# This code is part of a Qiskit project.
#
# (C) Copyright IBM 2018, 2023.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modifications or derivative works of this code must retain this
# copyright notice, and modified files need to carry a notice indicating
# that they have been altered from the originals.
"""The PySCF Driver."""
from __future__ import annotations
import inspect
import logging
import os
import tempfile
import warnings
from enum import Enum
from typing import Any
import numpy as np
from qiskit_algorithms.utils.validation import validate_min
from qiskit_nature.units import DistanceUnit
from qiskit_nature.exceptions import QiskitNatureError
from qiskit_nature.second_q.formats.molecule_info import MoleculeInfo
from qiskit_nature.second_q.formats.qcschema import QCSchema
from qiskit_nature.second_q.formats.qcschema_translator import qcschema_to_problem
from qiskit_nature.second_q.operators.symmetric_two_body import fold
from qiskit_nature.second_q.problems import ElectronicBasis, ElectronicStructureProblem
import qiskit_nature.optionals as _optionals
from qiskit_nature.utils import get_einsum
from ..electronic_structure_driver import ElectronicStructureDriver, MethodType, _QCSchemaData
logger = logging.getLogger(__name__)
warnings.filterwarnings("ignore", category=DeprecationWarning, module="pyscf")
[ドキュメント]class InitialGuess(Enum):
"""Initial Guess Enum"""
MINAO = "minao"
HCORE = "1e"
ONE_E = "1e"
ATOM = "atom"
[ドキュメント]@_optionals.HAS_PYSCF.require_in_instance
class PySCFDriver(ElectronicStructureDriver):
"""A Second-Quantization driver for Qiskit Nature using the PySCF library.
References:
https://pyscf.org/
"""
def __init__(
self,
atom: str | list[str] = "H 0.0 0.0 0.0; H 0.0 0.0 0.735",
*,
unit: DistanceUnit = DistanceUnit.ANGSTROM,
charge: int = 0,
spin: int = 0,
basis: str = "sto3g",
method: MethodType = MethodType.RHF,
xc_functional: str = "lda,vwn",
xcf_library: str = "libxc",
conv_tol: float = 1e-9,
max_cycle: int = 50,
init_guess: InitialGuess = InitialGuess.MINAO,
max_memory: int | None = None,
chkfile: str | None = None,
) -> None:
"""
Args:
atom: A string (or a list thereof) denoting the elements and coordinates of all atoms in
the system. Two formats are allowed; first, the PySCF-style `XYZ` format which is a
list of strings formatted as `{element symbol} {x_coord} {y_coord} {z_coord}`. If a
single string is given, the list entries should be joined by `;` as in the example:
`H 0.0 0.0 0.0; H 0.0 0.0 0.735`.
Second, the `Z-Matrix` format which is explained at 1_. The previous example
would be written as `H; H 3 0.735`.
See also 2_ for more details on geometry specifications supported by PySCF.
unit: Denotes the unit of coordinates. Valid values are given by the ``UnitsType`` enum.
charge: The charge of the molecule.
spin: The spin of the molecule. In accordance with PySCF's definition, the spin equals
:math:`2*S`, where :math:`S` is the total spin number of the molecule.
basis: A basis set name as recognized by PySCF (3_), e.g. `sto3g` (the default), `321g`,
etc. Note, that more advanced configuration options like a Dictionary or custom
basis sets are not allowed for the moment. Refer to 4_ for an extensive list of
PySCF's valid basis set names.
method: The SCF method type to be used for the PySCF calculation. While the name
refers to HF methods, the PySCFDriver also supports KS methods. Refer to the
``MethodType`` for a list of the supported methods.
xc_functional: One of the predefined Exchange-Correlation functional names as recognized
by PySCF (5_). Defaults to PySCF's default: 'lda,vwn'. __Note: this setting only has
an effect when a KS method is chosen for `method`.__
xcf_library: The Exchange-Correlation functional library to be used. This can be either
'libxc' (the default) or 'xcfun'. Depending on this value, a different set of values
for `xc_functional` will be available. Refer to 5_ for more details.
conv_tol: The SCF convergence tolerance. See 6_ for more details.
max_cycle: The maximum number of SCF iterations. See 6_ for more details.
init_guess: The method to make the initial guess for the SCF starting point. Valid
values are given by the ``InitialGuess`` enum. See 6_ for more details.
max_memory: The maximum memory that PySCF should use. See 6_ for more details.
chkfile: The path to a PySCF checkpoint file from which to load a previously run
calculation. The data stored in this file is assumed to be already converged.
