def get_chi(self, xc='RPA', q_c=[0, 0, 0], direction='x'):
""" Returns v^1/2 chi V^1/2"""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
G_G = pd.G2_qG[0]**0.5
nG = len(G_G)
if pd.kd.gamma:
G_G[0] = 1.0
if isinstance(direction, str):
d_v = {
'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]
}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
G_G /= (4 * pi)**0.5
if self.truncation == 'wigner-seitz':
kernel = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv,
self.chi0.calc.wfs.kd.N_c)
K_G = kernel.get_potential(pd)
K_G *= G_G**2
if pd.kd.gamma:
K_G[0] = 0.0
elif self.truncation == '2D':
K_G = truncated_coulomb(pd)
K_G *= G_G**2
else:
K_G = np.ones(nG)
K_GG = np.zeros((nG, nG), dtype=complex)
for i in range(nG):
K_GG[i, i] = K_G[i]
if xc != 'RPA':
R_av = self.chi0.calc.atoms.positions / Bohr
nt_sG = self.chi0.calc.density.nt_sG
K_GG += calculate_Kxc(pd,
nt_sG,
R_av,
self.chi0.calc.wfs.setups,
self.chi0.calc.density.D_asp,
functional=xc) * G_G * G_G[:, np.newaxis]
chi_wGG = []
for chi0_GG in chi0_wGG:
chi0_GG[:] = chi0_GG / G_G / G_G[:, np.newaxis]
chi_wGG.append(
np.dot(np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, K_GG)),
chi0_GG))
return chi0_wGG, np.array(chi_wGG)
def get_chi(self, xc='RPA', q_c=[0, 0, 0], direction='x'):
""" Returns v^1/2 chi V^1/2"""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
G_G = pd.G2_qG[0]**0.5
nG = len(G_G)
if pd.kd.gamma:
G_G[0] = 1.0
if isinstance(direction, str):
d_v = {'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
G_G /= (4 * pi)**0.5
if self.truncation == 'wigner-seitz':
kernel = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv,
self.chi0.calc.wfs.kd.N_c)
K_G = kernel.get_potential(pd)
K_G *= G_G**2
if pd.kd.gamma:
K_G[0] = 0.0
elif self.truncation == '2D':
K_G = truncated_coulomb(pd)
K_G *= G_G**2
else:
K_G = np.ones(nG)
K_GG = np.zeros((nG, nG), dtype=complex)
for i in range(nG):
K_GG[i, i] = K_G[i]
if xc != 'RPA':
R_av = self.chi0.calc.atoms.positions / Bohr
nt_sG = self.chi0.calc.density.nt_sG
K_GG += calculate_Kxc(pd, nt_sG, R_av, self.chi0.calc.wfs.setups,
self.chi0.calc.density.D_asp,
functional=xc) * G_G * G_G[:, np.newaxis]
chi_wGG = []
for chi0_GG in chi0_wGG:
chi0_GG[:] = chi0_GG / G_G / G_G[:, np.newaxis]
chi_wGG.append(np.dot(np.linalg.inv(np.eye(nG) -
np.dot(chi0_GG, K_GG)),
chi0_GG))
return chi0_wGG, np.array(chi_wGG)
class RPACorrelation:
def __init__(self, calc, xc='RPA', filename=None,
skip_gamma=False, qsym=True, nlambda=None,
nfrequencies=16, frequency_max=800.0, frequency_scale=2.0,
frequencies=None, weights=None,
world=mpi.world, nblocks=1, wstc=False,
txt=sys.stdout):
if isinstance(calc, str):
calc = GPAW(calc, txt=None, communicator=mpi.serial_comm)
self.calc = calc
if world.rank != 0:
txt = devnull
elif isinstance(txt, str):
txt = open(txt, 'w')
self.fd = txt
self.timer = Timer()
if frequencies is None:
frequencies, weights = get_gauss_legendre_points(nfrequencies,
frequency_max,
frequency_scale)
user_spec = False
else:
assert weights is not None
user_spec = True
self.omega_w = frequencies / Hartree
self.weight_w = weights / Hartree
if nblocks > 1:
assert len(self.omega_w) % nblocks == 0
assert wstc
self.wstc = wstc
self.nblocks = nblocks
self.world = world
self.skip_gamma = skip_gamma
self.ibzq_qc = None
self.weight_q = None
self.initialize_q_points(qsym)
# Energies for all q-vetors and cutoff energies:
self.energy_qi = []
self.filename = filename
self.print_initialization(xc, frequency_scale, nlambda, user_spec)
def initialize_q_points(self, qsym):
kd = self.calc.wfs.kd
self.bzq_qc = kd.get_bz_q_points(first=True)
if not qsym:
self.ibzq_qc = self.bzq_qc
self.weight_q = np.ones(len(self.bzq_qc)) / len(self.bzq_qc)
else:
U_scc = kd.symmetry.op_scc
self.ibzq_qc = kd.get_ibz_q_points(self.bzq_qc, U_scc)[0]
self.weight_q = kd.q_weights
def read(self):
lines = open(self.filename).readlines()[1:]
n = 0
self.energy_qi = []
nq = len(lines) // len(self.ecut_i)
for q_c in self.ibzq_qc[:nq]:
self.energy_qi.append([])
for ecut in self.ecut_i:
q1, q2, q3, ec, energy = [float(x)
for x in lines[n].split()]
self.energy_qi[-1].append(energy / Hartree)
n += 1
if (abs(q_c - (q1, q2, q3)).max() > 1e-4 or
abs(int(ecut * Hartree) - ec) > 0):
self.energy_qi = []
return
print('Read %d q-points from file: %s' % (nq, self.filename),
file=self.fd)
print(file=self.fd)
def write(self):
if self.world.rank == 0 and self.filename:
fd = open(self.filename, 'w')
print('#%9s %10s %10s %8s %12s' %
('q1', 'q2', 'q3', 'E_cut', 'E_c(q)'), file=fd)
for energy_i, q_c in zip(self.energy_qi, self.ibzq_qc):
for energy, ecut in zip(energy_i, self.ecut_i):
print('%10.4f %10.4f %10.4f %8d %r' %
(tuple(q_c) + (ecut * Hartree, energy * Hartree)),
file=fd)
def calculate(self, ecut, nbands=None, spin=False):
"""Calculate RPA correlation energy for one or several cutoffs.
ecut: float or list of floats
Plane-wave cutoff(s).
nbands: int
Number of bands (defaults to number of plane-waves).
spin: bool
Separate spin in response funtion.
(Only needed for beyond RPA methods that inherit this function).
"""
p = functools.partial(print, file=self.fd)
if isinstance(ecut, (float, int)):
ecut = ecut * (1 + 0.5 * np.arange(6))**(-2 / 3)
self.ecut_i = np.asarray(np.sort(ecut)) / Hartree
ecutmax = max(self.ecut_i)
if nbands is None:
p('Response function bands : Equal to number of plane waves')
else:
p('Response function bands : %s' % nbands)
p('Plane wave cutoffs (eV) :', end='')
for e in self.ecut_i:
p(' {0:.3f}'.format(e * Hartree), end='')
p()
p()
if self.filename and os.path.isfile(self.filename):
self.read()
self.world.barrier()
chi0 = Chi0(self.calc, 1j * Hartree * self.omega_w, eta=0.0,
intraband=False, hilbert=False,
txt=self.fd, timer=self.timer, world=self.world,
no_optical_limit=self.wstc,
nblocks=self.nblocks)
self.blockcomm = chi0.blockcomm
wfs = self.calc.wfs
if self.wstc:
with self.timer('WSTC-init'):
p('Using Wigner-Seitz truncated Coulomb potential.')
self.wstc = WignerSeitzTruncatedCoulomb(
wfs.gd.cell_cv, wfs.kd.N_c, self.fd)
nq = len(self.energy_qi)
nw = len(self.omega_w)
nGmax = max(count_reciprocal_vectors(ecutmax, wfs.gd, q_c)
for q_c in self.ibzq_qc[nq:])
mynGmax = (nGmax + self.nblocks - 1) // self.nblocks
nx = (1 + spin) * nw * mynGmax * nGmax
A1_x = np.empty(nx, complex)
if self.nblocks > 1:
A2_x = np.empty(nx, complex)
else:
A2_x = None
self.timer.start('RPA')
for q_c in self.ibzq_qc[nq:]:
if np.allclose(q_c, 0.0) and self.skip_gamma:
self.energy_qi.append(len(self.ecut_i) * [0.0])
self.write()
p('Not calculating E_c(q) at Gamma')
p()
continue
thisqd = KPointDescriptor([q_c])
pd = PWDescriptor(ecutmax, wfs.gd, complex, thisqd)
nG = pd.ngmax
mynG = (nG + self.nblocks - 1) // self.nblocks
chi0.Ga = self.blockcomm.rank * mynG
chi0.Gb = min(chi0.Ga + mynG, nG)
shape = (1 + spin, nw, chi0.Gb - chi0.Ga, nG)
chi0_swGG = A1_x[:np.prod(shape)].reshape(shape)
chi0_swGG[:] = 0.0
if self.wstc or np.allclose(q_c, 0.0):
# Wings (x=0,1) and head (G=0) for optical limit and three
# directions (v=0,1,2):
chi0_swxvG = np.zeros((1 + spin, nw, 2, 3, nG), complex)
chi0_swvv = np.zeros((1 + spin, nw, 3, 3), complex)
else:
chi0_swxvG = None
chi0_swvv = None
Q_aGii = chi0.initialize_paw_corrections(pd)
# First not completely filled band:
m1 = chi0.nocc1
p('# %s - %s' % (len(self.energy_qi), ctime().split()[-2]))
p('q = [%1.3f %1.3f %1.3f]' % tuple(q_c))
energy_i = []
for ecut in self.ecut_i:
if ecut == ecutmax:
# Nothing to cut away:
cut_G = None
m2 = nbands or nG
else:
cut_G = np.arange(nG)[pd.G2_qG[0] <= 2 * ecut]
m2 = len(cut_G)
p('E_cut = %d eV / Bands = %d:' % (ecut * Hartree, m2))
self.fd.flush()
energy = self.calculate_q(chi0, pd,
chi0_swGG, chi0_swxvG, chi0_swvv,
Q_aGii, m1, m2, cut_G, A2_x)
energy_i.append(energy)
m1 = m2
a = 1 / chi0.kncomm.size
if ecut < ecutmax and a != 1.0:
# Chi0 will be summed again over chicomm, so we divide
# by its size:
chi0_swGG *= a
if chi0_swxvG is not None:
chi0_swxvG *= a
chi0_swvv *= a
self.energy_qi.append(energy_i)
self.write()
p()
e_i = np.dot(self.weight_q, np.array(self.energy_qi))
p('==========================================================')
p()
p('Total correlation energy:')
for e_cut, e in zip(self.ecut_i, e_i):
p('%6.0f: %6.4f eV' % (e_cut * Hartree, e * Hartree))
p()
self.energy_qi = [] # important if another calculation is performed
if len(e_i) > 1:
self.extrapolate(e_i)
p('Calculation completed at: ', ctime())
p()
self.timer.stop('RPA')
self.timer.write(self.fd)
self.fd.flush()
return e_i * Hartree
@timer('chi0(q)')
def calculate_q(self, chi0, pd,
chi0_swGG, chi0_swxvG, chi0_swvv, Q_aGii, m1, m2, cut_G,
A2_x):
chi0_wGG = chi0_swGG[0]
if chi0_swxvG is not None:
chi0_wxvG = chi0_swxvG[0]
chi0_wvv = chi0_swvv[0]
else:
chi0_wxvG = None
chi0_wvv = None
chi0._calculate(pd, chi0_wGG, chi0_wxvG, chi0_wvv,
Q_aGii, m1, m2, [0, 1])
print('E_c(q) = ', end='', file=self.fd)
chi0_wGG = chi0.redistribute(chi0_wGG, A2_x)
if not pd.kd.gamma or self.wstc:
e = self.calculate_energy(pd, chi0_wGG, cut_G)
print('%.3f eV' % (e * Hartree), file=self.fd)
self.fd.flush()
else:
e = 0.0
for v in range(3):
chi0_wGG[:, 0] = chi0_wxvG[:, 0, v]
chi0_wGG[:, :, 0] = chi0_wxvG[:, 1, v]
chi0_wGG[:, 0, 0] = chi0_wvv[:, v, v]
ev = self.calculate_energy(pd, chi0_wGG, cut_G)
e += ev
print('%.3f' % (ev * Hartree), end='', file=self.fd)
if v < 2:
print('/', end='', file=self.fd)
else:
print(' eV', file=self.fd)
self.fd.flush()
e /= 3
return e
@timer('Energy')
def calculate_energy(self, pd, chi0_wGG, cut_G):
"""Evaluate correlation energy from chi0."""
