def fcidump(wfn, fname='INTDUMP', oe_ints=None):
"""Save integrals to file in FCIDUMP format as defined in Comp. Phys. Commun. 54 75 (1989)
Additional one-electron integrals, including orbital energies, can also be saved.
This latter format can be used with the HANDE QMC code but is not standard.
:returns: None
:raises: ValidationError when SCF wavefunction is not RHF
:type wfn: :py:class:`~psi4.core.Wavefunction`
:param wfn: set of molecule, basis, orbitals from which to generate cube files
:param fname: name of the integrals file, defaults to INTDUMP
:param oe_ints: list of additional one-electron integrals to save to file. So far only EIGENVALUES is a valid option.
:examples:
>>> # [1] Save one- and two-electron integrals to standard FCIDUMP format
>>> E, wfn = energy('scf', return_wfn=True)
>>> fcidump(wfn)
>>> # [2] Save orbital energies, one- and two-electron integrals.
>>> E, wfn = energy('scf', return_wfn=True)
>>> fcidump(wfn, oe_ints=['EIGENVALUES'])
"""
# Get some options
reference = core.get_option('SCF', 'REFERENCE')
ints_tolerance = core.get_global_option('INTS_TOLERANCE')
# Some sanity checks
if reference not in ['RHF', 'UHF']:
raise ValidationError(
'FCIDUMP not implemented for {} references\n'.format(reference))
if oe_ints is None:
oe_ints = []
molecule = wfn.molecule()
docc = wfn.doccpi()
frzcpi = wfn.frzcpi()
frzvpi = wfn.frzvpi()
active_docc = docc - frzcpi
active_socc = wfn.soccpi()
active_mopi = wfn.nmopi() - frzcpi - frzvpi
nbf = active_mopi.sum() if wfn.same_a_b_orbs() else 2 * active_mopi.sum()
nirrep = wfn.nirrep()
nelectron = 2 * active_docc.sum() + active_socc.sum()
irrep_map = _irrep_map(wfn)
wfn_irrep = 0
for h, n_socc in enumerate(active_socc):
if n_socc % 2 == 1:
wfn_irrep ^= h
core.print_out('Writing integrals in FCIDUMP format to ' + fname + '\n')
# Generate FCIDUMP header
header = '&FCI\n'
header += 'NORB={:d},\n'.format(nbf)
header += 'NELEC={:d},\n'.format(nelectron)
header += 'MS2={:d},\n'.format(wfn.nalpha() - wfn.nbeta())
header += 'UHF=.{}.,\n'.format(not wfn.same_a_b_orbs()).upper()
orbsym = ''
for h in range(active_mopi.n()):
for n in range(frzcpi[h], frzcpi[h] + active_mopi[h]):
orbsym += '{:d},'.format(irrep_map[h])
if not wfn.same_a_b_orbs():
orbsym += '{:d},'.format(irrep_map[h])
header += 'ORBSYM={}\n'.format(orbsym)
header += 'ISYM={:d},\n'.format(irrep_map[wfn_irrep])
header += '&END\n'
with open(fname, 'w') as intdump:
intdump.write(header)
# Get an IntegralTransform object
check_iwl_file_from_scf_type(core.get_global_option('SCF_TYPE'), wfn)
spaces = [core.MOSpace.all()]
trans_type = core.IntegralTransform.TransformationType.Restricted
if not wfn.same_a_b_orbs():
trans_type = core.IntegralTransform.TransformationType.Unrestricted
ints = core.IntegralTransform(wfn, spaces, trans_type)
ints.transform_tei(core.MOSpace.all(), core.MOSpace.all(),
core.MOSpace.all(), core.MOSpace.all())
core.print_out('Integral transformation complete!\n')
DPD_info = {
'instance_id': ints.get_dpd_id(),
'alpha_MO': ints.DPD_ID('[A>=A]+'),
'beta_MO': 0
}
if not wfn.same_a_b_orbs():
DPD_info['beta_MO'] = ints.DPD_ID("[a>=a]+")
# Write TEI to fname in FCIDUMP format
core.fcidump_tei_helper(nirrep, wfn.same_a_b_orbs(), DPD_info,
ints_tolerance, fname)
