def calc_me(atoms, nbands):
"""Do the calculation."""
molecule_name = atoms.get_chemical_formula()
atoms.set_initial_magnetic_moments([-1.0, 1.0])
fname = '.'.join([molecule_name, 'PBE-SIN'])
calc = GPAW(h=0.25,
xc='PBE',
eigensolver=CG(niter=5),
nbands=nbands,
txt=fname + '.log',
occupations=FermiDirac(0.0, fixmagmom=True),
convergence={
'energy': 0.005,
'bands': nbands,
'eigenstates': 1e-4,
'density': 1e-3
})
atoms.set_calculator(calc)
try:
atoms.get_potential_energy()
except KohnShamConvergenceError:
pass
if calc.scf.converged:
for calcp in calc_parms:
calc.set(**calcp)
try:
calc.calculate(system_changes=[])
except KohnShamConvergenceError:
break
if calc.scf.converged:
calc.write(fname + '.gpw', mode='all')
def gw_calc(kptsize=12, ecut=200.0, gwg_and_gw=False, gw_only=True):
"""Calculate the gw bandstructure"""
calc = GPAW('gs.gpw', txt=None)
kpts = {'size': (kptsize, kptsize, 1), 'gamma': True}
calc.set(kpts=kpts, fixdensity=True, txt='gs_gw.txt')
calc.get_potential_energy()
calc.diagonalize_full_hamiltonian(ecut=ecut)
calc.write('gs_gw_nowfs.gpw')
calc.write('gs_gw.gpw', mode='all')
lb, ub = get_bandrange(calc)
calc = G0W0(calc='gs_gw.gpw',
bands=(lb, ub),
ecut=ecut,
ecut_extrapolation=True,
truncation='2D',
nblocks=get_nblocks(world.size),
q0_correction=True,
filename='g0w0',
restartfile='g0w0.tmp',
savepckl=True)
calc.calculate()
def descriptors(cif):
f = open('a.cif', 'w')
f.write(cif)
f.flush()
f.close
a = read('a.cif')
descriptors_below = []
descriptors_above = []
try:
calc = GPAW(
mode='lcao',
xc='PBE',
maxiter=1,
# nbands=100,
# parallel={'domain': 1, 'band': 1},
# occupations=FermiDirac(width=0.01),
convergence={'density': 1},
kpts=[1, 1, 1],
txt='gs.txt')
# a.set_calculator(calc)
calc.calculate(a)
# a.get_potential_energy()
ev = pd.DataFrame(calc.get_eigenvalues())
ef = calc.get_fermi_level()
ev_below = ev.loc[ev.values <= ef]
ev_above = ev.loc[ev.values > ef]
for e in ev_below.values.tolist()[::-1]:
descriptors_below += e
if len(ev_below) > 50:
descriptors_below = descriptors_below[0:50]
elif len(ev_below) < 50:
for e in range(50 - len(ev_below)):
descriptors_below += [0]
descriptors_below = descriptors_below[::-1]
for e in ev_above.values.tolist():
descriptors_above += e
if len(ev_above) > 50:
descriptors_above = descriptors_above[0:50]
elif len(ev_above) < 50:
for e in range(50 - len(ev_above)):
descriptors_above += [0]
except Exception as e:
print('Problem in material:', e)
return descriptors_below + descriptors_above
def calc_gw(mater, ecut=250, band_num=3):
calc = GPAW(restart=gs_wfs(mater))
ne = calc.get_number_of_electrons()
nb = ne // 2
bands = (nb - band_num, nb + band_num)
del calc
calc = G0W0(calc=gs_wfs(mater),
bands=bands,
ecut=ecut,
ecut_extrapolation=True,
truncation="2D",
q0_correction=True,
filename=os.path.join(data_path, mater, "g0w0"),
restartfile=os.path.join(data_path, mater, "g0w0.tmp"),
savepckl=True)
calc.calculate()
def calc_gw(mater, band_num=3):
if not os.path.exists(es_wfs(mater)):
calc_es(mater)
calc = GPAW(restart=gs_wfs(mater))
ne = calc.get_number_of_electrons()
nb = int(ne // 2)
bands = (nb - band_num, nb + band_num)
print(bands)
del calc
calc = G0W0(
calc=es_wfs(mater),
nbands=nbs,
bands=bands,
nblocksmax=True,
# ecut_extrapolation=True,
truncation="2D",
q0_correction=True,
filename=os.path.join(data_path, mater, "g0w0"),
restartfile=os.path.join(data_path, mater, "g0w0.tmp"),
savepckl=True)
calc.calculate()
from gpaw.cluster import Cluster
from gpaw.test import equal
fname='H2_PBE.gpw'
fwfname='H2_wf_PBE.gpw'
txt = None
# write first if needed
try:
c = GPAW(fname, txt=txt)
c = GPAW(fwfname, txt=txt)
except:
s = Cluster([Atom('H'), Atom('H', [0,0,1])])
s.minimal_box(3.)
