示例#1
0
def setup_basis_set(
    n,
    l,
    s,
    h,
    u,
    dim=3,
    particle_charge=-1,
    np=None,
    includes_spin=False,
    anti_symmetrized_u=False,
    **kwargs,
):

    if np is None:
        import numpy as np

    bs = BasisSet(
        l,
        dim=dim,
        np=np,
        includes_spin=includes_spin,
        anti_symmetrized_u=anti_symmetrized_u,
    )

    bs.h = h
    bs.u = u
    bs.s = s
    bs.particle_charge = particle_charge

    if "position" in kwargs.keys():
        bs.position = kwargs["position"]

    if "momentum" in kwargs.keys():
        bs.momentum = kwargs["momentum"]

    if "nuclear_repulsion_energy" in kwargs.keys():
        bs.nuclear_repulsion_energy = kwargs["nuclear_repulsion_energy"]

    return bs
示例#2
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def construct_pyscf_system_rhf(
    molecule,
    basis="cc-pvdz",
    add_spin=True,
    anti_symmetrize=True,
    np=None,
    verbose=False,
    charge=0,
    cart=False,
    dip=None,
    **kwargs,
):
    """Convenience function setting up a closed-shell atom or a molecule from
    PySCF as a ``QuantumSystem`` in RHF-basis using PySCF's RHF-solver.

    Parameters
    ----------
    molecule : str
        String describing the atom or molecule. This gets passed to PySCF which
        means that we support all the same string options as PySCF.
    basis : str
        String describing the basis set. PySCF determines which options are
        available.
    add_spin : bool
        Whether or not to return a ``SpatialOrbitalSystem`` (``False``) or a
        ``GeneralOrbitalSystem`` (``True``). Default is ``True``.
    anti_symmetrize : bool
        Whether or not to anti-symmetrize the two-body elements in a
        ``GeneralOrbitalSystem``. This only applies if ``add_spin = True``.
        Default is ``True``.
    np : module
        Array- and linear algebra module.
    dip : list
        [position, momentum] f.ex. from Dalton
    Returns
    -------
    SpatialOrbitalSystem, GeneralOrbitalSystem
        Depending on the choice of ``add_spin`` we return a
        ``SpatialOrbitalSystem`` (``add_spin = False``), or a
        ``GeneralOrbitalSystem`` (``add_spin = True``).

    See Also
    -------
    PySCF

    Example
    -------
    >>> # Set up the Beryllium atom centered at (0, 0, 0)
    >>> system = construct_pyscf_system_rhf(
    ...     "be 0 0 0", basis="cc-pVDZ", add_spin=False
    ... ) # doctest.ELLIPSIS
    converged SCF energy = -14.5723...
    >>> # Compare the number of occupied basis functions
    >>> system.n == 4 // 2
    True
    >>> gos = system.construct_general_orbital_system()
    >>> gos.n == 4
    True
    >>> system = construct_pyscf_system_rhf(
    ...     "be 0 0 0", basis="cc-pVDZ"
    ... ) # doctest.ELLIPSIS
    converged SCF energy = -14.5723...
    >>> system.n == gos.n
    True
    """

    import pyscf

    if np is None:
        import numpy as np

    # Build molecule in AO-basis
    mol = pyscf.gto.Mole()
    mol.unit = "bohr"
    mol.charge = charge
    mol.cart = cart
    mol.build(atom=molecule, basis=basis, **kwargs)
    nuclear_repulsion_energy = mol.energy_nuc()

    n = mol.nelectron
    assert (
        n %
        2 == 0), "We require closed shell, with an even number of particles"

    l = mol.nao

    hf = pyscf.scf.RHF(mol)
    hf_energy = hf.kernel()

    if not hf.converged:
        warnings.warn("RHF calculation did not converge")

    if verbose:
        print(f"RHF energy: {hf.e_tot}")

    charges = mol.atom_charges()
    coords = mol.atom_coords()
    nuc_charge_center = np.einsum("z,zx->x", charges, coords) / charges.sum()
    mol.set_common_orig_(nuc_charge_center)