if self.wstc:
invG_G = (self.wstc.get_potential(pd) / (4 * pi))**0.5
else:
G_G = pd.G2_qG[0]**0.5 # |G+q|
if pd.kd.gamma:
G_G[0] = 1.0
invG_G = 1.0 / G_G
if cut_G is not None:
invG_G = invG_G[cut_G]
nG = len(invG_G)
e_w = []
for chi0_GG in chi0_wGG:
if cut_G is not None:
chi0_GG = chi0_GG.take(cut_G, 0).take(cut_G, 1)
e_GG = (np.eye(nG) -
4 * np.pi * chi0_GG * invG_G * invG_G[:, np.newaxis])
e = np.log(np.linalg.det(e_GG)) + nG - np.trace(e_GG)
e_w.append(e.real)
E_w = np.zeros_like(self.omega_w)
self.blockcomm.all_gather(np.array(e_w), E_w)
energy = np.dot(E_w, self.weight_w) / (2 * np.pi)
self.E_w = E_w
return energy
def extrapolate(self, e_i):
print('Extrapolated energies:', file=self.fd)
ex_i = []
for i in range(len(e_i) - 1):
e1, e2 = e_i[i:i + 2]
x1, x2 = self.ecut_i[i:i + 2]**-1.5
ex = (e1 * x2 - e2 * x1) / (x2 - x1)
ex_i.append(ex)
print(' %4.0f -%4.0f: %5.3f eV' % (self.ecut_i[i] * Hartree,
self.ecut_i[i + 1] * Hartree,
ex * Hartree),
file=self.fd)
print(file=self.fd)
self.fd.flush()
return e_i * Hartree
def print_initialization(self, xc, frequency_scale, nlambda, user_spec):
p = functools.partial(print, file=self.fd)
p('----------------------------------------------------------')
p('Non-self-consistent %s correlation energy' % xc)
p('----------------------------------------------------------')
p('Started at: ', ctime())
p()
p('Atoms :',
self.calc.atoms.get_chemical_formula(mode='hill'))
p('Ground state XC functional :', self.calc.hamiltonian.xc.name)
p('Valence electrons :', self.calc.wfs.setups.nvalence)
p('Number of bands :', self.calc.wfs.bd.nbands)
p('Number of spins :', self.calc.wfs.nspins)
p('Number of k-points :', len(self.calc.wfs.kd.bzk_kc))
p('Number of irreducible k-points :', len(self.calc.wfs.kd.ibzk_kc))
p('Number of q-points :', len(self.bzq_qc))
p('Number of irreducible q-points :', len(self.ibzq_qc))
p()
for q, weight in zip(self.ibzq_qc, self.weight_q):
p(' q: [%1.4f %1.4f %1.4f] - weight: %1.3f' %
(q[0], q[1], q[2], weight))
p()
p('----------------------------------------------------------')
p('----------------------------------------------------------')
p()
if nlambda is None:
p('Analytical coupling constant integration')
else:
p('Numerical coupling constant integration using', nlambda,
'Gauss-Legendre points')
p()
p('Frequencies')
if not user_spec:
p(' Gauss-Legendre integration with %s frequency points' %
len(self.omega_w))
p(' Transformed from [0,oo] to [0,1] using e^[-aw^(1/B)]')
p(' Highest frequency point at %5.1f eV and B=%1.1f' %
(self.omega_w[-1] * Hartree, frequency_scale))
else:
p(' User specified frequency integration with',
len(self.omega_w), 'frequency points')
p()
p('Parallelization')
p(' Total number of CPUs : % s' % self.world.size)
p(' G-vector decomposition : % s' % self.nblocks)
p(' K-point/band decomposition : % s' %
(self.world.size // self.nblocks))
p()
def calculate(self, ecut, nbands=None, spin=False):
"""Calculate RPA correlation energy for one or several cutoffs.
ecut: float or list of floats
Plane-wave cutoff(s).
nbands: int
Number of bands (defaults to number of plane-waves).
spin: bool
Separate spin in response funtion.
(Only needed for beyond RPA methods that inherit this function).
"""
p = functools.partial(print, file=self.fd)
if isinstance(ecut, (float, int)):
ecut = ecut * (1 + 0.5 * np.arange(6))**(-2 / 3)
self.ecut_i = np.asarray(np.sort(ecut)) / Hartree
ecutmax = max(self.ecut_i)
if nbands is None:
p('Response function bands : Equal to number of plane waves')
else:
p('Response function bands : %s' % nbands)
p('Plane wave cutoffs (eV) :', end='')
for e in self.ecut_i:
p(' {0:.3f}'.format(e * Hartree), end='')
p()
p()
if self.filename and os.path.isfile(self.filename):
self.read()
self.world.barrier()
chi0 = Chi0(self.calc, 1j * Hartree * self.omega_w, eta=0.0,
intraband=False, hilbert=False,
txt=self.fd, timer=self.timer, world=self.world,
no_optical_limit=self.wstc,
nblocks=self.nblocks)
self.blockcomm = chi0.blockcomm
wfs = self.calc.wfs
if self.wstc:
with self.timer('WSTC-init'):
p('Using Wigner-Seitz truncated Coulomb potential.')
self.wstc = WignerSeitzTruncatedCoulomb(
wfs.gd.cell_cv, wfs.kd.N_c, self.fd)
nq = len(self.energy_qi)
nw = len(self.omega_w)
nGmax = max(count_reciprocal_vectors(ecutmax, wfs.gd, q_c)
for q_c in self.ibzq_qc[nq:])
mynGmax = (nGmax + self.nblocks - 1) // self.nblocks
nx = (1 + spin) * nw * mynGmax * nGmax
A1_x = np.empty(nx, complex)
if self.nblocks > 1:
A2_x = np.empty(nx, complex)
else:
A2_x = None
self.timer.start('RPA')
for q_c in self.ibzq_qc[nq:]:
if np.allclose(q_c, 0.0) and self.skip_gamma:
self.energy_qi.append(len(self.ecut_i) * [0.0])
self.write()
p('Not calculating E_c(q) at Gamma')
p()
continue
thisqd = KPointDescriptor([q_c])
pd = PWDescriptor(ecutmax, wfs.gd, complex, thisqd)
nG = pd.ngmax
mynG = (nG + self.nblocks - 1) // self.nblocks
chi0.Ga = self.blockcomm.rank * mynG
chi0.Gb = min(chi0.Ga + mynG, nG)
shape = (1 + spin, nw, chi0.Gb - chi0.Ga, nG)
chi0_swGG = A1_x[:np.prod(shape)].reshape(shape)
chi0_swGG[:] = 0.0
if self.wstc or np.allclose(q_c, 0.0):
# Wings (x=0,1) and head (G=0) for optical limit and three
# directions (v=0,1,2):
chi0_swxvG = np.zeros((1 + spin, nw, 2, 3, nG), complex)
chi0_swvv = np.zeros((1 + spin, nw, 3, 3), complex)
else:
chi0_swxvG = None
chi0_swvv = None
Q_aGii = chi0.initialize_paw_corrections(pd)
# First not completely filled band:
m1 = chi0.nocc1
p('# %s - %s' % (len(self.energy_qi), ctime().split()[-2]))
p('q = [%1.3f %1.3f %1.3f]' % tuple(q_c))
energy_i = []
for ecut in self.ecut_i:
if ecut == ecutmax:
# Nothing to cut away:
cut_G = None
m2 = nbands or nG
else:
cut_G = np.arange(nG)[pd.G2_qG[0] <= 2 * ecut]
m2 = len(cut_G)
p('E_cut = %d eV / Bands = %d:' % (ecut * Hartree, m2))
self.fd.flush()
energy = self.calculate_q(chi0, pd,
chi0_swGG, chi0_swxvG, chi0_swvv,
Q_aGii, m1, m2, cut_G, A2_x)
energy_i.append(energy)
m1 = m2
a = 1 / chi0.kncomm.size
if ecut < ecutmax and a != 1.0:
# Chi0 will be summed again over chicomm, so we divide
# by its size:
chi0_swGG *= a
if chi0_swxvG is not None:
chi0_swxvG *= a
chi0_swvv *= a
self.energy_qi.append(energy_i)
self.write()
p()
e_i = np.dot(self.weight_q, np.array(self.energy_qi))
p('==========================================================')
p()
p('Total correlation energy:')
for e_cut, e in zip(self.ecut_i, e_i):
p('%6.0f: %6.4f eV' % (e_cut * Hartree, e * Hartree))
p()
self.energy_qi = [] # important if another calculation is performed
if len(e_i) > 1:
self.extrapolate(e_i)
p('Calculation completed at: ', ctime())
p()
self.timer.stop('RPA')
self.timer.write(self.fd)
self.fd.flush()
return e_i * Hartree
def get_dielectric_matrix(self, xc='RPA', q_c=[0, 0, 0],
direction='x', symmetric=True,
calculate_chi=False):
"""Returns the symmetrized dielectric matrix.
