def test_from_iodata():
"""Test gbasis.wrapper.from_iodata."""
pytest.importorskip("iodata")
from iodata import load_one
mol = load_one(find_datafile("data_iodata_water_sto3g_hf_g03.fchk"))
basis, coord_types = from_iodata(mol)
assert coord_types == ["cartesian"] * 5
assert all(isinstance(i, GeneralizedContractionShell) for i in basis)
assert basis[0].angmom == 0
assert np.allclose(basis[0].coord, mol.atcoords[0])
assert np.allclose(basis[0].exps,
np.array([130.7093214, 23.80886605, 6.443608313]))
assert np.allclose(
basis[0].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert np.allclose(basis[0].norm_cont, 1.0)
assert basis[1].angmom == 0
assert np.allclose(basis[1].coord, mol.atcoords[0])
assert np.allclose(basis[1].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[1].coeffs,
np.array([-0.09996722919, 0.3995128261, 0.7001154689]).reshape(-1, 1))
assert np.allclose(basis[1].norm_cont, 1.0)
assert basis[2].angmom == 1
assert np.allclose(basis[2].coord, mol.atcoords[0])
assert np.allclose(basis[2].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[2].coeffs,
np.array([0.1559162750, 0.6076837186, 0.3919573931]).reshape(-1, 1))
assert np.allclose(basis[2].norm_cont, 1.0)
assert basis[3].angmom == 0
assert np.allclose(basis[3].coord, mol.atcoords[1])
assert np.allclose(basis[3].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[3].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert np.allclose(basis[3].norm_cont, 1.0)
assert basis[4].angmom == 0
assert np.allclose(basis[4].coord, mol.atcoords[2])
assert np.allclose(basis[4].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[4].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert np.allclose(basis[4].norm_cont, 1.0)
# Artificially change angular momentum.
# The following few lines are commented out deliberately. The file
# "data_iodata_water_sto3g_hf_g03.fchk" does not contain "spherical"
# functions for angular momenta 0 and 1, so there is no need to have
# conventions for them. (This is a fairly common pattern in most QC codes.)
# -- BEGIN COMMENTED ASSERTS
# basis[2].angmom = 0
# assert basis[2].angmom_components_sph == (0,)
# basis[2].angmom = 1
# assert basis[2].angmom_components_sph == (1, -1, 0)
# -- END COMMENTED ASSERTS
basis[2].angmom = 2
assert basis[2].angmom_components_sph == ("c0", "c1", "s1", "c2", "s2")
basis[2].angmom = 3
assert basis[2].angmom_components_sph == ("c0", "c1", "s1", "c2", "s2",
"c3", "s3")
# NOTE: you shouldn't actually change the magnetic quantum number that is not compatible with
# the angular momentum, but we do so here to check that user input is accepted
mol.obasis.conventions[(0, "p")] = ["c1"]
basis, coord_types = from_iodata(mol)
basis[2].angmom = 0
assert coord_types == ["cartesian"] * 5
assert basis[2].angmom_components_sph == ("c1", )
assert np.allclose(basis[2].norm_cont, 1.0)
mol.obasis.conventions[(1, "p")] = ["c1", "c0", "s1"]
basis, coord_types = from_iodata(mol)
basis[2].angmom = 1
assert coord_types == ["cartesian"] * 5
assert basis[2].angmom_components_sph == ("c1", "c0", "s1")
assert np.allclose(basis[2].norm_cont, 1.0)
mol.obasis.conventions[(1, "c")] = ["z", "y", "x"]
basis, coord_types = from_iodata(mol)
basis[2].angmom = 1
assert np.allclose(np.array([[0, 0, 1], [0, 1, 0], [1, 0, 0]]),
basis[2].angmom_components_cart)
# Test Cartesian convention generation for missing angmom
# Needed for cases when only spherical basis is used in basis set
del mol.obasis.conventions[(1, "c")]
basis, coord_types = from_iodata(mol)
basis[2].angmom = 1
assert np.allclose(np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]),
basis[2].angmom_components_cart)
with pytest.raises(ValueError):
basis[2].angmom = 10
basis[2].angmom_components_sph
with pytest.raises(ValueError):
mol.obasis = mol.obasis._replace(primitive_normalization="L1")
basis, coord_types = from_iodata(mol)
from gbasis.integrals.point_charge import point_charge_integral
from Alchemical_tools import Alchemical_tools
import pylibxc
from gbasis.evals.density import evaluate_density
from gbasis.evals.eval import evaluate_basis
from gbasis.integrals.electron_repulsion import electron_repulsion_integral
from grid.onedgrid import GaussChebyshev
from grid.rtransform import BeckeTF
from grid.utils import get_cov_radii
from grid.atomic_grid import AtomicGrid
from grid.molgrid import MolGrid
from iodata import load_one
from gbasis.wrappers import from_iodata
molecule = load_one("h2o.fchk")
basis = from_iodata(molecule)
q = np.array([0.1])
R = np.array([[2.574156, -0.181816, -2.453822]])
alc_hf = Alchemical_tools(
basis,
molecule,
point_charge_positions=R,
point_charges_values=q,
coord_type="cartesian",
k="HF",
)
r0 = 1e-10
radii = get_cov_radii(molecule.atnums)
n_rad_points = 100
deg = 5
onedgrid = GaussChebyshev(n_rad_points)
def test_from_iodata():
"""Test gbasis.wrapper.from_iodata."""