c = GPAW(xc='PBE', h=.3, convergence={'density':1e-3, 'eigenstates':1e-3})
c.calculate(s)
c.write(fname)
c.write(fwfname, 'all')
# full information
c = GPAW(fwfname, txt=txt)
E_PBE = c.get_potential_energy()
try: # number of iterations needed in restart
niter_PBE = c.get_number_of_iterations()
except: pass
dE = c.get_xc_difference('TPSS')
E_1 = E_PBE + dE
print "E PBE, TPSS=", E_PBE, E_1
# no wfs
c = GPAW(fname, txt=txt)
ex = PointCharges()
ex.read('i' + fname)
ex.write('o' + fname)
convergence = {
'eigenstates': 1.e-4 * 40 * 1.5**3,
'density': 1.e-2,
'energy': 0.1
}
# without potential
if True:
if txt:
print('\n################## no potential')
c00 = GPAW(h=0.3, nbands=-1, convergence=convergence, txt=txt)
c00.calculate(H2)
eps00_n = c00.get_eigenvalues()
# 0 potential
if True:
if txt:
print('\n################## 0 potential')
cp0 = ConstantPotential(0.0)
c01 = GPAW(h=0.3,
nbands=-2,
external=cp0,
convergence=convergence,
txt=txt)
c01.calculate(H2)
# 1 potential
from ase import Atoms
from gpaw import GPAW
from gpaw.lrtddft import LrTDDFT
# Na2 cluster
atoms = Atoms(symbols='Na2',
positions=[(0, 0, 0), (3.0, 0, 0)],
pbc=False)
atoms.center(vacuum=6.0)
# Standard ground state calculation with empty states
calc = GPAW(nbands=100, h=0.4, setups={'Na': '1'})
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.set(convergence={'bands' : 90},
fixdensity=True,
eigensolver='cg')
calc.calculate()
calc.write('na2_gs_casida.gpw', mode='all')
# Standard Casida calculation
calc = GPAW('na2_gs_casida.gpw')
istart = 0
jend = 90
lr = LrTDDFT(calc, xc='LDA', istart=istart, jend=jend)
lr.diagonalize()
lr.write('na2_lr.dat.gz')
for atom in e_HOMO_cs.keys():
e_ref = e_HOMO_cs[atom]
# generate setup for the atom
if rank == 0 and not setups.has_key(atom):
g = Generator(atom, 'LB94', nofiles=True, txt=txt)
g.run(**parameters[atom])
setups[atom] = 1
barrier()
SS = Atoms([Atom(atom)], cell=(7, 7, 7), pbc=False)
SS.center()
c = GPAW(h=.3, xc='LB94', nbands=-2, txt=txt)
if atom in ['Mg']:
c.set(eigensolver='cg')
c.calculate(SS)
# find H**O energy
eps_n = c.get_eigenvalues(kpt=0, spin=0) / 27.211
f_n = c.get_occupation_numbers(kpt=0, spin=0)
for e, f in zip(eps_n, f_n):
if f < 0.99:
break
e_homo = e
e_homo = int( e_homo * 10000 + .5 ) / 10.
diff = e_ref + e_homo
print('%2s %8g %6.1f %4.1f' % (atom, e_ref, -e_homo, diff))
assert abs(diff) < 7
# H**O energy in mHa and magn. mom. for open shell atoms
e_HOMO_os = { 'He': [851, 0], # added for cross check
for atom in e_HOMO_cs.keys():
e_ref = e_HOMO_cs[atom]
# generate setup for the atom
if rank == 0 and not setups.has_key(atom):
g = Generator(atom, 'LB94', nofiles=True, txt=txt)
g.run(**parameters[atom])
setups[atom] = 1
barrier()
SS = Atoms([Atom(atom)], cell=(7, 7, 7), pbc=False)
SS.center()
c = GPAW(h=.3, xc='LB94', nbands=-2, txt=txt)
if atom in ['Mg']:
c.set(eigensolver='cg')
c.calculate(SS)
# find H**O energy
eps_n = c.get_eigenvalues(kpt=0, spin=0) / 27.211
f_n = c.get_occupation_numbers(kpt=0, spin=0)
for e, f in zip(eps_n, f_n):
if f < 0.99:
break
e_homo = e
e_homo = int( e_homo * 10000 + .5 ) / 10.