    C = np.asarray(hf.mo_coeff)

    h = pyscf.scf.hf.get_hcore(mol)
    s = mol.intor_symmetric("int1e_ovlp")
    u = mol.intor("int2e").reshape(l, l, l, l).transpose(0, 2, 1, 3)
    position = mol.intor("int1e_r").reshape(3, l, l)
    momentum = -1j * mol.intor("int1e_ipovlp").reshape(3, l, l)

    if dip is not None:
        diplen = dip[0]
        arr_eq0 = np.allclose(diplen[0], position[0])
        arr_eq1 = np.allclose(diplen[1], position[1])
        arr_eq2 = np.allclose(diplen[2], position[2])
        if not (arr_eq0 and arr_eq1 and arr_eq2):
            print('WARNING:')
            print('dipole_array_pyscf != dipole_array_dalton')

    bs = BasisSet(l, dim=3, np=np)
    bs.h = h
    bs.s = s
    bs.u = u
    bs.nuclear_repulsion_energy = nuclear_repulsion_energy
    bs.particle_charge = -1
    bs.position = position
    bs.momentum = momentum
    if dip is not None:
        bs.momentum = dip[1]
    bs.change_module(np=np)

    system = SpatialOrbitalSystem(n, bs)
    system.change_basis(C)

    return (system.construct_general_orbital_system(
        anti_symmetrize=anti_symmetrize) if add_spin else system)
示例#3
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def construct_pyscf_system_ao(
    molecule,
    basis="cc-pvdz",
    add_spin=True,
    anti_symmetrize=True,
    np=None,
    **kwargs,
):
    """Convenience function setting up an atom or a molecule from PySCF as a
    ``QuantumSystem``.

    Parameters
    ----------
    molecule : str
        String describing the atom or molecule. This gets passed to PySCF which
        means that we support all the same string options as PySCF.
    basis : str
        String describing the basis set. PySCF determines which options are
        available.
    add_spin : bool
        Whether or not to return a ``SpatialOrbitalSystem`` (``False``) or a
        ``GeneralOrbitalSystem`` (``True``). Default is ``True``.
    anti_symmetrize : bool
        Whether or not to anti-symmetrize the two-body elements in a
        ``GeneralOrbitalSystem``. This only applies if ``add_spin = True``.
        Default is ``True``.
    np : module
        Array- and linear algebra module.

    Returns
    -------
    SpatialOrbitalSystem, GeneralOrbitalSystem
        Depending on the choice of ``add_spin`` we return a
        ``SpatialOrbitalSystem`` (``add_spin = False``), or a
        ``GeneralOrbitalSystem`` (``add_spin = True``).

    See Also
    -------
    PySCF

    Example
    -------
    >>> # Set up the Beryllium atom centered at (0, 0, 0)
    >>> system = construct_pyscf_system_ao(
    ...     "be 0 0 0", basis="cc-pVDZ", add_spin=False
    ... )
    >>> # Compare the number of occupied basis functions
    >>> system.n == 4 // 2
    True
    >>> gos = system.construct_general_orbital_system()
    >>> gos.n == 4
    True
    """

    import pyscf

    if np is None:
        import numpy as np

    mol = pyscf.gto.Mole()
    mol.unit = "bohr"
    mol.build(atom=molecule, basis=basis, **kwargs)
    nuclear_repulsion_energy = mol.energy_nuc()

    n = mol.nelectron
    l = mol.nao

    # n_a = (mol.nelectron + mol.spin) // 2
    # n_b = n_a - mol.spin

    # assert n_b == n - n_a

    h = pyscf.scf.hf.get_hcore(mol)
    s = mol.intor_symmetric("int1e_ovlp")
    u = mol.intor("int2e").reshape(l, l, l, l).transpose(0, 2, 1, 3)
    position = mol.intor("int1e_r").reshape(3, l, l)

    bs = BasisSet(l, dim=3, np=np)
    bs.h = h
    bs.s = s
    bs.u = u
    bs.nuclear_repulsion_energy = nuclear_repulsion_energy
    bs.particle_charge = -1
    bs.position = position
    bs.change_module(np=np)

    system = SpatialOrbitalSystem(n, bs)

    return (system.construct_general_orbital_system(
        anti_symmetrize=anti_symmetrize) if add_spin else system)