def setUp(self):
geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))]
basis = '6-31g'
multiplicity = 1
charge = 0
self.molecule = PyscfMolecularData(geometry, basis, multiplicity,
charge)
mol = prepare_pyscf_molecule(self.molecule)
mol.verbose = 0
self.molecule._pyscf_data['mol'] = mol
self.molecule._pyscf_data['scf'] = mf = scf.RHF(mol).run()
self.molecule._pyscf_data['mp2'] = mp.MP2(mf).run()
self.molecule._pyscf_data['cisd'] = ci.CISD(mf).run()
self.molecule._pyscf_data['ccsd'] = cc.CCSD(mf).run()
self.molecule._pyscf_data['fci'] = fci.FCI(mf).run()
# See the License for the specific language governing permissions and
# limitations under the License.
"""Tests for molecular_data."""
from __future__ import absolute_import
import numpy
from openfermionpyscf import prepare_pyscf_molecule
from openfermionpyscf import PyscfMolecularData
from pyscf import scf, mp, ci, cc, fci
geometry = [('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))]
basis = '6-31g'
multiplicity = 1
charge = 0
molecule = PyscfMolecularData(geometry, basis, multiplicity, charge)
mol = prepare_pyscf_molecule(molecule)
mol.verbose = 0
molecule._pyscf_data['mol'] = mol
molecule._pyscf_data['scf'] = mf = scf.RHF(mol).run()
molecule._pyscf_data['mp2'] = mp.MP2(mf).run()
molecule._pyscf_data['cisd'] = ci.CISD(mf).run()
molecule._pyscf_data['ccsd'] = cc.CCSD(mf).run()
molecule._pyscf_data['fci'] = fci.FCI(mf).run()
def test_accessing_rdm():
mo = molecule.canonical_orbitals
overlap = molecule.overlap_integrals
h1 = molecule.one_body_integrals
def run_pyscf(molecule,
run_fci=False,
verbose=False,
n_frozen_orbital=0,
n_cancel_orbital=0,
cas_irrep_nocc=None,
cas_irrep_ncore=None): # ZZJ CHANGE
"""
This function runs a pyscf calculation.
Args:
molecule: An instance of the MolecularData or PyscfMolecularData class.
run_scf: Optional boolean to run SCF calculation.
run_mp2: Optional boolean to run MP2 calculation.
run_cisd: Optional boolean to run CISD calculation.
run_ccsd: Optional boolean to run CCSD calculation.
run_fci: Optional boolean to FCI calculation. ## NOTICE !!! FCI is changed to only done in the active space --- ZZJ CHANGE
verbose: Boolean whether to print calculation results to screen.
Returns:
molecule: The updated PyscfMolecularData object. Note the attributes
of the input molecule are also updated in this function.
"""
run_scf = True # ZZJ CHANGE scf must be run
# Prepare pyscf molecule.
pyscf_molecule = prepare_pyscf_molecule(molecule)
molecule.n_orbitals = int(pyscf_molecule.nao_nr())
molecule.n_qubits = 2 * molecule.n_orbitals
molecule.nuclear_repulsion = float(pyscf_molecule.energy_nuc())
# Run SCF.
pyscf_scf = compute_scf(pyscf_molecule)
pyscf_scf.verbose = 0
pyscf_scf.run()
molecule.hf_energy = float(pyscf_scf.e_tot)
if verbose:
print('Hartree-Fock energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.hf_energy))
# Hold pyscf data in molecule. They are required to compute density
# matrices and other quantities.
molecule._pyscf_data = pyscf_data = {}
pyscf_data['mol'] = pyscf_molecule
pyscf_data['scf'] = pyscf_scf
# Populate fields.
molecule.canonical_orbitals = pyscf_scf.mo_coeff.astype(float)
molecule.orbital_energies = pyscf_scf.mo_energy.astype(float)
# Get integrals.
one_body_integrals, two_body_integrals = compute_integrals(
pyscf_molecule, pyscf_scf)
molecule.one_body_integrals = one_body_integrals
molecule.two_body_integrals = two_body_integrals
molecule.overlap_integrals = pyscf_scf.get_ovlp()
# Run FCI.
if run_fci:
# pyscf_fci = fci.FCI(pyscf_scf)
# pyscf_fci.verbose = 0
# molecule.fci_energy, molecule.fci_wfn = pyscf_fci.kernel()
# pyscf_data['fci'] = pyscf_fci
# pyscf_data['fci_wfn'] = molecule.fci_wfn
nelec = molecule.n_electrons - n_frozen_orbital * 2
norb = molecule.n_orbitals - n_cancel_orbital - n_frozen_orbital
pyscf_fci = mcscf.CASCI(pyscf_scf, norb, nelec)
pyscf_fci.verbose = 0
if cas_irrep_nocc != None:
molecule.active_orbitals = mcscf.caslst_by_irrep(
pyscf_fci, pyscf_scf.mo_coeff, cas_irrep_nocc, cas_irrep_ncore)
mo = pyscf_fci.sort_mo_by_irrep(cas_irrep_nocc, cas_irrep_ncore)
frozen_orbitals_0 = [
i for i in range(molecule.active_orbitals[norb - 1] + 1)
]
for i in range(len(molecule.active_orbitals)):
molecule.active_orbitals[i] -= 1
frozen_orbitals_0[molecule.active_orbitals[i]] = -1
molecule.frozen_orbitals = []
for orb in frozen_orbitals_0:
if orb != -1:
molecule.frozen_orbitals.append(orb)
if n_frozen_orbital == len(molecule.frozen_orbitals):
break
pyscf_data['active_orbitals'] = molecule.active_orbitals
pyscf_data['frozen_orbitals'] = molecule.frozen_orbitals
else:
mo = None
molecule.active_orbitals = [
i for i in range(n_frozen_orbital, n_frozen_orbital + norb)
]
molecule.frozen_orbitals = [i for i in range(n_frozen_orbital)]
fci_result = pyscf_fci.kernel(mo)
pyscf_fci.analyze()
molecule.fci_energy = fci_result[0]
molecule.fci_wfn = fci_result[2]
if verbose:
print('FCI energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.fci_energy))
