def init_guess_by_chkfile(cell, chkfile_name, project=True, kpts=None):
'''Read the KHF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, 3D ndarray
'''
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if kpts is None:
kpts = scf_rec['kpts']
if 'kpt' in scf_rec:
chk_kpts = scf_rec['kpt'].reshape(-1, 3)
elif 'kpts' in scf_rec:
chk_kpts = scf_rec['kpts']
else:
chk_kpts = np.zeros((1, 3))
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if 'kpts' not in scf_rec: # gamma point or single k-point
if mo.ndim == 2:
mo = mo.reshape((1, ) + mo.shape)
mo_occ = mo_occ.reshape((1, ) + mo_occ.shape)
else: # UHF
mo = mo.reshape((2, 1) + mo.shape[1:])
mo_occ = mo_occ.reshape((2, 1) + mo_occ.shape[1:])
def fproj(mo, kpt):
if project:
return addons.project_mo_nr2nr(chk_cell, mo, cell, kpt)
else:
return mo
if kpts.shape == chk_kpts.shape and np.allclose(kpts, chk_kpts):
def makedm(mos, occs):
mos = [fproj(mo, None) for mo in mos]
return make_rdm1(mos, occs)
else:
where = [np.argmin(lib.norm(chk_kpts - kpt, axis=1)) for kpt in kpts]
def makedm(mos, occs):
mos = [
fproj(mos[w], chk_kpts[w] - kpts[i])
for i, w in enumerate(where)
]
return make_rdm1(mos, occs[where])
if mo.ndim == 3: # KRHF
dm = makedm(mo, mo_occ)
else: # KUHF
dm = makedm(mo[0], mo_occ[0]) + makedm(mo[1], mo_occ[1])
# Real DM for gamma point
if np.allclose(kpts, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=True, kpts=None):
'''Read the KHF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, 3D ndarray
'''
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if kpts is None:
kpts = scf_rec['kpts']
if 'kpt' in scf_rec:
chk_kpts = scf_rec['kpt'].reshape(-1,3)
elif 'kpts' in scf_rec:
chk_kpts = scf_rec['kpts']
else:
chk_kpts = np.zeros((1,3))
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if 'kpts' not in scf_rec: # gamma point or single k-point
if mo.ndim == 2:
mo = mo.reshape((1,)+mo.shape)
mo_occ = mo_occ.reshape((1,)+mo_occ.shape)
else: # UHF
mo = mo.reshape((2,1)+mo.shape[1:])
mo_occ = mo_occ.reshape((2,1)+mo_occ.shape[1:])
def fproj(mo, kpt):
if project:
return addons.project_mo_nr2nr(chk_cell, mo, cell, kpt)
else:
return mo
if kpts.shape == chk_kpts.shape and np.allclose(kpts, chk_kpts):
def makedm(mos, occs):
mos = [fproj(mo, None) for mo in mos]
return make_rdm1(mos, occs)
else:
where = [np.argmin(lib.norm(chk_kpts-kpt, axis=1)) for kpt in kpts]
def makedm(mos, occs):
mos = [fproj(mos[w], chk_kpts[w]-kpts[i]) for i,w in enumerate(where)]
return make_rdm1(mos, occs[where])
if mo.ndim == 3: # KRHF
dm = makedm(mo, mo_occ)
else: # KUHF
dm = makedm(mo[0], mo_occ[0]) + makedm(mo[1], mo_occ[1])
# Real DM for gamma point
if np.allclose(kpts, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=None, kpt=None):
'''Read the HF results from checkpoint file and make the density matrix
for UHF initial guess.