::
\tilde\epsilon_GG' = v^{-1/2}_G \epsilon_GG' v^{1/2}_G',
where::
epsilon_GG' = 1 - v_G * P_GG' and P_GG'
is the polarization.
::
In RPA: P = chi^0
In TDDFT: P = (1 - chi^0 * f_xc)^{-1} chi^0
The head of the inverse symmetrized dielectric matrix is equal
to the head of the inverse dielectric matrix (inverse dielectric
function)
"""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
G_G = pd.G2_qG[0]**0.5
nG = len(G_G)
if pd.kd.gamma:
G_G[0] = 1.0
if isinstance(direction, str):
d_v = {'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
if self.truncation == 'wigner-seitz':
kernel = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv,
self.chi0.calc.wfs.kd.N_c)
K_G = kernel.get_potential(pd)**0.5
if pd.kd.gamma:
K_G[0] = 0.0
elif self.truncation == '2D':
K_G = truncated_coulomb(pd)
if pd.kd.gamma:
K_G[0] = 0.0
else:
K_G = (4 * pi)**0.5 / G_G
if xc != 'RPA':
R_av = self.chi0.calc.atoms.positions / Bohr
nt_sG = self.chi0.calc.density.nt_sG
Kxc_sGG = calculate_Kxc(pd, nt_sG, R_av,
self.chi0.calc.wfs.setups,
self.chi0.calc.density.D_asp,
functional=xc)
if calculate_chi:
chi_wGG = []
for chi0_GG in chi0_wGG:
if xc == 'RPA':
P_GG = chi0_GG
else:
P_GG = np.dot(np.linalg.inv(np.eye(nG) -
np.dot(chi0_GG, Kxc_sGG[0])),
chi0_GG)
if symmetric:
e_GG = np.eye(nG) - P_GG * K_G * K_G[:, np.newaxis]
else:
K_GG = (K_G**2 * np.ones([nG, nG])).T
e_GG = np.eye(nG) - P_GG * K_GG
if calculate_chi:
K_GG = np.diag(K_G**2)
if xc != 'RPA':
K_GG += Kxc_sGG[0]
chi_wGG.append(np.dot(np.linalg.inv(np.eye(nG) -
np.dot(chi0_GG, K_GG)),
chi0_GG))
chi0_GG[:] = e_GG
# chi0_wGG is now the dielectric matrix
if not calculate_chi:
return chi0_wGG
else:
return pd, chi0_wGG, chi_wGG
def __init__(self, calc, xc=None, kpts=None, bands=None, ecut=None,
omega=None, world=mpi.world, txt=sys.stdout, timer=None):
PairDensity.__init__(self, calc, ecut, world=world, txt=txt,
timer=timer)
if xc is None or xc == 'EXX':
self.exx_fraction = 1.0
xc = XC(XCNull())
elif xc == 'PBE0':
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_PBEH')
elif xc == 'HSE03':
omega = 0.106
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE03')
elif xc == 'HSE06':
omega = 0.11
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE06')
elif xc == 'B3LYP':
self.exx_fraction = 0.2
xc = XC('HYB_GGA_XC_B3LYP')
self.xc = xc
self.omega = omega
self.exc = np.nan # density dependent part of xc-energy
self.kpts = select_kpts(kpts, self.calc)
if bands is None:
# Do all occupied bands:
bands = [0, self.nocc2]
prnt('Calculating exact exchange contributions for band index',
'%d-%d' % (bands[0], bands[1] - 1), file=self.fd)
prnt('for IBZ k-points with indices:',
', '.join(str(i) for i in self.kpts), file=self.fd)
self.bands = bands
if self.ecut is None:
self.ecut = self.calc.wfs.pd.ecut
prnt('Plane-wave cutoff: %.3f eV' % (self.ecut * Hartree),
file=self.fd)
shape = (self.calc.wfs.nspins, len(self.kpts), bands[1] - bands[0])
self.exxvv_sin = np.zeros(shape) # valence-valence exchange energies
self.exxvc_sin = np.zeros(shape) # valence-core exchange energies
self.f_sin = np.empty(shape) # occupation numbers
# The total EXX energy will not be calculated if we are only
# interested in a few eigenvalues for a few k-points
self.exx = np.nan # total EXX energy
self.exxvv = np.nan # valence-valence
self.exxvc = np.nan # valence-core
self.exxcc = 0.0 # core-core
self.mysKn1n2 = None # my (s, K, n1, n2) indices
self.distribute_k_points_and_bands(0, self.nocc2)
# All occupied states:
self.mykpts = [self.get_k_point(s, K, n1, n2)
for s, K, n1, n2 in self.mysKn1n2]
prnt('Using Wigner-Seitz truncated coulomb interaction.',
file=self.fd)
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.calc.wfs.kd.N_c,
self.fd)
self.iG_qG = {} # cache
# PAW matrices:
self.V_asii = [] # valence-valence correction
self.C_aii = [] # valence-core correction
self.initialize_paw_exx_corrections()
class EXX(PairDensity):
def __init__(self, calc, xc=None, kpts=None, bands=None, ecut=None,
omega=None, world=mpi.world, txt=sys.stdout, timer=None):
PairDensity.__init__(self, calc, ecut, world=world, txt=txt,
timer=timer)
if xc is None or xc == 'EXX':
self.exx_fraction = 1.0
xc = XC(XCNull())
elif xc == 'PBE0':
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_PBEH')
elif xc == 'HSE03':
omega = 0.106
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE03')
elif xc == 'HSE06':
omega = 0.11
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE06')
elif xc == 'B3LYP':
self.exx_fraction = 0.2
xc = XC('HYB_GGA_XC_B3LYP')
self.xc = xc
self.omega = omega
self.exc = np.nan # density dependent part of xc-energy
self.kpts = select_kpts(kpts, self.calc)
if bands is None:
# Do all occupied bands:
bands = [0, self.nocc2]
prnt('Calculating exact exchange contributions for band index',
'%d-%d' % (bands[0], bands[1] - 1), file=self.fd)
prnt('for IBZ k-points with indices:',
', '.join(str(i) for i in self.kpts), file=self.fd)
self.bands = bands
if self.ecut is None:
self.ecut = self.calc.wfs.pd.ecut
prnt('Plane-wave cutoff: %.3f eV' % (self.ecut * Hartree),
file=self.fd)
shape = (self.calc.wfs.nspins, len(self.kpts), bands[1] - bands[0])
self.exxvv_sin = np.zeros(shape) # valence-valence exchange energies
self.exxvc_sin = np.zeros(shape) # valence-core exchange energies
self.f_sin = np.empty(shape) # occupation numbers
# The total EXX energy will not be calculated if we are only
# interested in a few eigenvalues for a few k-points
self.exx = np.nan # total EXX energy
self.exxvv = np.nan # valence-valence
self.exxvc = np.nan # valence-core
self.exxcc = 0.0 # core-core
self.mysKn1n2 = None # my (s, K, n1, n2) indices
self.distribute_k_points_and_bands(0, self.nocc2)
# All occupied states:
self.mykpts = [self.get_k_point(s, K, n1, n2)
for s, K, n1, n2 in self.mysKn1n2]
prnt('Using Wigner-Seitz truncated coulomb interaction.',
file=self.fd)
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.calc.wfs.kd.N_c,
self.fd)
self.iG_qG = {} # cache
# PAW matrices:
self.V_asii = [] # valence-valence correction
self.C_aii = [] # valence-core correction
self.initialize_paw_exx_corrections()
def calculate(self):
kd = self.calc.wfs.kd
nspins = self.calc.wfs.nspins
for s in range(nspins):
for i, k1 in enumerate(self.kpts):
K1 = kd.ibz2bz_k[k1]
kpt1 = self.get_k_point(s, K1, *self.bands)
self.f_sin[s, i] = kpt1.f_n
for kpt2 in self.mykpts:
if kpt2.s == s:
self.calculate_q(i, kpt1, kpt2)
self.calculate_paw_exx_corrections(i, kpt1)
self.world.sum(self.exxvv_sin)
# Calculate total energy if we have everything needed:
if (len(self.kpts) == kd.nibzkpts and
self.bands[0] == 0 and
self.bands[1] >= self.nocc2):
exxvv_i = (self.exxvv_sin * self.f_sin).sum(axis=2).sum(axis=0)
exxvc_i = 2 * (self.exxvc_sin * self.f_sin).sum(axis=2).sum(axis=0)
self.exxvv = np.dot(kd.weight_k[self.kpts], exxvv_i) / nspins
self.exxvc = np.dot(kd.weight_k[self.kpts], exxvc_i) / nspins
self.exx = self.exxvv + self.exxvc + self.exxcc
prnt('Exact exchange energy:', file=self.fd)
for kind, exx in [('valence-valence', self.exxvv),
('valence-core', self.exxvc),
('core-core', self.exxcc),
('total', self.exx)]:
prnt('%16s%11.3f eV' % (kind + ':', exx * Hartree),
file=self.fd)
self.exc = self.calculate_hybrid_correction()
exx_sin = self.exxvv_sin + self.exxvc_sin
prnt('EXX eigenvalue contributions in eV:', file=self.fd)
prnt(np.array_str(exx_sin * Hartree, precision=3), file=self.fd)
def get_exx_energy(self):
return self.exx * Hartree
def get_total_energy(self):
ham = self.calc.hamiltonian
return (self.exx * self.exx_fraction + self.exc +
ham.Etot - ham.Exc) * Hartree
def get_eigenvalue_contributions(self):
if self.reader is not None:
self.calc.wfs.read_projections(self.reader)
b1, b2 = self.bands
e_sin = vxc(self.calc, self.xc)[:, self.kpts, b1:b2] / Hartree
e_sin += (self.exxvv_sin + self.exxvc_sin) * self.exx_fraction
return e_sin * Hartree
def calculate_q(self, i, kpt1, kpt2):
wfs = self.calc.wfs
q_c = wfs.kd.bzk_kc[kpt2.K] - wfs.kd.bzk_kc[kpt1.K]
qd = KPointDescriptor([q_c])
pd = PWDescriptor(self.ecut, wfs.gd, wfs.dtype, kd=qd)
Q_G = self.get_fft_indices(kpt1.K, kpt2.K, q_c, pd,
kpt1.shift_c - kpt2.shift_c)
Q_aGii = self.initialize_paw_corrections(pd, soft=True)
for n in range(kpt1.n2 - kpt1.n1):
ut1cc_R = kpt1.ut_nR[n].conj()
C1_aGi = [np.dot(Q_Gii, P1_ni[n].conj())
for Q_Gii, P1_ni in zip(Q_aGii, kpt1.P_ani)]
n_mG = self.calculate_pair_densities(ut1cc_R, C1_aGi, kpt2,
pd, Q_G)
e = self.calculate_n(pd, n, n_mG, kpt2)
self.exxvv_sin[kpt1.s, i, n] += e
def calculate_n(self, pd, n, n_mG, kpt2):
iG_G = self.get_coulomb_kernel(pd)
x = 4 * pi / self.calc.wfs.kd.nbzkpts / pd.gd.dv**2
e = 0.0
for f, n_G in zip(kpt2.f_n, n_mG):
x_G = n_G * iG_G
e -= x * f * pd.integrate(x_G, x_G).real
return e
def get_coulomb_kernel(self, pd):
if self.omega is not None:
G2_G = pd.G2_qG[0]
iG_G = np.empty_like(G2_G)
if pd.kd.gamma:
iG_G[0] = 1 / (2 * self.omega)
else:
iG_G[0] = ((1 - np.exp(-G2_G[0] / (4 * self.omega**2))) /
G2_G[0])**0.5
iG_G[1:] = ((1 - np.exp(-G2_G[1:] / (4 * self.omega**2))) /
G2_G[1:])**0.5
return iG_G
key = tuple((pd.kd.bzk_kc[0] * self.calc.wfs.kd.N_c).round())
iG_G = self.iG_qG.get(key)
if iG_G is None:
v_G = self.wstc.get_potential(pd)
iG_G = (v_G / (4 * pi))**0.5
self.iG_qG[key] = iG_G
return iG_G
def initialize_paw_exx_corrections(self):
for a, atomdata in enumerate(self.calc.wfs.setups):
V_sii = []
for D_p in self.calc.density.D_asp[a]:
D_ii = unpack2(D_p)
V_ii = pawexxvv(atomdata, D_ii)
V_sii.append(V_ii)
C_ii = unpack(atomdata.X_p)
self.V_asii.append(V_sii)
self.C_aii.append(C_ii)
self.exxcc += atomdata.ExxC
def calculate_paw_exx_corrections(self, i, kpt):
x = self.calc.wfs.nspins / self.world.size
s = kpt.s
for V_sii, C_ii, P_ni in zip(self.V_asii, self.C_aii, kpt.P_ani):
V_ii = V_sii[s]
v_n = (np.dot(P_ni, V_ii) * P_ni.conj()).sum(axis=1).real
c_n = (np.dot(P_ni, C_ii) * P_ni.conj()).sum(axis=1).real
self.exxvv_sin[s, i] -= v_n * x
self.exxvc_sin[s, i] -= c_n
def calculate_hybrid_correction(self):
dens = self.calc.density
if dens.nt_sg is None:
dens.interpolate_pseudo_density()
exc = self.xc.calculate(dens.finegd, dens.nt_sg)
for a, D_sp in dens.D_asp.items():
atomdata = dens.setups[a]
exc += self.xc.calculate_paw_correction(atomdata, D_sp)
return exc
def calculate_screened_potential(self):
"""Calculates the screened potential for each q-point in the 1st BZ.
