def test_Molecule_add_MoleculeBundle():
mol = molecule.Molecule(*eg.he)
bund1 = molecule.MoleculeBundle(molecule.Molecule(*eg.c2h4))
bund = mol + bund1
assert np.all(bund.molecules[0].elem[1:] == eg.he[0])
assert np.all(bund.molecules[0].xyz[1:] == eg.he[1])
assert np.all(bund.molecules[1].elem[1:] == eg.c2h4[0])
assert np.all(bund.molecules[1].xyz[1:] == eg.c2h4[1])
def test_Molecule_add_Molecule():
mol1 = molecule.Molecule(*eg.he)
mol2 = molecule.Molecule(*eg.c2h4)
bund = mol1 + mol2
assert np.all(bund.molecules[0].elem[1:] == eg.he[0])
assert np.all(bund.molecules[0].xyz[1:] == eg.he[1])
assert np.all(bund.molecules[1].elem[1:] == eg.c2h4[0])
assert np.all(bund.molecules[1].xyz[1:] == eg.c2h4[1])
def test_MoleculeBundle_copy():
mol1 = molecule.Molecule(*eg.he)
mol2 = molecule.Molecule(*eg.ch4)
bund1 = molecule.MoleculeBundle([mol1, mol2])
bund2 = bund1.copy()
assert np.all(bund1.molecules[0].elem == bund2.molecules[0].elem)
assert np.all(bund1.molecules[1].elem == bund2.molecules[1].elem)
assert np.allclose(bund1.molecules[0].xyz, bund2.molecules[0].xyz)
assert np.allclose(bund1.molecules[1].xyz, bund2.molecules[1].xyz)
def test_Molecule_match_to_ref():
mol5 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[5])
mol1 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[1])
mol2 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[2])
bund = molecule.MoleculeBundle([mol1, mol2])
ind = mol5.match_to_ref(bund)
assert np.all(np.abs(mol5.xyz - mol2.xyz) < 1)
assert not np.all(np.abs(mol5.xyz - mol1.xyz) < 1)
assert ind == 1
def test_MoleculeBundle_rearrange_old_ind():
mol1 = molecule.Molecule('He', np.zeros(3))
mol2 = molecule.Molecule('Ne', np.ones(3))
mol3 = molecule.Molecule('Ar', -np.ones(3))
bund = molecule.MoleculeBundle([mol1, mol2, mol3])
bund.rearrange(1, old_ind=0)
assert bund.molecules[0] == mol2
assert bund.molecules[1] == mol1
assert bund.molecules[2] == mol3
assert not bund.saved
def test_MoleculeBundle_add_molecules():
mol1 = molecule.Molecule('He', np.zeros(3))
mol2 = molecule.Molecule('Ne', np.ones(3))
mol3 = molecule.Molecule('Ar', -np.ones(3))
bund = molecule.MoleculeBundle(mol1)
bund.add_molecules([mol2, mol3])
assert bund.molecules[0] == mol1
assert bund.molecules[1] == mol2
assert bund.molecules[2] == mol3
assert not bund.saved
def test_MoleculeBundle_rm_molecules():
mol1 = molecule.Molecule('He', np.zeros(3))
mol2 = molecule.Molecule('Ne', np.ones(3))
mol3 = molecule.Molecule('Ar', -np.ones(3))
bund = molecule.MoleculeBundle([mol1, mol2, mol3])
bund.rm_molecules(1)
assert bund.nmol == 2
assert bund.molecules[0] == mol1
assert bund.molecules[1] == mol3
assert not bund.saved
def test_MoleculeBundle_match_to_ref():
mol1 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[1])
mol2 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[2])
mol3 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[3])
mol4 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[4])
mol5 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[5])
bund1 = molecule.MoleculeBundle([mol3, mol4, mol5])
bund2 = molecule.MoleculeBundle([mol1, mol2])
