def test_improper_fake(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Improper(connection_members=['fakesite1', 'fakesite2', 4.2])
def test_bond_fake_ctype(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
with pytest.raises(GMSOError):
Connection(connection_members=[site1, site2],
connection_type='Fake ctype',
name='fake')
def test_angle_fake_angletype(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
with pytest.raises(GMSOError):
Angle(connection_members=[site1, site2, site3],
connection_type='Fake angletype')
def test_set_with_atom_type(self):
lithium_type = AtomType(mass=6.941, charge=1)
site = Site(name='Lithium')
site.atom_type = lithium_type
assert site.charge == 1 * u.elementary_charge
assert site.mass == 6.941 * u.gram / u.mol
def _get_atoms(filename, topology, unit_style, type_list):
"""Function to 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 = Site(
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_dihedral_fake(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Dihedral(connection_members=['fakesite1', 'fakesite2', 4.2])
def test_dihedral_fake_dihedraltype(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Dihedral(connection_members=[site1, site2, site3, site4],
connection_type='Fake dihedraltype')
def test_improper_fake_impropertype(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
site4 = Site(name='site4')
with pytest.raises(GMSOError):
Improper(connection_members=[site1, site2, site3, site4],
connection_type='Fake impropertype')
def test_connection_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 1, 1])
ref_connection = Connection(connection_members=[site1, site2], )
same_connection = Connection(connection_members=[site1, site2], )
# Two connections are never equal
assert ref_connection != same_connection
def test_equivalence(self):
ref = Site(name='site', position=u.nm * np.zeros(3))
same_site = Site(name='site', position=u.nm * np.zeros(3))
other_pos = Site(name='site', position=u.nm * np.ones(3))
other_name = Site(name='site', position=u.nm * np.ones(3))
# Two sites are never equivalent
assert ref != same_site
assert ref != other_pos
assert ref != other_name
def test_add_connection_non_member(self):
site1, site2, site3 = (Site(), Site(), Site())
bond1, bond2, bond3 = (Bond([site1, site2]), Bond([site2, site3]),
Bond([site1, site3]))
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
with pytest.raises(GMSOError):
site3.add_connection(bond1)
site2.add_connection(bond3)
site1.add_connection(bond2)
def test_with_1000_atom_types(self):
top = Topology()
for i in range(1000):
site = Site()
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_connection(self):
top = Topology()
site1 = Site(name='site1')
site2 = Site(name='site2')
connect = Bond(connection_members=[site1, site2])
top.add_connection(connect)
top.add_site(site1)
top.add_site(site2)
assert len(top.connections) == 1
def test_connection_nonparametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
assert site1.n_connections == 0
assert site2.n_connections == 0
connect = Connection(connection_members=[site1, site2])
assert site1.n_connections == 1
assert site2.n_connections == 1
assert connect.connection_type is None
def test_bond_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 1, 1])
ref_connection = Bond(connection_members=[site1, site2], )
same_connection = Bond(connection_members=[site1, site2], )
diff_connection = Bond(connection_members=[site1, site2], )
assert ref_connection != same_connection
assert ref_connection != diff_connection
def test_add_connection_redundant(self):
site1, site2, site3 = (Site(), Site(), Site())
bond1, bond2, bond3 = (Bond([site1, site2]), Bond([site2, site3]),
Bond([site1, site3]))
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
site1.add_connection(bond1)
site1.add_connection(bond3)
site2.add_connection(bond1)
site2.add_connection(bond2)
site3.add_connection(bond3)
site3.add_connection(bond2)
assert site1.n_connections == site2.n_connections == site3.n_connections == 2
def test_angle_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 1, 1])
site3 = Site(name='site3', position=[1, 1, 1])
ref_angle = Angle(connection_members=[site1, site2, site3], )
same_angle = Angle(connection_members=[site1, site2, site3], )
diff_angle = Angle(connection_members=[site3, site2, site1], )
assert ref_angle != same_angle
assert ref_angle != diff_angle
def test_topology_atom_type_changes(self):
top = Topology()
for i in range(100):
site = Site(name='site{}'.format(i))
atom_type = AtomType(name='atom_type{}'.format(i % 10))
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 10
top.sites[0].atom_type.name = 'atom_type_changed'
assert id(top.sites[0].atom_type) == id(top.sites[10].atom_type)
assert top.sites[10].atom_type.name == 'atom_type_changed'