Since many q-points are related by symmetry, the actual calculation is
only done for q-points in the IBZ and the rest are obtained by symmetry
transformations. Results are returned as a generator to that it is not
necessary to store a huge matrix for each q-point in the memory."""
# The decorator $timer('W') doesn't work for generators, do we will
# have to manually start and stop the timer here:
self.timer.start('W')
print('Calculating screened Coulomb potential', file=self.fd)
if self.wstc:
print('Using Wigner-Seitz truncated Coloumb potential',
file=self.fd)
if self.ppa:
print('Using Godby-Needs plasmon-pole approximation:',
file=self.fd)
print(' Fitting energy: i*E0, E0 = %.3f Hartee' % self.E0,
file=self.fd)
# use small imaginary frequency to avoid dividing by zero:
frequencies = [1e-10j, 1j * self.E0 * Hartree]
parameters = {'eta': 0,
'hilbert': False,
'timeordered': False,
'frequencies': frequencies}
else:
print('Using full frequency integration:', file=self.fd)
print(' domega0: {0:g}'.format(self.domega0 * Hartree),
file=self.fd)
print(' omega2: {0:g}'.format(self.omega2 * Hartree),
file=self.fd)
parameters = {'eta': self.eta * Hartree,
'hilbert': True,
'timeordered': True,
'domega0': self.domega0 * Hartree,
'omega2': self.omega2 * Hartree}
chi0 = Chi0(self.calc,
nbands=self.nbands,
ecut=self.ecut * Hartree,
intraband=False,
real_space_derivatives=False,
txt=self.filename + '.w.txt',
timer=self.timer,
keep_occupied_states=True,
nblocks=self.blockcomm.size,
no_optical_limit=self.wstc,
**parameters)
if self.wstc:
wstc = WignerSeitzTruncatedCoulomb(
self.calc.wfs.gd.cell_cv,
self.calc.wfs.kd.N_c,
chi0.fd)
else:
wstc = None
self.omega_w = chi0.omega_w
self.omegamax = chi0.omegamax
htp = HilbertTransform(self.omega_w, self.eta, gw=True)
htm = HilbertTransform(self.omega_w, -self.eta, gw=True)
# Find maximum size of chi-0 matrices:
gd = self.calc.wfs.gd
nGmax = max(count_reciprocal_vectors(self.ecut, gd, q_c)
for q_c in self.qd.ibzk_kc)
nw = len(self.omega_w)
size = self.blockcomm.size
mynGmax = (nGmax + size - 1) // size
mynw = (nw + size - 1) // size
# Allocate memory in the beginning and use for all q:
A1_x = np.empty(nw * mynGmax * nGmax, complex)
A2_x = np.empty(max(mynw * nGmax, nw * mynGmax) * nGmax, complex)
# Need to pause the timer in between iterations
self.timer.stop('W')
for iq, q_c in enumerate(self.qd.ibzk_kc):
self.timer.start('W')
if self.savew:
wfilename = self.filename + '.w.q%d.pckl' % iq
fd = opencew(wfilename)
if self.savew and fd is None:
# Read screened potential from file
with open(wfilename) as fd:
pd, W = pickle.load(fd)
else:
# First time calculation
pd, W = self.calculate_w(chi0, q_c, htp, htm, wstc, A1_x, A2_x)
if self.savew:
pickle.dump((pd, W), fd, pickle.HIGHEST_PROTOCOL)
self.timer.stop('W')
# Loop over all k-points in the BZ and find those that are related
# to the current IBZ k-point by symmetry
Q1 = self.qd.ibz2bz_k[iq]
done = set()
for s, Q2 in enumerate(self.qd.bz2bz_ks[Q1]):
if Q2 >= 0 and Q2 not in done:
s = self.qd.sym_k[Q2]
self.s = s
self.U_cc = self.qd.symmetry.op_scc[s]
time_reversal = self.qd.time_reversal_k[Q2]
self.sign = 1 - 2 * time_reversal
Q_c = self.qd.bzk_kc[Q2]
d_c = self.sign * np.dot(self.U_cc, q_c) - Q_c
assert np.allclose(d_c.round(), d_c)
yield pd, W, Q_c
done.add(Q2)
class EXX(PairDensity):
def __init__(self,
calc,
xc=None,
kpts=None,
bands=None,
ecut=None,
omega=None,
world=mpi.world,
txt=sys.stdout,
timer=None):
PairDensity.__init__(self,
calc,
ecut,
world=world,
txt=txt,
timer=timer)
if xc is None or xc == 'EXX':
self.exx_fraction = 1.0
xc = XC(XCNull())
elif xc == 'PBE0':
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_PBEH')
elif xc == 'HSE03':
omega = 0.106
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE03')
elif xc == 'HSE06':
omega = 0.11
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE06')
elif xc == 'B3LYP':
self.exx_fraction = 0.2
xc = XC('HYB_GGA_XC_B3LYP')
self.xc = xc
self.omega = omega
self.exc = np.nan # density dependent part of xc-energy
self.kpts = select_kpts(kpts, self.calc)
if bands is None:
# Do all occupied bands:
bands = [0, self.nocc2]
prnt('Calculating exact exchange contributions for band index',
'%d-%d' % (bands[0], bands[1] - 1),
file=self.fd)
prnt('for IBZ k-points with indices:',
', '.join(str(i) for i in self.kpts),
file=self.fd)
self.bands = bands
if self.ecut is None:
self.ecut = self.calc.wfs.pd.ecut
prnt('Plane-wave cutoff: %.3f eV' % (self.ecut * Hartree),
file=self.fd)
shape = (self.calc.wfs.nspins, len(self.kpts), bands[1] - bands[0])
self.exxvv_sin = np.zeros(shape) # valence-valence exchange energies
self.exxvc_sin = np.zeros(shape) # valence-core exchange energies
self.f_sin = np.empty(shape) # occupation numbers
# The total EXX energy will not be calculated if we are only
# interested in a few eigenvalues for a few k-points
self.exx = np.nan # total EXX energy
self.exxvv = np.nan # valence-valence
self.exxvc = np.nan # valence-core
self.exxcc = 0.0 # core-core
self.mysKn1n2 = None # my (s, K, n1, n2) indices
self.distribute_k_points_and_bands(0, self.nocc2)
# All occupied states:
self.mykpts = [
self.get_k_point(s, K, n1, n2) for s, K, n1, n2 in self.mysKn1n2
]
prnt('Using Wigner-Seitz truncated coulomb interaction.', file=self.fd)
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.calc.wfs.kd.N_c, self.fd)
self.iG_qG = {} # cache
# PAW matrices:
self.V_asii = [] # valence-valence correction
self.C_aii = [] # valence-core correction
self.initialize_paw_exx_corrections()
def calculate(self):
kd = self.calc.wfs.kd
nspins = self.calc.wfs.nspins
for s in range(nspins):
for i, k1 in enumerate(self.kpts):
K1 = kd.ibz2bz_k[k1]
kpt1 = self.get_k_point(s, K1, *self.bands)
self.f_sin[s, i] = kpt1.f_n
for kpt2 in self.mykpts:
if kpt2.s == s:
self.calculate_q(i, kpt1, kpt2)
self.calculate_paw_exx_corrections(i, kpt1)
self.world.sum(self.exxvv_sin)
# Calculate total energy if we have everything needed:
if (len(self.kpts) == kd.nibzkpts and self.bands[0] == 0
and self.bands[1] >= self.nocc2):
exxvv_i = (self.exxvv_sin * self.f_sin).sum(axis=2).sum(axis=0)
exxvc_i = 2 * (self.exxvc_sin * self.f_sin).sum(axis=2).sum(axis=0)
self.exxvv = np.dot(kd.weight_k[self.kpts], exxvv_i) / nspins
self.exxvc = np.dot(kd.weight_k[self.kpts], exxvc_i) / nspins
self.exx = self.exxvv + self.exxvc + self.exxcc
prnt('Exact exchange energy:', file=self.fd)
for kind, exx in [('valence-valence', self.exxvv),
('valence-core', self.exxvc),
('core-core', self.exxcc), ('total', self.exx)]:
prnt('%16s%11.3f eV' % (kind + ':', exx * Hartree),
file=self.fd)
self.exc = self.calculate_hybrid_correction()
exx_sin = self.exxvv_sin + self.exxvc_sin
prnt('EXX eigenvalue contributions in eV:', file=self.fd)
prnt(np.array_str(exx_sin * Hartree, precision=3), file=self.fd)
def get_exx_energy(self):
return self.exx * Hartree
def get_total_energy(self):
ham = self.calc.hamiltonian
return (self.exx * self.exx_fraction + self.exc + ham.Etot -
ham.Exc) * Hartree
def get_eigenvalue_contributions(self):
if self.reader is not None:
self.calc.wfs.read_projections(self.reader)
b1, b2 = self.bands
e_sin = vxc(self.calc, self.xc)[:, self.kpts, b1:b2] / Hartree
e_sin += (self.exxvv_sin + self.exxvc_sin) * self.exx_fraction
return e_sin * Hartree