pytest.importorskip("iodata")
from iodata import load_one
mol = load_one(find_datafile("data_iodata_water_sto3g_hf_g03.fchk"))
basis = from_iodata(mol)
assert all(isinstance(i, GeneralizedContractionShell) for i in basis)
assert basis[0].angmom == 0
assert np.allclose(basis[0].coord, mol.atcoords[0])
assert np.allclose(basis[0].exps,
np.array([130.7093214, 23.80886605, 6.443608313]))
assert np.allclose(
basis[0].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert basis[1].angmom == 0
assert np.allclose(basis[1].coord, mol.atcoords[0])
assert np.allclose(basis[1].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[1].coeffs,
np.array([-0.09996722919, 0.3995128261, 0.7001154689]).reshape(-1, 1))
assert basis[2].angmom == 1
assert np.allclose(basis[2].coord, mol.atcoords[0])
assert np.allclose(basis[2].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[2].coeffs,
np.array([0.1559162750, 0.6076837186, 0.3919573931]).reshape(-1, 1))
assert basis[3].angmom == 0
assert np.allclose(basis[3].coord, mol.atcoords[1])
assert np.allclose(basis[3].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[3].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert basis[4].angmom == 0
assert np.allclose(basis[4].coord, mol.atcoords[2])
assert np.allclose(basis[4].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[4].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
with pytest.raises(ValueError):
basis[2].angmom_components_sph # pylint: disable=W0104
# artificially change angular momentum
basis[2].angmom = 2
assert basis[2].angmom_components_sph == (0, 1, -1, 2, -2)
basis[2].angmom = 3
assert basis[2].angmom_components_sph == (0, 1, -1, 2, -2, 3, -3)
with pytest.raises(ValueError):
mol.obasis = mol.obasis._replace(primitive_normalization="L1")
basis = from_iodata(mol)
def get_one_dm(mol, mole, verb_lvl=0):
"""Function to pass the one-particle density matrix
from a molecule IOdata object
to the format that PySCF uses.
Should work for restricted and unrestricted
The MO information is used to generate the density matrix.
Parameters
----------
mol
IOdata molecule object.
mole
PySCF mole object with the same or different basis set.
verb_lvl
Verbosity level integer flag.
Returns
-------
one_dm_2
One-particle density matrix understood by IOdata
projected and formatted in a PySCF-compatible way
(single 2d array or list for a,b 2d arrays)
coeffs
AO coefficient matrix understood by IOdata
projected and formatted in a PySCF-compatible way
(single 2d array or list for a,b 2d arrays)
occs
Occupation numbers formatted in a PySCF-compatible way
(single 1d array or list for a,b 1d arrays)
energies
MO energies formatted in a PySCF-compatible way
(single 1d array or list for a,b 1d arrays)
Raises
------
wrappyscferror
If the mol.mo information is not understood. Can be set manually by modifying the
mol.mo attribute in the mol object passed from IOData.
"""
basis_1 = from_iodata(mol)
basis_2 = from_pyscf(mole)
proj, s_2, s_1 = project(basis_2, basis_1)
try:
if mol.mo[0] == "unrestricted":
one_dm_a_1, one_dm_b_1, one_dm_1 = spin_dm(mol)
one_dm_a_2 = proj @ one_dm_a_1 @ np.linalg.inv(proj)
if verb_lvl > 0:
print("Total number of alpha electrons is {0}".format(
checkrdm(one_dm_a_2, s_2)))
one_dm_b_2 = proj @ one_dm_b_1 @ np.linalg.inv(proj)
if verb_lvl > 0:
print("Total number of beta electrons is {0}".format(
checkrdm(one_dm_b_2, s_2)))
one_dm_2 = one_dm_a_2 + one_dm_b_2
if verb_lvl > 0:
print("Total number of electrons is {0}".format(
checkrdm(one_dm_2, s_2)))
if np.allclose(one_dm_a_2, one_dm_b_2):
if verb_lvl > 1:
print(
"This will be treated a restricted wave function, alpha and beta orbitals are the same."