Refer to 6_ and 7_ for more details.
Raises:
QiskitNatureError: An invalid input was supplied.
.. _1: https://en.wikipedia.org/wiki/Z-matrix_(chemistry)
.. _2: https://pyscf.org/user/gto.html#geometry
.. _3: https://pyscf.org/user/gto.html#basis-set
.. _4: https://pyscf.org/pyscf_api_docs/pyscf.gto.basis.html#module-pyscf.gto.basis
.. _5: https://pyscf.org/user/dft.html#predefined-xc-functionals-and-functional-aliases
.. _6: https://pyscf.org/pyscf_api_docs/pyscf.scf.html#module-pyscf.scf.hf
.. _7: https://pyscf.org/pyscf_api_docs/pyscf.lib.html#module-pyscf.lib.chkfile
"""
super().__init__()
# pylint: disable=import-error
from pyscf import gto, scf
# First, ensure that PySCF supports the method
PySCFDriver.check_method_supported(method)
if isinstance(atom, list):
atom = ";".join(atom)
elif isinstance(atom, str):
atom = atom.replace("\n", ";")
else:
raise QiskitNatureError(
f"`atom` must be either a `str` or `list[str]`, but you passed {atom}"
)
validate_min("max_cycle", max_cycle, 1)
# we use the property-setter to deal with conversion
self.atom = atom
self._unit = unit
self._charge = charge
self._spin = spin
self._basis = basis
self._method = method
self._xc_functional = xc_functional
self.xcf_library = xcf_library # validate choice in property setter
self._conv_tol = conv_tol
self._max_cycle = max_cycle
self._init_guess = init_guess.value
self._max_memory = max_memory
self._chkfile = chkfile
self._mol: gto.Mole = None
self._calc: scf.HF = None
@property
def atom(self) -> str:
"""Returns the atom."""
return self._atom
@atom.setter
def atom(self, atom: str | list[str]) -> None:
"""Sets the atom."""
if isinstance(atom, list):
atom = ";".join(atom)
self._atom = atom.replace("\n", ";")
@property
def unit(self) -> DistanceUnit:
"""Returns the unit."""
return self._unit
@unit.setter
def unit(self, unit: DistanceUnit) -> None:
"""Sets the unit."""
self._unit = unit
@property
def charge(self) -> int:
"""Returns the charge."""
return self._charge
@charge.setter
def charge(self, charge: int) -> None:
"""Sets the charge."""
self._charge = charge
@property
def spin(self) -> int:
"""Returns the spin."""
return self._spin
@spin.setter
def spin(self, spin: int) -> None:
"""Sets the spin."""
self._spin = spin
@property
def basis(self) -> str:
"""return basis"""
return self._basis
@basis.setter
def basis(self, value: str) -> None:
"""set basis"""
self._basis = value
@property
def method(self) -> MethodType:
"""Returns Hartree-Fock/Kohn-Sham method"""
return self._method
@method.setter
def method(self, value: MethodType) -> None:
"""Sets Hartree-Fock/Kohn-Sham method"""
self._method = value
@property
def xc_functional(self) -> str:
"""Returns the Exchange-Correlation functional."""
return self._xc_functional
@xc_functional.setter
def xc_functional(self, xc_functional: str) -> None:
"""Sets the Exchange-Correlation functional."""
self._xc_functional = xc_functional
@property
def xcf_library(self) -> str:
"""Returns the Exchange-Correlation functional library."""
return self._xcf_library
@xcf_library.setter
def xcf_library(self, xcf_library: str) -> None:
"""Sets the Exchange-Correlation functional library."""
if xcf_library not in ("libxc", "xcfun"):
raise QiskitNatureError(
"Invalid XCF library. It can be either 'libxc' or 'xcfun', not " f"'{xcf_library}'"
)
self._xcf_library = xcf_library
@property
def conv_tol(self) -> float:
"""Returns the SCF convergence tolerance."""
return self._conv_tol
@conv_tol.setter
def conv_tol(self, conv_tol: float) -> None:
"""Sets the SCF convergence tolerance."""
self._conv_tol = conv_tol
@property
def max_cycle(self) -> int:
"""Returns the maximum number of SCF iterations."""
return self._max_cycle
@max_cycle.setter
def max_cycle(self, max_cycle: int) -> None:
"""Sets the maximum number of SCF iterations."""
self._max_cycle = max_cycle
@property
def init_guess(self) -> str:
"""Returns the method for the initial guess."""
