def test_add_phases_with_elements_wrong_use():
"""Test the wrong usage of addAqueousPhaseWithElements."""
editor = ChemicalEditor()
with pytest.raises(RuntimeError):
editor.addAqueousPhaseWithElements("H2O(l) C Ca")
with pytest.raises(RuntimeError):
editor.addAqueousPhaseWithElements(["H2O C Ca"])
def test_equilibrium_path(table_regression, tmpdir):
"""
An integration test that checks result's reproducibility of
the calculation of an equilibrium path between two states
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhaseWithElements("H O C Na Cl")
system = ChemicalSystem(editor)
problem1 = EquilibriumProblem(system)
problem1.add("H2O", 1, "kg")
problem1.add("CO2", 0.5, "mol")
problem1.add("HCl", 1, "mol")
problem2 = EquilibriumProblem(system)
problem2.add("H2O", 1, "kg")
problem2.add("CO2", 0.5, "mol")
problem2.add("NaOH", 2, "mol")
state1 = equilibrate(problem1)
state2 = equilibrate(problem2)
path = EquilibriumPath(system)
output = path.output()
output.precision(16)
output.filename(tmpdir.dirname + "/equilibriumPathResult.txt")
# Define which outputs will be written and checked
output.add("t")
output.add("pH")
output.add("speciesMolality(HCO3-)")
output.add("speciesMolality(CO2(aq))")
output.add("speciesMolality(CO3--)")
path.solve(state1, state2)
pathTable = pd.read_csv(
tmpdir.dirname + "/equilibriumPathResult.txt",
index_col=None,
delim_whitespace=True,
)
table_regression.check(pathTable, default_tol=dict(atol=1e-5, rtol=1e-14))
def test_add_phases_with_elements_right_use():
"""Test the normal use of addAqueousPhaseWithElements, addGaseousPhaseWithElements and addMineralPhaseWithElements."""
editor1 = ChemicalEditor()
editor1.addAqueousPhaseWithElements("H C O Ca")
editor1.addGaseousPhaseWithElements("H C O")
editor1.addMineralPhaseWithElements("Ca C O")
editor2 = ChemicalEditor()
editor2.addAqueousPhaseWithElements(["H", "C", "O", "Ca"])
editor2.addGaseousPhaseWithElements(["H", "C", "O"])
editor2.addMineralPhaseWithElements(["Ca", "C", "O"])
system1 = ChemicalSystem(editor1)
system2 = ChemicalSystem(editor2)
_check_equivalent_chemical_systems(system1, system2)
def equilibrium_inverse_with_h_o_na_cl_ca_c_calcite_ph_and_fixed_amounts():
"""
Build a problem with H, O, Na, Cl, Ca, C and Calcite with defined pH
and fixed species amount
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhaseWithElements("H O Na Cl Ca C")
editor.addMineralPhase("Calcite")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.pH(8.0, "HCl", "NaOH")
problem.fixSpeciesAmount("Calcite", 1, "mol")
return (system, problem)
def equilibrium_inverse_with_h_o_na_cl_ca_mg_c_defined_ph():
"""
Build a problem with H, Na, Cl, Ca, Mg, C with defined pH
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhaseWithElements("H O Na Cl Ca Mg C")
editor.addGaseousPhaseWithElements("H O C")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.add("CaCl2", 2, "mmol")
problem.add("MgCl2", 4, "mmol")
problem.pH(4.0, "CO2")
return (system, problem)
def equilibrium_inverse_with_h_o_na_cl_ca_mg_c_fixed_amount_and_activity():
"""
Build a problem with H, Na, Cl, Ca, Mg, C with fixed
species amount, activity and defined pH
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhaseWithElements("H O Na Cl Ca Mg C")
editor.addGaseousPhaseWithElements("H O C")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.add("CaCl2", 2, "mmol")
problem.add("MgCl2", 4, "mmol")
problem.pH(3.0, "HCl")
problem.fixSpeciesAmount("CO2(g)", 1.0, "mol")
problem.fixSpeciesActivity("O2(g)", 0.20)
return (system, problem)
def test_different_results(state_regression):
from reaktoro import ChemicalEditor, ChemicalState, ChemicalSystem, Database, EquilibriumProblem, EquilibriumSolver, Partition
database = Database('supcrt07.xml')
editor = ChemicalEditor(database)
aqueous_elements = ["C", "Ca", "Cl", "Fe", "H", "Na", "O", "S", "Ba", "Sr"]
aqueous_phase = editor.addAqueousPhaseWithElements(aqueous_elements)
assert aqueous_phase.name() == 'Aqueous'
mineral_species = [
"Anhydrite", "Barite", "Calcite", "Celestite", "Siderite", "Pyrrhotite"
]
for mineral in mineral_species:
editor.addMineralPhase(mineral)
gaseous_species = ["CO2(g)", "H2S(g)", "CH4(g)"]
editor.addGaseousPhase(gaseous_species)
chemical_system = ChemicalSystem(editor)
element_index = {
e.name(): index
for index, e in enumerate(chemical_system.elements())
}
species_index = {
s.name(): index
for index, s in enumerate(chemical_system.species())
}
phase_index = {
p.name(): index
for index, p in enumerate(chemical_system.phases())
}
reaktoro_case = get_reaktoro_case()
equilibrium_problem = EquilibriumProblem(chemical_system)
equilibrium_problem.setTemperature(reaktoro_case.temperature_in_K)
equilibrium_problem.setPressure(reaktoro_case.pressure_in_Pa)
partition = Partition(chemical_system)
partition.setInertPhases([phase_index['Gaseous']])
equilibrium_problem.setPartition(partition)
chemical_state = ChemicalState(chemical_system)
for name, index, molar_amount in reaktoro_case.species_amounts:
assert index == species_index[name]
chemical_state.setSpeciesAmount(index, molar_amount)
equilibrium_problem.addState(chemical_state)
solver = EquilibriumSolver(chemical_system)
solver.setPartition(partition)
result = solver.solve(chemical_state, equilibrium_problem)
assert result.optimum.succeeded
state_regression.check(chemical_state,
default_tol=dict(atol=1e-5, rtol=1e-14))
