def test_molecule_orbitals_fchk_uhf_ch4():
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
mol = Molecule.from_file(fname)
# check orbital energy
orb_energy = np.array([-1.12152085E+01, -9.42914385E-01, -5.43117091E-01, -5.43114279E-01,
-5.43101269E-01, 1.93295185E-01, 2.74358942E-01, 2.74359310E-01,
2.74359740E-01, 5.89328697E-01, 5.89342443E-01, 5.89343893E-01,
8.90214386E-01, 8.90219069E-01, 8.90222480E-01, 9.36275219E-01,
1.13182813E+00, 1.13184117E+00, 1.25675685E+00, 1.68763897E+00,
1.68764372E+00, 1.68765502E+00, 1.89570058E+00, 1.89570452E+00,
1.89571385E+00, 2.21323213E+00, 2.21324619E+00, 2.21328532E+00,
2.54691042E+00, 2.54694190E+00, 2.75532231E+00, 2.79906776E+00,
2.79907762E+00, 2.79908651E+00])
assert_almost_equal(mol.orbital_energy[0], orb_energy, decimal=6)
assert_almost_equal(mol.orbital_energy[1], orb_energy, decimal=6)
assert_almost_equal(mol.homo_energy[0], orb_energy[4], decimal=6)
assert_almost_equal(mol.homo_energy[1], orb_energy[4], decimal=6)
assert_almost_equal(mol.lumo_energy[0], orb_energy[5], decimal=6)
assert_almost_equal(mol.lumo_energy[1], orb_energy[5], decimal=6)
# check orbital coefficients
orb_coeff = np.array([9.97287609E-01, 1.86004593E-02, -8.24772487E-03])
assert_almost_equal(mol.orbital_coefficient[1][:3, 0], orb_coeff, decimal=6)
assert_almost_equal(mol.orbital_coefficient[0][:3, 0], orb_coeff, decimal=6)
assert_almost_equal(mol.orbital_coefficient[1][0, 1], -0.188285003, decimal=6)
assert_almost_equal(mol.orbital_coefficient[0][0, 1], -0.188285003, decimal=6)
assert_almost_equal(mol.orbital_coefficient[1][-1, -1], 1.02960200, decimal=6)
assert_almost_equal(mol.orbital_coefficient[0][-1, -1], 1.02960200, decimal=6)
# check overlap matrix
overlap = mol.compute_orbital_overlap()
assert_equal(overlap.shape, (34, 34))
assert_almost_equal(np.diag(overlap), np.ones(34), decimal=6)
assert_almost_equal(overlap, overlap.T, decimal=6)
def test_molecule_esp_fchk_uhf_ch4():
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
mol = Molecule.from_file(fname)
# check esp against Gaussian (printed in log file)
# check esp at the position of each nuclei (1.e-14 is added to avoid division by zero)
# excluding the nucleus itself.
point = mol.coordinates[0].reshape(1, 3) + 1.e-14
charge = np.array([0., 1., 1., 1., 1.])
assert_almost_equal(mol.compute_esp(point, charges=charge), [-14.745629], decimal=5)
point = mol.coordinates[1].reshape(1, 3) + 1.e-14
charge = np.array([6., 0., 1., 1., 1.])
assert_almost_equal(mol.compute_esp(point, charges=charge), [-1.116065], decimal=5)
point = mol.coordinates[2].reshape(1, 3) + 1.e-14
charge = np.array([6., 1., 0., 1., 1.])
assert_almost_equal(mol.compute_esp(point, charges=charge), [-1.116065], decimal=5)
point = mol.coordinates[3].reshape(1, 3) + 1.e-14
charge = np.array([6., 1., 1., 0., 1.])
assert_almost_equal(mol.compute_esp(point, charges=charge), [-1.116067], decimal=5)
point = mol.coordinates[4].reshape(1, 3) + 1.e-14
charge = np.array([6., 1., 1., 1., 0.])