return self._init_guess
@init_guess.setter
def init_guess(self, init_guess: str) -> None:
"""Sets the method for the initial guess."""
self._init_guess = init_guess
@property
def max_memory(self) -> int:
"""Returns the maximum memory allowance for the calculation."""
return self._max_memory
@max_memory.setter
def max_memory(self, max_memory: int) -> None:
"""Sets the maximum memory allowance for the calculation."""
self._max_memory = max_memory
@property
def chkfile(self) -> str:
"""Returns the path to the PySCF checkpoint file."""
return self._chkfile
@chkfile.setter
def chkfile(self, chkfile: str) -> None:
"""Sets the path to the PySCF checkpoint file."""
self._chkfile = chkfile
[ドキュメント] @staticmethod
def from_molecule(
molecule: MoleculeInfo,
*,
basis: str = "sto3g",
method: MethodType = MethodType.RHF,
driver_kwargs: dict[str, Any] | None = None,
) -> "PySCFDriver":
"""Creates a driver from a molecule.
Args:
molecule: the molecular information.
basis: the basis set.
method: the SCF method type.
driver_kwargs: keyword arguments to be passed to driver.
Returns:
The constructed driver instance.
"""
PySCFDriver.check_method_supported(method)
kwargs = {}
if driver_kwargs:
args = inspect.signature(PySCFDriver.__init__).parameters.keys()
for key, value in driver_kwargs.items():
if key not in ["self"] and key in args:
kwargs[key] = value
kwargs["atom"] = [
" ".join(map(str, (name, *coord)))
for name, coord in zip(molecule.symbols, molecule.coords)
]
kwargs["charge"] = molecule.charge
kwargs["spin"] = molecule.multiplicity - 1
kwargs["unit"] = molecule.units
kwargs["basis"] = PySCFDriver.to_driver_basis(basis)
kwargs["method"] = method
return PySCFDriver(**kwargs)
[ドキュメント] @staticmethod
def to_driver_basis(basis: str) -> str:
"""Converts basis to a driver acceptable basis.
Args:
basis: The basis set to be used.
Returns:
A driver acceptable basis.
"""
return basis
[ドキュメント] @staticmethod
def check_method_supported(method: MethodType) -> None:
"""Checks that PySCF supports this method.
Args:
method: the SCF method type.
Raises:
UnsupportMethodError: If the method is not supported.
"""
# supports all methods
pass
[ドキュメント] def run(self) -> ElectronicStructureProblem:
"""Runs the driver to produce a result.
Returns:
ElectronicStructureProblem produced by the run driver.
Raises:
QiskitNatureError: if an error during the PySCF setup or calculation occurred.
"""
self.run_pyscf()
return self.to_problem()
def _build_molecule(self) -> None:
"""Builds the PySCF molecule object.
Raises:
QiskitNatureError: If building the PySCF molecule object failed.
"""
# Get config from input parameters
# molecule is in PySCF atom string format e.g. "H .0 .0 .0; H .0 .0 0.2"
# or in Z-Matrix format e.g. "H; O 1 1.08; H 2 1.08 1 107.5"
# other parameters are as per PySCF got.Mole format
# pylint: disable=import-error
from pyscf import gto
from pyscf.lib import logger as pylogger
from pyscf.lib import param
atom = self._check_molecule_format(self.atom)
if self._max_memory is None:
self._max_memory = param.MAX_MEMORY
try:
verbose = pylogger.QUIET
output = None
if logger.isEnabledFor(logging.DEBUG):
verbose = pylogger.INFO
file, output = tempfile.mkstemp(suffix=".log")
os.close(file)
self._mol = gto.Mole(
atom=atom,
unit=self._unit.value,
basis=self._basis,
max_memory=self._max_memory,
verbose=verbose,
output=output,
)
self._mol.symmetry = False
self._mol.charge = self._charge
self._mol.spin = self._spin
self._mol.build(parse_arg=False)
if output is not None:
self._process_pyscf_log(output)
try:
os.remove(output)
except Exception: # pylint: disable=broad-except
pass
except Exception as exc:
raise QiskitNatureError("Failed to build the PySCF Molecule object.") from exc
@staticmethod
def _check_molecule_format(val: str) -> str | list[str]:
"""Ensures the molecule coordinates are in XYZ format.
This utility automatically converts a Z-matrix coordinate format into XYZ coordinates.
Args:
val: the atomic coordinates.
Raises:
QiskitNatureError: If the provided coordinate are badly formatted.
Returns:
The coordinates in XYZ format.
