def make_h3_2_5() -> Tuple[RestrictedHartreeFockObjective, of.MolecularData,
np.ndarray, np.ndarray, np.ndarray]:
# load the molecule from moelcular data
h3_2_5_path = os.path.join(
hfvqe.__path__[0],
'molecular_data/hydrogen_chains/h_3_p_sto-3g/bond_distance_2.5')
molfile = os.path.join(h3_2_5_path,
'H3_plus_sto-3g_singlet_linear_r-2.5.hdf5')
molecule = of.MolecularData(filename=molfile)
molecule.load()
S = np.load(os.path.join(h3_2_5_path, 'overlap.npy'))
Hcore = np.load(os.path.join(h3_2_5_path, 'h_core.npy'))
TEI = np.load(os.path.join(h3_2_5_path, 'tei.npy'))
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
scipy_result = rhf_minimization(rhf_objective)
return rhf_objective, molecule, scipy_result.x, obi, tbi
def make_h3_2_5(molecular_data_directory=None) \
-> Tuple[RestrictedHartreeFockObjective, of.MolecularData,
np.ndarray, np.ndarray, np.ndarray]:
if molecular_data_directory is None:
molecular_data_directory = _MOLECULAR_DATA_DIRECTORY
h3_2_5_path = f'{molecular_data_directory}/hydrogen_chains/h_3_p_sto-3g/bond_distance_2.5'
molfile = f'{h3_2_5_path}/H3_plus_sto-3g_singlet_linear_r-2.5.hdf5'
molecule = of.MolecularData(filename=molfile)
molecule.load()
S = np.load(os.path.join(h3_2_5_path, 'overlap.npy'))
Hcore = np.load(os.path.join(h3_2_5_path, 'h_core.npy'))
TEI = np.load(os.path.join(h3_2_5_path, 'tei.npy'))
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
scipy_result = rhf_minimization(rhf_objective)
return rhf_objective, molecule, scipy_result.x, obi, tbi
def h_n_linear_molecule(bond_distance: float,
n_hydrogens: int,
basis: str = 'sto-3g'):
# coverage: ignore
if n_hydrogens < 1 or n_hydrogens % 2 != 0:
raise ValueError('Must specify a positive, even number of hydrogens.')
molecule = of.MolecularData(
geometry=_h_n_linear_geometry(bond_distance, n_hydrogens),
charge=0,
basis=basis,
multiplicity=1,
description=f"linear_r-{bond_distance}",
)
if NO_OFPSI4:
raise NOOFPsi4Error("openfermion-psi4 is not installed")
molecule = run_psi4(molecule,
run_fci=False,
run_mp2=False,
run_cisd=False,
run_ccsd=False,
delete_input=False,
delete_output=False)
return molecule
def make_hn(
hcount, distance
) -> Tuple[RestrictedHartreeFockObjective, of.MolecularData, np.ndarray,
np.ndarray, np.ndarray]:
shcount = str(hcount)
sdistance = str(distance)
cwd = os.path.dirname(os.path.realpath(__file__))
hn_path = str(
Path(cwd + "/molecular_data/hydrogen_chains/h_" + shcount +
"_sto-3g/bond_distance_" + sdistance + "/"))
hdf5name = str("H" + shcount + "_sto-3g_singlet_linear_r-" + sdistance +
".hdf5")
molfile = os.path.join(hn_path, hdf5name)
molecule = of.MolecularData(filename=molfile)
molecule.load()
S = np.load(os.path.join(hn_path, 'overlap.npy'))
Hcore = np.load(os.path.join(hn_path, 'h_core.npy'))
TEI = np.load(os.path.join(hn_path, 'tei.npy'))
_, X = sp.linalg.eigh(Hcore, S)
obi = of.general_basis_change(Hcore, X, (1, 0))
tbi = np.einsum('psqr', of.general_basis_change(TEI, X, (1, 0, 1, 0)))
molecular_hamiltonian = generate_hamiltonian(obi, tbi,
molecule.nuclear_repulsion)
rhf_objective = RestrictedHartreeFockObjective(molecular_hamiltonian,
molecule.n_electrons)
scipy_result = rhf_minimization(rhf_objective)
return rhf_objective, molecule, scipy_result.x, obi, tbi
def load_molecular_hamiltonian(
geometry,
basis,
multiplicity,
description,
n_active_electrons,
n_active_orbitals):
molecule = openfermion.MolecularData(
geometry, basis, multiplicity, description=description)
molecule.load()
n_core_orbitals = (molecule.n_electrons - n_active_electrons) // 2
occupied_indices = list(range(n_core_orbitals))
active_indices = list(range(n_core_orbitals,
n_core_orbitals + n_active_orbitals))
return molecule.get_molecular_hamiltonian(
occupied_indices=occupied_indices,
active_indices=active_indices)
def main():