diff = e_ref + e_homo
print '%2s %8g %6.1f %4.1f' % (atom, e_ref, -e_homo, diff)
assert abs(diff) < 7
# H**O energy in mHa and magn. mom. for open shell atoms
e_HOMO_os = { 'He': [851, 0], # added for cross check
h=.4
q=3
spin=True
s = Atoms([Atom('Fe')])
s.center(vacuum=2.5)
convergence={'eigenstates':0.01, 'density':0.1, 'energy':0.1}
# use Hunds rules
c = GPAW(charge=q, h=h, nbands=5,
hund=True,
eigensolver='rmm-diis',
occupations=FermiDirac(width=0.1),
convergence=convergence
)
c.calculate(s)
equal(c.get_magnetic_moment(0), 5, 0.1)
# set magnetic moment
mm = [5]
s.set_initial_magnetic_moments(mm)
c = GPAW(charge=q, h=h, nbands=5,
occupations=FermiDirac(width=0.1, fixmagmom=True),
convergence=convergence
)
c.calculate(s)
equal(c.get_magnetic_moment(0), 5, 0.1)
txt = 'mgga_sc.txt'
s = Cluster([Atom('H')])
s.minimal_box(4., h=h)
s.set_initial_magnetic_moments([1])
# see https://trac.fysik.dtu.dk/projects/gpaw/ticket/244
s.set_cell((8.400000, 8.400000, 8.400000))
c = GPAW(xc='TPSS',
h=h,
nbands=5,
txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
c.calculate(s)
cpbe = GPAW(xc='PBE',
h=h,
nbands=5,
txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
cpbe.calculate(s)
cpbe.set(xc='TPSS')
cpbe.calculate()
print("Energy difference",
(cpbe.get_potential_energy() - c.get_potential_energy()))
equal(cpbe.get_potential_energy(), c.get_potential_energy(), 0.002)
"""Test Hirshfeld for spin/no spin consitency"""
from ase import Atom
from gpaw import GPAW
from ase.parallel import parprint
from gpaw.analyse.hirshfeld import HirshfeldPartitioning
from gpaw import FermiDirac
from gpaw.cluster import Cluster
from gpaw.test import equal
h = 0.25
box = 3
atoms = Cluster()
atoms.append(Atom('H'))
atoms.minimal_box(box)
volumes = []
for spinpol in [False, True]:
calc = GPAW(h=h,
occupations=FermiDirac(0.1, fixmagmom=True),
experimental={'niter_fixdensity': 2},
spinpol=spinpol)
calc.calculate(atoms)
volumes.append(HirshfeldPartitioning(calc).get_effective_volume_ratios())
parprint(volumes)
equal(volumes[0][0], volumes[1][0], 4e-9)
h = 0.4
box = 2
nbands = 4
txt = '-'
txt = None
np.set_printoptions(precision=3, suppress=True)
H2 = Cluster(molecule('H2'))
H2.minimal_box(box, h)
c1 = GPAW(h=h,
txt=txt,
eigensolver='dav',
nbands=nbands,
convergence={'eigenstates': nbands})
c1.calculate(H2)
lr1 = LrTDDFT(c1)
parprint('sanity --------')
ov = Overlap(c1).pseudo(c1)
parprint('pseudo(normalized):\n', ov)
ov = Overlap(c1).pseudo(c1, False)
parprint('pseudo(not normalized):\n', ov)
ov = Overlap(c1).full(c1)
parprint('full:\n', ov)
equal(ov[0], np.eye(ov[0].shape[0], dtype=ov.dtype), 1e-10)
def show(c2):
c2.calculate(H2)
ov = Overlap(c1).pseudo(c2)
# Wigner-Seitz ----------------------------------------
if 1:
ws = WignerSeitz(calc.density.finegd, mol, calc)
vr = ws.get_effective_volume_ratios()
parprint('Wigner-Seitz:', vr)
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
# calculate
parprint('fresh:')
mol = Cluster(molecule('H2O'))
mol.minimal_box(3, h=h)
calc = GPAW(nbands=6,
h = h,
txt=None)
calc.calculate(mol)
calc.write(gpwname)
lastres = run()