assert_almost_equal(mol.compute_esp(point, charges=charge), [-1.116065], decimal=5)
# check esp at non-nuclei points
points = np.array([[ 0.5, 0.5, 0.5],
[-0.5, -0.5, -0.5],
[-0.5, 0.5, 0.5],
[-0.5, -0.5, 0.5],
[-0.5, 0.5, -0.5],
[ 0.5, -0.5, -0.5],
[ 0.5, -0.5, 0.5],
[ 0.5, 0.5, -0.5]]) / 0.529177
expected_esp = np.array([0.895650, 0.237257, 0.234243, 0.708301,
0.499083, 0.479275, 0.241434, 0.235102])
assert_almost_equal(mol.compute_esp(points), expected_esp, decimal=5)
def test_horton_molecule_basic_fchk_o2_uhf():
with path('chemtools.data', 'o2_uhf_virtual.fchk') as fname:
mol = Molecule.from_file(fname)
# print mol.nelectrons
# check basic numerics
assert_equal(mol.natom, 2)
assert_equal(mol.nelectrons, (9, 7))
assert_equal(mol.nbasis, 44)
assert_equal(mol.numbers, [8, 8])
assert_equal(mol.pseudo_numbers, [8, 8])
assert_equal(mol.homo_index, (9, 7))
assert_equal(mol.lumo_index, (10, 8))
assert_equal(mol.orbital_occupation[0], np.array([1] * 9 + [0] * 35))
assert_equal(mol.orbital_occupation[1], np.array([1] * 7 + [0] * 37))
assert_almost_equal(mol.energy, -1.496641407696776E+02, decimal=8)
# check coordinates
coord = np.array([[0.0, 0.0, 1.09452498], [0.0, 0.0, -1.09452498]])
assert_almost_equal(mol.coordinates, coord, decimal=6)
# energy of alpha orbitals
orb_energy_a = np.array([
-2.07520003E+01, -2.07511624E+01, -1.77073830E+00, -1.19176563E+00,
-8.67505123E-01, -8.67505123E-01, -7.86590608E-01, -5.41367609E-01,
-5.41367609E-01, 1.75551613E-01, 1.79578059E-01, 2.12136240E-01,
2.12136240E-01, 2.82746427E-01, 2.82746427E-01, 2.85693824E-01,
4.25803814E-01, 5.48137441E-01, 1.13330121E+00, 1.13563801E+00,
1.13563801E+00, 1.21130153E+00, 1.21130153E+00, 1.21869395E+00,
1.42273629E+00, 1.74301463E+00, 2.54671907E+00, 2.54671907E+00,
2.83314193E+00, 2.83314193E+00, 3.16996201E+00, 3.16996201E+00,
3.35513494E+00, 3.91418793E+00, 3.91418793E+00, 4.32509152E+00,
5.22427895E+00, 5.22427895E+00, 5.43561012E+00, 5.51122695E+00,
5.51122695E+00, 6.78081131E+00, 5.12932061E+01, 5.15031931E+01
])
# energy of beta orbitals
orb_energy_b = np.array([
-2.06970266E+01, -2.06955835E+01, -1.64286825E+00, -9.81871414E-01,
-7.18265821E-01, -6.01903968E-01, -6.01903968E-01, 1.04744787E-01,
1.04744787E-01, 1.82240025E-01, 1.84775146E-01, 2.25175431E-01,
2.25175431E-01, 2.81988319E-01, 3.22590360E-01, 3.22590360E-01,
4.31522630E-01, 6.25012892E-01, 1.14414927E+00, 1.21805822E+00,
1.21805822E+00, 1.24392742E+00, 1.30587863E+00, 1.30587863E+00,
1.45650216E+00, 1.79253113E+00, 2.62926234E+00, 2.62926234E+00,
2.95890359E+00, 2.95890359E+00, 3.32630000E+00, 3.32630000E+00,
3.42846106E+00, 3.99627997E+00, 3.99627997E+00, 4.36808390E+00,
5.33007026E+00, 5.33007026E+00, 5.45827702E+00, 5.61601037E+00,
5.61601037E+00, 6.81582045E+00, 5.13257489E+01, 5.15352582E+01
])
# check orbital energy
assert_almost_equal(mol.orbital_energy[0], orb_energy_a, decimal=6)
assert_almost_equal(mol.orbital_energy[1], orb_energy_b, decimal=6)
assert_almost_equal(mol.homo_energy[0], orb_energy_a[8], decimal=6)
assert_almost_equal(mol.homo_energy[1], orb_energy_b[6], decimal=6)
assert_almost_equal(mol.lumo_energy[0], orb_energy_a[9], decimal=6)
assert_almost_equal(mol.lumo_energy[1], orb_energy_b[7], decimal=6)
assert_almost_equal(mol.mulliken_charges, 0.0, decimal=6)
# check orbital coefficients
assert_almost_equal(mol.orbital_coefficient[0][:3, 0],
np.array([0.389497609, 0.333421243, 0.]),