# Read-in OEI and write them to fname in FCIDUMP format
# Indexing functions to translate from zero-based (C and Python) to
# one-based (Fortran)
mo_idx = lambda x: x + 1
alpha_mo_idx = lambda x: 2 * x + 1
beta_mo_idx = lambda x: 2 * (x + 1)
with open(fname, 'a') as intdump:
core.print_out('Writing frozen core operator in FCIDUMP format to ' +
fname + '\n')
if reference == 'RHF':
PSIF_MO_FZC = 'MO-basis Frozen-Core Operator'
moH = core.Matrix(PSIF_MO_FZC, wfn.nmopi(), wfn.nmopi())
moH.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC = moH.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = mo_idx(il[0][index] + offset)
col = mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E}{:4d}{:4d}{:4d}{:4d}\n'.format(
x, row, col, 0, 0))
offset += block.shape[0]
# Additional one-electron integrals as requested in oe_ints
# Orbital energies
core.print_out('Writing orbital energies in FCIDUMP format to ' +
fname + '\n')
if 'EIGENVALUES' in oe_ints:
eigs_dump = write_eigenvalues(
wfn.epsilon_a().get_block(mo_slice).to_array(), mo_idx)
intdump.write(eigs_dump)
else:
PSIF_MO_A_FZC = 'MO-basis Alpha Frozen-Core Oper'
moH_A = core.Matrix(PSIF_MO_A_FZC, wfn.nmopi(), wfn.nmopi())
moH_A.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC_A = moH_A.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC_A.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = alpha_mo_idx(il[0][index] + offset)
col = alpha_mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E}{:4d}{:4d}{:4d}{:4d}\n'.format(
x, row, col, 0, 0))
offset += block.shape[0]
PSIF_MO_B_FZC = 'MO-basis Beta Frozen-Core Oper'
moH_B = core.Matrix(PSIF_MO_B_FZC, wfn.nmopi(), wfn.nmopi())
moH_B.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC_B = moH_B.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC_B.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = beta_mo_idx(il[0][index] + offset)
col = beta_mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E}{:4d}{:4d}{:4d}{:4d}\n'.format(
x, row, col, 0, 0))
offset += block.shape[0]
# Additional one-electron integrals as requested in oe_ints
# Orbital energies
core.print_out('Writing orbital energies in FCIDUMP format to ' +
fname + '\n')
if 'EIGENVALUES' in oe_ints:
alpha_eigs_dump = write_eigenvalues(
wfn.epsilon_a().get_block(mo_slice).to_array(),
alpha_mo_idx)
beta_eigs_dump = write_eigenvalues(
wfn.epsilon_b().get_block(mo_slice).to_array(),
beta_mo_idx)
intdump.write(alpha_eigs_dump + beta_eigs_dump)
# Dipole integrals
#core.print_out('Writing dipole moment OEI in FCIDUMP format to ' + fname + '\n')
# Traceless quadrupole integrals
#core.print_out('Writing traceless quadrupole moment OEI in FCIDUMP format to ' + fname + '\n')
# Frozen core + nuclear repulsion energy
core.print_out(
'Writing frozen core + nuclear repulsion energy in FCIDUMP format to '
+ fname + '\n')
e_fzc = ints.get_frozen_core_energy()
e_nuc = molecule.nuclear_repulsion_energy(
wfn.get_dipole_field_strength())
intdump.write('{:29.20E}{:4d}{:4d}{:4d}{:4d}\n'.format(
e_fzc + e_nuc, 0, 0, 0, 0))
core.print_out(
'Done generating {} with integrals in FCIDUMP format.\n'.format(fname))
def fcidump(wfn, fname='INTDUMP', oe_ints=None):
"""Save integrals to file in FCIDUMP format as defined in Comp. Phys. Commun. 54 75 (1989)
Additional one-electron integrals, including orbital energies, can also be saved.
