def test_atom_invalid_position(self):
atom = Atom(name='invalidSite')
with pytest.raises(ValueError) as e:
atom.position = [0, 0, 0, 0]
assert 'Position of shape (3,) is not valid. ' \
'Accepted values: (a.) 3-tuple, (b.) list of length 3 ' \
'(c.) np.array or unyt.unyt_array of shape (3,)' in e
def test_dihedral_fake(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Dihedral(connection_members=["fakeatom1", "fakeatom2", 4.2])
def test_set_with_atom_type(self):
lithium_type = AtomType(mass=6.941, charge=1)
atom = Atom(name="Lithium")
atom.atom_type = lithium_type
assert atom.charge == 1 * u.elementary_charge
assert atom.mass == 6.941 * u.gram / u.mol
def test_square_with_bridge(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
c24 = Bond(connection_members=[s2, s4])
mytop.add_site(s1, update_types=False)
mytop.add_site(s2, update_types=False)
mytop.add_site(s3, update_types=False)
mytop.add_site(s4, update_types=False)
mytop.add_connection(c12, update_types=False)
mytop.add_connection(c23, update_types=False)
mytop.add_connection(c34, update_types=False)
mytop.add_connection(c41, update_types=False)
mytop.add_connection(c24, update_types=False)
assert mytop.n_bonds == 5
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 5
assert mytop.n_angles == 8
assert mytop.n_dihedrals == 6
assert mytop.n_impropers == 2
def test_angle_nonparametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
connect = Angle(connection_members=[atom1, atom2, atom3])
assert connect.angle_type is None
def test_improper_fake(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Improper(connection_members=["fakeatom1", "fakeatom2", 4.2])
def _get_atoms(filename, topology, unit_style, type_list):
"""Parse the atom information in the LAMMPS data file."""
with open(filename, "r") as lammps_file:
for i, line in enumerate(lammps_file):
if "atoms" in line.split():
n_atoms = int(line.split()[0])
if "Atoms" in line.split():
break
atom_lines = open(filename, "r").readlines()[i + 2:i + n_atoms + 2]
for line in atom_lines:
atom_line = line.split()
atom_type = atom_line[2]
charge = u.unyt_quantity(float(atom_line[3]),
get_units(unit_style)["charge"])
coord = u.angstrom * u.unyt_array(
[float(atom_line[4]),
float(atom_line[5]),
float(atom_line[6])])
site = Atom(
charge=charge,
position=coord,
atom_type=type_list[int(atom_type) - 1],
)
element = element_by_mass(site.atom_type.mass.value)
site.name = element.name
site.element = element
topology.add_site(site)
topology.update_sites()
return topology
def test_bond_nonparametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
connect = Bond(connection_members=[atom1, atom2])
assert connect.bond_type is None
def test_improper_fake(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Improper(connection_members=['fakeatom1', 'fakeatom2', 4.2])
def test_square(self):
mytop = Topology()
s1 = Atom(name="1")
s2 = Atom(name="2")
s3 = Atom(name="3")
s4 = Atom(name="4")
c12 = Bond(connection_members=[s1, s2])
c23 = Bond(connection_members=[s2, s3])
c34 = Bond(connection_members=[s3, s4])
c41 = Bond(connection_members=[s4, s1])
for site in [s1, s2, s3, s4]:
mytop.add_site(site, update_types=False)
for conn in [c12, c23, c34, c41]:
mytop.add_connection(conn, update_types=False)
assert mytop.n_bonds == 4
assert mytop.n_angles == 0
assert mytop.n_dihedrals == 0
assert mytop.n_impropers == 0
mytop.identify_connections()
assert mytop.n_bonds == 4
assert mytop.n_angles == 4
assert mytop.n_dihedrals == 4
assert mytop.n_impropers == 0
def test_angle_fake_angletype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
with pytest.raises(ValidationError):
Angle(connection_members=[atom1, atom2, atom3],
angle_type='Fake angletype')
def test_dihedral_fake(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Dihedral(connection_members=['fakeatom1', 'fakeatom2', 4.2])
def test_improper_constituent_types(self):
atom1 = Atom(name="atom1",
position=[0, 0, 0],
atom_type=AtomType(name="A"))
atom2 = Atom(name="atom2",
position=[1, 0, 0],
atom_type=AtomType(name="B"))
atom3 = Atom(name="atom3",
position=[1, 1, 0],
atom_type=AtomType(name="C"))
atom4 = Atom(name="atom4",
position=[1, 1, 4],
atom_type=AtomType(name="D"))
imptype = ImproperType(member_types=[
atom1.atom_type.name,
atom2.atom_type.name,
atom3.atom_type.name,
atom4.atom_type.name,
])
imp = Improper(connection_members=[atom1, atom2, atom3, atom4], )
imp.improper_type = imp.connection_type = imptype
assert "A" in imp.connection_type.member_types
assert "B" in imp.connection_type.member_types
assert "C" in imp.connection_type.member_types
assert "D" in imp.connection_type.member_types
def test_dihedral_constituent_types(self):
atom1 = Atom(name="atom1",
position=[0, 0, 0],
atom_type=AtomType(name="A"))
atom2 = Atom(name="atom2",
position=[1, 0, 0],
atom_type=AtomType(name="B"))
atom3 = Atom(name="atom3",
position=[1, 1, 0],
