def read_geom(filename: str, verb=0):
"""Very simple wrapper for iodata load_one.
Parameters
----------
filename
A string that contains the path to an input file.
verb
Verbosity level integer flag.
Returns
-------
mol
An IOdata molecule object.
Raises
------
readereerror
If the file is not found.
"""
path = os.path.abspath(filename)
try:
assert os.path.exists(path)
assert os.path.isfile(path)
except:
raise readererror("Could not load the file {0}.".format(path))
mol = load_one(path)
if verb > 1:
print("File loaded using IOData.")
if verb > 2:
pp.pprint(mol)
return mol
def atom_coordinates_iodata(sdf_name):
r"""Load atomic coordinates from a sdf file with iodata.
Parameters
----------
sdf_name : string
SDF file name.
Returns
-------
coords : ndarray
3D atomic coordinates.
"""
mol = load_one(sdf_name)
coords = mol.atcoords
return coords
def read_one(filename: str, verb=0):
"""Very simple wrapper for iodata load_one.
Parameters
----------
filename
A string that contains the path to an input file.
verb
Verbosity level integer flag.
Returns
-------
mol
An IOdata molecule object.
Raises
------
readereerror
If the file is not found or is not a file, or
does not contain the basis set information needed
to calculate the one-particle density matrix etc.
"""
path = os.path.abspath(filename)
try:
assert os.path.exists(path)
assert os.path.isfile(path)
except:
raise readererror("Could not load the file {0}.".format(path))
mol = load_one(path)
try:
mol.mo.coeffsa
except:
raise readererror(
"Basis set coefficients were not understood or are not present.")
if verb > 1:
print("File loaded using IOData.")
if verb > 2:
pprint(mol)
return mol
def write_orbitals(self, filename='None'):
# Assign filename depending if it is given as an input
# or if it has to be generated from the elements.
if filename == 'None':
filename = '../data/molden-fchk_files/' + self.scheme[
0] + '/' + self.generate_molname()
else:
filename = '../data/molden-fchk_files/' + filename
# Write out the molden file using psi4
psi4.molden(self.model.wavefunction, filename + '.molden')
# Using IOData, we load in the molden file. We alter the
# values of the coefficients using the localized coefficients.
# Finally we write them out to a FCHK file and remove the molden file
molecule = load_one(filename + '.molden')
molecule_mo = molecule.mo
mo_coeffs = molecule_mo.coeffs
# replace the occupied orbital coefficients with the localized ones.
self.L_occ = np.dot(self.C_occ, self.W)
mo_coeffs[:, :self.N_occ] = self.L_occ
molecule_mo.coeffs = mo_coeffs
dump_one(molecule, filename + '.fchk')
os.remove(filename + '.molden')
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)
import pytest
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
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 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)