def test_bs(self):
sb = StructureBuilder()
atoms, *_ = sb.get_structure("C", "diamond")
# print(atoms)
base_dir = os.path.join(os.path.dirname(__file__),
"../../tmp/C-class/")
m_calc = MaterCalc(atoms=atoms,
base_dir=base_dir)
self.assertTrue(m_calc.relax(fmax=0.002)) # Very tight limit!
self.assertTrue(m_calc.ground_state())
# get the PBE BS
lattice_type = get_cellinfo(m_calc.atoms.cell).lattice
self.assertTrue(lattice_type in special_paths.keys())
kpts_bs = dict(path=special_paths[lattice_type],
npoints=120)
# HSE06 base generate
gs_file = os.path.join(base_dir, "gs.gpw")
_calc = GPAW(restart=gs_file)
atoms = _calc.atoms.copy()
calc = GPAW(**_calc.parameters)
calc.set(kpts=dict(gamma=True,
density=4)) # low density calculations
calc.atoms = atoms
del _calc
calc.get_potential_energy()
calc.write(os.path.join(base_dir, "hse.gpw"), mode="all")
calc = GPAW(restart=os.path.join(base_dir, "hse.gpw"),
txt=None)
ns = calc.get_number_of_spins()
nk = len(calc.get_ibz_k_points())
nbands = calc.get_number_of_bands()
eigen_pbe = numpy.array([[calc.get_eigenvalues(spin=s,
kpt=k) \
for k in range(nk)]\
for s in range(ns)])
parprint("EIGEN_PBE", eigen_pbe.shape)
vxc_pbe = vxc(calc, "PBE")
parprint("VXC_PBE", vxc_pbe.shape)
# world.barrier()
# HSE06 now
calc_hse = EXX(os.path.join(base_dir, "hse.gpw"),
xc="HSE06",
bands=[0, nbands])
calc_hse.calculate()
vxc_hse = calc_hse.get_eigenvalue_contributions()
parprint(vxc_hse.shape)
parprint(vxc_hse)
eigen_hse = eigen_pbe - vxc_pbe + vxc_hse
# HSE bandgap from just kpts
bg_hse_min, *_ = bandgap(eigenvalues=eigen_hse,
efermi=calc.get_fermi_level(),
direct=False)
bg_hse_dir, *_ = bandgap(eigenvalues=eigen_hse,
efermi=calc.get_fermi_level(),
direct=True)
parprint("HSE: E_min \t E_dir")
parprint("{:.3f}\t{:.3f}".format(bg_hse_min, bg_hse_dir))
"""
def calculate_exact_exchange(self):
name = self.filename + '.exx.npy'
fd = opencew(name)
if fd is None:
print('Reading EXX contribution from file:', name, file=self.fd)
with open(name) as fd:
self.exx_sin = np.load(fd)
assert self.exx_sin.shape == self.shape, self.exx_sin.shape
return
print('Calculating EXX contribution', file=self.fd)
exx = EXX(self.calc, kpts=self.kpts, bands=self.bands,
txt=self.filename + '.exx.txt', timer=self.timer)
exx.calculate()
self.exx_sin = exx.get_eigenvalue_contributions() / Hartree
np.save(fd, self.exx_sin)
def calculate_exact_exchange(self):
name = self.filename + '.exx.npy'
fd = opencew(name)
if fd is None:
print('Reading EXX contribution from file:', name, file=self.fd)
with open(name) as fd:
self.exx_sin = np.load(fd)
assert self.exx_sin.shape == self.shape, self.exx_sin.shape
return
print('Calculating EXX contribution', file=self.fd)
exx = EXX(self.calc, kpts=self.kpts, bands=self.bands,
txt=self.filename + '.exx.txt', timer=self.timer)
exx.calculate()
self.exx_sin = exx.get_eigenvalue_contributions() / Hartree
np.save(fd, self.exx_sin)
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()
ibzk_kc = atoms.calc.get_ibz_k_points()
n = int(atoms.calc.get_number_of_electrons()) // 2
ibzk = []
eps_kn = []
for k_c in [(0, 0, 0), (0.5, 0.5, 0), (0.5, 0.5, 0.5)]:
k = abs(ibzk_kc - k_c).max(1).argmin()
ibzk.append(k)
eps_kn.append(atoms.calc.get_eigenvalues(k)[n - 1:n + 1])
if name == 'Ar':
break
deps_kn = vxc(atoms.calc, 'PBE')[0, ibzk, n - 1:n + 1]