def calculate_q(self, i, kpt1, kpt2):
wfs = self.calc.wfs
q_c = wfs.kd.bzk_kc[kpt2.K] - wfs.kd.bzk_kc[kpt1.K]
qd = KPointDescriptor([q_c])
pd = PWDescriptor(self.ecut, wfs.gd, wfs.dtype, kd=qd)
Q_G = self.get_fft_indices(kpt1.K, kpt2.K, q_c, pd,
kpt1.shift_c - kpt2.shift_c)
Q_aGii = self.initialize_paw_corrections(pd, soft=True)
for n in range(kpt1.n2 - kpt1.n1):
ut1cc_R = kpt1.ut_nR[n].conj()
C1_aGi = [
np.dot(Q_Gii, P1_ni[n].conj())
for Q_Gii, P1_ni in zip(Q_aGii, kpt1.P_ani)
]
n_mG = self.calculate_pair_densities(ut1cc_R, C1_aGi, kpt2, pd,
Q_G)
e = self.calculate_n(pd, n, n_mG, kpt2)
self.exxvv_sin[kpt1.s, i, n] += e
def calculate_n(self, pd, n, n_mG, kpt2):
iG_G = self.get_coulomb_kernel(pd)
x = 4 * pi / self.calc.wfs.kd.nbzkpts / pd.gd.dv**2
e = 0.0
for f, n_G in zip(kpt2.f_n, n_mG):
x_G = n_G * iG_G
e -= x * f * pd.integrate(x_G, x_G).real
return e
def get_coulomb_kernel(self, pd):
if self.omega is not None:
G2_G = pd.G2_qG[0]
iG_G = np.empty_like(G2_G)
if pd.kd.gamma:
iG_G[0] = 1 / (2 * self.omega)
else:
iG_G[0] = ((1 - np.exp(-G2_G[0] / (4 * self.omega**2))) /
G2_G[0])**0.5
iG_G[1:] = ((1 - np.exp(-G2_G[1:] / (4 * self.omega**2))) /
G2_G[1:])**0.5
return iG_G
key = tuple((pd.kd.bzk_kc[0] * self.calc.wfs.kd.N_c).round())
iG_G = self.iG_qG.get(key)
if iG_G is None:
v_G = self.wstc.get_potential(pd)
iG_G = (v_G / (4 * pi))**0.5
self.iG_qG[key] = iG_G
return iG_G
def initialize_paw_exx_corrections(self):
for a, atomdata in enumerate(self.calc.wfs.setups):
V_sii = []
for D_p in self.calc.density.D_asp[a]:
D_ii = unpack2(D_p)
V_ii = pawexxvv(atomdata, D_ii)
V_sii.append(V_ii)
C_ii = unpack(atomdata.X_p)
self.V_asii.append(V_sii)
self.C_aii.append(C_ii)
self.exxcc += atomdata.ExxC
def calculate_paw_exx_corrections(self, i, kpt):
x = self.calc.wfs.nspins / self.world.size
s = kpt.s
for V_sii, C_ii, P_ni in zip(self.V_asii, self.C_aii, kpt.P_ani):
V_ii = V_sii[s]
v_n = (np.dot(P_ni, V_ii) * P_ni.conj()).sum(axis=1).real
c_n = (np.dot(P_ni, C_ii) * P_ni.conj()).sum(axis=1).real
self.exxvv_sin[s, i] -= v_n * x
self.exxvc_sin[s, i] -= c_n
def calculate_hybrid_correction(self):
dens = self.calc.density
if dens.nt_sg is None:
dens.interpolate_pseudo_density()
exc = self.xc.calculate(dens.finegd, dens.nt_sg)
for a, D_sp in dens.D_asp.items():
atomdata = dens.setups[a]
exc += self.xc.calculate_paw_correction(atomdata, D_sp)
return exc
def __init__(self,
calc=None,
spinors=False,
ecut=10.,
scale=1.0,
nbands=None,
valence_bands=None,
conduction_bands=None,
eshift=None,
gw_skn=None,
truncation=None,
integrate_gamma=1,
txt=sys.stdout,
mode='BSE',
wfile=None,
write_h=False,
write_v=False):
"""Creates the BSE object
calc: str or calculator object
The string should refer to the .gpw file contaning KS orbitals
ecut: float
Plane wave cutoff energy (eV)
nbands: int
Number of bands used for the screened interaction
valence_bands: list
Valence bands used in the BSE Hamiltonian
conduction_bands: list
Conduction bands used in the BSE Hamiltonian
eshift: float
Scissors operator opening the gap (eV)
gw_skn: list / array
List or array defining the gw quasiparticle energies used in
the BSE Hamiltonian. Should match spin, k-points and
valence/conduction bands
truncation: str
Coulomb truncation scheme. Can be either wigner-seitz,
2D, 1D, or 0D
integrate_gamma: int
Method to integrate the Coulomb interaction. 1 is a numerical
integration at all q-points with G=[0,0,0] - this breaks the
symmetry slightly. 0 is analytical integration at q=[0,0,0] only -
this conserves the symmetry. integrate_gamma=2 is the same as 1,
but the average is only carried out in the non-periodic directions.
txt: str
txt output
mode: str
Theory level used. can be RPA TDHF or BSE. Only BSE is screened.
wfile: str
File for saving screened interaction and some other stuff
needed later
write_h: bool
If True, write the BSE Hamiltonian to H_SS.ulm.
write_v: bool
If True, write eigenvalues and eigenstates to v_TS.ulm
"""
# Calculator
if isinstance(calc, str):
calc = GPAW(calc, txt=None, communicator=serial_comm)
self.calc = calc
self.spinors = spinors
self.scale = scale
assert mode in ['RPA', 'TDHF', 'BSE']
# assert calc.wfs.kd.nbzkpts % world.size == 0
# txt file
if world.rank != 0:
txt = devnull
elif isinstance(txt, str):
txt = open(txt, 'w', 1)
self.fd = txt
self.ecut = ecut / Hartree
self.nbands = nbands
self.mode = mode
self.truncation = truncation
if integrate_gamma == 0 and truncation is not None:
print('***WARNING*** Analytical Coulomb integration is ' +
'not expected to work with Coulomb truncation. ' +
'Use integrate_gamma=1', file=self.fd)
self.integrate_gamma = integrate_gamma
self.wfile = wfile
self.write_h = write_h
self.write_v = write_v
# Find q-vectors and weights in the IBZ:
self.kd = calc.wfs.kd
if -1 in self.kd.bz2bz_ks:
print('***WARNING*** Symmetries may not be right ' +
'Use gamma-centered grid to be sure', file=self.fd)
offset_c = 0.5 * ((self.kd.N_c + 1) % 2) / self.kd.N_c
bzq_qc = monkhorst_pack(self.kd.N_c) + offset_c
self.qd = KPointDescriptor(bzq_qc)
self.qd.set_symmetry(self.calc.atoms, self.kd.symmetry)
self.vol = abs(np.linalg.det(calc.wfs.gd.cell_cv))
# bands
self.spins = self.calc.wfs.nspins
if self.spins == 2:
if self.spinors:
self.spinors = False
print('***WARNING*** Presently the spinor version' +
'does not work for spin-polarized calculations.' +
'Performing scalar calculation', file=self.fd)
assert len(valence_bands[0]) == len(valence_bands[1])
assert len(conduction_bands[0]) == len(conduction_bands[1])
if valence_bands is None:
nv = self.calc.wfs.setups.nvalence
valence_bands = [[nv // 2 - 1]]
if self.spins == 2:
valence_bands *= 2
if conduction_bands is None:
conduction_bands = [[valence_bands[-1] + 1]]
if self.spins == 2:
conduction_bands *= 2
self.val_sn = np.array(valence_bands)
if len(np.shape(self.val_sn)) == 1:
self.val_sn = np.array([self.val_sn])
self.con_sn = np.array(conduction_bands)
if len(np.shape(self.con_sn)) == 1:
self.con_sn = np.array([self.con_sn])
self.td = True
for n in self.val_sn[0]:
if n in self.con_sn[0]:
self.td = False
if len(self.val_sn) == 2:
for n in self.val_sn[1]:
if n in self.con_sn[1]:
self.td = False
self.nv = len(self.val_sn[0])
self.nc = len(self.con_sn[0])
if eshift is not None:
eshift /= Hartree
if gw_skn is not None:
assert self.nv + self.nc == len(gw_skn[0, 0])
assert self.kd.nibzkpts == len(gw_skn[0])
gw_skn = gw_skn[:, self.kd.bz2ibz_k]
# assert self.kd.nbzkpts == len(gw_skn[0])
gw_skn /= Hartree
self.gw_skn = gw_skn
self.eshift = eshift
# Number of pair orbitals
self.nS = self.kd.nbzkpts * self.nv * self.nc * self.spins
self.nS *= (self.spinors + 1)**2
# Wigner-Seitz stuff
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.kd.N_c, self.fd)
else:
self.wstc = None
self.print_initialization(self.td, self.eshift, self.gw_skn)
def get_chi(self,
xc='RPA',
q_c=[0, 0, 0],
spin='all',
direction='x',
return_VchiV=True,
q_v=None,
RSrep='gpaw',
spinpol_cut=None,
density_cut=None,
fxc_scaling=None):
""" Returns v^1/2 chi v^1/2 for the density response and chi for the
spin response. The truncated Coulomb interaction is included as
v^-1/2 v_t v^-1/2. This is in order to conform with
the head and wings of chi0, which is treated specially for q=0.
spin : str or int
If 'all' then include all spins.