# Return updated molecule instance.
pyscf_molecular_data = PyscfMolecularData.__new__(PyscfMolecularData)
pyscf_molecular_data.__dict__.update(molecule.__dict__)
pyscf_molecular_data.save()
return pyscf_molecular_data
def run_pyscf(molecule,
run_scf=True,
run_mp2=False,
run_cisd=False,
run_ccsd=False,
run_fci=False,
verbose=False):
"""
This function runs a pyscf calculation.
Args:
molecule: An instance of the MolecularData or PyscfMolecularData class.
run_scf: Optional boolean to run SCF calculation.
run_mp2: Optional boolean to run MP2 calculation.
run_cisd: Optional boolean to run CISD calculation.
run_ccsd: Optional boolean to run CCSD calculation.
run_fci: Optional boolean to FCI calculation.
verbose: Boolean whether to print calculation results to screen.
Returns:
molecule: The updated PyscfMolecularData object. Note the attributes
of the input molecule are also updated in this function.
"""
# Prepare pyscf molecule.
pyscf_molecule = prepare_pyscf_molecule(molecule)
molecule.n_orbitals = int(pyscf_molecule.nao_nr())
molecule.n_qubits = 2 * molecule.n_orbitals
molecule.nuclear_repulsion = float(pyscf_molecule.energy_nuc())
# Run SCF.
pyscf_scf = compute_scf(pyscf_molecule)
pyscf_scf.verbose = 0
# Custom properties
pyscf_scf.chkfile = 'chkfiles/rohf.chk'
pyscf_scf.init_guess = 'chkfile'
#pyscf_scf.max_cycle = 1000
pyscf_scf.max_cycle = 0 # Use chkfile
pyscf_scf.verbose = 4
pyscf_scf.run()
pyscf_scf.analyze()
molecule.hf_energy = float(pyscf_scf.e_tot)
if verbose:
print('Hartree-Fock energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.hf_energy))
# Hold pyscf data in molecule. They are required to compute density
# matrices and other quantities.
molecule._pyscf_data = pyscf_data = {}
pyscf_data['mol'] = pyscf_molecule
pyscf_data['scf'] = pyscf_scf
# Populate fields.
molecule.canonical_orbitals = pyscf_scf.mo_coeff.astype(float)
molecule.orbital_energies = pyscf_scf.mo_energy.astype(float)
# Get integrals.
# Try to load integrals from file if they exist
try:
print("Attempting to load integrals...")
one_body_integrals = np.load("1e-integrals.npy")
two_body_integrals = np.load("2e-integrals.npy")
except FileNotFoundError:
print("Integrals not found. Recalculating...")
one_body_integrals, two_body_integrals = compute_integrals(
pyscf_molecule, pyscf_scf)
np.save("1e-integrals.npy", one_body_integrals)
np.save("2e-integrals.npy", two_body_integrals)
print("Integrals loaded")
molecule.one_body_integrals = one_body_integrals
molecule.two_body_integrals = two_body_integrals
molecule.overlap_integrals = pyscf_scf.get_ovlp()
# Run MP2.
if run_mp2:
if molecule.multiplicity != 1:
print("WARNING: RO-MP2 is not available in PySCF.")
else:
pyscf_mp2 = mp.MP2(pyscf_scf)
pyscf_mp2.verbose = 0
pyscf_mp2.run()
# molecule.mp2_energy = pyscf_mp2.e_tot # pyscf-1.4.4 or higher
molecule.mp2_energy = pyscf_scf.e_tot + pyscf_mp2.e_corr
pyscf_data['mp2'] = pyscf_mp2
if verbose:
print('MP2 energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.mp2_energy))
# Run CISD.
if run_cisd:
pyscf_cisd = ci.CISD(pyscf_scf)
pyscf_cisd.verbose = 0
pyscf_cisd.run()
molecule.cisd_energy = pyscf_cisd.e_tot
pyscf_data['cisd'] = pyscf_cisd
if verbose:
print('CISD energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.cisd_energy))
# Run CCSD.
if run_ccsd:
pyscf_ccsd = cc.CCSD(pyscf_scf)
pyscf_ccsd.verbose = 0
pyscf_ccsd.run()
molecule.ccsd_energy = pyscf_ccsd.e_tot
pyscf_data['ccsd'] = pyscf_ccsd
if verbose:
print('CCSD energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.ccsd_energy))
# Run FCI.
if run_fci:
pyscf_fci = fci.FCI(pyscf_molecule, pyscf_scf.mo_coeff)
pyscf_fci.verbose = 0
molecule.fci_energy = pyscf_fci.kernel()[0]
pyscf_data['fci'] = pyscf_fci
if verbose:
print('FCI energy for {} ({} electrons) is {}.'.format(
molecule.name, molecule.n_electrons, molecule.fci_energy))
# Return updated molecule instance.
print("Ending pyscf...")
pyscf_molecular_data = PyscfMolecularData.__new__(PyscfMolecularData)
pyscf_molecular_data.__dict__.update(molecule.__dict__)
print("Saving...")
#pyscf_molecular_data.save()
print("Saved")
return pyscf_molecular_data