)
coeffs = proj @ mol.mo.coeffsa
energies = np.asarray(mol.mo.energies[:mol.mo.norba])
occs = np.asarray(np.around(mol.mo.occsa) * 2)
return one_dm_2, coeffs, occs, energies
else:
if verb_lvl > 2:
print("This is a true unrestricted wave function.")
energies_a = np.asarray(mol.mo.energies[:mol.mo.norba])
energies_b = np.asarray(mol.mo.energies[mol.mo.norbb:])
occs_a = np.asarray(np.around(mol.mo.occsa))
occs_b = np.asarray(np.around(mol.mo.occsb))
coeffs_a = proj @ mol.mo.coeffsa
coeffs_b = proj @ mol.mo.coeffsb
return (
np.array((one_dm_a_2, one_dm_b_2)),
np.array((coeffs_a, coeffs_b)),
np.array((occs_a, occs_b)),
np.array((energies_a, energies_b)),
)
if mol.mo[0] == "restricted":
one_dm_1 = spin_dm(mol)[2]
one_dm_2 = proj @ one_dm_1 @ np.linalg.inv(proj)
coeffs = np.asarray(proj @ mol.mo.coeffsa)
occs = np.asarray(np.around(mol.mo.occsa) * 2)
energies = np.asarray(mol.mo.energies)
if verb_lvl > 2:
print("This is a restricted wave function.")
if verb_lvl > 0:
print("Total number of electrons is {0}".format(
checkrdm(one_dm_2, s_2)))
return one_dm_2, coeffs, occs, energies
except:
raise wrappyscferror(
"Could not understand if the passed data is restricted or unrestricted. You may set it manually."
)
def test_from_iodata():
"""Test gbasis.wrapper.from_iodata."""
pytest.importorskip("iodata")
from iodata import load_one
mol = load_one(find_datafile("data_iodata_water_sto3g_hf_g03.fchk"))
basis = from_iodata(mol)
assert all(isinstance(i, GeneralizedContractionShell) for i in basis)
assert basis[0].angmom == 0
assert np.allclose(basis[0].coord, mol.atcoords[0])
assert np.allclose(basis[0].exps,
np.array([130.7093214, 23.80886605, 6.443608313]))
assert np.allclose(
basis[0].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert basis[1].angmom == 0
assert np.allclose(basis[1].coord, mol.atcoords[0])
assert np.allclose(basis[1].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[1].coeffs,
np.array([-0.09996722919, 0.3995128261, 0.7001154689]).reshape(-1, 1))
assert basis[2].angmom == 1
assert np.allclose(basis[2].coord, mol.atcoords[0])
assert np.allclose(basis[2].exps,
np.array([5.033151319, 1.169596125, 0.3803889600]))
assert np.allclose(
basis[2].coeffs,
np.array([0.1559162750, 0.6076837186, 0.3919573931]).reshape(-1, 1))
assert basis[3].angmom == 0
assert np.allclose(basis[3].coord, mol.atcoords[1])
assert np.allclose(basis[3].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[3].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
assert basis[4].angmom == 0
assert np.allclose(basis[4].coord, mol.atcoords[2])
assert np.allclose(basis[4].exps,
np.array([3.425250914, 0.6239137298, 0.1688554040]))
assert np.allclose(
basis[4].coeffs,
np.array([0.1543289673, 0.5353281423, 0.4446345422]).reshape(-1, 1))
# artificially change angular momentum
basis[2].angmom = 0
assert basis[2].angmom_components_sph == (0, )
basis[2].angmom = 1
assert basis[2].angmom_components_sph == (1, -1, 0)
basis[2].angmom = 2
assert basis[2].angmom_components_sph == (0, 1, -1, 2, -2)
basis[2].angmom = 3
assert basis[2].angmom_components_sph == (0, 1, -1, 2, -2, 3, -3)
# NOTE: you shouldn't actually change the magnetic quantum number that is not compatible with
# the angular momentum, but we do so here to check that user input is accepted
mol.obasis.conventions[(0, "p")] = ["sc1"]
basis = from_iodata(mol)
basis[2].angmom = 0
assert basis[2].angmom_components_sph == (1, )
mol.obasis.conventions[(1, "p")] = ["pc1", "pc0", "ps1"]
basis = from_iodata(mol)
basis[2].angmom = 1
assert basis[2].angmom_components_sph == (1, 0, -1)
with pytest.raises(ValueError):
basis[2].angmom = -1
basis[2].angmom_components_sph
with pytest.raises(ValueError):
mol.obasis = mol.obasis._replace(primitive_normalization="L1")
basis = from_iodata(mol)