from itertools import product
import pyscf
import openfermion as of
from openfermion.chem.molecular_data import spinorb_from_spatial
from openfermionpyscf import run_pyscf
from pyscf.cc.addons import spatial2spin
import numpy as np
basis = 'cc-pvdz'
mol = pyscf.M(atom='H 0 0 0; B 0 0 {}'.format(1.6), basis=basis)
mf = mol.RHF().run()
mycc = mf.CCSD().run()
print('CCSD correlation energy', mycc.e_corr)
molecule = of.MolecularData(geometry=[['H', (0, 0, 0)], ['B',
(0, 0, 1.6)]],
basis=basis,
charge=0,
multiplicity=1)
molecule = run_pyscf(molecule, run_ccsd=True)
oei, tei = molecule.get_integrals()
norbs = int(mf.mo_coeff.shape[1])
occ = mf.mo_occ
nele = int(sum(occ))
nocc = nele // 2
assert np.allclose(np.transpose(mycc.t2, [1, 0, 3, 2]), mycc.t2)
soei, stei = spinorb_from_spatial(oei, tei)
astei = np.einsum('ijkl', stei) - np.einsum('ijlk', stei)
# put in physics notation. OpenFermion stores <12|2'1'>
gtei = astei.transpose(0, 1, 3, 2)
eps = np.kron(molecule.orbital_energies, np.ones(2))
n = np.newaxis
o = slice(None, 2 * nocc)
v = slice(2 * nocc, None)
e_abij = 1 / (-eps[v, n, n, n] - eps[n, v, n, n] + eps[n, n, o, n] +
eps[n, n, n, o])
e_ai = 1 / (-eps[v, n] + eps[n, o])
fock = soei + np.einsum('piiq->pq', astei[:, o, o, :])
hf_energy = 0.5 * np.einsum('ii', (fock + soei)[o, o])
hf_energy_test = 1.0 * einsum('ii', fock[o, o]) - 0.5 * einsum(
'ijij', gtei[o, o, o, o])
print(hf_energy_test, hf_energy)
assert np.isclose(hf_energy + molecule.nuclear_repulsion,
molecule.hf_energy)
g = gtei
nsvirt = 2 * (norbs - nocc)
nsocc = 2 * nocc
t1f, t2f = kernel(np.zeros((nsvirt, nsocc)),
np.zeros((nsvirt, nsvirt, nsocc, nsocc)), fock, g, o, v,
e_ai, e_abij)
print(ccsd_energy(t1f, t2f, fock, g, o, v) - hf_energy)
t1f, t2f = kernel(np.zeros((nsvirt, nsocc)),
np.zeros((nsvirt, nsvirt, nsocc, nsocc)),
fock,
g,
o,
v,
e_ai,
e_abij,
diis_size=8,
diis_start_cycle=4)
print(ccsd_energy(t1f, t2f, fock, g, o, v) - hf_energy)
def main():
"""
Example for solving CC3 amplitude equations
"""
import pyscf
import openfermion as of
from openfermion.chem.molecular_data import spinorb_from_spatial
from openfermionpyscf import run_pyscf
from pyscf.cc.addons import spatial2spin
from pyscf import cc
import numpy as np
np.set_printoptions(linewidth=500)
# run pyscf for some reason
basis = '6-31g'
mol = pyscf.M(
atom='H 0 0 0; F 0 0 {}'.format(1.6),
basis=basis)
mf = mol.RHF()
mf.verbose = 0
mf.run()
# build molecule and run pyscf again for some reason
molecule = of.MolecularData(geometry=[['H', (0, 0, 0)], ['F', (0, 0, 1.6)]],
basis=basis, charge=0, multiplicity=1)
molecule = run_pyscf(molecule,run_ccsd=False)
# 1-, 2-electron integrals
oei, tei = molecule.get_integrals()
# Number of orbitals, number of electrons. apparently only works for closed shells
occ = mf.mo_occ
nele = int(sum(occ))
nocc = nele // 2
norbs = oei.shape[0]
nsvirt = 2 * (norbs - nocc)
nsocc = 2 * nocc
soei, stei = spinorb_from_spatial(oei, tei)
astei = np.einsum('ijkl', stei) - np.einsum('ijlk', stei)
gtei = astei.transpose(0, 1, 3, 2)
eps = np.kron(molecule.orbital_energies, np.ones(2))
n = np.newaxis
o = slice(None, nsocc)
v = slice(nsocc, None)
e_abcijk = 1 / (- eps[v, n, n, n, n, n] - eps[n, v, n, n, n, n] - eps[n, n, v, n, n, n]
+ eps[n, n, n, o, n, n] + eps[n, n, n, n, o, n] + eps[n, n, n, n, n, o] )
e_abij = 1 / (-eps[v, n, n, n] - eps[n, v, n, n] + eps[n, n, o, n] + eps[
n, n, n, o])
e_ai = 1 / (-eps[v, n] + eps[n, o])
fock = soei + np.einsum('piiq->pq', astei[:, o, o, :])
hf_energy = 0.5 * np.einsum('ii', (fock + soei)[o, o])
hf_energy_test = 1.0 * einsum('ii', fock[o, o]) -0.5 * einsum('ijij', gtei[o, o, o, o])
print("")
print(" SCF Total Energy: {: 20.12f}".format(hf_energy + molecule.nuclear_repulsion))
print("")
assert np.isclose(hf_energy, mf.e_tot - molecule.nuclear_repulsion)
