def test_class_method(self):
template = PotentialTemplateLibrary()['HarmonicBondPotential']
params = {'k': 1.0 * u.dimensionless,
'r_eq': 1.0 * u.dimensionless}
harmonic_potential_from_template = ParametricPotential.from_template(template, params)
harmonic_potential = ParametricPotential(name='HarmonicBondPotential',
expression='0.5 * k * (r-r_eq)**2',
independent_variables={'r'},
parameters=params)
assert harmonic_potential.name == harmonic_potential_from_template.name
assert harmonic_potential.expression == harmonic_potential_from_template.expression
assert harmonic_potential.independent_variables == harmonic_potential_from_template.independent_variables
def test_class_method(self):
template = PotentialTemplateLibrary()["HarmonicBondPotential"]
params = {"k": 1.0 * u.dimensionless, "r_eq": 1.0 * u.dimensionless}
harmonic_potential_from_template = ParametricPotential.from_template(
template, params)
harmonic_potential = ParametricPotential(
name="HarmonicBondPotential",
expression="0.5 * k * (r-r_eq)**2",
independent_variables={"r"},
parameters=params,
)
assert harmonic_potential.name == harmonic_potential_from_template.name
assert (harmonic_potential.expression ==
harmonic_potential_from_template.expression)
assert (harmonic_potential.independent_variables ==
harmonic_potential_from_template.independent_variables)
def test_ethane_periodic(self, typed_ethane):
from gmso.lib.potential_templates import PotentialTemplateLibrary
from gmso.core.parametric_potential import ParametricPotential
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 = ParametricPotential.from_template(
potential_template=per_torsion,
parameters=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_class_method_with_error(self):
template = object()
with pytest.raises(GMSOError):
ParametricPotential.from_template(template, parameters=None)