def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.data_source_factories[3]
self.data_source = self.factory.create_data_source()
self.traj_file = gromacs_coordinate_file
self.formulation = ProbeFormulation()
def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.notification_listener_factories[0]
self.notification_listener = self.factory.create_listener()
self.model = self.factory.create_model()
self.notification_listener.initialize(self.model)
self.surfactant = ProbePrimaryIngredient()
self.salt = ProbeSaltIngredient()
self.solvent = ProbeSolventIngredient()
self.surfactant.name = "Primary Surfactant"
self.salt.name = "Sodium Chloride"
self.solvent.name = "Water"
self.parameters = [
DataValue(name="surfactant_name", value="best chemical ever"),
DataValue(name="surfactant_conc", value=1.0),
DataValue(name="salt_conc", value=5.0),
]
self.kpis = [
DataValue(name="viscosity", value=5.7),
DataValue(name="cost", value=10),
]
def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.data_source_factories[4]
self.data_source = self.factory.create_data_source()
self.model = self.factory.create_model()
self.formulation = ProbeFormulation()
self.input = [self.formulation]
def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.mco_factories[0]
self.mco = self.factory.create_optimizer()
self.model = self.factory.create_model()
self.parameters = [
IngredientMCOParameter(
mock.Mock(spec=IngredientMCOParameterFactory),
categories=["A", "B"],
),
FixedMCOParameter(mock.Mock(spec=FixedMCOParameterFactory),
value=12.0),
ListedMCOParameter(mock.Mock(spec=ListedMCOParameterFactory),
levels=[0.1, 2.5]),
RangedMCOParameter(
mock.Mock(spec=RangedMCOParameterFactory),
upper_bound=1.5,
n_samples=3,
),
]
def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.data_source_factories[1]
self.data_source = self.factory.create_data_source()
#: Example input values
self.size = 4000
self.name = "test_experiment"
self.martini_parameters = "test_martini.itp"
self.md_min_parameters = "test_min_parm.mdp"
self.md_prod_parameters = "test_prod_parm.mdp"
self.model = self.factory.create_model()
self.model.n_molecule_types = 4
self.model.martini_parameters = self.martini_parameters
self.model.md_prod_parameters = self.md_prod_parameters
self.model.md_min_parameters = self.md_min_parameters
self.model.size = self.size
self.model.name = self.name
self.surfactants = [
ProbePrimaryIngredient(),
ProbeSecondaryIngredient(),
]
self.salt = ProbeSaltIngredient()
self.solvent = ProbeSolventIngredient()
self.ingredients = self.surfactants + [self.salt] + [self.solvent]
self.concentrations = [12, 4, 0.5, 83.5]
self.formulation = Formulation(ingredients=self.ingredients,
concentrations=self.concentrations)
self.input_values = [self.formulation]
self.masses = [
self.surfactants[0].mass,
self.surfactants[1].mass,
self.salt.mass,
self.solvent.mass,
]
def setUp(self):
self.plugin = SurfactantPlugin()
self.factory = self.plugin.data_source_factories[0]
self.data_source = self.factory.create_data_source()