decimal=6)
def test_molecule_basics_fchk_uhf_ch4():
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
molecule = Molecule.from_file(fname)
# check basics
check_molecule_basics(molecule)
# check charges
esp = np.array([-0.502277518, 0.125567970, 0.125569655, 0.125566743, 0.125573150])
assert_almost_equal(molecule.esp_charges, esp, decimal=6)
npa = np.array([-0.791299253, 0.197824989, 0.197825250, 0.197824326, 0.197824689])
assert_almost_equal(molecule.npa_charges, npa, decimal=6)
mul = np.array([-0.139702704, 0.0349253868, 0.0349266071, 0.0349235395, 0.0349271707])
assert_almost_equal(molecule.mulliken_charges, mul, decimal=6)
def test_molecule_density_matrix_fchk_uhf_ch4():
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
mol = Molecule.from_file(fname)
# check density matrix against Gaussian (printed in log fname)
expected_diag = np.array([1.03003, 0.13222, 0.05565, 0.17944, 0.17944, 0.17944, 0.03891,
0.03891, 0.03891, 0.00028, 0.00064, 0.00045, 0.00011, 0.00072,
0.18575, 0.02710, 0.00044, 0.00072, 0.00038, 0.18575, 0.02710,
0.00057, 0.00074, 0.00023, 0.18575, 0.02710, 0.00069, 0.00029,
0.00056, 0.18575, 0.02710, 0.00035, 0.00030, 0.00089])
# column 5, rows 15-21
expected_05 = np.array([0.12066, 0.05027, -0.00560, -0.00252, -0.00502, -0.12275, -0.05114])
# column 15, rows 16-34
expected_15 = np.array([ 0.06838, -0.00691, -0.00996, -0.00619, -0.01612, -0.01573, 0.00244,
0.00393, 0.00238, -0.01612, -0.01573, 0.00277, 0.00383, 0.00217,
-0.01612, -0.01573, 0.00270, 0.00366, 0.00253])
# column 19, rows 20-34
expected_19 = np.array([-0.00130, 0.00004, 0.00004, -0.00033, 0.00002, 0.00302, 0.00184,
0.00001, -0.00010, -0.00003, -0.00438, -0.00125, -0.00032, 0.00003,
-0.00035])
# column 29, rows 30-34
expected_29 = np.array([-0.00442, -0.00106, -0.00003, 0.00029, -0.00047])
# check alpha density matrix
dm_array_a = mol.compute_density_matrix(spin="a")
assert_almost_equal(np.diag(dm_array_a), expected_diag, decimal=5)
assert_almost_equal(dm_array_a, dm_array_a.T, decimal=5)
assert_almost_equal(dm_array_a[0, 1:3], np.array([-0.04982, -0.05262]), decimal=5)
assert_almost_equal(dm_array_a[4, 14:21], expected_05, decimal=5)
assert_almost_equal(dm_array_a[14, 15:], expected_15, decimal=5)
assert_almost_equal(dm_array_a[18, 19:], expected_19, decimal=5)
assert_almost_equal(dm_array_a[28, 29:], expected_29, decimal=5)
# check beta density matrix
dm_array_b = mol.compute_density_matrix(spin="b")
assert_almost_equal(np.diag(dm_array_b), expected_diag, decimal=5)
assert_almost_equal(dm_array_b, dm_array_b.T, decimal=5)
assert_almost_equal(dm_array_b[0, 1:3], np.array([-0.04982, -0.05262]), decimal=5)
assert_almost_equal(dm_array_b[4, 14:21], expected_05, decimal=5)
assert_almost_equal(dm_array_b[14, 15:], expected_15, decimal=5)
assert_almost_equal(dm_array_b[18, 19:], expected_19, decimal=5)
assert_almost_equal(dm_array_b[28, 29:], expected_29, decimal=5)
# check total density matrix
dm_array_ab = mol.compute_density_matrix(spin="ab")
assert_almost_equal(np.diag(dm_array_ab), 2 * expected_diag, decimal=5)
assert_almost_equal(dm_array_ab, dm_array_ab.T, decimal=5)
assert_almost_equal(dm_array_ab[0, 1:3], 2*np.array([-0.04982, -0.05262]), decimal=5)
assert_almost_equal(dm_array_ab[4, 14:21], 2*expected_05, decimal=5)
assert_almost_equal(dm_array_ab[14, 15:], 2*expected_15, decimal=5)
assert_almost_equal(dm_array_ab[18, 19:], 2*expected_19, decimal=5)
