def test_topology_get_index(self):
top = Topology()
conn_members = [Site(), Site(), Site(), Site()]
for i in range(5):
top.add_site(Site())
top.add_connection(Bond(
connection_members=[conn_members[0], conn_members[1]]))
top.add_connection(Angle(
connection_members=[conn_members[0], conn_members[1], conn_members[2]]))
top.add_connection(Dihedral(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
top.add_connection(Improper(
connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]]))
a_bond = Bond(connection_members=[conn_members[0], conn_members[1]])
an_angle = Angle(connection_members=[conn_members[0], conn_members[1], conn_members[2]])
a_site = Site()
a_dihedral = Dihedral(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
an_improper = Improper(connection_members=[conn_members[0], conn_members[1], conn_members[2], conn_members[3]])
top.add_site(a_site)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_site) == 9
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
def test_angle_eq(self):
atom1 = Atom(name='atom1', position=[0, 0, 0])
atom2 = Atom(name='atom2', position=[1, 1, 1])
atom3 = Atom(name='atom3', position=[1, 1, 1])
ref_angle = Angle(connection_members=[atom1, atom2, atom3], )
same_angle = Angle(connection_members=[atom1, atom2, atom3], )
diff_angle = Angle(connection_members=[atom3, atom2, atom1], )
assert ref_angle != same_angle
assert ref_angle != diff_angle
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_get_index(self):
top = Topology()
conn_members = [Atom() for _ in range(10)]
for atom in conn_members:
top.add_site(atom)
for i in range(5):
top.add_connection(
Bond(connection_members=[conn_members[i], conn_members[i +
1]]))
top.add_connection(
Angle(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2]
]))
top.add_connection(
Dihedral(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
top.add_connection(
Improper(connection_members=[
conn_members[i], conn_members[i + 1], conn_members[i + 2],
conn_members[i + 3]
]))
a_atom = Atom()
a_bond = Bond(connection_members=[conn_members[6], conn_members[7]])
an_angle = Angle(connection_members=[
conn_members[6], conn_members[7], conn_members[8]
])
a_dihedral = Dihedral(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
an_improper = Improper(connection_members=[
conn_members[6], conn_members[7], conn_members[8], conn_members[9]
])
top.add_site(a_atom)
top.add_connection(a_bond)
top.add_connection(an_angle)
top.add_connection(a_dihedral)
top.add_connection(an_improper)
assert top.get_index(a_atom) == 10
assert top.get_index(a_bond) == 5
assert top.get_index(an_angle) == 5
assert top.get_index(a_dihedral) == 5
assert top.get_index(an_improper) == 5
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_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_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_add_equivalent_connections(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
angle = Angle(connection_members=[atom1, atom2, atom3])
angle_eq = Angle(connection_members=[atom3, atom2, atom1])
angle_not_eq = Angle(connection_members=[atom1, atom3, atom2])
top = Topology()
top.add_connection(angle)
top.add_connection(angle_eq)
assert top.n_angles == 1
top.add_connection(angle_not_eq)
assert top.n_angles == 2
def test_equivalent_members_set(self):
atom1 = Atom(name="AtomA")
atom2 = Atom(name="AtomB")
atom3 = Atom(name="AtomC")
angle = Angle(connection_members=[atom1, atom2, atom3])
angle_eq = Angle(connection_members=[atom3, atom2, atom1])
angle_not_eq = Angle(connection_members=[atom1, atom3, atom2])
assert tuple(angle_eq.connection_members) in angle.equivalent_members()
assert tuple(angle.connection_members) in angle_eq.equivalent_members()
assert not (tuple(angle.connection_members)
in angle_not_eq.equivalent_members())
def test_angle_to_json_loop(self, typed_ethane, are_equivalent_atoms):
for angle in typed_ethane.angles:
angle_json = angle.json()
angle_copy = Angle.parse_raw(angle_json)
for member1, member2 in zip(angle.connection_members,
angle_copy.connection_members):
assert are_equivalent_atoms(member1, member2)
assert angle.angle_type == angle_copy.angle_type
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_angle_parametrized(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
