def test_basis_function_3d_grids_same_in_pyscf_and_mdt(molkey, request):
mol = request.getfixturevalue(molkey)
randocoords = 6.0 * u.angstrom * (np.random.rand(200, 3) - 0.5)
pyscf_vals = basis_values(mol, mol.wfn.aobasis, randocoords)
with np.errstate(under='ignore'):
mdt_vals = mol.wfn.aobasis(randocoords)
helpers.assert_almost_equal(mdt_vals, pyscf_vals, decimal=5)
def test_basis_function_3d_grids_same_in_pyscf_and_mdt(molkey, request):
mol = request.getfixturevalue(molkey)
randocoords = 6.0 * u.angstrom * (np.random.rand(200, 3) - 0.5)
pyscf_vals = basis_values(mol, mol.wfn.aobasis, randocoords)
with np.errstate(under='ignore'):
mdt_vals = mol.wfn.aobasis(randocoords)
helpers.assert_almost_equal(mdt_vals, pyscf_vals, decimal=5)
def test_pyscf_basis_function_space_integral_normalized(molkey, request):
mol = request.getfixturevalue(molkey)
grid = mdt.mathutils.padded_grid(mol.positions, 8.0 * u.angstrom, npoints=150)
points = grid.allpoints()
pyscf_vals = basis_values(mol, mol.wfn.aobasis, points)
assert pyscf_vals.shape == (len(points), len(mol.wfn.aobasis))
pyscf_normsqr = (pyscf_vals ** 2).sum(axis=0) * grid.dx * grid.dy * grid.dz
helpers.assert_almost_equal(pyscf_normsqr, 1.0,
decimal=4)
def test_pyscf_basis_function_space_integral_normalized(molkey, request):
mol = request.getfixturevalue(molkey)
grid = mdt.mathutils.padded_grid(mol.positions,
8.0 * u.angstrom,
npoints=150)
points = grid.allpoints()
pyscf_vals = basis_values(mol, mol.wfn.aobasis, points)
assert pyscf_vals.shape == (len(points), len(mol.wfn.aobasis))
pyscf_normsqr = (pyscf_vals**2).sum(axis=0) * grid.dx * grid.dy * grid.dz
helpers.assert_almost_equal(pyscf_normsqr, 1.0, decimal=4)
def test_pyscf_orbital_grid_works(h2_rhf_augccpvdz):
""" Tests the basic input/output of the pyscf basis_values function
Doesn't actually test the values directly - just that the answers are mathematically consistent
"""
mol = h2_rhf_augccpvdz
wfn = mol.wfn
nbasis = len(wfn.aobasis)
coords = u.array([
mol.com,
np.zeros(3) * u.angstrom, 10.0 * np.ones(3) * u.angstrom,
np.ones(3) * u.nm
])
# First - check that the shape is appropriate if called without orbital coefficients
values_nocoeffs = basis_values(mol, wfn.aobasis, coords)
assert values_nocoeffs.shape == (len(coords), nbasis)
assert (values_nocoeffs[-1] == values_nocoeffs[-2]
).all() # these 2 coordinates are the same
# Second - explicitly send orbital coefficients for first 2 basis functions
coeffs = np.zeros((2, nbasis))
coeffs[:2, :2] = np.identity(2)
vals_b0 = basis_values(mol, wfn.aobasis, coords, coeffs=coeffs)
assert vals_b0.shape == (len(coords), len(coeffs))
np.testing.assert_allclose(values_nocoeffs[:, :2], vals_b0)
# Third - send symmetric and anti-symmetric combinations of basis functions and check answers
plusminus = np.zeros((2, nbasis))
plusminus[:2, :2] = 1.0 / np.sqrt(2)
plusminus[1, 1] = -1.0 / np.sqrt(2)
vals_plusminus = basis_values(mol, wfn.aobasis, coords, coeffs=plusminus)
assert vals_plusminus.shape == (len(coords), len(coeffs))
helpers.assert_almost_equal(vals_plusminus[:, 0],
(vals_b0[:, 0] + vals_b0[:, 1]) / np.sqrt(2))
helpers.assert_almost_equal(vals_plusminus[:, 1],
(vals_b0[:, 0] - vals_b0[:, 1]) / np.sqrt(2))
def test_pyscf_orbital_grid_works(h2_rhf_augccpvdz):
""" Tests the basic input/output of the pyscf basis_values function
Doesn't actually test the values directly - just that the answers are mathematically consistent
"""
mol = h2_rhf_augccpvdz
wfn = mol.wfn
nbasis = len(wfn.aobasis)
coords = u.array([mol.com,
np.zeros(3)*u.angstrom,
10.0 * np.ones(3) * u.angstrom,
np.ones(3)*u.nm])
# First - check that the shape is appropriate if called without orbital coefficients
values_nocoeffs = basis_values(mol, wfn.aobasis, coords)
assert values_nocoeffs.shape == (len(coords), nbasis)
assert (values_nocoeffs[-1] == values_nocoeffs[-2]).all() # these 2 coordinates are the same
# Second - explicitly send orbital coefficients for first 2 basis functions
coeffs = np.zeros((2, nbasis))
coeffs[:2, :2] = np.identity(2)
vals_b0 = basis_values(mol, wfn.aobasis, coords, coeffs=coeffs)
assert vals_b0.shape == (len(coords), len(coeffs))
np.testing.assert_allclose(values_nocoeffs[:,:2], vals_b0)
# Third - send symmetric and anti-symmetric combinations of basis functions and check answers
plusminus = np.zeros((2, nbasis))
plusminus[:2, :2] = 1.0 / np.sqrt(2)
plusminus[1,1] = -1.0 / np.sqrt(2)
vals_plusminus = basis_values(mol, wfn.aobasis, coords, coeffs=plusminus)
assert vals_plusminus.shape == (len(coords), len(coeffs))
helpers.assert_almost_equal(vals_plusminus[:,0],
(vals_b0[:,0] + vals_b0[:,1])/np.sqrt(2))
helpers.assert_almost_equal(vals_plusminus[:,1],
(vals_b0[:,0] - vals_b0[:,1])/np.sqrt(2))
def __call__(self, coords, coeffs=None):
"""Calculate the value of each basis function at the specified coordinates.
Note:
This is just a pass-through to a specific implementation - PYSCF's eval_ao routine
for now.
Args:
coords (Array[length]): List of coordinates.
coeffs (Vector): List of ao coefficients (optional; if not passed, all basis fn
values are returned)
Returns:
Array[length]: if ``coeffs`` is not passed, an array of basis fn values at each
coordinate. Otherwise, a list of orbital values at each coordinate
"""
from moldesign.interfaces.pyscf_interface import basis_values
return basis_values(self.wfn.mol, self, coords, coeffs=coeffs,
positions=self.wfn.positions)
def __call__(self, coords, coeffs=None):
"""Calculate the value of each basis function at the specified coordinates.
Note:
This is just a pass-through to a specific implementation - PYSCF's eval_ao routine
for now.
Args:
coords (Array[length]): List of coordinates.
coeffs (Vector): List of ao coefficients (optional; if not passed, all basis fn
values are returned)
Returns:
Array[length]: if ``coeffs`` is not passed, an array of basis fn values at each
coordinate. Otherwise, a list of orbital values at each coordinate
"""
from moldesign.interfaces.pyscf_interface import basis_values
return basis_values(self.wfn.mol,
self,
coords,
coeffs=coeffs,
positions=self.wfn.positions)