def test_set_expression_bad(self):
potential = Potential(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_set_params_partial(self):
potential = Potential(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_class_method(self):
template = PotentialTemplateLibrary()['HarmonicBondPotential']
params = {'k': 1.0 * u.dimensionless, 'r_eq': 1.0 * u.dimensionless}
harmonic_potential_from_template = Potential.from_template(
template, params)
harmonic_potential = Potential(name='HarmonicBondPotential',
expression='0.5 * k * (r-r_eq)**2',
independent_variables={'r'},
parameters=params,
template=False)
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(self):
# Try changing the expression but keep the parameters
potential = Potential(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_equivalance(self):
ref_potential = Potential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
same_potential = Potential(
name='mypotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_name = Potential(
name='nopotential',
expression='a*x+b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_expression = Potential(
name='mypotential',
expression='a+x*b',
parameters={
'a': 1.0*u.g,
'b': 1.0*u.m},
independent_variables={'x'}
)
diff_params = Potential(
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_expression_and_params_mismatch(self):
potential = Potential(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 = Potential()
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 = Potential(
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_expression_consistency(self):
new_potential = Potential(
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_new_potential(self):
new_potential = Potential(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(new_potential.parameters['a'], 1.0 * u.g)
assert allclose(new_potential.parameters['b'], 1.0 * u.m)
assert new_potential.independent_variables == {sympy.symbols('x')}
def test_connection_parametrized(self):
site1 = Site(name='site1')
site2 = Site(name='site2')
assert site1.n_connections == 0
assert site2.n_connections == 0
c_type = Potential()
name = 'name'
connect = Connection(connection_members=[site1, site2],
connection_type=c_type,
name=name)
assert site1.n_connections == 1
assert site2.n_connections == 1
assert len(connect.connection_members) == 2
assert connect.connection_type is not None
assert connect.name == name
def test_incorrect_expression(self):
with pytest.raises(ValueError):
Potential(name='mytype', expression=4.2)
def test_incorrect_indep_vars(self):
with pytest.raises(ValueError):
Potential(expression='x*y', independent_variables='z')
def test_class_method_with_error(self):
template = object()
with pytest.raises(GMSOError):
Potential.from_template(template, parameters=None)