Returns:
Density matrix, (nao,nao) ndarray
'''
from pyscf import gto
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if project is None:
project = not gto.same_basis_set(chk_cell, cell)
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if kpt is None:
kpt = np.zeros(3)
if 'kpt' in scf_rec:
chk_kpt = scf_rec['kpt']
elif 'kpts' in scf_rec:
kpts = scf_rec['kpts'] # the closest kpt from KRHF results
where = np.argmin(lib.norm(kpts - kpt, axis=1))
chk_kpt = kpts[where]
if getattr(mo[0], 'ndim', None) == 2: # KRHF
mo = mo[where]
mo_occ = mo_occ[where]
else: # KUHF
mo = [mo[0][where], mo[1][where]]
mo_occ = [mo_occ[0][where], mo_occ[1][where]]
else: # from molecular code
chk_kpt = np.zeros(3)
if project:
s = cell.pbc_intor('int1e_ovlp', kpt=kpt)
def fproj(mo):
if project:
mo = addons.project_mo_nr2nr(chk_cell, mo, cell, chk_kpt - kpt)
norm = np.einsum('pi,pi->i', mo.conj(), s.dot(mo))
mo /= np.sqrt(norm)
return mo
if getattr(mo, 'ndim', None) == 2:
mo = fproj(mo)
mo_occa = (mo_occ > 1e-8).astype(np.double)
mo_occb = mo_occ - mo_occa
dm = mol_uhf.make_rdm1([mo, mo], [mo_occa, mo_occb])
else: # UHF
dm = mol_uhf.make_rdm1([fproj(mo[0]), fproj(mo[1])], mo_occ)
# Real DM for gamma point
if kpt is None or np.allclose(kpt, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=None, kpt=None):
'''Read the HF results from checkpoint file and make the density matrix
for UHF initial guess.
Returns:
Density matrix, (nao,nao) ndarray
'''
from pyscf import gto
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if project is None:
project = not gto.same_basis_set(chk_cell, cell)
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if kpt is None:
kpt = np.zeros(3)
if 'kpt' in scf_rec:
chk_kpt = scf_rec['kpt']
elif 'kpts' in scf_rec:
kpts = scf_rec['kpts'] # the closest kpt from KRHF results
where = np.argmin(lib.norm(kpts-kpt, axis=1))
chk_kpt = kpts[where]
if getattr(mo[0], 'ndim', None) == 2: # KRHF
mo = mo[where]
mo_occ = mo_occ[where]
else: # KUHF
mo = [mo[0][where], mo[1][where]]
mo_occ = [mo_occ[0][where], mo_occ[1][where]]
else: # from molecular code
chk_kpt = np.zeros(3)
if project:
s = cell.pbc_intor('int1e_ovlp', kpt=kpt)
def fproj(mo):
if project:
mo = addons.project_mo_nr2nr(chk_cell, mo, cell, chk_kpt-kpt)
norm = np.einsum('pi,pi->i', mo.conj(), s.dot(mo))
mo /= np.sqrt(norm)
return mo
if getattr(mo, 'ndim', None) == 2:
mo = fproj(mo)
mo_occa = (mo_occ>1e-8).astype(np.double)
mo_occb = mo_occ - mo_occa
dm = mol_uhf.make_rdm1([mo,mo], [mo_occa,mo_occb])
else: # UHF
dm = mol_uhf.make_rdm1([fproj(mo[0]),fproj(mo[1])], mo_occ)
# Real DM for gamma point
if kpt is None or np.allclose(kpt, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=True, kpt=None):
'''Read the HF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, (nao,nao) ndarray
'''
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if kpt is None:
kpt = np.zeros(3)
if 'kpt' in scf_rec:
chk_kpt = scf_rec['kpt']
elif 'kpts' in scf_rec:
kpts = scf_rec['kpts'] # the closest kpt from KRHF results
where = np.argmin(lib.norm(kpts - kpt, axis=1))
chk_kpt = kpts[where]
if mo[0].ndim == 2: # KRHF
mo = mo[where]
mo_occ = mo_occ[where]
else:
mo = mo[:, where]