pbe0 = EXX(name + '.gpw', 'PBE0', ibzk, (n - 1, n + 1), txt=name + '.exx')
pbe0.calculate()
deps0_kn = pbe0.get_eigenvalue_contributions()[0]
eps0_kn = eps_kn - deps_kn + deps0_kn
data = {}
for k, point in enumerate('GXL'):
data[point] = [eps_kn[k][1] - eps_kn[0][0],
eps0_kn[k, 1] - eps0_kn[0, 0]]
data[point] += bfb[name][2 + k * 4:6 + k * 4]
if name == 'Ar':
break
c.write(atoms, name=name, data=data)
del c[id]
ibzk_kc = atoms.calc.get_ibz_k_points()
n = int(atoms.calc.get_number_of_electrons()) // 2
ibzk = []
eps_kn = []
for k_c in [(0, 0, 0), (0.5, 0.5, 0), (0.5, 0.5, 0.5)]:
k = abs(ibzk_kc - k_c).max(1).argmin()
ibzk.append(k)
eps_kn.append(atoms.calc.get_eigenvalues(k)[n - 1:n + 1])
if name == 'Ar':
break
deps_kn = vxc(atoms.calc, 'PBE')[0, ibzk, n - 1:n + 1]
pbe0 = EXX(name, 'PBE0', ibzk, (n - 1, n + 1), txt=name + '.exx')
pbe0.calculate()
deps0_kn = pbe0.get_eigenvalue_contributions()[0]
eps0_kn = eps_kn - deps_kn + deps0_kn
data = {}
for k, point in enumerate('GXL'):
data[point] = [eps_kn[k][1] - eps_kn[0][0],
eps0_kn[k, 1] - eps0_kn[0, 0]]
data[point] += bfb[name][2 + k * 4:6 + k * 4]
if name == 'Ar':
break
c.write(atoms, name=name, data=data)
del c[id]
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)
def hse(base_dir="./", kdens=6.0):
emptybands = 20
convbands = 10
# If pbc in z direction, use vdW for relaxation as default!
# if atoms.pbc[-1]: # Do not compare with np.bool_ !
# use_vdW = True
# else:
# use_vdW = False
curr_dir = os.path.dirname(os.path.abspath(__file__))
param_file = os.path.join(curr_dir, "../parameters.json")
gpw_file = os.path.join(base_dir, "gs.gpw")
hse_file = os.path.join(base_dir, "hse.gpw")
hse_nowfs_file = os.path.join(base_dir, "hse_nowfs.gpw")
hse_eigen_file = os.path.join(base_dir, "hse_eigenvalues.npz")
if not os.path.exists(gpw_file):
parprint("No ground state calculation? Exit...")
return 0
if os.path.exists(param_file):
params = json.load(open(param_file, "r"))
else:
raise FileNotFoundError("no parameter file!")
if not os.path.exists(hse_file):
calc = GPAW(gpw_file) # reload the calculation
atoms = calc.get_atoms()
kpts = get_kpts_size(atoms, kdens)
calc.set(nbands=-emptybands,
fixdensity=True,
kpts=kpts,
convergence={'bands': -convbands})
calc.get_potential_energy()
calc.write(hse_file, 'all')
calc.write(hse_nowfs_file) # no wavefunction
mpi.world.barrier()
time.sleep(10) # is this needed?
calc = GPAW(hse_file, txt=None)
ns = calc.get_number_of_spins()
nk = len(calc.get_ibz_k_points())
nb = calc.get_number_of_bands()
vxc_pbe_skn = vxc(calc, 'PBE')
vxc_pbe_nsk = numpy.ascontiguousarray(vxc_pbe_skn.transpose(2, 0, 1))
vxc_pbe_nsk = calc.wfs.bd.collect(vxc_pbe_nsk, broadcast=True)
vxc_pbe_skn = vxc_pbe_nsk.transpose(1, 2, 0)[:, :, :-convbands]
e_pbe_skn = np.zeros((ns, nk, nb))
for s in range(ns):
for k in range(nk):
e_pbe_skn[s, k, :] = calc.get_eigenvalues(spin=s, kpt=k)
e_pbe_skn = e_pbe_skn[:, :, :-convbands]
hse_calc = EXX(hse_file, xc='HSE06', bands=[0, nb - convbands])
hse_calc.calculate()
vxc_hse_skn = hse_calc.get_eigenvalue_contributions()
e_hse_skn = e_pbe_skn - vxc_pbe_skn + vxc_hse_skn
ranks = [0]
if mpi.world.rank in ranks:
dct = dict(vxc_hse_skn=vxc_hse_skn,
e_pbe_skn=e_pbe_skn,
vxc_pbe_skn=vxc_pbe_skn,
e_hse_skn=e_hse_skn)
with open(hse_eigen_file, 'wb') as f:
numpy.savez(f, **dct)
parprint("Single HSE06 finished!")
