def test_water_top(self, water_system):
top = water_system
ff = gmso.ForceField(get_path('tip3p.xml'))
for site in top.sites:
site.atom_type = ff.atom_types[site.name]
top.update_sites()
top.update_atom_types()
for bond in top.bonds:
bond.bond_type = bond.connection_type = ff.bond_types[
'opls_111~opls_112']
top.update_bonds()
top.update_bond_types()
for subtop in top.subtops:
angle = gmso.core.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_angles()
top.update_angle_types()
write_top(top, 'water.top')
def test_modified_potentials(self, ar_system):
top = ar_system
ff = gmso.ForceField(get_fn('ar.xml'))
for site in top.sites:
site.atom_type = ff.atom_types['Ar']
top.update_topology()
top.atom_types[0].set_expression('sigma + epsilon*r')
with pytest.raises(EngineIncompatibilityError):
write_top(top, 'out.top')
alternate_lj = '4*epsilon*sigma**12/r**12 - 4*epsilon*sigma**6/r**6'
top.atom_types[0].set_expression(alternate_lj)
write_top(top, 'ar.top')
def _parse_gmso(self, forcefield_files, **kwargs):
"""Parse metadata information when using GMSO as backend."""
if forcefield_files:
self.ff = gmso.ForceField(forcefield_files, **kwargs)
self._version = self.ff.version
self._name = self.ff.name
for name, atype in self.ff.atom_types.items():
self.atomTypeDefinitions[name] = atype.definition
self.atomTypeOverrides[name] = atype.overrides
self.atomTypeDesc[name] = atype.description
self.atomTypeRefs[name] = set(atype.doi.split(","))
self.atomTypeClasses[name] = atype.atomclass
if atype.tags.get("element"):
ele = atype.tags["element"]
if element.element_by_symbol(ele):
self.atomTypeElements[atype.name] = ele
else:
self.non_element_types[ele] = None
else:
# Register atomtype with missing atomtype as atomistic (empty string)
self.atomTypeElements[name] = ""
return None