assert top.is_typed()
def test_bond_constituent_types(self):
site1 = Site(name='site1',
position=[0, 0, 0],
atom_type=AtomType(name='A'))
site2 = Site(name='site2',
position=[1, 0, 0],
atom_type=AtomType(name='B'))
bondtype = BondType(
member_types=[site1.atom_type.name, site2.atom_type.name])
bond = Bond(connection_members=[site1, site2],
connection_type=bondtype)
assert 'A' in bond.connection_type.member_types
assert 'B' in bond.connection_type.member_types
def test_top_update(self):
top = Topology()
top.update_topology()
assert top.n_sites == 0
assert len(top.atom_types) == 0
assert len(top.atom_type_expressions) == 0
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
atomtype = AtomType()
site1 = Site(name='site1', atom_type=atomtype)
top.add_site(site1)
site2 = Site(name='site2', atom_type=atomtype)
top.add_site(site2)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
ctype = BondType()
connection_12 = Bond(connection_members=[site1, site2],
connection_type=ctype)
top.add_connection(connection_12)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
site1.atom_type = AtomType(expression='sigma*epsilon')
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
top.update_atom_types()
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
def test_add_untyped_bond_update(self):
site1 = Site(atom_type=None)
site2 = Site(atom_type=None)
bond = Bond(connection_members=[site1, site2], connection_type=None)
top = Topology()
assert len(top.bond_types) == 0
top.add_connection(bond, update_types=False)
assert len(top.bond_types) == 0
top = Topology()
assert len(top.bond_types) == 0
top.add_connection(bond, update_types=True)
assert len(top.bond_types) == 0
def test_improper_constituent_types(self):
site1 = Site(name='site1', position=[0,0,0], atom_type=AtomType(name='A'))
site2 = Site(name='site2', position=[1,0,0], atom_type=AtomType(name='B'))
site3 = Site(name='site3', position=[1,1,0], atom_type=AtomType(name='C'))
site4 = Site(name='site4', position=[1,1,4], atom_type=AtomType(name='D'))
imptype = ImproperType(member_types=[site1.atom_type.name,
site2.atom_type.name,
site3.atom_type.name,
site4.atom_type.name])
imp = Improper(connection_members=[site1, site2, site3, site4],
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_angle_nonparametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
assert site1.n_connections == 0
assert site2.n_connections == 0
assert site3.n_connections == 0
connect = Angle(connection_members=[site1, site2, site3])
assert site1.n_connections == 1
assert site2.n_connections == 1
assert site3.n_connections == 1
assert connect.connection_type is None
def test_add_site_parent(self):
top = Topology()
subtop = SubTopology()
site1 = Site(position=u.nm * np.zeros(3))
site2 = Site(position=u.nm * np.ones(3))
top.add_subtopology(subtop)
assert top.n_sites == 0
assert subtop.n_sites == 0
subtop.add_site(site1)
assert top.n_sites == 1
assert subtop.n_sites == 1
top.add_site(site2)
assert top.n_sites == 2
assert subtop.n_sites == 1
def test_add_site(self):
top = Topology()
site = Site(name='site')
assert top.n_sites == 0
top.add_site(site)
assert top.n_sites == 1
def test_to_mbuild_name_none(self):
top = Top()
top.add_site(Site())
top.name = None
compound = to_mbuild(top)
assert compound.name == 'Compound'
def test_bond_bondtype_update(self):
top = Topology()
atype1 = AtomType(expression='sigma + epsilon')
atype2 = AtomType(expression='sigma * epsilon')
site1 = Site('a', atom_type=atype1)
site2 = Site('b', atom_type=atype2)
btype = BondType()
bond = Bond(connection_members=[site1, site2], connection_type=btype)
top.add_site(site1)
top.add_site(site2)
top.add_connection(bond)
assert top.n_bonds == 1
assert len(top.bond_types) == 1
assert len(top.bond_type_expressions) == 1
def test_subtop_add_site(self):
subtop = SubTopology()
site = Site()
subtop.add_site(site)
assert subtop.n_sites == 1
def test_atomtype_update(self):
top = Topology()
assert top.n_sites == 0
assert top.n_bonds == 0
assert top.n_connections == 0
atype1 = AtomType(expression='sigma + epsilon')
atype2 = AtomType(expression='sigma * epsilon')
site1 = Site('a', atom_type=atype1)
site2 = Site('b', atom_type=atype2)
top.add_site(site1)
top.add_site(site2)
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
def test_dihedral_eq(self):
site1 = Site(name='site1', position=[0, 0, 0])
site2 = Site(name='site2', position=[1, 0, 0])
site3 = Site(name='site3', position=[1, 1, 0])
site4 = Site(name='site4', position=[1, 1, 1])
ref_dihedral = Dihedral(
connection_members=[site1, site2, site3, site4], )
same_dihedral = Dihedral(
connection_members=[site1, site2, site3, site4], )
diff_dihedral = Dihedral(
connection_members=[site1, site2, site3, site4], )
assert ref_dihedral != same_dihedral
assert ref_dihedral != diff_dihedral
