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"""Module with utility function for dumping the Hamiltonian to file in FCIDUMP format."""
from __future__ import division
from datetime import datetime
import numpy as np
from psi4.driver import constants
from psi4.driver.p4util.util import compare_values, success
from psi4.driver.procrouting.proc_util import check_iwl_file_from_scf_type
from .exceptions import *
[docs]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(), constants.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(), constants.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(), constants.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))
[docs]def write_eigenvalues(eigs, mo_idx):
"""Prepare multi-line string with one-particle eigenvalues to be written to the FCIDUMP file.
"""
eigs_dump = ''
iorb = 0
for h, block in enumerate(eigs):
for idx, x in np.ndenumerate(block):
eigs_dump += '{: 29.20E} {:4d} {:4d} {:4d} {:4d}\n'.format(x, mo_idx(iorb), 0, 0, 0)
iorb += 1
return eigs_dump
[docs]def fcidump_from_file(fname):
"""Function to read in a FCIDUMP file.
:returns: a dictionary with FCIDUMP header and integrals
The key-value pairs are:
- 'norb' : number of basis functions
- 'nelec' : number of electrons
- 'ms2' : spin polarization of the system
- 'isym' : symmetry of state (if present in FCIDUMP)
- 'orbsym' : list of symmetry labels of each orbital
- 'uhf' : whether restricted or unrestricted
- 'enuc' : nuclear repulsion plus frozen core energy
- 'epsilon' : orbital energies
- 'hcore' : core Hamiltonian
- 'eri' : electron-repulsion integrals
:param fname: FCIDUMP file name
"""
intdump = {}
with open(fname, 'r') as handle:
assert '&FCI' == handle.readline().strip()
skiplines = 1
read = True
while True:
skiplines += 1
line = handle.readline()
if 'END' in line:
break
key, value = line.split('=')
value = value.strip().rstrip(',')
if key == 'UHF':
value = 'TRUE' in value
elif key == 'ORBSYM':
value = [int(x) for x in value.split(',')]
else:
value = int(value.replace(',', ''))
intdump[key.lower()] = value
# Read the data and index, skip header
raw_ints = np.genfromtxt(fname, skip_header=skiplines)
# Read last line, i.e. Enuc + Efzc
intdump['enuc'] = raw_ints[-1, 0]
# Read in integrals and indices
ints = raw_ints[:-1, 0]
# Get dimensions and indices
nbf = intdump['norb']
idxs = raw_ints[:, 1:].astype(np.int) - 1
# Slices
sl = slice(ints.shape[0] - nbf, ints.shape[0])
# Extract orbital energies
epsilon = np.zeros(nbf)
epsilon[idxs[sl, 0]] = ints[sl]
intdump['epsilon'] = epsilon
# Count how many 2-index intdump we have
sl = slice(sl.start - nbf * nbf, sl.stop - nbf)
two_index = np.all(idxs[sl, 2:] == -1, axis=1).sum()
sl = slice(sl.stop - two_index, sl.stop)
# Extract Hcore
Hcore = np.zeros((nbf, nbf))
Hcore[(idxs[sl, 0], idxs[sl, 1])] = ints[sl]
Hcore[(idxs[sl, 1], idxs[sl, 0])] = ints[sl]
intdump['hcore'] = Hcore
# Extract ERIs
sl = slice(0, sl.start)
eri = np.zeros((nbf, nbf, nbf, nbf))
eri[(idxs[sl, 0], idxs[sl, 1], idxs[sl, 2], idxs[sl, 3])] = ints[sl]
eri[(idxs[sl, 0], idxs[sl, 1], idxs[sl, 3], idxs[sl, 2])] = ints[sl]
eri[(idxs[sl, 1], idxs[sl, 0], idxs[sl, 2], idxs[sl, 3])] = ints[sl]
eri[(idxs[sl, 1], idxs[sl, 0], idxs[sl, 3], idxs[sl, 2])] = ints[sl]
eri[(idxs[sl, 2], idxs[sl, 3], idxs[sl, 0], idxs[sl, 1])] = ints[sl]
eri[(idxs[sl, 3], idxs[sl, 2], idxs[sl, 0], idxs[sl, 1])] = ints[sl]
eri[(idxs[sl, 2], idxs[sl, 3], idxs[sl, 1], idxs[sl, 0])] = ints[sl]
eri[(idxs[sl, 3], idxs[sl, 2], idxs[sl, 1], idxs[sl, 0])] = ints[sl]
intdump['eri'] = eri
return intdump
[docs]def compare_fcidumps(expected, computed, label):
"""Function to compare two FCIDUMP files. Prints :py:func:`util.success`
when value *computed* matches value *expected*.
