try:
self.basis = r['BasisSet']
except KeyError:
pass
self.gpts = ((r.dimension('ngptsx') + 1) // 2 * 2,
(r.dimension('ngptsy') + 1) // 2 * 2,
(r.dimension('ngptsz') + 1) // 2 * 2)
self.lmax = r['MaximumAngularMomentum']
self.setups = r['SetupTypes']
self.fixdensity = r['FixDensity']
if version <= 0.4:
# Old version: XXX
print('# Warning: Reading old version 0.3/0.4 restart files ' +
'will be disabled some day in the future!')
self.convergence['eigenstates'] = r['Tolerance']
else:
self.convergence = {
'density': r['DensityConvergenceCriterion'],
'energy': r['EnergyConvergenceCriterion'] * Hartree,
'eigenstates': r['EigenstatesConvergenceCriterion'],
'bands': r['NumberOfBandsToConverge']
}
if version <= 0.6:
mixer = 'Mixer'
weight = r['MixMetric']
elif version <= 0.7:
mixer = r['MixClass']
weight = r['MixWeight']
metric = r['MixMetric']
if metric is None:
weight = 1.0
else:
mixer = r['MixClass']
weight = r['MixWeight']
if mixer == 'Mixer':
from gpaw.mixer import Mixer
elif mixer == 'MixerSum':
from gpaw.mixer import MixerSum as Mixer
elif mixer == 'MixerSum2':
from gpaw.mixer import MixerSum2 as Mixer
elif mixer == 'MixerDif':
from gpaw.mixer import MixerDif as Mixer
elif mixer == 'DummyMixer':
from gpaw.mixer import DummyMixer as Mixer
else:
Mixer = None
if Mixer is None:
self.mixer = None
else:
self.mixer = Mixer(r['MixBeta'], r['MixOld'], weight)
if version == 0.3:
# Old version: XXX
print('# Warning: Reading old version 0.3 restart files is ' +
'dangerous and will be disabled some day in the future!')
self.stencils = (2, 3)
self.charge = 0.0
fixmom = False
else:
self.stencils = (r['KohnShamStencil'], r['InterpolationStencil'])
if r['PoissonStencil'] == 999:
self.poissonsolver = FFTPoissonSolver()
else:
self.poissonsolver = PoissonSolver(nn=r['PoissonStencil'])
self.charge = r['Charge']
fixmom = r['FixMagneticMoment']
self.occupations = FermiDirac(r['FermiWidth'] * Hartree,
fixmagmom=fixmom)
try:
self.mode = r['Mode']
except KeyError:
self.mode = 'fd'
try:
dtype = r['DataType']
if dtype == 'Float':
self.dtype = float
else:
self.dtype = complex
except KeyError:
self.dtype = float
k = KPoint()
def f(occ, x):
k.eps_n[0] = x
n, dnde, x, S = occ.distribution(k, 0.0)
return n, dnde, S
def test(occ):
print(occ)
for e in [-0.3 / Hartree, 0, 0.1 / Hartree, 1.2 / Hartree]:
n0, d0, S0 = f(occ, e)
x = 0.000001
np, dp, Sp = f(occ, e + x)
nm, dm, Sm = f(occ, e - x)
d = -(np - nm) / (2 * x)
dS = Sm - Sp
dn = np - nm
print(d - d0, dS - e * dn)
assert abs(d - d0) < 3e-5
assert abs(dS - e * dn) < 1e-13
for w in [0.1, 0.5]:
test(FermiDirac(w))
for n in range(4):
test(MethfesselPaxton(w, n))
def __init__(self, width, *args, **kwargs):
raise NotImplementedError
FermiDirac.__init__(self, width, fermi)
self.set_fermi_level(epsF)
self.niter = 0
print("#" * 60)
print("GPAW benchmark: Carbon Fullerenes on a Lead Surface")
print(" grid spacing: h=%f" % h)
print(" Brillouin-zone sampling: kpts=" + str(kpts))
print(" MPI tasks: %d" % size)
print(" using CUDA (GPGPU): " + str(use_cuda))
print(" using pyMIC (KNC) : " + str(use_mic))
print(" using CPU (or KNL): " + str(use_cpu))
print("#" * 60)
print("")
# setup parameters
args = {
'h': h,
'nbands': -180,
'occupations': FermiDirac(0.2),
'kpts': kpts,
'xc': 'PBE',
'mixer': Mixer(0.1, 5, 100),
'eigensolver': 'rmm-diis',
'maxiter': maxiter,
'xc_thread': False,
'txt': txt
}
if use_cuda:
args['gpu'] = {'cuda': True, 'hybrid_blas': False}
try:
args['parallel'] = parallel
except:
pass
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'