inds = bund1.match_to_ref(bund2)
assert np.allclose(inds, [0, 0, 1])
def test_MoleculeBundle_iadd_Molecule():
mol1 = molecule.Molecule(*eg.he)
mol2 = molecule.Molecule(*eg.ch4)
mol3 = molecule.Molecule(*eg.c2h4)
bund = molecule.MoleculeBundle([mol1, mol2])
bund += mol3
assert np.all(bund.molecules[0].elem[1:] == eg.he[0])
assert np.all(bund.molecules[0].xyz[1:] == eg.he[1])
assert np.all(bund.molecules[1].elem[1:] == eg.ch4[0])
assert np.all(bund.molecules[1].xyz[1:] == eg.ch4[1])
assert np.all(bund.molecules[2].elem[1:] == eg.c2h4[0])
assert np.all(bund.molecules[2].xyz[1:] == eg.c2h4[1])
def test_MoleculeBundle_add_MoleculeBundle():
mol1 = molecule.Molecule(*eg.he)
mol2 = molecule.Molecule(*eg.ch4)
mol3 = molecule.Molecule(*eg.c2h4)
bund1 = molecule.MoleculeBundle(mol1)
bund23 = molecule.MoleculeBundle([mol2, mol3])
bund = bund1 + bund23
assert np.all(bund.molecules[0].elem[1:] == eg.he[0])
assert np.all(bund.molecules[0].xyz[1:] == eg.he[1])
assert np.all(bund.molecules[1].elem[1:] == eg.ch4[0])
assert np.all(bund.molecules[1].xyz[1:] == eg.ch4[1])
assert np.all(bund.molecules[2].elem[1:] == eg.c2h4[0])
assert np.all(bund.molecules[2].xyz[1:] == eg.c2h4[1])
def test_Molecule_read_openfile_vec(tmpdir):
f = ef.tmpf(tmpdir, ef.xyz_vec)
mol = molecule.Molecule()
mol.read(f, hasvec=True)
assert np.all(mol.elem[1:] == eg.ch4[0])
assert np.allclose(mol.xyz[1:], eg.ch4[1])
assert not mol.saved
def test_Molecule_copy():
mol1 = molecule.Molecule(*eg.c2h4)
mol2 = mol1.copy()
assert np.all(mol1.elem[1:] == eg.c2h4[0])
assert np.all(mol2.elem[1:] == eg.c2h4[0])
assert np.allclose(mol1.xyz[1:], eg.c2h4[1])
assert np.allclose(mol2.xyz[1:], eg.c2h4[1])
def test_MoleculeBundle_write_vec(tmpdir):
f = tmpdir.join('tmp.xyz')
vec = np.ones((5, 3))
mol = molecule.Molecule(*eg.ch4, vec=vec, comment='comment line')
bund = molecule.MoleculeBundle([mol, mol])
bund.write(f.open(mode='w'))
assert f.read() == 2 * ef.xyz_vec
def test_Molecule_centre_mass():
mol = molecule.Molecule(*eg.ch4)
mol.xyz[1] += 2
mol.centre_mass()
mass = mol.get_mass()
cm = np.sum(mass[:, np.newaxis] * mol.xyz, axis=0) / np.sum(mass)
assert np.allclose(mol.xyz[0], np.zeros(3))
assert np.allclose(cm, np.zeros(3))
def test_Molecule_read_filename(tmpdir):
f = tmpdir.join('tmp.xyz')
f.write(ef.xyz_novec)
mol = molecule.Molecule()
mol.read(str(f.realpath()))
assert np.all(mol.elem[1:] == eg.ch4[0])
assert np.allclose(mol.xyz[1:], eg.ch4[1])
assert not mol.saved
def test_Molecule_rearrange_all():
mol = molecule.Molecule(*eg.ch4)
ind = [5, 3, 4, 1, 2]
oind = [i - 1 for i in ind]
mol.rearrange(ind)
assert np.all(mol.elem[1:] == eg.ch4[0][oind])
assert np.allclose(mol.xyz[1:], eg.ch4[1][oind])
assert not mol.saved
def test_empty_Molecule():
mol = molecule.Molecule()
assert len(mol.elem) == 0
assert len(mol.xyz) == 0
assert len(mol.vec) == 0
assert mol.comment == ''
assert str(mol) == '[]'
assert repr(mol) == 'Molecule(\'\', [])'
def test_Molecule_subst_vec():
mol = molecule.Molecule(*eg.c2h4)
mol.print_vec = True
mol.vec = np.ones_like(mol.xyz)
mol.subst('ch3', 3, pl=2)
newvec = np.vstack((np.ones((2, 3)), np.zeros((4, 3)), np.ones((3, 3))))
