def xc(filename, xc, ecut=None):
"""Calculate non self-consitent energy.
filename: str
Name of restart-file.
xc: str
Functional
ecut: float
Plane-wave cutoff for exact exchange.
"""
name, ext = filename.rsplit('.', 1)
assert ext == 'gpw'
if xc in ['EXX', 'PBE0', 'B3LYP']:
from gpaw.xc.exx import EXX
exx = EXX(filename, xc, ecut=ecut, txt=name + '-exx.txt')
exx.calculate()
e = exx.get_total_energy()
else:
from gpaw import GPAW
calc = GPAW(filename, txt=None)
e = calc.get_potential_energy() + calc.get_xc_difference(xc)
print(e, 'eV')
def xc(filename, xc, ecut=None):
"""Calculate non self-consitent energy.
filename: str
Name of restart-file.
xc: str
Functional
ecut: float
Plane-wave cutoff for exact exchange.
"""
name, ext = filename.rsplit(".", 1)
assert ext == "gpw"
if xc in ["EXX", "PBE0", "B3LYP"]:
from gpaw.xc.exx import EXX
exx = EXX(filename, xc, ecut=ecut, txt=name + "-exx.txt")
exx.calculate()
e = exx.get_total_energy()
else:
from gpaw import GPAW
calc = GPAW(filename, txt=None)
e = calc.get_potential_energy() + calc.get_xc_difference(xc)
print(e, "eV")
isolated_calc = GPAW(
mode=PW(pwcutoff),
dtype=complex,
kpts=(1, 1, 1),
xc="PBE",
txt="si_isolated_pbe.txt",
occupations=FermiDirac(0.01, fixmagmom=True),
spinpol=True,
hund=True,
convergence={"density": 1.0e-6},
mixer=Mixer(beta=0.05, nmaxold=5, weight=50.0),
)
isolated_silicon.set_calculator(isolated_calc)
e0_isolated_pbe = isolated_silicon.get_potential_energy()
isolated_calc.write("si.pbe+exx.isolated.gpw", mode="all")
# Now the exact exchange
exx = EXX("si.pbe+exx.isolated.gpw", txt="si_isolated_exx.txt")
exx.calculate()
si_isolated_exx = exx.get_total_energy()
s = str(L)
s += " "
s += str(e0_isolated_pbe)
s += " "
s += str(si_isolated_exx)
s += "\n"
myresults.write(s)
'size': (k, k, k),
'gamma': True
},
xc='PBE',
occupations=FermiDirac(0.01),
txt='si.pbe+exx.pbe_output.txt',
parallel={'band': 1})
bulk_crystal.set_calculator(bulk_calc)
e0_bulk_pbe = bulk_crystal.get_potential_energy()
# Write to file
bulk_calc.write('bulk.gpw', mode='all')
# Now the exact exchange
exx_bulk = EXX('bulk.gpw', txt='si.pbe+exx.exx_output.txt')
exx_bulk.calculate()
e0_bulk_exx = exx_bulk.get_total_energy()
s = str(alat)
s += ' '
s += str(k)
s += ' '
s += str(pwcutoff)
s += ' '
s += str(e0_bulk_pbe)
s += ' '
s += str(e0_bulk_exx)
s += '\n'
resultfile.write(s)
N2 = molecule('N2')
N2.center(vacuum=2.0)
calc = GPAW(mode=PW(force_complex_dtype=True),
xc='PBE',
parallel={'domain': 1},
eigensolver='rmm-diis')
N2.set_calculator(calc)
E_n2_pbe = N2.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=104, scalapack=True)
calc.write('N2.gpw', mode='all')
exx = EXX('N2.gpw')
exx.calculate()
E_n2_hf = exx.get_total_energy()
rpa = RPACorrelation('N2.gpw', nfrequencies=8)
E_n2_rpa = rpa.calculate(ecut=[ecut])
N = molecule('N')
N.set_cell(N2.cell)
calc = GPAW(mode=PW(force_complex_dtype=True),
xc='PBE',
parallel={'domain': 1},
eigensolver='rmm-diis')
N.set_calculator(calc)
