def convert_projection_data(symbols, V_qnM, H_qMM, S_qMM, P_aqMi,
originaltype='dzp', newtype='sz'):
Nq = len(H_qMM)
mask = basis_subset2(symbols, originaltype, newtype)
mask2 = np.outer(mask, mask)
NMnew = len(mask.nonzero()[0])
V_qnM = V_qnM[..., mask]
H_qMM = H_qMM[:, mask2].reshape(Nq, NMnew, NMnew)
S_qMM = S_qMM[:, mask2].reshape(Nq, NMnew, NMnew)
P2_aqMi = {}
for a, P_qMi in P_aqMi.items():
P2_aqMi[a] = P_qMi[:, mask, :]
return V_qnM, H_qMM, S_qMM, P2_aqMi
def convert_projection_data(symbols, V_qnM, H_qMM, S_qMM, P_aqMi,
originaltype='dzp', newtype='sz'):
Nq = len(H_qMM)
mask = basis_subset2(symbols, originaltype, newtype)
mask2 = np.outer(mask, mask)
NMnew = len(mask.nonzero()[0])
V_qnM = V_qnM[..., mask]
H_qMM = H_qMM[:, mask2].reshape(Nq, NMnew, NMnew)
S_qMM = S_qMM[:, mask2].reshape(Nq, NMnew, NMnew)
P2_aqMi = {}
for a, P_qMi in P_aqMi.items():
P2_aqMi[a] = P_qMi[:, mask, :]
return V_qnM, H_qMM, S_qMM, P2_aqMi
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))