assert_almost_equal(dm_array_ab[28, 29:], 2*expected_29, decimal=5)
def test_molecule_density_matrix_index_fchk_uhf_ch4():
# check get_density_matrix for different values of the index/
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
mol = Molecule.from_file(fname)
dm_full = mol._get_density_matrix("a")._array
# errors
assert_raises(ValueError, mol._get_density_matrix, "a", [[1]])
assert_raises(ValueError, mol._get_density_matrix, "a", [0])
# one index
for i in range(1, mol.nbasis + 1):
assert np.allclose(dm_full[i - 1, i - 1], mol._get_density_matrix("a", i)._array)
# multiple indices
for i in range(1, mol.nbasis + 1):
for j in range(1, mol.nbasis + 1):
# NOTE: indices can be repeated
indices = np.array([i -1, j - 1])
assert np.allclose(dm_full[indices[:, None], indices[None, :]],
mol._get_density_matrix("a", [i, j])._array)
def test_molecule_horton_ch4():
with path("chemtools.data", "data_horton_fchk_ch4_uhf_ccpvdz.npz") as fname:
data = np.load(str(fname))
with path("chemtools.data", "ch4_uhf_ccpvdz.fchk") as fname:
mol = Molecule.from_file(fname)
# check properties computed at nucleus against HORTON
points = data["coords"]
assert np.allclose(mol.compute_density(points), data["nuc_dens"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_gradient(points), data["nuc_grad"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_hessian(points), data["nuc_hess"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_ked(points), data["nuc_ked_pd"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_esp(points), data["nuc_esp"], rtol=0., atol=1.e-6)
# check properties computed on a grid against HORTON
assert np.allclose(mol.compute_density(data["points"]), data["dens"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_gradient(data["points"]), data["grad"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_hessian(data["points"]), data["hess"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_ked(data["points"]), data["ked_pd"], rtol=0., atol=1.e-6)
assert np.allclose(mol.compute_esp(data["points"]), data["esp"], rtol=0., atol=1.e-6)
def test_molecule_raises_wfn_uhf_ch4():
with path("chemtools.data", "ch4_uhf_ccpvdz.wfn") as fname:
molecule = Molecule.from_file(fname)
check_molecule_raises(molecule)
def test_molecule_grid_fortran_fchk_rhf_ch4():
# make an instance of molecule
with path("chemtools.data", "ch4_rhf_ccpvdz.fchk") as fname:
molecule = Molecule.from_file(fname)
check_molecule_against_fortran_ch4(molecule)
def test_molecule_grid_g09_wfn_uhf_ch4():
# make an instance of molecule from wfn file
with path("chemtools.data", "ch4_uhf_ccpvdz.wfn") as fname:
molecule = Molecule.from_file(fname)
check_molecule_against_gaussian_ch4(molecule)
def test_horton_molecule_grid_fortran_fchk_ch4_rhf_ccpvdz():
# make an instance of molecule
with path('chemtools.data', 'ch4_rhf_ccpvdz.fchk') as fname:
molecule = Molecule.from_file(fname)
check_horton_molecule_against_fortran_ch4_uhf_ccpvdz(molecule)
def test_horton_molecule_grid_gaussian_wfn_ch4_uhf_ccpvdz():
# make an instance of molecule from wfn file
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
molecule = Molecule.from_file(fname)
check_horton_molecule_against_gaussian_ch4_uhf_ccpvdz(molecule)
def test_horton_molecule_check_raises_wfn_ch4_uhf_ccpvdz():
with path('chemtools.data', 'ch4_uhf_ccpvdz.wfn') as fname:
molecule = Molecule.from_file(fname)
check_horton_molecule_raises(molecule)