assert np.isclose(hf_energy_test, hf_energy)
g = gtei
t1z = np.zeros((nsvirt, nsocc))
t2z = np.zeros((nsvirt, nsvirt, nsocc, nsocc))
t3z = np.zeros((nsvirt, nsvirt, nsvirt, nsocc, nsocc, nsocc))
t1f, t2f, t3f = kernel(t1z, t2z, t3z, fock, g, o, v, e_ai, e_abij,e_abcijk,hf_energy,
stopping_eps=1e-10)
en = ccsd_energy(t1f, t2f, fock, g, o, v)
# determine triples amplitudes
residual_triples = triples_residual(t1f, t2f, t3f, fock, g, o, v)
fock_e_abcijk = np.reciprocal(e_abcijk)
triples_res = residual_triples + fock_e_abcijk * t3f
t3f = triples_res * e_abcijk
# determine (t) correction ... need to transpose t1 t2 first (TODO: fix)
l1 = t1f.transpose(1, 0)
l2 = t2f.transpose(2, 3, 0, 1)
t_en = t_energy(l1, l2, t3f, fock, g, o, v)
print("")
print(" CCSD Correlation Energy: {: 20.12f}".format(en - hf_energy))
print(" CCSD Total Energy: {: 20.12f}".format(en + molecule.nuclear_repulsion))
print("")
print(" (T) Energy: {: 20.12f}".format(t_en))
print(" CCSD(T) Total Energy: {: 20.12f}".format(en + molecule.nuclear_repulsion + t_en))
print("")
assert np.isclose(t_en,-0.003382913092468,atol=1e-9)
assert np.isclose(en+molecule.nuclear_repulsion+t_en,-100.009057558929399,atol=1e-9)
import openfermion
diatomic_bond_length = .7414
geometry = [('H', (0., 0., 0.)), ('H', (0., 0., diatomic_bond_length))]
basis = 'sto-3g'
multiplicity = 1
charge = 0
description = format(diatomic_bond_length)
molecule = openfermion.MolecularData(geometry,
basis,
multiplicity,
description=description)
molecule.load()
hamiltonian = molecule.get_molecular_hamiltonian()
print("Bond Length in Angstroms: {}".format(diatomic_bond_length))
print("Hartree Fock (mean-field) energy in Hartrees: {}".format(
molecule.hf_energy))
print("FCI (Exact) energy in Hartrees: {}".format(molecule.fci_energy))
import cirq
import openfermioncirq
import sympy
class MyAnsatz(openfermioncirq.VariationalAnsatz):
def params(self):
"""The parameters of the ansatz."""
return [sympy.Symbol('theta_0')]
uses_bounds=False)
optimization_params = OptimizationParams(algorithm=algorithm)
# Wave Function Ansatz (parameterized guess) U(theta)
ansatz = MyAnsatz()
q0, q1, _, _ = ansatz.qubits
# Initialize to |11> state
## U(theta)|11> --> best guess ground state
preparation_circuit = cq.Circuit.from_ops(cq.X(q0), cq.X(q1))
#%%
## Run a study on a single bond length
molecule = of.MolecularData([('H', (0., 0., 0.)), ('H', (0., 0., 0.7414))],
'sto-3g', 1, 0)
molecule.load()
objective = ofcq.HamiltonianObjective(molecule.get_molecular_hamiltonian())
study = ofcq.VariationalStudy(name='my_hydrogen_study',
ansatz=ansatz,
objective=objective,
preparation_circuit=preparation_circuit)
result = study.optimize(optimization_params)
print("Initial state energy in Hartrees: {}".format(molecule.hf_energy))
print("Optimized energy result in Hartree: {}".format(result.optimal_value))
print("Exact energy result in Hartees for reference: {}".format(
molecule.fci_energy))
#%%
)
guess_vecs = [guess_wfn1, guess_wfn2]
dl_w, dl_v = davidsonliu_fqe(elec_hamil,
1,
guess_vecs,
nele=nele,
sz=sz,
norb=norb)
# dummy geometry
geometry = [["Li", [0, 0, 0], ["H", [0, 0, 1.4]]]]
charge = 0
multiplicity = 1
molecule = of.MolecularData(
geometry=geometry,
basis="sto-3g",
charge=charge,
multiplicity=multiplicity,
)
molecule.one_body_integrals = h1e
molecule.two_body_integrals = np.einsum("ijlk", -2 * h2e)
molecular_hamiltonian = molecule.get_molecular_hamiltonian()
molecular_hamiltonian.constant = 0
ham_fop = of.get_fermion_operator(molecular_hamiltonian)
ham_mat = of.get_sparse_operator(of.jordan_wigner(ham_fop)).toarray()
cirq_ci = fqe.to_cirq(wfn)
cirq_ci = cirq_ci.reshape((2**12, 1))
assert np.isclose(cirq_ci.conj().T @ ham_mat @ cirq_ci, ecalc)
hf_idx = int("111100000000", 2)
hf_idx2 = int("111001000000", 2)