"""
# pylint: disable=import-error
from pyscf import gto
atoms = [x.strip() for x in val.split(";")]
if atoms is None or len(atoms) < 1:
raise QiskitNatureError("Molecule format error: " + val)
# An xyz format has 4 parts in each atom, if not then do zmatrix convert
# Allows dummy atoms, using symbol 'X' in zmatrix format for coord computation to xyz
parts = [x.strip() for x in atoms[0].split()]
if len(parts) != 4:
try:
newval = []
for entry in gto.mole.from_zmatrix(val):
if entry[0].upper() != "X":
newval.append(entry)
return newval
except Exception as exc:
raise QiskitNatureError("Failed to convert atom string: " + val) from exc
return val
[ドキュメント] def run_pyscf(self) -> None:
"""Runs the PySCF calculation.
This method is part of the public interface to allow the user to easily overwrite it in a
subclass to further tailor the behavior to some specific use case.
Raises:
QiskitNatureError: If an invalid HF method type was supplied.
"""
self._build_molecule()
# pylint: disable=import-error
from pyscf import dft, scf
from pyscf.lib import chkfile as lib_chkfile
method_name = None
method_cls = None
try:
# attempt to gather the SCF-method class specified by the MethodType
method_name = self.method.value.upper()
method_cls = getattr(scf, method_name)
except AttributeError as exc:
raise QiskitNatureError(f"Failed to load {method_name} HF object.") from exc
self._calc = method_cls(self._mol)
if method_name in ("RKS", "ROKS", "UKS"):
self._calc._numint.libxc = getattr(dft, self.xcf_library)
self._calc.xc = self.xc_functional
if self._chkfile is not None and os.path.exists(self._chkfile):
self._calc.__dict__.update(lib_chkfile.load(self._chkfile, "scf"))
logger.info("PySCF loaded from chkfile e(hf): %s", self._calc.e_tot)
else:
self._calc.conv_tol = self._conv_tol
self._calc.max_cycle = self._max_cycle
self._calc.init_guess = self._init_guess
self._calc.kernel()
logger.info(
"PySCF kernel() converged: %s, e(hf): %s",
self._calc.converged,
self._calc.e_tot,
)
[ドキュメント] def to_qcschema(self, *, include_dipole: bool = True) -> QCSchema:
# pylint: disable=import-error
from pyscf import __version__ as pyscf_version
from pyscf import ao2mo, gto
from pyscf.tools import dump_mat
einsum_func, _ = get_einsum()
data = _QCSchemaData()
data.overlap = self._calc.get_ovlp()
data.mo_coeff, data.mo_coeff_b = self._expand_mo_object(
self._calc.mo_coeff, array_dimension=3
)
data.mo_energy, data.mo_energy_b = self._expand_mo_object(self._calc.mo_energy)
data.mo_occ, data.mo_occ_b = self._expand_mo_object(self._calc.mo_occ)
if logger.isEnabledFor(logging.DEBUG):
# Add some more to PySCF output...
# First analyze() which prints extra information about MO energy and occupation
self._mol.stdout.write("\n")
self._calc.analyze()
# Now labelled orbitals for contributions to the MOs for s,p,d etc of each atom
self._mol.stdout.write("\n\n--- Alpha Molecular Orbitals ---\n\n")
dump_mat.dump_mo(self._mol, data.mo_coeff, digits=7, start=1)
if data.mo_coeff_b is not None:
self._mol.stdout.write("\n--- Beta Molecular Orbitals ---\n\n")
dump_mat.dump_mo(self._mol, data.mo_coeff_b, digits=7, start=1)
self._mol.stdout.flush()
data.hij = self._calc.get_hcore()
data.hij_mo = np.dot(np.dot(data.mo_coeff.T, data.hij), data.mo_coeff)
if data.mo_coeff_b is not None:
data.hij_mo_b = np.dot(np.dot(data.mo_coeff_b.T, data.hij), data.mo_coeff_b)
data.eri = self._mol.intor("int2e", aosym=8)
data.eri_mo = fold(ao2mo.full(self._mol, data.mo_coeff, aosym=4))
if data.mo_coeff_b is not None:
data.eri_mo_bb = fold(ao2mo.full(self._mol, data.mo_coeff_b, aosym=4))
data.eri_mo_ba = fold(
ao2mo.general(
self._mol,
[data.mo_coeff_b, data.mo_coeff_b, data.mo_coeff, data.mo_coeff],