E_n_pbe = N.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=104, scalapack=True)
CO = Atoms('CO', [(0, 0, 0), (0, 0, 1.1283)])
CO.set_pbc(True)
CO.center(vacuum=3.0)
calc = GPAW(mode=PW(600, force_complex_dtype=True),
parallel={'domain': 1},
xc='PBE',
txt='CO.ralda_01_CO_pbe.txt',
convergence={'density': 1.e-6})
CO.set_calculator(calc)
E0_pbe = CO.get_potential_energy()
exx = EXX(calc, txt='CO.ralda_01_CO_exx.txt')
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,
CO = Atoms('CO', [(0, 0, 0), (0, 0, 1.1283)])
CO.set_pbc(True)
CO.center(vacuum=3.0)
calc = GPAW(mode=PW(600),
dtype=complex,
xc='PBE',
txt='CO_pbe.txt',
convergence={'density': 1.e-6})
CO.set_calculator(calc)
E0_pbe= CO.get_potential_energy()
exx = EXX(calc, txt='CO_exx.txt')
exx.calculate()
E0_hf = exx.get_total_energy()
calc.diagonalize_full_hamiltonian()
calc.write('CO.gpw', mode='all')
# C -------------------------------------------
C = Atoms('C')
C.set_pbc(True)
C.set_cell(CO.cell)
C.center()
calc = GPAW(mode=PW(600),
dtype=complex,
xc='PBE',
mixer=MixerSum(beta=0.1, nmaxold=5, weight=50.0),
hund=True,
pbc=(1, 1, 1))
isolated_calc = GPAW(mode=PW(pwcutoff),
dtype=complex,
kpts=(1, 1, 1),
xc='PBE',
txt='si_isolated_pbe.txt',
occupations=FermiDirac(0.01, fixmagmom=True),
spinpol=True,
hund=True,
convergence={'density': 1.e-6},
mixer=Mixer(beta=0.05, nmaxold=5, weight=50.0))
isolated_silicon.set_calculator(isolated_calc)
e0_isolated_pbe = isolated_silicon.get_potential_energy()
isolated_calc.write('si.pbe+exx.isolated.gpw', mode='all')
# Now the exact exchange
exx = EXX('si.pbe+exx.isolated.gpw', txt='si_isolated_exx.txt')
exx.calculate()
si_isolated_exx = exx.get_total_energy()
s = str(L)
s += ' '
s += str(e0_isolated_pbe)
s += ' '
s += str(si_isolated_exx)
s += '\n'
myresults.write(s)
pos = slab.get_positions()
add_adsorbate(slab, 'C', d, position=(pos[3,0], pos[3,1]))
add_adsorbate(slab, 'C', d, position=(cell[0,0]/3 + cell[1,0]/3,
cell[0,1]/3 + cell[1,1]/3))
#view(slab)
calc = GPAW(xc='PBE',
eigensolver='cg',
mode=PW(600),
kpts=kpts,
occupations=FermiDirac(width=0.01),
mixer=MixerSum(beta=0.1, nmaxold=5, weight=50.0),
convergence={'density': 1.e-6},
maxiter=300,
parallel={'domain': 1,
'band': 1},
txt='gs_%s.txt' % d)
slab.set_calculator(calc)
E = slab.get_potential_energy()
exx = EXX(calc, txt='exx_%s.txt' % d)
exx.calculate()
E_hf = exx.get_total_energy()
calc.diagonalize_full_hamiltonian()
calc.write('gs_%s.gpw' % d, mode='all')
f = paropen('hf_acdf.dat', 'a')
print(d, E, E_hf, file=f)
f.close()
del slab[-2:]
cell = bulk('C', 'fcc', a=3.553).get_cell()
a = Atoms('C2',
cell=cell,
pbc=True,
scaled_positions=((0, 0, 0), (0.25, 0.25, 0.25)))
calc = GPAW(mode=PW(600),
xc='PBE',
occupations=FermiDirac(width=0.01),
convergence={'density': 1.e-6},
kpts=kpts,
parallel={'domain': 1},
txt='diamond.ralda_01_pbe.txt')
a.set_calculator(calc)
E_pbe = a.get_potential_energy()
exx = EXX(calc, txt='diamond.ralda_01_exx.txt')
