def get_lcao_xc(calc, P_aqMi, bfs=None, spin=0):
nq = len(calc.wfs.ibzk_qc)
nao = calc.wfs.setups.nao
dtype = calc.wfs.dtype
if bfs is None:
bfs = get_bfs(calc)
if calc.density.nt_sg is None:
calc.density.interpolate()
nt_sg = calc.density.nt_sg
vxct_sg = calc.density.finegd.zeros(calc.wfs.nspins)
calc.hamiltonian.xc.calculate(calc.density.finegd, nt_sg, vxct_sg)
vxct_G = calc.wfs.gd.zeros()
calc.hamiltonian.restrict(vxct_sg[spin], vxct_G)
Vxc_qMM = np.zeros((nq, nao, nao), dtype)
for q, Vxc_MM in enumerate(Vxc_qMM):
bfs.calculate_potential_matrix(vxct_G, Vxc_MM, q)
tri2full(Vxc_MM, "L")
# Add atomic PAW corrections
for a, P_qMi in P_aqMi.items():
D_sp = calc.density.D_asp[a][:]
H_sp = np.zeros_like(D_sp)
calc.wfs.setups[a].xc_correction.calculate(calc.hamiltonian.xc, D_sp, H_sp)
H_ii = unpack(H_sp[spin])
for Vxc_MM, P_Mi in zip(Vxc_qMM, P_qMi):
Vxc_MM += dots(P_Mi, H_ii, P_Mi.T.conj())
return Vxc_qMM * Hartree
def get_lcao_xc(calc, P_aqMi, bfs=None, spin=0):
nq = len(calc.wfs.kd.ibzk_qc)
nao = calc.wfs.setups.nao
dtype = calc.wfs.dtype
if bfs is None:
bfs = get_bfs(calc)
if calc.density.nt_sg is None:
calc.density.interpolate_pseudo_density()
nt_sg = calc.density.nt_sg
vxct_sg = calc.density.finegd.zeros(calc.wfs.nspins)
calc.hamiltonian.xc.calculate(calc.density.finegd, nt_sg, vxct_sg)
vxct_G = calc.wfs.gd.zeros()
calc.hamiltonian.restrict_and_collect(vxct_sg[spin], vxct_G)
Vxc_qMM = np.zeros((nq, nao, nao), dtype)
for q, Vxc_MM in enumerate(Vxc_qMM):
bfs.calculate_potential_matrix(vxct_G, Vxc_MM, q)
tri2full(Vxc_MM, 'L')
# Add atomic PAW corrections
for a, P_qMi in P_aqMi.items():
D_sp = calc.density.D_asp[a][:]
H_sp = np.zeros_like(D_sp)
calc.hamiltonian.xc.calculate_paw_correction(calc.wfs.setups[a], D_sp,
H_sp)
H_ii = unpack(H_sp[spin])
for Vxc_MM, P_Mi in zip(Vxc_qMM, P_qMi):
Vxc_MM += dots(P_Mi, H_ii, P_Mi.T.conj())
return Vxc_qMM * Hartree
def __init__(
self,
gpwfilename,
fixedenergy=0.0,
spin=0,
ibl=True,
basis="sz",
zero_fermi=False,
pwfbasis=None,
lcaoatoms=None,
projection_data=None,
):
calc = GPAW(gpwfilename, txt=None, basis=basis)
assert calc.wfs.gd.comm.size == 1
assert calc.wfs.kpt_comm.size == 1
assert calc.wfs.band_comm.size == 1
if zero_fermi:
try:
Ef = calc.get_fermi_level()
except NotImplementedError:
Ef = calc.get_homo_lumo().mean()
else:
Ef = 0.0
self.ibzk_kc = calc.get_ibz_k_points()
self.nk = len(self.ibzk_kc)
self.eps_kn = [calc.get_eigenvalues(kpt=q, spin=spin) - Ef for q in range(self.nk)]
self.M_k = [sum(eps_n <= fixedenergy) for eps_n in self.eps_kn]
print "Fixed states:", self.M_k
self.calc = calc
self.dtype = self.calc.wfs.dtype
self.spin = spin
self.ibl = ibl