# load previous calculation
parprint('reloaded:')
calc = GPAW(gpwname, txt=None)
mol = calc.get_atoms()
run(lastres)
from gpaw.cluster import Cluster
from gpaw.test import equal
h=0.40
txt = None
txt = 'mgga_sc.txt'
s = Cluster([Atom('H')])
s.minimal_box(4., h=h)
s.set_initial_magnetic_moments([1])
# see https://trac.fysik.dtu.dk/projects/gpaw/ticket/244
s.set_cell((8.400000,8.400000,8.400000))
c = GPAW(xc='TPSS', h=h, nbands=5, txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
c.calculate(s)
cpbe = GPAW(xc='PBE', h=h, nbands=5, txt=txt,
eigensolver='rmm-diis',
fixmom=True,
maxiter=300)
cpbe.calculate(s)
cpbe.set(xc='TPSS')
cpbe.calculate()
print "Energy difference", (cpbe.get_potential_energy() -
c.get_potential_energy())
equal(cpbe.get_potential_energy(), c.get_potential_energy(), 0.002)
from ase import Atoms
from gpaw import GPAW
from gpaw.lrtddft import LrTDDFT
# Na2 cluster
atoms = Atoms(symbols='Na2', positions=[(0, 0, 0), (3.0, 0, 0)], pbc=False)
atoms.center(vacuum=6.0)
# Standard ground state calculation with empty states
calc = GPAW(nbands=100, h=0.4, setups={'Na': '1'})
atoms.set_calculator(calc)
energy = atoms.get_potential_energy()
calc.set(convergence={'bands': 90}, fixdensity=True, eigensolver='cg')
calc.calculate()
calc.write('na2_gs_casida.gpw', mode='all')
# Standard Casida calculation
calc = GPAW('na2_gs_casida.gpw')
istart = 0
jend = 90
lr = LrTDDFT(calc, xc='LDA', istart=istart, jend=jend)
lr.diagonalize()
lr.write('na2_lr.dat.gz')
lr_vspin = LrTDDFT(calc, xc=xc, nspins=2)
singlet, triplet = lr_vspin.singlets_triplets()
lr_vspin.diagonalize()
# the triplet is lower, so that the second is the first singlet
# excited state
t2 = lr_vspin[1]
print 'with virtual/wo spin t2, t1=', t2.get_energy(), t1 .get_energy()
equal(t1.get_energy(), t2.get_energy(), 5.e-7)
if not load:
c_spin = GPAW(xc='PBE', nbands=2,
spinpol=True, parallel={'domain': world.size},
txt=txt)
H2.set_calculator(c_spin)
c_spin.calculate(H2)
## c_spin.write('H2spin.gpw', 'all')
else:
c_spin = GPAW('H2spin.gpw', txt=txt)
lr_spin = LrTDDFT(c_spin, xc=xc)
lr_spin.diagonalize()
for i in range(2):
print 'i, real, virtual spin: ', i, lr_vspin[i], lr_spin[i]
equal(lr_vspin[i].get_energy(), lr_spin[i].get_energy(), 5.e-6)
# singlet/triplet separation
precision = 1.e-5
singlet.diagonalize()
equal(singlet[0].get_energy(), lr_spin[1].get_energy(), precision)
equal(singlet[0].get_oscillator_strength()[0],
lr_spin[1].get_oscillator_strength()[0], precision)
nbands = 4
unocc = True
load = False
# usual calculation
fname = 'Be2.gpw'
if not load:
xco = HybridXC(xc)
cocc = GPAW(h=0.3,
eigensolver='rmm-diis',
xc=xco,
nbands=nbands,
convergence={'eigenstates': 1e-4},
txt=txt)
cocc.calculate(loa)
else:
cocc = GPAW(fname)
cocc.converge_wave_functions()
fo_n = 1. * cocc.get_occupation_numbers()
eo_n = 1. * cocc.get_eigenvalues()
if unocc:
# apply Fock opeartor also to unoccupied orbitals
xcu = HybridXC(xc, unocc=True)
cunocc = GPAW(h=0.3,
eigensolver='rmm-diis',
xc=xcu,
nbands=nbands,
convergence={'eigenstates': 1e-4},
txt=txt)
gd = lr.calculator.density.gd