angle_type = AngleType()
connect = Angle(connection_members=[atom1, atom2, atom3],
angle_type=angle_type,
name='angle_name')
assert len(connect.connection_members) == 3
assert connect.angle_type is not None
assert connect.name == 'angle_name'
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_angle_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'))
angtype = AngleType(member_types=[
site1.atom_type.name, site2.atom_type.name, site3.atom_type.name
])
ang = Angle(connection_members=[site1, site2, site3],
connection_type=angtype)
assert 'A' in ang.connection_type.member_types
assert 'B' in ang.connection_type.member_types
assert 'C' in ang.connection_type.member_types
def test_angle_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'))
angtype = AngleType(member_types=[
atom1.atom_type.name, atom2.atom_type.name, atom3.atom_type.name
])
ang = Angle(connection_members=[atom1, atom2, atom3],
angle_type=angtype)
assert 'A' in ang.angle_type.member_types
assert 'B' in ang.angle_type.member_types
assert 'C' in ang.angle_type.member_types
def test_angle_angletype_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)
site3 = Site('c', atom_type=atype2)
atype = AngleType()
angle = Angle(connection_members=[site1, site2, site3], connection_type=atype, name='angle_name')
top.add_site(site1)
top.add_site(site2)
top.add_site(site3)
top.add_connection(angle)
assert top.n_angles == 1
assert len(top.angle_types) == 1
assert len(top.angle_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
def test_angle_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"))
angtype = AngleType(member_types=[
atom1.atom_type.name,
atom2.atom_type.name,
atom3.atom_type.name,
])
ang = Angle(connection_members=[atom1, atom2, atom3],
angle_type=angtype)
assert "A" in ang.angle_type.member_types
assert "B" in ang.angle_type.member_types
assert "C" in ang.angle_type.member_types
def test_angle_parametrized(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
angle_type = AngleType()
connect = Angle(connection_members=[site1, site2, site3],
connection_type=angle_type,
name='angle_name')
assert site1.n_connections == 1
assert site2.n_connections == 1
assert site3.n_connections == 1
assert len(connect.connection_members) == 3
assert connect.connection_type is not None
assert connect.name == 'angle_name'
def test_angle_angletype_update(self):
top = Topology()
atype1 = AtomType(expression='sigma + epsilon*r')
atype2 = AtomType(expression='sigma * epsilon*r')
atom1 = Atom(name='a', atom_type=atype1)
atom2 = Atom(name='b', atom_type=atype2)
atom3 = Atom(name='c', atom_type=atype2)
atype = AngleType()
angle = Angle(connection_members=[atom1, atom2, atom3],
angle_type=atype,
name='angle_name')
top.add_site(atom1)
top.add_site(atom2)
top.add_site(atom3)
top.add_connection(angle)
assert top.n_angles == 1
assert len(top.angle_types) == 1
assert len(top.angle_type_expressions) == 1
assert len(top.atom_type_expressions) == 2
def typed_water_system(self, water_system):
top = water_system
ff = ForceField(get_path('tip3p.xml'))
element_map = {"O": "opls_111", "H": "opls_112"}
for atom in top.sites:
atom.atom_type = ff.atom_types[atom.name]
for bond in top.bonds:
bond.connection_type = ff.bond_types["opls_111~opls_112"]
for subtop in top.subtops:
angle = Angle(
connection_members=[site for site in subtop.sites],
name="opls_112~opls_111~opls_112",
connection_type=ff.angle_types["opls_112~opls_111~opls_112"])
top.add_connection(angle)
top.update_topology()
return top
def _get_connection(filename, topology, unit_style, connection_type):
"""General function to parse connection types
"""
with open(filename, 'r') as lammps_file:
types = False
for i, line in enumerate(lammps_file):
if connection_type in line.split():
n_connection_types = int(line.split()[0])
types = True
if connection_type.capitalize() in line.split():
break
if types == False:
return topology
connection_type_lines = open(filename, 'r').readlines()[i+2:i+n_connection_types+2]
connection_type_list = list()
for line in connection_type_lines:
if connection_type == 'bond':
c_type = BondType(name=line.split()[0]
)
# Multiply 'k' by 2 since LAMMPS includes 1/2 in the term
c_type.parameters['k']=float(line.split()[1])*u.Unit(
get_units(unit_style)['energy']/
get_units(unit_style)['distance']**2