Performs a system exit on failure. Used in input files in the test suite.
:returns: a dictionary of energies computed from the MO integrals.
The key-value pairs are:
- 'NUCLEAR REPULSION ENERGY' : nuclear repulsion plus frozen core energy
- 'ONE-ELECTRON ENERGY' : SCF one-electron energy
- 'TWO-ELECTRON ENERGY' : SCF two-electron energy
- 'SCF TOTAL ENERGY' : SCF total energy
- 'MP2 CORRELATION ENERGY' : MP2 correlation energy
:param expected: reference FCIDUMP file
:param computed: computed FCIDUMP file
:param label: string labelling the test
"""
try:
from deepdiff import DeepDiff
except ImportError:
raise ImportError("""Install deepdiff. `conda install deepdiff -c conda-forge` or `pip install deepdiff`""")
# Grab expected header and integrals
ref_intdump = fcidump_from_file(expected)
intdump = fcidump_from_file(computed)
# Compare headers
header_diff = DeepDiff(
ref_intdump,
intdump,
ignore_order=True,
exclude_paths={"root['enuc']", "root['hcore']", "root['eri']", "root['epsilon']"})
if header_diff:
message = ("\tComputed FCIDUMP file header does not match expected header.\n")
raise TestComparisonError(header_diff)
ref_energies = _energies_from_fcidump(ref_intdump)
energies = _energies_from_fcidump(intdump)
pass_1el = compare_values(ref_energies['ONE-ELECTRON ENERGY'], energies['ONE-ELECTRON ENERGY'], 7, label + '. 1-electron energy')
pass_2el = compare_values(ref_energies['TWO-ELECTRON ENERGY'], energies['TWO-ELECTRON ENERGY'], 7, label + '. 2-electron energy')
pass_scf = compare_values(ref_energies['SCF TOTAL ENERGY'], energies['SCF TOTAL ENERGY'], 10, label + '. SCF total energy')
pass_mp2 = compare_values(ref_energies['MP2 CORRELATION ENERGY'], energies['MP2 CORRELATION ENERGY'], 10, label + '. MP2 correlation energy')
if (pass_1el and pass_2el and pass_scf and pass_mp2):
success(label)
return True
def _energies_from_fcidump(intdump):
energies = {}
energies['NUCLEAR REPULSION ENERGY'] = intdump['enuc']
epsilon = intdump['epsilon']
Hcore = intdump['hcore']
eri = intdump['eri']
# Compute SCF energy
energies['ONE-ELECTRON ENERGY'], energies['TWO-ELECTRON ENERGY'] = _scf_energy(Hcore, eri,
np.where(epsilon < 0)[0],
intdump['uhf'])
# yapf: disable
energies['SCF TOTAL ENERGY'] = energies['ONE-ELECTRON ENERGY'] + energies['TWO-ELECTRON ENERGY'] + energies['NUCLEAR REPULSION ENERGY']
# yapf: enable
# Compute MP2 energy
energies['MP2 CORRELATION ENERGY'] = _mp2_energy(eri, epsilon, intdump['uhf'])
return energies
def _scf_energy(Hcore, ERI, occ_sl, unrestricted):
scf_1el_e = np.einsum('ii->', Hcore[np.ix_(occ_sl, occ_sl)])
if not unrestricted:
scf_1el_e *= 2
coulomb = np.einsum('iijj->', ERI[np.ix_(occ_sl, occ_sl, occ_sl, occ_sl)])
exchange = np.einsum('ijij->', ERI[np.ix_(occ_sl, occ_sl, occ_sl, occ_sl)])
if unrestricted:
scf_2el_e = 0.5 * (coulomb - exchange)
else:
scf_2el_e = 2.0 * coulomb - exchange
return scf_1el_e, scf_2el_e
def _mp2_energy(ERI, epsilon, unrestricted):
# Occupied and virtual slices
occ_sl = np.where(epsilon < 0)[0]
vir_sl = np.where(epsilon > 0)[0]
eocc = epsilon[occ_sl]
evir = epsilon[vir_sl]
denom = 1 / (eocc.reshape(-1, 1, 1, 1) - evir.reshape(-1, 1, 1) + eocc.reshape(-1, 1) - evir)
MO = ERI[np.ix_(occ_sl, vir_sl, occ_sl, vir_sl)]
if unrestricted:
mp2_e = 0.5 * np.einsum("abrs,abrs,abrs->", MO, MO - MO.swapaxes(1, 3), denom)
else:
mp2_e = np.einsum('iajb,iajb,iajb->', MO, MO, denom) + np.einsum('iajb,iajb,iajb->', MO - MO.swapaxes(1, 3),
MO, denom)
return mp2_e