exx.calculate()
E_hf = exx.get_total_energy()
E_C = np.loadtxt('CO.ralda.PBE_HF_C.dat')
f = paropen('diamond.ralda.PBE_HF_diamond.dat', 'w')
print('PBE: ', E_pbe / 2 - E_C[0], file=f)
print('HF: ', E_hf / 2 - E_C[1], file=f)
f.close()
calc.diagonalize_full_hamiltonian()
calc.write('diamond.ralda.pbe_wfcs.gpw', mode='all')
(0.0000, 0.0000, -1.1560)]),
'Be2': ('Be2', [(0.0000, 0.0000, 0.0000),
(0.0000, 0.0000, 2.460)])}
c = ase.db.connect('results.db')
for name in ex_atomization.keys() + 'H Li Be B C N O F Cl P'.split():
id = c.reserve(name=name)
if id is None:
continue
if name in extra:
a = Atoms(*extra[name])
else:
a = molecule(name)
if name in bondlengths:
a.set_distance(0, 1, bondlengths[name])
a.cell = [11, 12, 13]
a.center()
a.calc = GPAW(xc='PBE', mode=PW(500), txt=name + '.txt', dtype=complex)
a.get_potential_energy()
exx = EXX(a.calc)
exx.calculate()
eexx = exx.get_total_energy()
c.write(a, name=name, exx=eexx)
del c[id]
ecut = 25
N2 = molecule("N2")
N2.center(vacuum=2.0)
calc = GPAW(mode="pw", dtype=complex, xc="PBE", eigensolver="rmm-diis")
N2.set_calculator(calc)
E_n2_pbe = N2.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=104, scalapack=True)
calc.write("N2.gpw", mode="all")
exx = EXX("N2.gpw")
exx.calculate()
E_n2_hf = exx.get_total_energy()
rpa = RPACorrelation("N2.gpw", nfrequencies=8)
E_n2_rpa = rpa.calculate(ecut=[ecut])
# -------------------------------------------------------------------------
N = molecule("N")
N.set_cell(N2.cell)
calc = GPAW(mode="pw", dtype=complex, xc="PBE", eigensolver="rmm-diis")
N.set_calculator(calc)
E_n_pbe = N.get_potential_energy()
calc.diagonalize_full_hamiltonian(nbands=104, scalapack=True)
calc.write("N.gpw", mode="all")
mode = PW(pwcutoff),
kpts={'size': (k, k, k), 'gamma': True},
dtype=complex,
xc='PBE',
txt='si.pbe+exx.pbe_output.txt',
parallel={'band':1}
)
bulk_crystal.set_calculator(bulk_calc)
e0_bulk_pbe = bulk_crystal.get_potential_energy()
# Write to file
bulk_calc.write('bulk.gpw',mode='all')
# Now the exact exchange
exx_bulk = EXX('bulk.gpw', txt='si.pbe+exx.exx_output.txt')
exx_bulk.calculate()
e0_bulk_exx = exx_bulk.get_total_energy()
s = str(alat)
s += ' '
s += str(k)
s += ' '
s += str(pwcutoff)
s += ' '
s += str(e0_bulk_pbe)
s += ' '
s += str(e0_bulk_exx)
s += '\n'
resultfile.write(s)
import ase.db
from ase.build import bulk
import numpy as np
from gpaw.xc.exx import EXX
from gpaw import GPAW, PW
a0 = 5.43
con = ase.db.connect('si.db')
for k in range(2, 9):
for a in np.linspace(a0 - 0.04, a0 + 0.04, 5):
id = con.reserve(a=a, k=k)
if id is None:
continue
si = bulk('Si', 'diamond', a)
si.calc = GPAW(kpts=(k, k, k),
mode=PW(400),
xc='PBE',
eigensolver='rmm-diis',
txt=None)
si.get_potential_energy()
name = 'si-{0:.2f}-{1}'.format(a, k)
si.calc.write(name + '.gpw', mode='all')
pbe0 = EXX(name + '.gpw', 'PBE0', txt=name + '.pbe0.txt')
pbe0.calculate()
epbe0 = pbe0.get_total_energy()
con.write(si, a=a, k=k, epbe0=epbe0)
del con[id]