)*2
c_type.parameters['r_eq']=float(line.split()[2])*(get_units(unit_style)['distance']**2)
elif connection_type == 'angle':
c_type = AngleType(name=line.split()[0]
)
# Multiply 'k' by 2 since LAMMPS includes 1/2 in the term
c_type.parameters['k']=float(line.split()[1])*u.Unit(
get_units(unit_style)['energy']/
get_units(unit_style)['angle_k']**2
)*2
c_type.parameters['theta_eq']=float(line.split()[2])*u.Unit(
get_units(unit_style)['angle'])
connection_type_list.append(c_type)
with open(filename, 'r') as lammps_file:
for i, line in enumerate(lammps_file):
if connection_type + 's' in line.split():
n_connections = int(line.split()[0])
if connection_type.capitalize() + 's' in line.split():
break
connection_lines = open(filename, 'r').readlines()[i+2:i+n_connections+2]
# Determine number of sites to generate
if connection_type == 'bond':
n_sites = 2
elif connection_type == 'angle':
n_sites = 3
else:
n_sites = 4
for i, line in enumerate(connection_lines):
site_list = list()
for j in range(n_sites):
site = topology.sites[int(line.split()[j+2])-1]
site_list.append(site)
if connection_type == 'bond':
connection = Bond(
connection_members=site_list,
connection_type=connection_type_list[int(line.split()[1])-1],
)
elif connection_type == 'angle':
connection = Angle(
connection_members=site_list,
connection_type=connection_type_list[int(line.split()[1])-1],
)
topology.add_connection(connection)
return topology
def test_angle_fake(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
site3 = Site(name='site3')
with pytest.raises(GMSOError):
Angle(connection_members=['fakesite1', 'fakesite2', 4.2])
def _get_connection(filename, topology, unit_style, connection_type):
"""Parse connection types."""
with open(filename, "r") as lammps_file:
types = False
for i, line in enumerate(lammps_file):
if connection_type in line.split():
n_connection_types = int(line.split()[0])
types = True
if connection_type.capitalize() in line.split():
break
if types == False:
return topology
connection_type_lines = open(
filename, "r").readlines()[i + 2:i + n_connection_types + 2]
connection_type_list = list()
for line in connection_type_lines:
if connection_type == "bond":
c_type = BondType(name=line.split()[0])
# Multiply 'k' by 2 since LAMMPS includes 1/2 in the term
c_type.parameters["k"] = (float(line.split()[1]) * u.Unit(
get_units(unit_style)["energy"] /
get_units(unit_style)["distance"]**2) * 2)
c_type.parameters["r_eq"] = float(
line.split()[2]) * (get_units(unit_style)["distance"]**2)
elif connection_type == "angle":
c_type = AngleType(name=line.split()[0])
# Multiply 'k' by 2 since LAMMPS includes 1/2 in the term
c_type.parameters["k"] = (float(line.split()[1]) * u.Unit(
get_units(unit_style)["energy"] /
get_units(unit_style)["angle_k"]**2) * 2)
c_type.parameters["theta_eq"] = float(line.split()[2]) * u.Unit(
get_units(unit_style)["angle"])
connection_type_list.append(c_type)
with open(filename, "r") as lammps_file:
for i, line in enumerate(lammps_file):
if connection_type + "s" in line.split():
n_connections = int(line.split()[0])
if connection_type.capitalize() + "s" in line.split():
break
connection_lines = open(filename,
"r").readlines()[i + 2:i + n_connections + 2]
# Determine number of sites to generate
if connection_type == "bond":
n_sites = 2
elif connection_type == "angle":
n_sites = 3
else:
n_sites = 4
for i, line in enumerate(connection_lines):
site_list = list()
for j in range(n_sites):
site = topology.sites[int(line.split()[j + 2]) - 1]
site_list.append(site)
if connection_type == "bond":
connection = Bond(
connection_members=site_list,
bond_type=connection_type_list[int(line.split()[1]) - 1],
)
elif connection_type == "angle":
connection = Angle(
connection_members=site_list,
angle_type=connection_type_list[int(line.split()[1]) - 1],
)
topology.add_connection(connection)
return topology
def test_angle_fake(self):
atom1 = Atom(name='atom1')
atom2 = Atom(name='atom2')
atom3 = Atom(name='atom3')
with pytest.raises(ValidationError):
Angle(connection_members=['fakesite1', 'fakesite2', 4.2])
def test_angle_fake(self):
atom1 = Atom(name="atom1")
atom2 = Atom(name="atom2")
atom3 = Atom(name="atom3")
with pytest.raises(ValidationError):
Angle(connection_members=["fakesite1", "fakesite2", 4.2])