self.pwf_q = []
self.norms_qn = []
self.S_qww = []
self.H_qww = []
if ibl:
if pwfbasis is not None:
pwfmask = basis_subset2(calc.atoms.get_chemical_symbols(), basis, pwfbasis)
if lcaoatoms is not None:
lcaoindices = get_bfi2(calc.atoms.get_chemical_symbols(), basis, lcaoatoms)
else:
lcaoindices = None
self.bfs = get_bfs(calc)
if projection_data is None:
V_qnM, H_qMM, S_qMM, self.P_aqMi = get_lcao_projections_HSP(
calc, bfs=self.bfs, spin=spin, projectionsonly=False
)
else:
V_qnM, H_qMM, S_qMM, self.P_aqMi = projection_data
H_qMM -= Ef * S_qMM
for q, M in enumerate(self.M_k):
if pwfbasis is None:
pwf = ProjectedWannierFunctionsIBL(V_qnM[q], S_qMM[q], M, lcaoindices)
else:
pwf = PWFplusLCAO(V_qnM[q], S_qMM[q], M, pwfmask, lcaoindices)
self.pwf_q.append(pwf)
self.norms_qn.append(pwf.norms_n)
self.S_qww.append(pwf.S_ww)
self.H_qww.append(pwf.rotate_matrix(self.eps_kn[q][:M], H_qMM[q]))
else:
if projection_data is None:
V_qnM = get_lcao_projections_HSP(calc, spin=spin)
else:
V_qnM = projection_data
for q, M in enumerate(self.M_k):
pwf = ProjectedWannierFunctionsFBL(V_qnM[q], M, ortho=False)
self.pwf_q.append(pwf)
self.norms_qn.append(pwf.norms_n)
self.S_qww.append(pwf.S_ww)
self.H_qww.append(pwf.rotate_matrix(self.eps_kn[q]))
for S in self.S_qww:
print "Condition number: %0.1e" % condition_number(S)
def __init__(self,
gpwfilename,
fixedenergy=0.,
spin=0,
ibl=True,
basis='sz',
zero_fermi=False,
pwfbasis=None,
lcaoatoms=None,
projection_data=None):
calc = GPAW(gpwfilename, txt=None, basis=basis)
assert calc.wfs.gd.comm.size == 1
assert calc.wfs.kd.comm.size == 1
assert calc.wfs.bd.comm.size == 1
if zero_fermi:
try:
Ef = calc.get_fermi_level()
except NotImplementedError:
Ef = calc.get_homo_lumo().mean()
else:
Ef = 0.0
self.ibzk_kc = calc.get_ibz_k_points()
self.nk = len(self.ibzk_kc)
self.eps_kn = [
calc.get_eigenvalues(kpt=q, spin=spin) - Ef for q in range(self.nk)
]
self.M_k = [sum(eps_n <= fixedenergy) for eps_n in self.eps_kn]
print('Fixed states:', self.M_k)
self.calc = calc
self.dtype = self.calc.wfs.dtype
self.spin = spin
self.ibl = ibl
self.pwf_q = []
self.norms_qn = []
self.S_qww = []
self.H_qww = []
if ibl:
if pwfbasis is not None:
pwfmask = basis_subset2(calc.atoms.get_chemical_symbols(),
basis, pwfbasis)
if lcaoatoms is not None:
lcaoindices = get_bfi2(calc.atoms.get_chemical_symbols(),
basis, lcaoatoms)
else:
lcaoindices = None
self.bfs = get_bfs(calc)
if projection_data is None:
V_qnM, H_qMM, S_qMM, self.P_aqMi = get_lcao_projections_HSP(
calc, bfs=self.bfs, spin=spin, projectionsonly=False)
else:
V_qnM, H_qMM, S_qMM, self.P_aqMi = projection_data
H_qMM -= Ef * S_qMM
for q, M in enumerate(self.M_k):