This latter format can be used with the HANDE QMC code but is not standard.
:returns: None
:raises: ValidationError when SCF wavefunction is not RHF
:type wfn: :py:class:`~psi4.core.Wavefunction`
:param wfn: set of molecule, basis, orbitals from which to generate cube files
:param fname: name of the integrals file, defaults to INTDUMP
:param oe_ints: list of additional one-electron integrals to save to file.
So far only EIGENVALUES is a valid option.
:examples:
>>> # [1] Save one- and two-electron integrals to standard FCIDUMP format
>>> E, wfn = energy('scf', return_wfn=True)
>>> fcidump(wfn)
>>> # [2] Save orbital energies, one- and two-electron integrals.
>>> E, wfn = energy('scf', return_wfn=True)
>>> fcidump(wfn, oe_ints=['EIGENVALUES'])
"""
# Get some options
reference = core.get_option('SCF', 'REFERENCE')
ints_tolerance = core.get_global_option('INTS_TOLERANCE')
# Some sanity checks
if reference not in ['RHF', 'UHF']:
raise ValidationError('FCIDUMP not implemented for {} references\n'.format(reference))
if oe_ints is None:
oe_ints = []
molecule = wfn.molecule()
docc = wfn.doccpi()
frzcpi = wfn.frzcpi()
frzvpi = wfn.frzvpi()
active_docc = docc - frzcpi
active_socc = wfn.soccpi()
active_mopi = wfn.nmopi() - frzcpi - frzvpi
nbf = active_mopi.sum() if wfn.same_a_b_orbs() else 2 * active_mopi.sum()
nirrep = wfn.nirrep()
nelectron = 2 * active_docc.sum() + active_socc.sum()
core.print_out('Writing integrals in FCIDUMP format to ' + fname + '\n')
# Generate FCIDUMP header
header = '&FCI\n'
header += 'NORB={:d},\n'.format(nbf)
header += 'NELEC={:d},\n'.format(nelectron)
header += 'MS2={:d},\n'.format(wfn.nalpha() - wfn.nbeta())
header += 'UHF=.{}.,\n'.format(not wfn.same_a_b_orbs()).upper()
orbsym = ''
for h in range(active_mopi.n()):
for n in range(frzcpi[h], frzcpi[h] + active_mopi[h]):
orbsym += '{:d},'.format(h + 1)
if not wfn.same_a_b_orbs():
orbsym += '{:d},'.format(h + 1)
header += 'ORBSYM={}\n'.format(orbsym)
header += '&END\n'
with open(fname, 'w') as intdump:
intdump.write(header)
# Get an IntegralTransform object
check_iwl_file_from_scf_type(core.get_global_option('SCF_TYPE'), wfn)
spaces = [core.MOSpace.all()]
trans_type = core.IntegralTransform.TransformationType.Restricted
if not wfn.same_a_b_orbs():
trans_type = core.IntegralTransform.TransformationType.Unrestricted
ints = core.IntegralTransform(wfn, spaces, trans_type)
ints.transform_tei(core.MOSpace.all(), core.MOSpace.all(), core.MOSpace.all(), core.MOSpace.all())
core.print_out('Integral transformation complete!\n')
DPD_info = {'instance_id': ints.get_dpd_id(), 'alpha_MO': ints.DPD_ID('[A>=A]+'), 'beta_MO': 0}
if not wfn.same_a_b_orbs():
DPD_info['beta_MO'] = ints.DPD_ID("[a>=a]+")
# Write TEI to fname in FCIDUMP format
core.fcidump_tei_helper(nirrep, wfn.same_a_b_orbs(), DPD_info, ints_tolerance, fname)
# Read-in OEI and write them to fname in FCIDUMP format
# Indexing functions to translate from zero-based (C and Python) to
# one-based (Fortran)
mo_idx = lambda x: x + 1
alpha_mo_idx = lambda x: 2 * x + 1