finegd = lr.calculator.density.finegd
ddiff = gd.integrate(abs(den - den_vspin))
parprint(' density integral, difference=',
gd.integrate(den), gd.integrate(den_vspin), ddiff)
parprint(' aed density integral',
finegd.integrate(ex.get_all_electron_density() * Bohr**3),
finegd.integrate(ex_vspin.get_all_electron_density() * Bohr**3))
assert(ddiff < 1.e-4)
if not load:
c_spin = GPAW(xc='PBE', nbands=2,
spinpol=True, parallel={'domain': world.size},
txt=txt)
H2.set_calculator(c_spin)
c_spin.calculate(H2)
## c_spin.write('H2spin.gpw', 'all')
else:
c_spin = GPAW('H2spin.gpw', txt=txt)
lr_spin = LrTDDFT(c_spin, xc=xc)
lr_spin.diagonalize()
for i in range(2):
parprint('i, real, virtual spin: ', i, lr_vspin[i], lr_spin[i])
equal(lr_vspin[i].get_energy(), lr_spin[i].get_energy(), 6.e-6)
ex_vspin = ExcitedState(lr_vspin, i)
den_vspin = ex_vspin.get_pseudo_density() * Bohr**3
ex_spin = ExcitedState(lr_spin, i)
den_spin = ex_spin.get_pseudo_density() * Bohr**3
ddiff = gd.integrate(abs(den_vspin - den_spin))
parprint(' density integral, difference=',
gd.integrate(den_vspin), gd.integrate(den_spin),
if len(lastres):
equal(vr, lastres.pop(0), 1.e-10)
results.append(vr)
return results
mol = Cluster(molecule('H2O'))
mol.minimal_box(2.5, h=h)
# calculate
if 1:
parprint('### fresh:')
calc = GPAW(nbands=6, h=h, txt=None)
if 1:
calc.calculate(mol)
calc.write(gpwname)
lastres = run()
# load previous calculation
if 1:
parprint('### reloaded:')
calc = GPAW(gpwname, txt=None)
mol = calc.get_atoms()
run(lastres)
# periodic modulo test
parprint('### periodic:')
mol.set_pbc(True)
mol.translate(-mol[0].position)
mol.translate([-1.e-24, 0, 0])
)
f.close()
world.barrier()
ex = PointCharges()
ex.read("i" + fname)
ex.write("o" + fname)
convergence = {"eigenstates": 1.0e-4 * 40 * 1.5 ** 3, "density": 1.0e-2, "energy": 0.1}
# without potential
if True:
if txt:
print("\n################## no potential")
c00 = GPAW(h=0.3, nbands=-1, convergence=convergence, txt=txt)
c00.calculate(H2)
eps00_n = c00.get_eigenvalues()
# 0 potential
if True:
if txt:
print("\n################## 0 potential")
cp0 = ConstantPotential(0.0)
c01 = GPAW(h=0.3, nbands=-2, external=cp0, convergence=convergence, txt=txt)
c01.calculate(H2)
# 1 potential
if True:
if txt:
print("################## 1 potential")
cp1 = ConstantPotential(-1.0 / Hartree)
loa = Atoms("Be2", [(0, 0, 0), (2.45, 0, 0)], cell=[5.9, 4.8, 5.0])
loa.center()
txt = None
xc = "PBE0"
nbands = 4
unocc = True
load = False
# usual calculation
fname = "Be2.gpw"
if not load:
xco = HybridXC(xc)
cocc = GPAW(h=0.3, eigensolver="rmm-diis", xc=xco, nbands=nbands, convergence={"eigenstates": 1e-4}, txt=txt)
cocc.calculate(loa)
else:
cocc = GPAW(fname)
cocc.converge_wave_functions()
fo_n = 1.0 * cocc.get_occupation_numbers()
eo_n = 1.0 * cocc.get_eigenvalues()
if unocc:
# apply Fock opeartor also to unoccupied orbitals
xcu = HybridXC(xc, unocc=True)
cunocc = GPAW(h=0.3, eigensolver="rmm-diis", xc=xcu, nbands=nbands, convergence={"eigenstates": 1e-4}, txt=txt)
cunocc.calculate(loa)
parprint(" HF occ HF unocc diff")
parprint(
"Energy %10.4f %10.4f %10.4f"