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_custom_defaults(self, typed_ethane):
write_top(typed_ethane, 'system.top',
top_vars={"gen-pairs": "yes", "fudgeLJ": 0.5, "fudgeQQ":0.5})
struct = pmd.load_file('system.top')
assert struct.defaults.gen_pairs == "yes"
assert struct.defaults.fudgeLJ == 0.5
assert struct.defaults.fudgeQQ == 0.5
def test_ethane_periodic(self, typed_ethane):
from gmso.lib.potential_templates import PotentialTemplateLibrary
per_torsion = PotentialTemplateLibrary()["PeriodicTorsionPotential"]
params = {
"k": 10 * u.Unit("kJ / mol"),
"phi_eq": 15 * u.Unit("degree"),
"n": 3 * u.Unit("dimensionless")
}
periodic_dihedral_type = gmso.core.potential.Potential.from_template(
per_torsion, params)
for dihedral in typed_ethane.dihedrals:
dihedral.connection_type = periodic_dihedral_type
typed_ethane.update_connection_types()
write_top(typed_ethane, 'system.top')
struct = pmd.load_file('system.top')
assert len(struct.dihedrals) == 9
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 test_pmd_loop(self, top, request):
top = request.getfixturevalue(top)
write_top(top, 'system.top')
pmd.load_file('system.top')
def test_write_top(self, typed_ar_system):
top = typed_ar_system
write_top(top, 'ar.top')
def test_pmd_loop(self, typed_ar_system):
top = typed_ar_system
write_top(top, 'ar.top')
pmd.load_file('ar.top')