If 0 or 1, only include this specific spin.
(not used in transverse reponse functions)
RSrep : str
real space representation of kernel ('gpaw' or 'grid')
spinpol_cut : float
cutoff spin polarization below which f_xc is evaluated in
unpolarized limit (make sure divergent terms cancel out correctly)
density_cut : float
cutoff density below which f_xc is set to zero
fxc_scaling : list
Possible scaling of kernel to hit Goldstone mode.
If w=0 is included in the present calculation and
fxc_scaling=[True, None], the fxc_scaling to match
kappaM_w[0] = 0. will be calculated. If
fxc_scaling = [True, float], Kxc will be scaled by float.
Default is None, i.e. no scaling
"""
# XXX generalize to kernel check
response = self.chi0.response
if response in ['+-', '-+']:
assert xc in ('ALDA_x', 'ALDA_X', 'ALDA')
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c, spin)
if response == 'density':
N_c = self.chi0.calc.wfs.kd.N_c
Kbare_G = get_coulomb_kernel(pd, N_c, truncation=None, q_v=q_v)
vsqr_G = Kbare_G**0.5
nG = len(vsqr_G)
if self.truncation is not None:
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv, N_c)
else:
self.wstc = None
Ktrunc_G = get_coulomb_kernel(pd,
N_c,
truncation=self.truncation,
wstc=self.wstc,
q_v=q_v)
K_GG = np.diag(Ktrunc_G / Kbare_G)
else:
K_GG = np.eye(nG, dtype=complex)
if pd.kd.gamma:
if isinstance(direction, str):
d_v = {
'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]
}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
if xc != 'RPA':
Kxc_GG = get_xc_kernel(pd,
self.chi0,
functional=xc,
chi0_wGG=chi0_wGG,
density_cut=density_cut)
K_GG += Kxc_GG / vsqr_G / vsqr_G[:, np.newaxis]
# Invert Dyson eq.
chi_wGG = []
for chi0_GG in chi0_wGG:
"""v^1/2 chi0 V^1/2"""
chi0_GG[:] = chi0_GG * vsqr_G * vsqr_G[:, np.newaxis]
chi_GG = np.dot(
np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, K_GG)), chi0_GG)
if not return_VchiV:
chi0_GG /= vsqr_G * vsqr_G[:, np.newaxis]
chi_GG /= vsqr_G * vsqr_G[:, np.newaxis]
chi_wGG.append(chi_GG)
if len(chi_wGG):
chi_wGG = np.array(chi_wGG)
else:
chi_wGG = np.zeros((0, nG, nG), complex)
# Spin response
else:
Kxc_GG = get_xc_kernel(pd,
self.chi0,
functional=xc,
kernel=response[::-1],
RSrep=RSrep,
chi0_wGG=chi0_wGG,
fxc_scaling=fxc_scaling,
density_cut=density_cut,
spinpol_cut=spinpol_cut)
# Invert Dyson equation
chi_wGG = []
for chi0_GG in chi0_wGG:
chi_GG = np.dot(
np.linalg.inv(
np.eye(len(chi0_GG)) - np.dot(chi0_GG, Kxc_GG)),
chi0_GG)
chi_wGG.append(chi_GG)
return pd, chi0_wGG, np.array(chi_wGG)
def calculate(self, ecut, nbands=None, spin=False):
"""Calculate RPA correlation energy for one or several cutoffs.
ecut: float or list of floats
Plane-wave cutoff(s).
nbands: int
Number of bands (defaults to number of plane-waves).
spin: bool
Separate spin in response function.
(Only needed for beyond RPA methods that inherit this function).
"""
p = functools.partial(print, file=self.fd)
if isinstance(ecut, (float, int)):
ecut = ecut * (1 + 0.5 * np.arange(6))**(-2 / 3)
self.ecut_i = np.asarray(np.sort(ecut)) / Hartree
ecutmax = max(self.ecut_i)
if nbands is None:
p('Response function bands : Equal to number of plane waves')
else:
p('Response function bands : %s' % nbands)
p('Plane wave cutoffs (eV) :', end='')
for e in self.ecut_i:
p(' {0:.3f}'.format(e * Hartree), end='')
p()
if self.truncation is not None:
p('Using %s Coulomb truncation' % self.truncation)
p()
if self.filename and os.path.isfile(self.filename):
self.read()
self.world.barrier()
chi0 = Chi0(self.calc, 1j * Hartree * self.omega_w, eta=0.0,
intraband=False, hilbert=False,
txt='chi0.txt', timer=self.timer, world=self.world,
nblocks=self.nblocks)
self.blockcomm = chi0.blockcomm
wfs = self.calc.wfs
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(wfs.gd.cell_cv,
wfs.kd.N_c, self.fd)
else:
self.wstc = None
nq = len(self.energy_qi)
nw = len(self.omega_w)
nGmax = max(count_reciprocal_vectors(ecutmax, wfs.gd, q_c)
for q_c in self.ibzq_qc[nq:])
mynGmax = (nGmax + self.nblocks - 1) // self.nblocks
nx = (1 + spin) * nw * mynGmax * nGmax
A1_x = np.empty(nx, complex)
if self.nblocks > 1:
A2_x = np.empty(nx, complex)
else:
A2_x = None
self.timer.start('RPA')
for q_c in self.ibzq_qc[nq:]:
if np.allclose(q_c, 0.0) and self.skip_gamma:
self.energy_qi.append(len(self.ecut_i) * [0.0])
self.write()
p('Not calculating E_c(q) at Gamma')
p()
continue
thisqd = KPointDescriptor([q_c])
pd = PWDescriptor(ecutmax, wfs.gd, complex, thisqd)
nG = pd.ngmax
mynG = (nG + self.nblocks - 1) // self.nblocks
chi0.Ga = self.blockcomm.rank * mynG
chi0.Gb = min(chi0.Ga + mynG, nG)
shape = (1 + spin, nw, chi0.Gb - chi0.Ga, nG)
chi0_swGG = A1_x[:np.prod(shape)].reshape(shape)
chi0_swGG[:] = 0.0
if np.allclose(q_c, 0.0):
chi0_swxvG = np.zeros((1 + spin, nw, 2, 3, nG), complex)
chi0_swvv = np.zeros((1 + spin, nw, 3, 3), complex)
else:
chi0_swxvG = None
chi0_swvv = None
# First not completely filled band:
m1 = chi0.nocc1
p('# %s - %s' % (len(self.energy_qi), ctime().split()[-2]))
p('q = [%1.3f %1.3f %1.3f]' % tuple(q_c))
energy_i = []
for ecut in self.ecut_i:
if ecut == ecutmax:
# Nothing to cut away:
cut_G = None
m2 = nbands or nG
else:
cut_G = np.arange(nG)[pd.G2_qG[0] <= 2 * ecut]
m2 = len(cut_G)
p('E_cut = %d eV / Bands = %d:' % (ecut * Hartree, m2))
self.fd.flush()
energy = self.calculate_q(chi0, pd,
chi0_swGG, chi0_swxvG, chi0_swvv,
m1, m2, cut_G, A2_x)
energy_i.append(energy)
m1 = m2
a = 1 / chi0.kncomm.size
if ecut < ecutmax and a != 1.0:
# Chi0 will be summed again over chicomm, so we divide
# by its size:
chi0_swGG *= a
if chi0_swxvG is not None:
chi0_swxvG *= a
chi0_swvv *= a
self.energy_qi.append(energy_i)
self.write()
p()
e_i = np.dot(self.weight_q, np.array(self.energy_qi))
p('==========================================================')
p()
p('Total correlation energy:')
for e_cut, e in zip(self.ecut_i, e_i):
p('%6.0f: %6.4f eV' % (e_cut * Hartree, e * Hartree))
p()
self.energy_qi = [] # important if another calculation is performed
if len(e_i) > 1:
self.extrapolate(e_i)
p('Calculation completed at: ', ctime())
p()
self.timer.stop('RPA')
self.timer.write(self.fd)
self.fd.flush()
return e_i * Hartree
def get_dielectric_matrix(self,
xc='RPA',
q_c=[0, 0, 0],
direction='x',
symmetric=True,
calculate_chi=False):
"""Returns the symmetrized dielectric matrix.
::
\tilde\epsilon_GG' = v^{-1/2}_G \epsilon_GG' v^{1/2}_G',
where::
epsilon_GG' = 1 - v_G * P_GG' and P_GG'
is the polarization.