beta_mo_idx = lambda x: 2 * (x + 1)
with open(fname, 'a') as intdump:
core.print_out('Writing frozen core operator in FCIDUMP format to ' + fname + '\n')
if reference == 'RHF':
PSIF_MO_FZC = 'MO-basis Frozen-Core Operator'
moH = core.Matrix(PSIF_MO_FZC, wfn.nmopi(), wfn.nmopi())
moH.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC = moH.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = mo_idx(il[0][index] + offset)
col = mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E} {:4d} {:4d} {:4d} {:4d}\n'.format(x, row, col, 0, 0))
offset += block.shape[0]
# Additional one-electron integrals as requested in oe_ints
# Orbital energies
core.print_out('Writing orbital energies in FCIDUMP format to ' + fname + '\n')
if 'EIGENVALUES' in oe_ints:
eigs_dump = write_eigenvalues(wfn.epsilon_a().get_block(mo_slice).to_array(), mo_idx)
intdump.write(eigs_dump)
else:
PSIF_MO_A_FZC = 'MO-basis Alpha Frozen-Core Oper'
moH_A = core.Matrix(PSIF_MO_A_FZC, wfn.nmopi(), wfn.nmopi())
moH_A.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC_A = moH_A.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC_A.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = alpha_mo_idx(il[0][index] + offset)
col = alpha_mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E} {:4d} {:4d} {:4d} {:4d}\n'.format(x, row, col, 0, 0))
offset += block.shape[0]
PSIF_MO_B_FZC = 'MO-basis Beta Frozen-Core Oper'
moH_B = core.Matrix(PSIF_MO_B_FZC, wfn.nmopi(), wfn.nmopi())
moH_B.load(core.IO.shared_object(), psif.PSIF_OEI)
mo_slice = core.Slice(frzcpi, active_mopi)
MO_FZC_B = moH_B.get_block(mo_slice, mo_slice)
offset = 0
for h, block in enumerate(MO_FZC_B.nph):
il = np.tril_indices(block.shape[0])
for index, x in np.ndenumerate(block[il]):
row = beta_mo_idx(il[0][index] + offset)
col = beta_mo_idx(il[1][index] + offset)
if (abs(x) > ints_tolerance):
intdump.write('{:29.20E} {:4d} {:4d} {:4d} {:4d}\n'.format(x, row, col, 0, 0))
offset += block.shape[0]
# Additional one-electron integrals as requested in oe_ints
# Orbital energies
core.print_out('Writing orbital energies in FCIDUMP format to ' + fname + '\n')
if 'EIGENVALUES' in oe_ints:
alpha_eigs_dump = write_eigenvalues(wfn.epsilon_a().get_block(mo_slice).to_array(), alpha_mo_idx)
beta_eigs_dump = write_eigenvalues(wfn.epsilon_b().get_block(mo_slice).to_array(), beta_mo_idx)
intdump.write(alpha_eigs_dump + beta_eigs_dump)
# Dipole integrals
#core.print_out('Writing dipole moment OEI in FCIDUMP format to ' + fname + '\n')
# Traceless quadrupole integrals
#core.print_out('Writing traceless quadrupole moment OEI in FCIDUMP format to ' + fname + '\n')
# Frozen core + nuclear repulsion energy
core.print_out('Writing frozen core + nuclear repulsion energy in FCIDUMP format to ' + fname + '\n')
e_fzc = ints.get_frozen_core_energy()
e_nuc = molecule.nuclear_repulsion_energy(wfn.get_dipole_field_strength())
intdump.write('{: 29.20E} {:4d} {:4d} {:4d} {:4d}\n'.format(e_fzc + e_nuc, 0, 0, 0, 0))
core.print_out('Done generating {} with integrals in FCIDUMP format.\n'.format(fname))