def do_make_molecule(self, *args, **kwargs):
"""
Parameters
----------
args
kwargs
Returns
-------
"""
# integrals need to be passed in base class
assert ("one_body_integrals" in kwargs)
assert ("two_body_integrals" in kwargs)
assert ("nuclear_repulsion" in kwargs)
assert ("n_orbitals" in kwargs)
molecule = MolecularData(**self.parameters.molecular_data_param)
molecule.one_body_integrals = kwargs["one_body_integrals"]
molecule.two_body_integrals = kwargs["two_body_integrals"]
molecule.nuclear_repulsion = kwargs["nuclear_repulsion"]
molecule.n_orbitals = kwargs["n_orbitals"]
molecule.save()
return molecule
def make_molecule(self, *args, **kwargs) -> MolecularData:
"""Creates a molecule in openfermion format by running psi4 and extracting the data
Will check for previous outputfiles before running
Will not recompute if a file was found
Parameters
----------
parameters :
An instance of ParametersQC, which also holds an instance of ParametersPsi4 via parameters.psi4
The molecule will be saved in parameters.filename, if this file exists before the call the molecule will be imported from the file
Returns
-------
type
the molecule in openfermion.MolecularData format
"""
molecule = MolecularData(**self.parameters.molecular_data_param)
# try to load
do_compute = True
try:
import os
if os.path.exists(self.parameters.filename):
molecule.load()
do_compute = False
except OSError:
do_compute = True
if do_compute:
molecule = self.do_make_molecule(*args, **kwargs)
molecule.save()
return molecule
def create_molecule():
geometry = make_geometry()
basis = 'sto-3g'
charge = 0
multiplicity = 1
moleculefilename = '/app/moleculefile.hdf5'
molecule = MolecularData(geometry,
basis,
multiplicity,
charge,
description,
filename=moleculefilename)
# openfermion's run_psi4
molecule = run_psi4(molecule,
run_scf=1,
run_mp2=1,
run_cisd=0,
run_ccsd=0,
run_fci=0,
verbose=1,
tolerate_error=1)
molecule.save()
def generate_and_save(geometry, basis, multiplicity, charge, description,
mfilename):
# initialize the molecule
molecule = MolecularData(geometry,
basis,
multiplicity,
charge,
description=description,
filename=mfilename)
molecule.save()
# compute the active space integrals
print('-computing integrals-')
molecule = run_psi4(molecule,
run_mp2=True,
run_cisd=True,
run_ccsd=True,
run_fci=True)
print(molecule.filename)
print(molecule.two_body_integrals)
print(molecule.canonical_orbitals)
molecule.save()
print('Successful generation')
# Add points for a full dissociation curve from 0.1 to 3.0 angstroms
spacings += [0.1 * r for r in range(1, 30)]
# Set run options
run_scf = 1
run_mp2 = 1
run_cisd = 1
run_ccsd = 1
run_fci = 1
verbose = 1
tolerate_error = 1
# Run Diatomic Curve
for spacing in spacings:
description = "{:.2f}".format(spacing)
geometry = [['Be', [0, 0, 0]], ['H', [0, 0, spacing]],
['H', [0, 0, -spacing]]]
molecule = MolecularData(geometry, basis, multiplicity, charge,
description)
molecule = run_psi4(molecule,
run_scf=run_scf,
run_mp2=run_mp2,
run_cisd=run_cisd,
run_ccsd=run_ccsd,
run_fci=run_fci,
verbose=verbose,
tolerate_error=tolerate_error)
molecule.save()
