def test_cube_h2o_dimer():
# test against previous generated .cube files
with path('chemtools.data', 'h2o_dimer_pbe_sto3g-dens.cube') as file_path:
cube = UniformGrid.from_cube(file_path)
mol1 = Molecule.from_file(str(file_path))
with tmpdir('chemtools.test.test_base.test_cube_h2o_dimer') as dn:
cube2 = '%s/%s' % (dn, 'h2o_dimer_pbe_sto3g-dens.cube')
cube.generate_cube(cube2, mol1.cube_data)
cube2 = '%s/%s' % (dn, 'h2o_dimer_pbe_sto3g-dens.cube')
mol2 = Molecule.from_file(cube2)
# Check coordinates
np.testing.assert_array_almost_equal(mol1.coordinates, mol2.coordinates, decimal=6)
np.testing.assert_equal(mol1.numbers, mol2.numbers)
# Check grid data
ugrid1 = mol1.grid
ugrid2 = mol2.grid
np.testing.assert_array_almost_equal(ugrid1.grid_rvecs, ugrid2.grid_rvecs, decimal=6)
np.testing.assert_equal(ugrid1.shape, ugrid2.shape)
data1 = mol1.cube_data / mol1.cube_data
data2 = mol2.cube_data / mol1.cube_data
np.testing.assert_array_almost_equal(data1, data2, decimal=4)
np.testing.assert_equal(mol1.pseudo_numbers, mol2.pseudo_numbers)
def load_molecule_and_grid(fname, cube):
"""Return instances of molecule and uniform cubic grid.
Parameters
----------
fname : str
Path to wave-function file.
cube : str
Uniform cubic grid specifications.
"""
# load molecule
mol = Molecule.from_file(fname)
if cube.endswith(".cube"):
# load & check cube file
cube = UniformGrid.from_cube(cube)
if np.allclose(mol.numbers, cube.numbers):
raise ValueError(
"Atomic number in {0} & {1} should be the same!".format(
fname, cube))
if np.allclose(mol.coordinates, cube.coordinates):
raise ValueError(
"Atomic coordinates in {0} & {1} should be the same!".format(
cube.fname, cube.cube))
elif len(cube.split(",")) == 2:
# make a cubic grid
spacing, extension = [float(item) for item in cube.split(",")]
cube = UniformGrid.from_molecule(mol,
spacing=spacing,
extension=extension,
rotate=True)
else:
raise ValueError("Argument cube={0} is not recognized!".format(cube))
return mol, cube