def test_conversion_from_folder(names, tmpdir, requires_babel):
r"""Test the conversion of molecular structure file with different formats"""
filename = os.path.join(ref_dir, names[0])
qchem.read_structure(filename, outpath=tmpdir)
with open(tmpdir.join("structure.xyz")) as g:
gen_file = g.readlines()[2:]
with open(os.path.join(ref_dir, names[1])) as f:
ref_file = f.readlines()[2:]
assert gen_file == ref_file
def test_reading_xyz_file(tmpdir):
r"""Test reading of the generated file 'structure.xyz'"""
ref_symbols = ["C", "C", "N", "H", "H", "H", "H", "H"]
ref_coords = np.array([
0.68219113,
-0.85415621,
-1.04123909,
-1.34926445,
0.23621577,
0.61794044,
1.29068294,
0.25133357,
1.40784596,
0.83525895,
-2.88939124,
-1.16974047,
1.26989596,
0.19275206,
-2.69852891,
-2.57758643,
-1.05824663,
1.61949529,
-2.17129532,
2.04090421,
0.11338357,
2.06547065,
2.00877887,
1.20186582,
])
name = os.path.join(ref_dir, "gdb3.mol5.XYZ")
symbols, coordinates = qchem.read_structure(name, outpath=tmpdir)
assert symbols == ref_symbols
assert np.allclose(coordinates, ref_coords)
def test_subprocess_run(monkeypatch, requires_babel):
r"""Test 'subprocess.run' function running babel to convert the molecular structure
file to xyz format"""
with monkeypatch.context() as m:
def fake_run(*args, **kwargs):
raise subprocess.CalledProcessError(1, "obabel")
m.setattr(subprocess, "run", fake_run)
with pytest.raises(
RuntimeError,
match=
"Open Babel error. See the following Open Babel output for details"
):
qchem.read_structure("fake_mol_geo.SDF")
def test_reading_xyz_file(tmpdir):
r"""Test reading of the generated file 'structure.xyz'"""
ref_geometry = [
["C", (0.361, -0.452, -0.551)],
["C", (-0.714, 0.125, 0.327)],
["N", (0.683, 0.133, 0.745)],
["H", (0.442, -1.529, -0.619)],
["H", (0.672, 0.102, -1.428)],
["H", (-1.364, -0.56, 0.857)],
["H", (-1.149, 1.08, 0.060)],
["H", (1.093, 1.063, 0.636)],
]
name = os.path.join(ref_dir, "gdb3.mol5.XYZ")
geometry = qchem.read_structure(name, outpath=tmpdir)
assert geometry == ref_geometry
Sit down, brew a hot drink, and let's take a look!
Importing the molecular structure
---------------------------------
The first step is to import the QChem package from PennyLane.
"""
from pennylane import qchem
##############################################################################
# In this example, we construct the electronic Hamiltonian of one of the most unique
# molecules: water. We begin by reading the positions of the oxygen and hydrogen atoms. The
# equilibrium geometry of water is read from the file :download:`h2o.xyz </demonstrations/h2o.xyz>`
# and stored in a list containing the symbol and the Cartesian coordinates of each atomic
# species:
geometry = qchem.read_structure('h2o.xyz')
print("The total number of atoms is: {}".format(len(geometry)))
print(geometry)
##############################################################################
# .. note::
#
# The xyz format is supported out of the box.
# If `Open Babel <http://openbabel.org/wiki/Main_Page>`_ is installed, any
# format recognized by Open Babel is also supported by PennyLane, such as
# ``.mol`` and ``.sdf``.
#
# Please see the :func:`~.pennylane_qchem.qchem.read_structure` and Open Babel documentation
# for more information on installing Open Babel.
#
# Calling the function :func:`~.pennylane_qchem.qchem.read_structure` also creates the file
Sit down, brew a hot drink, and let's take a look!
Importing the molecular structure
---------------------------------
The first step is to import the QChem package from PennyLane.