::
In RPA: P = chi^0
In TDDFT: P = (1 - chi^0 * f_xc)^{-1} chi^0
The head of the inverse symmetrized dielectric matrix is equal
to the head of the inverse dielectric matrix (inverse dielectric
function)
"""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
G_G = pd.G2_qG[0]**0.5
nG = len(G_G)
if pd.kd.gamma:
G_G[0] = 1.0
if isinstance(direction, str):
d_v = {
'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]
}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
if self.truncation == 'wigner-seitz':
kernel = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv,
self.chi0.calc.wfs.kd.N_c)
K_G = kernel.get_potential(pd)**0.5
if pd.kd.gamma:
K_G[0] = 0.0
elif self.truncation == '2D':
K_G = truncated_coulomb(pd)
if pd.kd.gamma:
K_G[0] = 0.0
else:
K_G = (4 * pi)**0.5 / G_G
if xc != 'RPA':
R_av = self.chi0.calc.atoms.positions / Bohr
nt_sG = self.chi0.calc.density.nt_sG
Kxc_sGG = calculate_Kxc(pd,
nt_sG,
R_av,
self.chi0.calc.wfs.setups,
self.chi0.calc.density.D_asp,
functional=xc)
if calculate_chi:
chi_wGG = []
for chi0_GG in chi0_wGG:
if xc == 'RPA':
P_GG = chi0_GG
else:
P_GG = np.dot(
np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, Kxc_sGG[0])),
chi0_GG)
if symmetric:
e_GG = np.eye(nG) - P_GG * K_G * K_G[:, np.newaxis]
else:
K_GG = (K_G**2 * np.ones([nG, nG])).T
e_GG = np.eye(nG) - P_GG * K_GG
if calculate_chi:
K_GG = np.diag(K_G**2)
if xc != 'RPA':
K_GG += Kxc_sGG[0]
chi_wGG.append(
np.dot(np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, K_GG)),
chi0_GG))
chi0_GG[:] = e_GG
# chi0_wGG is now the dielectric matrix
if not calculate_chi:
return chi0_wGG
else:
return pd, chi0_wGG, chi_wGG
def get_chi(self,
xc='RPA',
q_c=[0, 0, 0],
direction='x',
return_VchiV=True,
q_v=None):
""" Returns v^1/2 chi v^1/2. The truncated Coulomb interaction is
then included as v^-1/2 v_t v^-1/2. This is in order to conform with
the head and wings of chi0, which is treated specially for q=0."""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
N_c = self.chi0.calc.wfs.kd.N_c
Kbare_G = get_coulomb_kernel(pd, N_c, truncation=None, q_v=q_v)
vsqr_G = Kbare_G**0.5
nG = len(vsqr_G)
if self.truncation is not None:
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv, N_c)
else:
self.wstc = None
Ktrunc_G = get_coulomb_kernel(pd,
N_c,
truncation=self.truncation,
wstc=self.wstc,
q_v=q_v)
K_GG = np.diag(Ktrunc_G / Kbare_G)
else:
K_GG = np.eye(nG, dtype=complex)
if pd.kd.gamma:
if isinstance(direction, str):
d_v = {
'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]
}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
if xc != 'RPA':
Kxc_sGG = get_xc_kernel(pd,
self.chi0,
functional=xc,
chi0_wGG=chi0_wGG)
K_GG += Kxc_sGG[0] / vsqr_G / vsqr_G[:, np.newaxis]
chi_wGG = []
for chi0_GG in chi0_wGG:
"""v^1/2 chi0 V^1/2"""
chi0_GG[:] = chi0_GG * vsqr_G * vsqr_G[:, np.newaxis]
chi_GG = np.dot(np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, K_GG)),
chi0_GG)
if not return_VchiV:
chi0_GG /= vsqr_G * vsqr_G[:, np.newaxis]
chi_GG /= vsqr_G * vsqr_G[:, np.newaxis]
chi_wGG.append(chi_GG)
return pd, chi0_wGG, np.array(chi_wGG)
def __init__(self,
calc,
xc=None,
kpts=None,
bands=None,
ecut=None,
omega=None,
world=mpi.world,
txt=sys.stdout,
timer=None):
PairDensity.__init__(self,
calc,
ecut,
world=world,
txt=txt,
timer=timer)
if xc is None or xc == 'EXX':
self.exx_fraction = 1.0
xc = XC(XCNull())
elif xc == 'PBE0':
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_PBEH')
elif xc == 'HSE03':
omega = 0.106
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE03')
elif xc == 'HSE06':
omega = 0.11
self.exx_fraction = 0.25
xc = XC('HYB_GGA_XC_HSE06')
elif xc == 'B3LYP':
self.exx_fraction = 0.2
xc = XC('HYB_GGA_XC_B3LYP')
self.xc = xc
self.omega = omega
self.exc = np.nan # density dependent part of xc-energy
self.kpts = select_kpts(kpts, self.calc)
if bands is None:
# Do all occupied bands:
bands = [0, self.nocc2]
prnt('Calculating exact exchange contributions for band index',
'%d-%d' % (bands[0], bands[1] - 1),
file=self.fd)
prnt('for IBZ k-points with indices:',
', '.join(str(i) for i in self.kpts),
file=self.fd)
self.bands = bands
if self.ecut is None:
self.ecut = self.calc.wfs.pd.ecut
prnt('Plane-wave cutoff: %.3f eV' % (self.ecut * Hartree),
file=self.fd)
shape = (self.calc.wfs.nspins, len(self.kpts), bands[1] - bands[0])
self.exxvv_sin = np.zeros(shape) # valence-valence exchange energies
self.exxvc_sin = np.zeros(shape) # valence-core exchange energies
self.f_sin = np.empty(shape) # occupation numbers
# The total EXX energy will not be calculated if we are only
# interested in a few eigenvalues for a few k-points
self.exx = np.nan # total EXX energy
self.exxvv = np.nan # valence-valence
self.exxvc = np.nan # valence-core
self.exxcc = 0.0 # core-core
self.mysKn1n2 = None # my (s, K, n1, n2) indices
self.distribute_k_points_and_bands(0, self.nocc2)
# All occupied states:
self.mykpts = [
self.get_k_point(s, K, n1, n2) for s, K, n1, n2 in self.mysKn1n2
]
prnt('Using Wigner-Seitz truncated coulomb interaction.', file=self.fd)
self.wstc = WignerSeitzTruncatedCoulomb(self.calc.wfs.gd.cell_cv,
self.calc.wfs.kd.N_c, self.fd)
self.iG_qG = {} # cache
# PAW matrices:
self.V_asii = [] # valence-valence correction
self.C_aii = [] # valence-core correction
self.initialize_paw_exx_corrections()
def get_dielectric_matrix(self,
xc='RPA',
q_c=[0, 0, 0],
direction='x',
symmetric=True,
calculate_chi=False,
q_v=None,
add_intraband=True):
"""Returns the symmetrized dielectric matrix.
::
\tilde\epsilon_GG' = v^{-1/2}_G \epsilon_GG' v^{1/2}_G',
where::
epsilon_GG' = 1 - v_G * P_GG' and P_GG'
is the polarization.
::
In RPA: P = chi^0
In TDDFT: P = (1 - chi^0 * f_xc)^{-1} chi^0
in addition to RPA one can use the kernels, ALDA, rALDA, rAPBE,
Bootstrap and LRalpha (long-range kerne), where alpha is a user
specified parameter (for example xc='LR0.25')
The head of the inverse symmetrized dielectric matrix is equal
to the head of the inverse dielectric matrix (inverse dielectric
function)"""
pd, chi0_wGG, chi0_wxvG, chi0_wvv = self.calculate_chi0(q_c)
N_c = self.chi0.calc.wfs.kd.N_c
if self.truncation == 'wigner-seitz':
self.wstc = WignerSeitzTruncatedCoulomb(pd.gd.cell_cv, N_c)
else:
self.wstc = None
K_G = get_coulomb_kernel(pd,
N_c,
truncation=self.truncation,
wstc=self.wstc,
q_v=q_v)**0.5
nG = len(K_G)
if pd.kd.gamma:
if isinstance(direction, str):
d_v = {
'x': [1, 0, 0],
'y': [0, 1, 0],
'z': [0, 0, 1]
}[direction]
else:
d_v = direction
d_v = np.asarray(d_v) / np.linalg.norm(d_v)
W = slice(self.w1, self.w2)
if add_intraband:
chi0_wGG[:, 0] = np.dot(d_v, chi0_wxvG[W, 0])
chi0_wGG[:, :, 0] = np.dot(d_v, chi0_wxvG[W, 1])
chi0_wGG[:, 0, 0] = np.dot(d_v, np.dot(chi0_wvv[W], d_v).T)
if q_v is not None:
print('Restoring q dependence of head and wings of chi0')
chi0_wGG[:, 1:, 0] *= np.dot(q_v, d_v)
chi0_wGG[:, 0, 1:] *= np.dot(q_v, d_v)
chi0_wGG[:, 0, 0] *= np.dot(q_v, d_v)**2
if xc != 'RPA':
Kxc_sGG = get_xc_kernel(pd,
self.chi0,
functional=xc,
chi0_wGG=chi0_wGG)
if calculate_chi:
chi_wGG = []
for chi0_GG in chi0_wGG:
if xc == 'RPA':
P_GG = chi0_GG
else:
P_GG = np.dot(
np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, Kxc_sGG[0])),
chi0_GG)
if symmetric:
e_GG = np.eye(nG) - P_GG * K_G * K_G[:, np.newaxis]
else:
K_GG = (K_G**2 * np.ones([nG, nG])).T
e_GG = np.eye(nG) - P_GG * K_GG
if calculate_chi:
K_GG = np.diag(K_G**2)
if xc != 'RPA':
K_GG += Kxc_sGG[0]
chi_wGG.append(
np.dot(np.linalg.inv(np.eye(nG) - np.dot(chi0_GG, K_GG)),
chi0_GG))
chi0_GG[:] = e_GG
# chi0_wGG is now the dielectric matrix
if not calculate_chi:
return chi0_wGG
else:
# chi_wGG is the full density response function..
return pd, chi0_wGG, np.array(chi_wGG)
class RPACorrelation:
def __init__(self,
calc,
xc='RPA',
filename=None,
skip_gamma=False,
qsym=True,
nlambda=None,
nfrequencies=16,
frequency_max=800.0,
frequency_scale=2.0,
frequencies=None,
weights=None,
world=mpi.world,
nblocks=1,
wstc=False,
txt=sys.stdout):
if isinstance(calc, str):
calc = GPAW(calc, txt=None, communicator=mpi.serial_comm)
self.calc = calc
if world.rank != 0:
txt = devnull
elif isinstance(txt, str):
txt = open(txt, 'w')
self.fd = txt
self.timer = Timer()
if frequencies is None:
frequencies, weights = get_gauss_legendre_points(
nfrequencies, frequency_max, frequency_scale)
user_spec = False
else:
assert weights is not None
user_spec = True
self.omega_w = frequencies / Hartree
self.weight_w = weights / Hartree
if nblocks > 1:
assert len(self.omega_w) % nblocks == 0
assert wstc
self.wstc = wstc
self.nblocks = nblocks
self.world = world
self.skip_gamma = skip_gamma
self.ibzq_qc = None
self.weight_q = None
self.initialize_q_points(qsym)
# Energies for all q-vetors and cutoff energies:
self.energy_qi = []
self.filename = filename
self.print_initialization(xc, frequency_scale, nlambda, user_spec)
def initialize_q_points(self, qsym):
kd = self.calc.wfs.kd
self.bzq_qc = kd.get_bz_q_points(first=True)
if not qsym:
self.ibzq_qc = self.bzq_qc
self.weight_q = np.ones(len(self.bzq_qc)) / len(self.bzq_qc)
else:
U_scc = kd.symmetry.op_scc
self.ibzq_qc = kd.get_ibz_q_points(self.bzq_qc, U_scc)[0]
self.weight_q = kd.q_weights
def read(self):
lines = open(self.filename).readlines()[1:]
n = 0
self.energy_qi = []
nq = len(lines) // len(self.ecut_i)
for q_c in self.ibzq_qc[:nq]:
self.energy_qi.append([])
for ecut in self.ecut_i:
q1, q2, q3, ec, energy = [float(x) for x in lines[n].split()]
self.energy_qi[-1].append(energy / Hartree)
n += 1
if (abs(q_c - (q1, q2, q3)).max() > 1e-4
or abs(int(ecut * Hartree) - ec) > 0):
self.energy_qi = []
return
print('Read %d q-points from file: %s' % (nq, self.filename),
file=self.fd)
print(file=self.fd)
def write(self):
if self.world.rank == 0 and self.filename:
fd = open(self.filename, 'w')
print('#%9s %10s %10s %8s %12s' %
('q1', 'q2', 'q3', 'E_cut', 'E_c(q)'),
file=fd)
for energy_i, q_c in zip(self.energy_qi, self.ibzq_qc):
for energy, ecut in zip(energy_i, self.ecut_i):
print('%10.4f %10.4f %10.4f %8d %r' %
(tuple(q_c) + (ecut * Hartree, energy * Hartree)),
file=fd)
def calculate(self, ecut, nbands=None, spin=False):
"""Calculate RPA correlation energy for one or several cutoffs.
ecut: float or list of floats
Plane-wave cutoff(s).
nbands: int
Number of bands (defaults to number of plane-waves).
spin: bool
Separate spin in response funtion.