if pwfbasis is None:
pwf = ProjectedWannierFunctionsIBL(V_qnM[q], S_qMM[q], M,
lcaoindices)
else:
pwf = PWFplusLCAO(V_qnM[q], S_qMM[q], M, pwfmask,
lcaoindices)
self.pwf_q.append(pwf)
self.norms_qn.append(pwf.norms_n)
self.S_qww.append(pwf.S_ww)
self.H_qww.append(
pwf.rotate_matrix(self.eps_kn[q][:M], H_qMM[q]))
else:
if projection_data is None:
V_qnM = get_lcao_projections_HSP(calc, spin=spin)
else:
V_qnM = projection_data
for q, M in enumerate(self.M_k):
pwf = ProjectedWannierFunctionsFBL(V_qnM[q], M, ortho=False)
self.pwf_q.append(pwf)
self.norms_qn.append(pwf.norms_n)
self.S_qww.append(pwf.S_ww)
self.H_qww.append(pwf.rotate_matrix(self.eps_kn[q]))
for S in self.S_qww:
print('Condition number: %0.1e' % condition_number(S))
spos_ac = bulk.get_scaled_positions()
tci = TwoCenterIntegrals(calc.wfs.gd, setups, calc.wfs.gamma, calc.wfs.ibzk_qc)
tci.set_positions(spos_ac)
# Calculate projector overlaps, and (lower triangle of-) S and T matrices
S_qMM = np.zeros((nq, nao, nao), dtype)
T_qMM = np.zeros((nq, nao, nao), dtype)
P_aqMi = {}
for a in range(len(spos_ac)):
ni = calc.wfs.setups[a].ni
P_aqMi[a] = np.zeros((nq, nao, ni), dtype)
tci.calculate(spos_ac, S_qMM, T_qMM, P_aqMi)
# Calculate projections using BFS
bfs = get_bfs(calc)
V_qnM = np.zeros((nq, nbands, nao), dtype)
for q, V_nM in enumerate(V_qnM):
bfs.integrate2(kpt_q[q].psit_nG[:], V_nM, q)
for a, P_ni in kpt_q[q].P_ani.items():
P_Mi = P_aqMi[a][q]
V_nM += np.dot(np.dot(P_ni, setups[a].dO_ii), P_Mi.T.conj())
bfs_qnM = V_qnM.copy()
# Calculate projections using LFC
lfc = get_lfc(calc)
V_qnM = np.zeros((nq, nbands, nao), dtype)
V_qAni = [lfc.dict(nbands) for q in range(nq)]
for q, V_Ani in enumerate(V_qAni):
lfc.integrate(kpt_q[q].psit_nG[:], V_Ani, q)
tci = TwoCenterIntegrals(calc.wfs.gd, setups, calc.wfs.gamma, calc.wfs.ibzk_qc)
tci.set_positions(spos_ac)
# Calculate projector overlaps, and (lower triangle of-) S and T matrices
S_qMM = np.zeros((nq, nao, nao), dtype)
T_qMM = np.zeros((nq, nao, nao), dtype)
P_aqMi = {}
for a in range(len(spos_ac)):
ni = calc.wfs.setups[a].ni
P_aqMi[a] = np.zeros((nq, nao, ni), dtype)
tci.calculate(spos_ac, S_qMM, T_qMM, P_aqMi)
# Calculate projections using BFS
bfs = get_bfs(calc)
V_qnM = np.zeros((nq, nbands, nao), dtype)
for q, V_nM in enumerate(V_qnM):
bfs.integrate2(kpt_q[q].psit_nG[:], V_nM, q)
for a, P_ni in kpt_q[q].P_ani.items():
P_Mi = P_aqMi[a][q]
V_nM += np.dot(np.dot(P_ni, setups[a].dO_ii), P_Mi.T.conj())
bfs_qnM = V_qnM.copy()
# Calculate projections using LFC
lfc = get_lfc(calc)
V_qnM = np.zeros((nq, nbands, nao), dtype)
V_qAni = [lfc.dict(nbands) for q in range(nq)]
for q, V_Ani in enumerate(V_qAni):
