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(mol, chkfile, project=True):
from pyscf.scf import addons
if isinstance(chkfile, pyscf.gto.Mole):
raise TypeError('''
You see this error message because of the API updates.
The first argument is chkfile file name.''')
chk_mol, scf_rec = pyscf.scf.chkfile.load_scf(chkfile)
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_mol, mo, mol)
else:
return mo
if scf_rec['mo_coeff'].ndim == 2:
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if numpy.iscomplexobj(mo):
raise NotImplementedError(
'TODO: project DHF orbital to ROHF orbital')
dm = make_rdm1(fproj(mo), mo_occ)
else: # UHF
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
dm = uhf.make_rdm1((fproj(mo[0]), fproj(mo[1])), mo_occ)
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(mol, chkfile, project=True):
from pyscf.scf import addons
if isinstance(chkfile, pyscf.gto.Mole):
raise TypeError('''
You see this error message because of the API updates.
The first argument is chkfile file name.''')
chk_mol, scf_rec = pyscf.scf.chkfile.load_scf(chkfile)
def fproj(mo):
if project:
return addons.project_mo_nr2nr(chk_mol, mo, mol)
else:
return mo
if scf_rec['mo_coeff'].ndim == 2:
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if numpy.iscomplexobj(mo):
raise NotImplementedError('TODO: project DHF orbital to ROHF orbital')
dm = make_rdm1(fproj(mo), mo_occ)
else: # UHF
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
dm = uhf.make_rdm1((fproj(mo[0]),fproj(mo[1])), mo_occ)
return dm
def init_guess_by_chkfile(mol, chkfile_name, project=None):
'''Read SCF chkfile and make the density matrix for GHF initial guess.
Kwargs:
project : None or bool
Whether to project chkfile's orbitals to the new basis. Note when
the geometry of the chkfile and the given molecule are very
different, this projection can produce very poor initial guess.
In PES scanning, it is recommended to swith off project.
If project is set to None, the projection is only applied when the
basis sets of the chkfile's molecule are different to the basis
sets of the given molecule (regardless whether the geometry of
the two molecules are different). Note the basis sets are
considered to be different if the two molecules are derived from
the same molecule with different ordering of atoms.
'''
from pyscf.scf import addons
chk_mol, scf_rec = chkfile.load_scf(chkfile_name)
if project is None:
project = not gto.same_basis_set(chk_mol, mol)
# Check whether the two molecules are similar
if abs(mol.inertia_moment() - chk_mol.inertia_moment()).sum() > 0.5:
logger.warn(
mol, "Large deviations found between the input "
"molecule and the molecule from chkfile\n"
"Initial guess density matrix may have large error.")
if project:
s = hf.get_ovlp(mol)
def fproj(mo):
if project:
mo = addons.project_mo_nr2nr(chk_mol, mo, mol)
norm = numpy.einsum('pi,pi->i', mo.conj(), s.dot(mo))
mo /= numpy.sqrt(norm)
return mo
nao = chk_mol.nao_nr()
mo = scf_rec['mo_coeff']
mo_occ = scf_rec['mo_occ']
if getattr(mo[0], 'ndim', None) == 1: # RHF/GHF/DHF
if nao * 2 == mo.shape[0]: # GHF or DHF
if project:
raise NotImplementedError('Project initial guess from '
'different geometry')
else:
dm = hf.make_rdm1(mo, mo_occ)
else: # RHF
mo_coeff = fproj(mo)
mo_occa = (mo_occ > 1e-8).astype(numpy.double)
mo_occb = mo_occ - mo_occa
dma, dmb = uhf.make_rdm1([mo_coeff] * 2, (mo_occa, mo_occb))
dm = scipy.linalg.block_diag(dma, dmb)
else: #UHF
if getattr(mo[0][0], 'ndim', None) == 2: # KUHF
logger.warn(
mol, 'k-point UHF results are found. Density matrix '
'at Gamma point is used for the molecular SCF initial guess')
mo = mo[0]
dma, dmb = uhf.make_rdm1([fproj(mo[0]), fproj(mo[1])], mo_occ)
dm = scipy.linalg.block_diag(dma, dmb)
return dm