mo_occ = mo_occ[:, where]
else: # from molecular code
chk_kpt = np.zeros(3)
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_cell, mo, cell, chk_kpt - kpt)
else:
return mo
if mo.ndim == 2:
mo = fproj(mo)
mo_occa = (mo_occ > 1e-8).astype(np.double)
mo_occb = mo_occ - mo_occa
dm = mol_uhf.make_rdm1([mo, mo], [mo_occa, mo_occb])
else: # UHF
dm = mol_uhf.make_rdm1([fproj(mo[0]), fproj(mo[1])], mo_occ)
# Real DM for gamma point
if kpt is None or np.allclose(kpt, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=True, kpt=None):
'''Read the HF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, (nao,nao) ndarray
'''
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if kpt is None:
kpt = np.zeros(3)
if 'kpt' in scf_rec:
chk_kpt = scf_rec['kpt']
elif 'kpts' in scf_rec:
kpts = scf_rec['kpts'] # the closest kpt from KRHF results
where = np.argmin(lib.norm(kpts - kpt, axis=1))
chk_kpt = kpts[where]
if mo.ndim == 3: # KRHF:
mo = mo[where]
mo_occ = mo_occ[where]
else:
mo = mo[:, where]
mo_occ = mo_occ[:, where]
else:
chk_kpt = np.zeros(3)
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_cell, mo, cell, chk_kpt - kpt)
else:
return mo
if mo.ndim == 2:
dm = pyscf.scf.hf.make_rdm1(fproj(mo), mo_occ)
else: # UHF
dm = np.asarray((pyscf.scf.hf.make_rdm1(fproj(mo[0]), mo_occ[0]),
pyscf.scf.hf.make_rdm1(fproj(mo[1]), mo_occ[1])))
# Real DM for gamma point
if kpt is None or np.allclose(kpt, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=True, kpt=None):
'''Read the HF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, (nao,nao) ndarray
'''
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if kpt is None:
kpt = np.zeros(3)
if 'kpt' in scf_rec:
chk_kpt = scf_rec['kpt']
elif 'kpts' in scf_rec:
kpts = scf_rec['kpts'] # the closest kpt from KRHF results
where = np.argmin(lib.norm(kpts-kpt, axis=1))
chk_kpt = kpts[where]
if mo.ndim == 3: # KRHF:
mo = mo[where]
mo_occ = mo_occ[where]
else:
mo = mo[:,where]
mo_occ = mo_occ[:,where]
else:
chk_kpt = np.zeros(3)
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_cell, mo, cell, chk_kpt-kpt)
else:
return mo
if mo.ndim == 2:
dm = pyscf.scf.hf.make_rdm1(fproj(mo), mo_occ)
else: # UHF
dm = np.asarray((pyscf.scf.hf.make_rdm1(fproj(mo[0]), mo_occ[0]),
pyscf.scf.hf.make_rdm1(fproj(mo[1]), mo_occ[1])))
# Real DM for gamma point
if kpt is None or np.allclose(kpt, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=None, kpts=None):
'''Read the KHF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, 3D ndarray
'''
from pyscf import gto
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if project is None:
project = not gto.same_basis_set(chk_cell, cell)
if kpts is None:
kpts = scf_rec['kpts']
if 'kpt' in scf_rec:
chk_kpts = scf_rec['kpt'].reshape(-1, 3)
elif 'kpts' in scf_rec:
chk_kpts = scf_rec['kpts']
else:
chk_kpts = np.zeros((1, 3))
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if 'kpts' not in scf_rec: # gamma point or single k-point
if mo.ndim == 2:
mo = np.expand_dims(mo, axis=0)
mo_occ = np.expand_dims(mo_occ, axis=0)
else: # UHF
mo = [np.expand_dims(mo[0], axis=0), np.expand_dims(mo[1], axis=0)]
mo_occ = [
np.expand_dims(mo_occ[0], axis=0),
np.expand_dims(mo_occ[1], axis=0)
