def test_equivalance(self):
ref_potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
same_potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
diff_name = ParametricPotential(
name="nopotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
diff_expression = ParametricPotential(
name="mypotential",
expression="a+x*b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
diff_params = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 2.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
assert ref_potential == same_potential
assert ref_potential != diff_name
assert ref_potential != diff_expression
assert ref_potential != diff_params
assert same_potential != diff_name
assert same_potential != diff_expression
assert same_potential != diff_params
assert diff_name != diff_expression
assert diff_expression != diff_params
def test_set_params_bad(self):
potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
with pytest.raises(ValueError):
potential.set_expression(parameters={'aa': 4.0*u.g, 'bb': 4.0*u.m})
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_set_params_partial(self):
potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
potential.set_expression(parameters={'a': 4.0*u.g})
assert potential.expression == sympy.sympify('a*x+b')
assert potential.parameters == {'a': 4*u.g, 'b': 1*u.m}
def test_set_expression_bad(self):
potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
with pytest.raises(ValueError):
potential.set_expression(expression="a*x**2+b*x+c")
def test_equivalance(self):
ref_potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
same_potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_name = ParametricPotential(
name='nopotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_expression = ParametricPotential(
name='mypotential',
expression='a+x*b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_params = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 2.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
assert ref_potential == same_potential
assert ref_potential != diff_name
assert ref_potential != diff_expression
assert ref_potential != diff_params
assert same_potential != diff_name
assert same_potential != diff_expression
assert same_potential != diff_params
assert diff_name != diff_expression
assert diff_expression != diff_params
def test_set_params_partial(self):
potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
potential.set_expression(parameters={"a": 4.0 * u.g})
assert potential.expression == sympy.sympify("a*x+b")
assert potential.parameters == {"a": 4 * u.g, "b": 1 * u.m}
def test_set_expression(self):
# Try changing the expression but keep the parameters
potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
potential.set_expression(expression='a*x**2+b')
assert potential.expression == sympy.sympify('a*x**2+b')
assert potential.parameters == {'a': 1*u.g, 'b': 1*u.m}
def test_set_expression(self):
# Try changing the expression but keep the parameters
potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
potential.set_expression(expression="a*x**2+b")
assert potential.expression == sympy.sympify("a*x**2+b")
assert potential.parameters == {"a": 1 * u.g, "b": 1 * u.m}
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_set_expression_and_params_mismatch(self):
potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
with pytest.raises(ValueError):
potential.set_expression(
expression='c*x+d',
parameters={
'u': 1.0*u.g,
'v': 1.0*u.m},
)
def test_setters(self):
new_potential = ParametricPotential()
new_potential.name = "SettingName"
new_potential.set_expression(
independent_variables=sympy.symbols({'r'}),
expression='r*sigma*epsilon',
parameters={
'sigma': 1 * u.nm,
'epsilon': 10 * u.Unit('kcal / mol')
}
)
assert new_potential.name == "SettingName"
assert new_potential.independent_variables == {sympy.symbols('r')}
assert new_potential.parameters == {
'sigma': 1 * u.nm,
'epsilon': 10 * u.Unit('kcal / mol')
}
assert new_potential.expression == sympy.sympify('r * sigma * epsilon')
def test_set_expression_and_params(self):
potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
potential.set_expression(
expression='u*r+v',
parameters={
'u': 1.0*u.g,
'v': 1.0*u.m},
independent_variables={'r'}
)
assert potential.expression == sympy.sympify('u*r+v')
assert potential.parameters == { 'u': 1*u.g, 'v': 1*u.m}
def test_set_expression_and_params_mismatch(self):
potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
with pytest.raises(ValueError):
potential.set_expression(
expression="c*x+d",
parameters={
"u": 1.0 * u.g,
"v": 1.0 * u.m
},
)
def test_setters(self):
new_potential = ParametricPotential()
new_potential.name = "SettingName"
new_potential.set_expression(
independent_variables=sympy.symbols({"r"}),
expression="r*sigma*epsilon",
parameters={
"sigma": 1 * u.nm,
"epsilon": 10 * u.Unit("kcal / mol"),
},
)
assert new_potential.name == "SettingName"
assert new_potential.independent_variables == {sympy.symbols("r")}
assert new_potential.parameters == {
"sigma": 1 * u.nm,
"epsilon": 10 * u.Unit("kcal / mol"),
}
assert new_potential.expression == sympy.sympify("r * sigma * epsilon")
def test_expression_consistency(self):
new_potential = ParametricPotential(
name='mypotential',
parameters={'x': 1*u.m, 'y': 10*u.m},
expression='x + y * z',
independent_variables='z'
)
symbol_x, symbol_y, symbol_z = sympy.symbols('x y z')
correct_expr = sympy.sympify('x+y*z')
assert new_potential.expression.free_symbols == set([symbol_x, symbol_y, symbol_z])
assert correct_expr == new_potential.expression
def test_set_expression_and_params(self):
potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
potential.set_expression(
expression="u*r+v",
parameters={
"u": 1.0 * u.g,
"v": 1.0 * u.m
},
independent_variables={"r"},
)
assert potential.expression == sympy.sympify("u*r+v")
assert potential.parameters == {"u": 1 * u.g, "v": 1 * u.m}
def test_new_potential(self):
new_potential = ParametricPotential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
assert new_potential.name == 'mypotential'
assert new_potential.expression == sympy.sympify('a*x+b')
assert_allclose_units(new_potential.parameters['a'], 1.0 * u.g, rtol=1e-5, atol=1e-8)
assert_allclose_units(new_potential.parameters['b'], 1.0 * u.m, rtol=1e-5, atol=1e-8)
assert new_potential.independent_variables == {sympy.symbols('x')}
def test_expression_consistency(self):
new_potential = ParametricPotential(
name="mypotential",
parameters={
"x": 1 * u.m,
"y": 10 * u.m
},
expression="x + y * z",
independent_variables="z",
)
symbol_x, symbol_y, symbol_z = sympy.symbols("x y z")
correct_expr = sympy.sympify("x+y*z")
assert new_potential.expression.free_symbols == set(
[symbol_x, symbol_y, symbol_z])
assert correct_expr == new_potential.expression
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_new_potential(self):
new_potential = ParametricPotential(
name="mypotential",
expression="a*x+b",
parameters={
"a": 1.0 * u.g,
"b": 1.0 * u.m
},
independent_variables={"x"},
)
assert new_potential.name == "mypotential"
assert new_potential.expression == sympy.sympify("a*x+b")
assert_allclose_units(new_potential.parameters["a"],
1.0 * u.g,
rtol=1e-5,
atol=1e-8)
assert_allclose_units(new_potential.parameters["b"],
1.0 * u.m,
rtol=1e-5,
atol=1e-8)
assert new_potential.independent_variables == {sympy.symbols("x")}
def test_incorrect_expression(self):
with pytest.raises(ValueError):
ParametricPotential(name='mytype', expression=4.2)
def test_incorrect_indep_vars(self):
with pytest.raises(ValueError):
ParametricPotential(expression='x*y', independent_variables='z')
def test_class_method_with_error(self):
template = object()
with pytest.raises(GMSOError):
ParametricPotential.from_template(template, parameters=None)