aosym=4,
)
)
data.e_nuc = gto.mole.energy_nuc(self._mol)
data.e_ref = self._calc.e_tot
data.symbols = [self._mol.atom_pure_symbol(i) for i in range(self._mol.natm)]
data.coords = self._mol.atom_coords(unit="Bohr").ravel().tolist()
data.multiplicity = self._spin + 1
data.charge = self._charge
data.masses = list(self._mol.atom_mass_list())
data.method = self._method.value.upper()
data.basis = self._basis
data.creator = "PySCF"
data.version = pyscf_version
data.nbasis = self._mol.nbas
data.nmo = self._mol.nao
data.nalpha = self._mol.nelec[0]
data.nbeta = self._mol.nelec[1]
if include_dipole:
self._mol.set_common_orig((0, 0, 0))
ao_dip = self._mol.intor_symmetric("int1e_r", comp=3)
d_m = self._calc.make_rdm1(self._calc.mo_coeff, self._calc.mo_occ)
if not (isinstance(d_m, np.ndarray) and d_m.ndim == 2):
d_m = d_m[0] + d_m[1]
elec_dip = np.negative(einsum_func("xij,ji->x", ao_dip, d_m).real)
elec_dip = np.round(elec_dip, decimals=8)
nucl_dip = einsum_func("i,ix->x", self._mol.atom_charges(), self._mol.atom_coords())
nucl_dip = np.round(nucl_dip, decimals=8)
ref_dip = nucl_dip + elec_dip
logger.info("HF Electronic dipole moment: %s", elec_dip)
logger.info("Nuclear dipole moment: %s", nucl_dip)
logger.info("Total dipole moment: %s", ref_dip)
data.dip_nuc = nucl_dip
data.dip_ref = ref_dip
data.dip_x = ao_dip[0]
data.dip_y = ao_dip[1]
data.dip_z = ao_dip[2]
data.dip_mo_x_a = np.dot(np.dot(data.mo_coeff.T, data.dip_x), data.mo_coeff)
data.dip_mo_y_a = np.dot(np.dot(data.mo_coeff.T, data.dip_y), data.mo_coeff)
data.dip_mo_z_a = np.dot(np.dot(data.mo_coeff.T, data.dip_z), data.mo_coeff)
if data.mo_coeff_b is not None:
data.dip_mo_x_b = np.dot(np.dot(data.mo_coeff_b.T, data.dip_x), data.mo_coeff_b)
data.dip_mo_y_b = np.dot(np.dot(data.mo_coeff_b.T, data.dip_y), data.mo_coeff_b)
data.dip_mo_z_b = np.dot(np.dot(data.mo_coeff_b.T, data.dip_z), data.mo_coeff_b)
return self._to_qcschema(data, include_dipole=include_dipole)
[ドキュメント] def to_problem(
self,
*,
basis: ElectronicBasis = ElectronicBasis.MO,
include_dipole: bool = True,
) -> ElectronicStructureProblem:
qcschema = self.to_qcschema(include_dipole=include_dipole)
problem = qcschema_to_problem(qcschema, basis=basis, include_dipole=include_dipole)
if include_dipole and problem.properties.electronic_dipole_moment is not None:
problem.properties.electronic_dipole_moment.reverse_dipole_sign = True
return problem
def _expand_mo_object(
self,
mo_object: tuple[np.ndarray | None, np.ndarray | None] | np.ndarray,
array_dimension: int = 2,
) -> tuple[np.ndarray, np.ndarray]:
"""Expands the molecular orbital object into alpha- and beta-spin components.
Since PySCF 1.6.2, the alpha and beta components are no longer stored as a tuple but as a
multi-dimensional numpy array. This utility takes care of differentiating these cases.
Args:
mo_object: the molecular orbital object to expand.
array_dimension: This argument specifies the dimension of the numpy array (if a tuple
is not encountered). Making this configurable permits this function to be used to
expand both, MO coefficients (3D array) and MO energies (2D array).
Returns:
The (alpha, beta) tuple of MO data.
"""
if isinstance(mo_object, tuple):
return mo_object
if len(mo_object.shape) == array_dimension:
return mo_object[0], mo_object[1]
return mo_object, None
def _process_pyscf_log(self, logfile: str) -> None:
"""Processes a PySCF logfile.
Args:
logfile: the path of the PySCF logfile.
"""
with open(logfile, "r", encoding="utf8") as file:
contents = file.readlines()
for i, content in enumerate(contents):
if content.startswith("System:"):
contents = contents[i:]
break
logger.debug("PySCF processing messages log:\n%s", "".join(contents))