]
if project:
s = cell.pbc_intor('int1e_ovlp', kpts=kpts)
def fproj(mo, kpts):
if project:
mo = addons.project_mo_nr2nr(chk_cell, mo, cell, kpts)
for k, c in enumerate(mo):
norm = np.einsum('pi,pi->i', c.conj(), s[k].dot(c))
mo[k] /= np.sqrt(norm)
return mo
if kpts.shape == chk_kpts.shape and np.allclose(kpts, chk_kpts):
def makedm(mos, occs):
moa, mob = mos
mos = ([fproj(mo, None)
for mo in moa], [fproj(mo, None) for mo in mob])
return make_rdm1(mos, occs)
else:
def makedm(mos, occs):
where = [
np.argmin(lib.norm(chk_kpts - kpt, axis=1)) for kpt in kpts
]
moa, mob = mos
occa, occb = occs
dkpts = [chk_kpts[w] - kpts[i] for i, w in enumerate(where)]
mos = (fproj([moa[w] for w in where],
dkpts), fproj([mob[w] for w in where], dkpts))
occs = ([occa[i] for i in where], [occb[i] for i in where])
return make_rdm1(mos, occs)
if getattr(mo[0], 'ndim', None) == 2: # KRHF
mo_occa = [(occ > 1e-8).astype(np.double) for occ in mo_occ]
mo_occb = [occ - mo_occa[k] for k, occ in enumerate(mo_occ)]
dm = makedm((mo, mo), (mo_occa, mo_occb))
else: # KUHF
dm = makedm(mo, mo_occ)
# Real DM for gamma point
if np.allclose(kpts, 0):
dm = dm.real
return dm
def init_guess_by_chkfile(cell, chkfile_name, project=None, kpts=None):
'''Read the KHF results from checkpoint file, then project it to the
basis defined by ``cell``
Returns:
Density matrix, 3D ndarray
'''
from pyscf import gto
chk_cell, scf_rec = chkfile.load_scf(chkfile_name)
if project is None:
project = not gto.same_basis_set(chk_cell, cell)
if kpts is None:
kpts = scf_rec['kpts']
if 'kpt' in scf_rec:
chk_kpts = scf_rec['kpt'].reshape(-1,3)
elif 'kpts' in scf_rec:
chk_kpts = scf_rec['kpts']
else:
chk_kpts = np.zeros((1,3))
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if 'kpts' not in scf_rec: # gamma point or single k-point
if mo.ndim == 2:
mo = np.expand_dims(mo, axis=0)
mo_occ = np.expand_dims(mo_occ, axis=0)
else: # UHF
mo = [np.expand_dims(mo[0], axis=0),
np.expand_dims(mo[1], axis=0)]
mo_occ = [np.expand_dims(mo_occ[0], axis=0),
np.expand_dims(mo_occ[1], axis=0)]
if project:
s = cell.pbc_intor('int1e_ovlp', kpts=kpts)
def fproj(mo, kpts):
if project:
mo = addons.project_mo_nr2nr(chk_cell, mo, cell, kpts)
for k, c in enumerate(mo):
norm = np.einsum('pi,pi->i', c.conj(), s[k].dot(c))
mo[k] /= np.sqrt(norm)
return mo
if kpts.shape == chk_kpts.shape and np.allclose(kpts, chk_kpts):
def makedm(mos, occs):
moa, mob = mos
mos =([fproj(mo, None) for mo in moa],
[fproj(mo, None) for mo in mob])
return make_rdm1(mos, occs)
else:
def makedm(mos, occs):
where = [np.argmin(lib.norm(chk_kpts-kpt, axis=1)) for kpt in kpts]
moa, mob = mos
occa, occb = occs
dkpts = [chk_kpts[w]-kpts[i] for i,w in enumerate(where)]
mos = (fproj([moa[w] for w in where], dkpts),
fproj([mob[w] for w in where], dkpts))
occs = ([occa[i] for i in where], [occb[i] for i in where])
return make_rdm1(mos, occs)
if getattr(mo[0], 'ndim', None) == 2: # KRHF
mo_occa = [(occ>1e-8).astype(np.double) for occ in mo_occ]
mo_occb = [occ-mo_occa[k] for k,occ in enumerate(mo_occ)]
dm = makedm((mo, mo), (mo_occa, mo_occb))
else: # KUHF
dm = makedm(mo, mo_occ)
# Real DM for gamma point
if np.allclose(kpts, 0):
dm = dm.real
return dm