def test_eleven_atom_BaseMolecule():
mol = molecule.BaseMolecule(*eg.c3h8)
assert mol.natm == 11
assert np.all(mol.elem == eg.c3h8[0])
assert np.allclose(mol.xyz, eg.c3h8[1])
assert '...' in str(mol)
assert '...' in repr(mol)
def test_BaseMolecule_rearrange_all():
mol = molecule.BaseMolecule(*eg.ch4)
ind = [4, 2, 3, 0, 1]
mol.rearrange(ind)
assert np.all(mol.elem == eg.ch4[0][ind])
assert np.allclose(mol.xyz, eg.ch4[1][ind])
assert not mol.saved
def test_BaseMolecule_copy():
mol1 = molecule.BaseMolecule(*eg.c2h4)
mol2 = mol1.copy()
assert np.all(mol1.elem == eg.c2h4[0])
assert np.all(mol2.elem == eg.c2h4[0])
assert np.allclose(mol1.xyz, eg.c2h4[1])
assert np.allclose(mol2.xyz, eg.c2h4[1])
def test_BaseMolecule_add_atoms_multiple():
mol = molecule.BaseMolecule(*eg.he)
mol.add_atoms(*eg.ch4)
soln_elem = np.hstack((eg.he[0], eg.ch4[0]))
soln_xyz = np.vstack((eg.he[1], eg.ch4[1]))
assert np.all(mol.elem == soln_elem)
assert np.allclose(mol.xyz, soln_xyz)
assert not mol.saved
def test_BaseMolecule_add_atoms_single():
mol = molecule.BaseMolecule(*eg.he)
mol.add_atoms('H', np.ones(3))
soln_elem = np.hstack((eg.he[0], 'H'))
soln_xyz = np.vstack((eg.he[1], np.ones(3)))
assert np.all(mol.elem == soln_elem)
assert np.allclose(mol.xyz, soln_xyz)
assert not mol.saved
def test_empty_BaseMolecule():
mol = molecule.BaseMolecule()
assert len(mol.elem) == 0
assert len(mol.xyz) == 0
assert len(mol.vec) == 0
assert mol.comment == ''
assert str(mol) == '[]'
assert repr(mol) == 'BaseMolecule(\'\', [])'
def test_BaseMolecule_add_atoms_new_vec():
mol = molecule.BaseMolecule(*eg.he)
mol.add_atoms('H', np.ones(3), new_vec=2 * np.ones(3))
soln_elem = np.hstack((eg.he[0], 'H'))
soln_xyz = np.vstack((eg.he[1], np.ones(3)))
soln_vec = np.vstack((np.zeros(3), 2 * np.ones(3)))
assert np.all(mol.elem == soln_elem)
assert np.allclose(mol.xyz, soln_xyz)
assert np.allclose(mol.vec, soln_vec)
def test_BaseMolecule_rearrange_old_ind():
mol = molecule.BaseMolecule(*eg.ch4)
ninds = [1, 2]
oinds = [3, 4]
mol.rearrange(ninds, old_ind=oinds)
soln_elem = eg.ch4[0][[0, 3, 4, 1, 2]]
soln_xyz = eg.ch4[1][[0, 3, 4, 1, 2]]
assert np.all(mol.elem == soln_elem)
assert np.allclose(mol.xyz, soln_xyz)
assert not mol.saved
def test_BaseMolecule_revert():
mol = molecule.BaseMolecule(*eg.he)
mol.elem = np.array(['H'])
mol.xyz = np.ones((1, 3))
mol.comment = 'comment'
mol.revert()
assert mol.saved
assert np.all(mol.elem == eg.he[0])
assert np.allclose(mol.xyz, eg.he[1])
assert mol.comment == ''
def test_BaseMolecule_save():
mol = molecule.BaseMolecule(*eg.he)
mol.elem = np.array(['H'])
mol.xyz = np.ones((1, 3))
mol.comment = 'comment'
mol.save()
assert mol.saved
assert np.all(mol.save_elem == ['H'])
assert np.allclose(mol.save_xyz, np.ones((1, 3)))
assert mol.save_comment == 'comment'
def test_single_atom_vec_BaseMolecule():
mol = molecule.BaseMolecule(*eg.he, vec=np.ones(3))
zf = 3 * '{:14.8f}'.format(0)
of = 3 * '{:14.8f}'.format(1)
ze = ','.join(3 * ['{:16.8e}'.format(0)])
oe = ','.join(3 * ['{:16.8e}'.format(1)])
assert mol.natm == 1
assert np.all(mol.elem == ['He'])
assert np.allclose(mol.xyz, np.zeros((1, 3)))
assert str(mol) == '[[He' + zf + '\n ' + of + ']]'
assert repr(mol) == ('BaseMolecule(\'\',\n [[He,' + ze + ',\n ' + oe +
']])')
def test_BaseMolecule_rm_atoms_single():
mol = molecule.BaseMolecule(*eg.ch4)
mol.rm_atoms(0)
assert np.all(mol.elem == eg.ch4[0][1:])
assert np.allclose(mol.xyz, eg.ch4[1][1:])
assert not mol.saved
def test_BaseMolecule_len_elem_not_equal_len_xyz():
with pytest.raises(ValueError, match=r'Number of element labels .*'):
mol = molecule.BaseMolecule('H', np.zeros((2, 3)))
def test_BaseMolecule_xyz_vec_different_shape():
with pytest.raises(ValueError, match=r'Cartesian geometry and vector .*'):
mol = molecule.BaseMolecule(['H', 'H'], np.zeros((2, 3)),
np.ones((1, 3)))
def test_BaseMolecule_vec_not_3d():
with pytest.raises(ValueError, match=r'Molecular vector must be 3.*'):
mol = molecule.BaseMolecule('H', np.zeros(3), vec=np.ones(2))
def test_BaseMolecule_xyz_not_3d():
with pytest.raises(ValueError, match=r'Molecular geometry must be 3.*'):
mol = molecule.BaseMolecule('H', np.zeros(2))
def test_BaseMolecule_rm_atoms_multiple():
mol = molecule.BaseMolecule(*eg.ch4)
mol.rm_atoms((1, 2, 3, 4))
assert np.all(mol.elem == eg.ch4[0][0])
assert np.allclose(mol.xyz, eg.ch4[1][0])
assert not mol.saved
def test_two_atom_comment_BaseMolecule():
mol = molecule.BaseMolecule(*eg.h2, comment='comment')
assert mol.natm == 2
assert np.all(mol.elem == eg.h2[0])
assert np.allclose(mol.xyz, eg.h2[1])
assert 'comment' in str(mol)
def test_BaseMolecule_rearrange_fails():
mol = molecule.BaseMolecule(*eg.ch4)
with pytest.raises(IndexError, match=r'Old and new indices must be .*'):
mol.rearrange([1, 3])