"""
from pennylane import qchem
##############################################################################
# In this example, we construct the electronic Hamiltonian of one of the most unique
# molecules: water. We begin by reading the positions of the oxygen and hydrogen atoms. The
# equilibrium geometry of water is read from the file :download:`h2o.xyz </demonstrations/h2o.xyz>`
# which retrieves the symbol and the Cartesian coordinates of each atomic species:
symbols, coordinates = qchem.read_structure('h2o.xyz')
print("The total number of atoms is: {}".format(len(symbols)))
print(symbols)
print(coordinates)
##############################################################################
# .. note::
#
# The xyz format is supported out of the box.
# If `Open Babel <http://openbabel.org/wiki/Main_Page>`_ is installed, any
# format recognized by Open Babel is also supported by PennyLane, such as
# ``.mol`` and ``.sdf``.
#
# Please see the :func:`~.pennylane_qchem.qchem.read_structure` and Open Babel documentation
# for more information on installing Open Babel.
#
1.7: "vqe_parallel/h2_1.70.xyz",
1.9: "vqe_parallel/h2_1.90.xyz",
2.1: "vqe_parallel/h2_2.10.xyz",
}
##############################################################################
# The next step is to create the qubit Hamiltonians for each value of the inter-atomic distance.
# We do this by first reading the molecular geometry from the external file using the
# :func:`~.pennylane_qchem.qchem.read_structure` function and passing the atomic symbols
# and coordinates to :func:`~.pennylane_qchem.qchem.molecular_hamiltonian`.
hamiltonians = []
for separation, file in data.items():
symbols, coordinates = qchem.read_structure(file)
h = qchem.molecular_hamiltonian(symbols, coordinates, name=str(separation))[0]
hamiltonians.append(h)
##############################################################################
# Each Hamiltonian can be written as a linear combination of fifteen tensor products of Pauli
# matrices. Let's take a look more closely at one of the Hamiltonians:
h = hamiltonians[0]
print("Number of terms: {}\n".format(len(h.ops)))
for op in h.ops:
print("Measurement {} on wires {}".format(op.name, op.wires))
##############################################################################
# Defining the energy function
# set of 3 Gaussian functions are contracted to represent an atomic Slater-type orbital (STO):
basis_set = 'sto-3g'
##############################################################################
# At this stage, to compute the molecule's Hamiltonian in the Pauli basis, several
# calculations need to be performed. With PennyLane, these can all be done in a
# single line by calling the function :func:`~.pennylane_qchem.qchem.molecular_hamiltonian`.
# The charge, multiplicity, and basis set can also be specified as keyword arguments. Finally,
# the number of active electrons and active orbitals may be indicated, as well as the
# fermionic-to-qubit mapping, which can be either Jordan-Wigner (``jordan_wigner``) or Bravyi-Kitaev
# (``bravyi_kitaev``). The atomic symbols and their nuclear coordinates can be read directly
# from the geometry file. The outputs of the function are the qubit Hamiltonian of the molecule
# and the number of qubits needed to represent it:
symbols, coordinates = qchem.read_structure(geometry)
h, qubits = qchem.molecular_hamiltonian(symbols,
coordinates,
charge=charge,
mult=multiplicity,
basis=basis_set,
active_electrons=2,
active_orbitals=2,
mapping='jordan_wigner')
print('Number of qubits = ', qubits)
print('Hamiltonian is ', h)
##############################################################################
# That's it! From here on, we can use PennyLane as usual, employing its entire stack of
Importing the molecular structure
---------------------------------
The first step is to import the QChem package from PennyLane.
"""
from pennylane import qchem
##############################################################################
# In this example, we construct the electronic Hamiltonian of one of the most unique
# molecules: water. We begin by reading the positions of the oxygen and hydrogen atoms. The
# equilibrium geometry of water is read from the file :download:`h2o.xyz </demonstrations/h2o.xyz>`
# and stored in a list containing the symbol and the Cartesian coordinates of each atomic
# species:
geometry = qchem.read_structure(
'/workspace/my-examples-for-quantum-computing/pennylaneai/qml-demos/alldata/h2o.xyz'
)
print("The total number of atoms is: {}".format(len(geometry)))
print(geometry)
##############################################################################
# .. note::
#
# The xyz format is supported out of the box.
# If `Open Babel <http://openbabel.org/wiki/Main_Page>`_ is installed, any
# format recognized by Open Babel is also supported by PennyLane, such as
# ``.mol`` and ``.sdf``.
#
# Please see the :func:`~.pennylane_qchem.qchem.read_structure` and Open Babel documentation
# for more information on installing Open Babel.
#