assert np.all(mol.elem[1:] == eg.c2h3me[0])
assert np.allclose(mol.xyz[1:], eg.c2h3me[1])
assert np.allclose(mol.vec[1:], newvec)
def test_single_atom_MoleculeBundle():
mol = molecule.Molecule(*eg.he)
bund = molecule.MoleculeBundle(mol)
zf = 3 * '{:14.8f}'.format(0)
ze = 3 * ',{:16.8e}'.format(0)
assert bund.nmol == 1
assert str(bund) == '[[[He' + zf + ']]]'
assert repr(bund) == ('MoleculeBundle(\n Molecule(\'\',\n [[XM' + ze +
'],\n [He' + ze + ']]))')
def test_eleven_atom_Molecule():
mol = molecule.Molecule(*eg.c3h8)
assert mol.natm == 11
assert np.all(mol.elem == np.hstack(('XM', eg.c3h8[0])))
assert np.allclose(mol.xyz,
np.vstack((np.zeros(3), eg.c3h8[1])),
atol=1e-7)
assert '...' in str(mol)
assert '...' in repr(mol)
def test_MoleculeBundle_save():
mol = molecule.Molecule(*eg.he)
bund = molecule.MoleculeBundle([mol, mol])
bund.molecules = [mol]
bund.molecules[0].xyz += 1
bund.molecules[0].elem[1] = 'H'
bund.save()
assert bund.saved
assert bund.molecules[0].saved
assert len(bund.save_molecules) == 1
def test_single_atom_vec_Molecule():
mol = molecule.Molecule(*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 == ['XM', 'He'])
assert np.allclose(mol.xyz, np.zeros((2, 3)))
assert str(mol) == '[[He' + zf + '\n ' + of + ']]'
assert repr(mol) == ('Molecule(\'\',\n [[XM,' + ze + ',\n ' + ze +
'],\n [He,' + ze + ',\n ' + oe + ']])')
def test_MoleculeBundle_measure():
mol1 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[1])
mol2 = molecule.Molecule(eg.ch2f2[0], eg.ch2f2[2])
bund = molecule.MoleculeBundle([mol1, mol2])
stre = bund.measure('stre', 2, 3)
assert np.allclose(stre, [np.sqrt(2), 2.04])
def test_MoleculeBundle_write_openfile(tmpdir):
f = tmpdir.join('tmp.xyz')
mol = molecule.Molecule(*eg.ch4, comment='comment line')
bund = molecule.MoleculeBundle([mol, mol])
bund.write(f.open(mode='w'))
assert f.read() == 2 * ef.xyz_novec
def test_MoleculeBundle_write_filename(tmpdir):
f = tmpdir.join('tmp.xyz')
mol = molecule.Molecule(*eg.ch4, comment='comment line')
bund = molecule.MoleculeBundle([mol, mol])
bund.write(str(f.realpath()))
assert f.read() == 2 * ef.xyz_novec
def test_Molecule_rotate_no_vec():
mol = molecule.Molecule(*eg.c2h4)
mol.rotate(np.pi / 2, 'Z')
soln = np.array([-eg.c2h4[1][:, 1], -eg.c2h4[1][:, 0], eg.c2h4[1][:, 2]]).T
assert np.allclose(mol.xyz[1:], soln)
def test_Molecule_rotate_vec():
mol = molecule.Molecule(*eg.c2h4, vec=np.ones((6, 3)))
mol.rotate(np.pi / 2, 'Z')
soln = np.ones_like(eg.c2h4[1])
soln[:, 0] = -1
assert np.allclose(mol.vec[1:], soln)
def test_Molecule_subst():
mol = molecule.Molecule(*eg.c2h4)
mol.subst('ch3', 3, pl=2)
assert np.all(mol.elem[1:] == eg.c2h3me[0])
assert np.allclose(mol.xyz[1:], eg.c2h3me[1])
def test_MoleculeBundle_add_wrong_type():
bund1 = molecule.MoleculeBundle(molecule.Molecule(*eg.he))
with pytest.raises(TypeError,
match=r'Addition not supported for types .*'):
bund = bund1 + np.ones(3)
def test_seven_molecule_MoleculeBundle():
mol = molecule.Molecule(*eg.he)
bund = molecule.MoleculeBundle(7 * [mol])
assert bund.nmol == 7
assert '...' in str(bund)
assert '...' in repr(bund)