atom_type=AtomType(name="C"))
atom4 = Atom(name="atom4",
position=[1, 1, 4],
atom_type=AtomType(name="D"))
dihtype = DihedralType(member_types=[
atom1.atom_type.name,
atom2.atom_type.name,
atom3.atom_type.name,
atom4.atom_type.name,
])
dih = Dihedral(connection_members=[atom1, atom2, atom3, atom4], )
dih.dihedral_type = dihtype
assert "A" in dih.connection_type.member_types
assert "B" in dih.connection_type.member_types
assert "C" in dih.connection_type.member_types
assert "D" in dih.connection_type.member_types
def test_dihedral_fake_dihedraltype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Dihedral(connection_members=[atom1, atom2, atom3, atom4],
dihedral_type='Fake dihedraltype')
def test_improper_fake_impropertype(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
atom4 = Atom(name='atom4')
with pytest.raises(ValidationError):
Improper(connection_members=[atom1, atom2, atom3, atom4],
connection_type='Fake impropertype')
def test_improper_nonparametrized(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
connect = Improper(connection_members=[atom1, atom2, atom3, atom4])
assert connect.connection_type is None
def test_angle_fake_angletype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
with pytest.raises(ValidationError):
Angle(
connection_members=[atom1, atom2, atom3],
angle_type="Fake angletype",
)
def test_dihedral_nonparametrized(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom1")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
connect = Dihedral(connection_members=[atom1, atom2, atom3, atom4])
assert connect.connection_type is None
def test_equivalence(self):
ref = Atom(name="atom", position=u.nm * np.zeros(3))
same_atom = Atom(name="atom", position=u.nm * np.zeros(3))
other_pos = Atom(name="atom", position=u.nm * np.ones(3))
other_name = Atom(name="atom", position=u.nm * np.ones(3))
# Two sites are never equivalent
assert ref != same_atom
assert ref != other_pos
assert ref != other_name
def test_equivalent_members_set(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom2, atom1])
assert (tuple(bond_eq.connection_members) in bond.equivalent_members())
assert (tuple(bond.connection_members) in bond_eq.equivalent_members())
def test_improper_fake_impropertype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Improper(
connection_members=[atom1, atom2, atom3, atom4],
connection_type="Fake impropertype",
)
def test_dihedral_fake_dihedraltype(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
atom4 = Atom(name="atom4")
with pytest.raises(ValidationError):
Dihedral(
connection_members=[atom1, atom2, atom3, atom4],
dihedral_type="Fake dihedraltype",
)
def test_with_1000_atom_types(self):
top = Topology()
for i in range(1000):
site = Atom()
atom_type = AtomType()
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 1
assert top.n_sites == 1000
def test_add_equivalent_connections(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom2, atom1])
top = Topology()
top.add_connection(bond)
top.add_connection(bond_eq)
assert top.n_bonds == 1
def test_add_duplicate_connected_atom(self):
top = Topology()
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
bond = Bond(connection_members=[atom1, atom2])
bond_eq = Bond(connection_members=[atom1, atom2])
top.add_connection(bond)
top.add_connection(bond_eq)
top.update_topology()
assert top.n_connections == 1
def test_add_connection(self):
top = Topology()
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
connect = Bond(connection_members=[atom1, atom2])
top.add_connection(connect)
top.add_site(atom1)
top.add_site(atom2)
assert len(top.connections) == 1
def test_bond_constituent_types(self):
atom1 = Atom(name='atom1',
position=[0, 0, 0],
atom_type=AtomType(name='A'))
atom2 = Atom(name='atom2',
position=[1, 0, 0],
atom_type=AtomType(name='B'))
bondtype = BondType(
member_types=[atom1.atom_type.name, atom2.atom_type.name])
bond = Bond(connection_members=[atom1, atom2], bond_type=bondtype)
assert 'A' in bond.connection_type.member_types
assert 'B' in bond.connection_type.member_types
def test_bond_constituent_types(self):
atom1 = Atom(name="atom1",
position=[0, 0, 0],
atom_type=AtomType(name="A"))
atom2 = Atom(name="atom2",
position=[1, 0, 0],
atom_type=AtomType(name="B"))
bondtype = BondType(
member_types=[atom1.atom_type.name, atom2.atom_type.name])
bond = Bond(connection_members=[atom1, atom2], bond_type=bondtype)
assert "A" in bond.connection_type.member_types
assert "B" in bond.connection_type.member_types
def test_bond_eq(self):
atom1 = Atom(name='atom1', position=[0, 0, 0])
atom2 = Atom(name='atom2', position=[1, 1, 1])
ref_connection = Bond(connection_members=[atom1, atom2], )
same_connection = Bond(connection_members=[atom1, atom2], )
diff_connection = Bond(connection_members=[atom1, atom2], )
assert ref_connection != same_connection
assert ref_connection != diff_connection