(Only needed for beyond RPA methods that inherit this function).
"""
p = functools.partial(print, file=self.fd)
if isinstance(ecut, (float, int)):
ecut = ecut * (1 + 0.5 * np.arange(6))**(-2 / 3)
self.ecut_i = np.asarray(np.sort(ecut)) / Hartree
ecutmax = max(self.ecut_i)
if nbands is None:
p('Response function bands : Equal to number of plane waves')
else:
p('Response function bands : %s' % nbands)
p('Plane wave cutoffs (eV) :', end='')
for e in self.ecut_i:
p(' {0:.3f}'.format(e * Hartree), end='')
p()
p()
if self.filename and os.path.isfile(self.filename):
self.read()
self.world.barrier()
chi0 = Chi0(self.calc,
1j * Hartree * self.omega_w,
eta=0.0,
intraband=False,
hilbert=False,
txt=self.fd,
timer=self.timer,
world=self.world,
no_optical_limit=self.wstc,
nblocks=self.nblocks)
self.blockcomm = chi0.blockcomm
wfs = self.calc.wfs
if self.wstc:
with self.timer('WSTC-init'):
p('Using Wigner-Seitz truncated Coulomb potential.')
self.wstc = WignerSeitzTruncatedCoulomb(
wfs.gd.cell_cv, wfs.kd.N_c, self.fd)
nq = len(self.energy_qi)
nw = len(self.omega_w)
nGmax = max(
count_reciprocal_vectors(ecutmax, wfs.gd, q_c)
for q_c in self.ibzq_qc[nq:])
mynGmax = (nGmax + self.nblocks - 1) // self.nblocks
nx = (1 + spin) * nw * mynGmax * nGmax
A1_x = np.empty(nx, complex)
if self.nblocks > 1:
A2_x = np.empty(nx, complex)
else:
A2_x = None
self.timer.start('RPA')
for q_c in self.ibzq_qc[nq:]:
if np.allclose(q_c, 0.0) and self.skip_gamma:
self.energy_qi.append(len(self.ecut_i) * [0.0])
self.write()
p('Not calculating E_c(q) at Gamma')
p()
continue
thisqd = KPointDescriptor([q_c])
pd = PWDescriptor(ecutmax, wfs.gd, complex, thisqd)
nG = pd.ngmax
mynG = (nG + self.nblocks - 1) // self.nblocks
chi0.Ga = self.blockcomm.rank * mynG
chi0.Gb = min(chi0.Ga + mynG, nG)
shape = (1 + spin, nw, chi0.Gb - chi0.Ga, nG)
chi0_swGG = A1_x[:np.prod(shape)].reshape(shape)
chi0_swGG[:] = 0.0
if self.wstc or np.allclose(q_c, 0.0):
# Wings (x=0,1) and head (G=0) for optical limit and three
# directions (v=0,1,2):
chi0_swxvG = np.zeros((1 + spin, nw, 2, 3, nG), complex)
chi0_swvv = np.zeros((1 + spin, nw, 3, 3), complex)
else:
chi0_swxvG = None
chi0_swvv = None
Q_aGii = chi0.initialize_paw_corrections(pd)
# First not completely filled band:
m1 = chi0.nocc1
p('# %s - %s' % (len(self.energy_qi), ctime().split()[-2]))
p('q = [%1.3f %1.3f %1.3f]' % tuple(q_c))
energy_i = []
for ecut in self.ecut_i:
if ecut == ecutmax:
# Nothing to cut away:
cut_G = None
m2 = nbands or nG
else:
cut_G = np.arange(nG)[pd.G2_qG[0] <= 2 * ecut]
m2 = len(cut_G)
p('E_cut = %d eV / Bands = %d:' % (ecut * Hartree, m2))
self.fd.flush()
energy = self.calculate_q(chi0, pd, chi0_swGG, chi0_swxvG,
chi0_swvv, Q_aGii, m1, m2, cut_G,
A2_x)
energy_i.append(energy)
m1 = m2
a = 1 / chi0.kncomm.size
if ecut < ecutmax and a != 1.0:
# Chi0 will be summed again over chicomm, so we divide
# by its size:
chi0_swGG *= a
if chi0_swxvG is not None:
chi0_swxvG *= a
chi0_swvv *= a
self.energy_qi.append(energy_i)
self.write()
p()
e_i = np.dot(self.weight_q, np.array(self.energy_qi))
p('==========================================================')
p()
p('Total correlation energy:')
for e_cut, e in zip(self.ecut_i, e_i):
p('%6.0f: %6.4f eV' % (e_cut * Hartree, e * Hartree))
p()
self.energy_qi = [] # important if another calculation is performed
if len(e_i) > 1:
self.extrapolate(e_i)
p('Calculation completed at: ', ctime())
p()
self.timer.stop('RPA')
self.timer.write(self.fd)
self.fd.flush()
return e_i * Hartree
@timer('chi0(q)')
def calculate_q(self, chi0, pd, chi0_swGG, chi0_swxvG, chi0_swvv, Q_aGii,
m1, m2, cut_G, A2_x):
chi0_wGG = chi0_swGG[0]
if chi0_swxvG is not None:
chi0_wxvG = chi0_swxvG[0]
chi0_wvv = chi0_swvv[0]
else:
chi0_wxvG = None
chi0_wvv = None
chi0._calculate(pd, chi0_wGG, chi0_wxvG, chi0_wvv, Q_aGii, m1, m2,
[0, 1])
print('E_c(q) = ', end='', file=self.fd)
chi0_wGG = chi0.redistribute(chi0_wGG, A2_x)
if not pd.kd.gamma or self.wstc:
e = self.calculate_energy(pd, chi0_wGG, cut_G)
print('%.3f eV' % (e * Hartree), file=self.fd)
self.fd.flush()
else:
e = 0.0
for v in range(3):
chi0_wGG[:, 0] = chi0_wxvG[:, 0, v]
chi0_wGG[:, :, 0] = chi0_wxvG[:, 1, v]
chi0_wGG[:, 0, 0] = chi0_wvv[:, v, v]
ev = self.calculate_energy(pd, chi0_wGG, cut_G)
e += ev
print('%.3f' % (ev * Hartree), end='', file=self.fd)
if v < 2:
print('/', end='', file=self.fd)
else:
print(' eV', file=self.fd)
self.fd.flush()
e /= 3
return e
@timer('Energy')
def calculate_energy(self, pd, chi0_wGG, cut_G):
"""Evaluate correlation energy from chi0."""
if self.wstc:
invG_G = (self.wstc.get_potential(pd) / (4 * pi))**0.5
else:
G_G = pd.G2_qG[0]**0.5 # |G+q|
if pd.kd.gamma:
G_G[0] = 1.0
invG_G = 1.0 / G_G
if cut_G is not None:
invG_G = invG_G[cut_G]
nG = len(invG_G)
e_w = []
for chi0_GG in chi0_wGG:
if cut_G is not None:
chi0_GG = chi0_GG.take(cut_G, 0).take(cut_G, 1)
e_GG = (np.eye(nG) -
4 * np.pi * chi0_GG * invG_G * invG_G[:, np.newaxis])
e = np.log(np.linalg.det(e_GG)) + nG - np.trace(e_GG)
e_w.append(e.real)
E_w = np.zeros_like(self.omega_w)
self.blockcomm.all_gather(np.array(e_w), E_w)
energy = np.dot(E_w, self.weight_w) / (2 * np.pi)
self.E_w = E_w
return energy
def extrapolate(self, e_i):
print('Extrapolated energies:', file=self.fd)
ex_i = []
for i in range(len(e_i) - 1):
e1, e2 = e_i[i:i + 2]
x1, x2 = self.ecut_i[i:i + 2]**-1.5
ex = (e1 * x2 - e2 * x1) / (x2 - x1)
ex_i.append(ex)
print(' %4.0f -%4.0f: %5.3f eV' %
(self.ecut_i[i] * Hartree, self.ecut_i[i + 1] * Hartree,
ex * Hartree),
file=self.fd)
print(file=self.fd)
self.fd.flush()
return e_i * Hartree
def print_initialization(self, xc, frequency_scale, nlambda, user_spec):
p = functools.partial(print, file=self.fd)
p('----------------------------------------------------------')
p('Non-self-consistent %s correlation energy' % xc)
p('----------------------------------------------------------')
p('Started at: ', ctime())
p()
p('Atoms :',
self.calc.atoms.get_chemical_formula(mode='hill'))
p('Ground state XC functional :', self.calc.hamiltonian.xc.name)
p('Valence electrons :', self.calc.wfs.setups.nvalence)
p('Number of bands :', self.calc.wfs.bd.nbands)
p('Number of spins :', self.calc.wfs.nspins)
p('Number of k-points :', len(self.calc.wfs.kd.bzk_kc))
p('Number of irreducible k-points :', len(self.calc.wfs.kd.ibzk_kc))
p('Number of q-points :', len(self.bzq_qc))
p('Number of irreducible q-points :', len(self.ibzq_qc))
p()
for q, weight in zip(self.ibzq_qc, self.weight_q):
p(' q: [%1.4f %1.4f %1.4f] - weight: %1.3f' %
(q[0], q[1], q[2], weight))
p()
p('----------------------------------------------------------')
p('----------------------------------------------------------')
p()
if nlambda is None:
p('Analytical coupling constant integration')
else:
p('Numerical coupling constant integration using', nlambda,
'Gauss-Legendre points')
p()
p('Frequencies')
if not user_spec:
p(' Gauss-Legendre integration with %s frequency points' %
len(self.omega_w))
p(' Transformed from [0,oo] to [0,1] using e^[-aw^(1/B)]')
p(' Highest frequency point at %5.1f eV and B=%1.1f' %
(self.omega_w[-1] * Hartree, frequency_scale))
else:
p(' User specified frequency integration with',
len(self.omega_w), 'frequency points')
p()
p('Parallelization')
p(' Total number of CPUs : % s' % self.world.size)
p(' G-vector decomposition : % s' % self.nblocks)
p(' K-point/band decomposition : % s' %
(self.world.size // self.nblocks))
p()