def equilibrium_problem_with_h2o_feoh2_feoh3_nh3_magnetite():
'''
Build a problem with H2O, Fe(OH)2, Fe(OH)3, NH3 and Magnetite
'''
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O Fe(OH)2 Fe(OH)3 NH3")
editor.addGaseousPhase("NH3(g)")
editor.addMineralPhase("Magnetite")
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.add("H2O", 1, "kg")
problem.add("Fe(OH)2", 1, "mol")
problem.add("Fe(OH)3", 2, "mol")
problem.add("NH3", 1, "mol")
return (system, problem)
def equilibrium_inverse_with_h2o_nacl_caco3_co2_calcite_fixed_phase_volume():
'''
Build a problem with H2O, NaCl, CaCO3, CO2 and Calcite
with fixed values of phase volume
'''
editor = ChemicalEditor()
editor.addAqueousPhase("H2O NaCl CaCO3")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Calcite")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.fixPhaseVolume("Gaseous", 0.2, "m3", "CO2")
problem.fixPhaseVolume("Aqueous", 0.3, "m3", "1 kg H2O; 0.1 mol NaCl")
problem.fixPhaseVolume("Calcite", 0.5, "m3", "CaCO3")
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.addAqueousPhase("H O Na Cl Ca Mg C")
editor.addGaseousPhase("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_h2o_nacl_caco3_co2_fixed_mass_amount_and_alkalinity():
"""
Build a problem with H2O, NaCl, CaCO3, CO2 and Calcite
with fixed values of Species Mass, Amount and alkalinity
"""
editor = ChemicalEditor()
editor.addAqueousPhaseWithElementsOf("H2O NaCl CaCO3")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Calcite")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.fixSpeciesMass("Calcite", 100, "g")
problem.fixSpeciesAmount("CO2(g)", 1.0, "mol")
problem.alkalinity(25.0, "meq/L", "Cl")
return (system, problem)
def test_add_phases_wrong_use():
"""Test the wrong usage of addAqueousPhase, addGaseousPhase and addMineralPhase."""
editor = ChemicalEditor()
with pytest.raises(RuntimeError):
editor.addAqueousPhase("H2O(l) C Ca")
with pytest.raises(RuntimeError):
editor.addAqueousPhase(["H2O C Ca"])
with pytest.raises(RuntimeError):
editor.addGaseousPhase("CO2(g) H")
with pytest.raises(RuntimeError):
editor.addGaseousPhase(["CO2"])
with pytest.raises(RuntimeError):
editor.addMineralPhase("Siderita C")
with pytest.raises(RuntimeError):
editor.addMineralPhase(["CaCO3"])
def test_equilibrium_CH4_liq_gas(temperature, pressure, num_regression):
db = Database("supcrt98.xml")
editor = ChemicalEditor(db)
eos_params = CubicEOSParams()
eos_params.phase_identification_method = PhaseIdentificationMethod.GibbsEnergyAndEquationOfStateMethod
editor.addGaseousPhase(["CH4(g)"]).setChemicalModelPengRobinson(eos_params)
editor.addLiquidPhase(["CH4(liq)"
]).setChemicalModelPengRobinson(eos_params)
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.setTemperature(temperature, "K")
problem.setPressure(pressure, "Pa")
problem.add("CH4(g)", 1.0, "mol")
solver = EquilibriumSolver(problem.system())
options = EquilibriumOptions()
options.hessian = GibbsHessian.Exact
options.nonlinear.max_iterations = 100
options.optimum.max_iterations = 200
options.optimum.ipnewton.step = StepMode.Conservative
options.optimum.tolerance = 1e-17
solver.setOptions(options)
state = ChemicalState(system)
result = solver.solve(state, problem)
assert result.optimum.succeeded
species_amounts = {
"CH4(g)": np.asarray([state.speciesAmount("CH4(g)")]),
"CH4(liq)": np.asarray([state.speciesAmount("CH4(liq)")]),
}
num_regression.check(species_amounts)
def equilibrium_inverse_with_h2o_nacl_caco3_calcilte_and_fixed_mass():
"""
Build a problem with H2O, NaCL, CaCO3, CO2, Calcite with fixed
species mass and amount
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O NaCl CaCO3")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Calcite")
system = ChemicalSystem(editor)
problem = EquilibriumInverseProblem(system)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 0.1, "mol")
problem.fixSpeciesMass("Calcite", 100, "g")
problem.fixSpeciesAmount("CO2(g)", 1.0, "mol")
return (system, problem)
def equilibrium_problem_with_h2o_co2_nacl_halite_60C_300bar():
"""
Build a problem with 1 kg of H2O, 100 g of CO2 and 0.1 mol of NaCl
at 60 °C and 300 bar
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O NaCl CO2")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Halite")
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.add("H2O", 1, "kg")
problem.add("CO2", 100, "g")
problem.add("NaCl", 0.1, "mol")
problem.setTemperature(60, "celsius")
problem.setPressure(300, "bar")
return (system, problem)
def test_chemical_editor_create_system():
expected = [
"H2O(l)", "H+", "OH-", "H2O(g)", "CO2(g)", "H2O(liq)", "CO2(liq)",
"Graphite"
]
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O(l) H+ OH-")
editor.addGaseousPhase("H2O(g) CO2(g)")
editor.addLiquidPhase("H2O(liq) CO2(liq)")
editor.addMineralPhase("Graphite")
system = ChemicalSystem(editor)
species_name = []
for specie in system.species():
species_name.append(specie.name())
assert species_name == expected
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.addAqueousPhase("H O Na Cl Ca Mg C")
editor.addGaseousPhase("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 equilibrium_problem_with_h2o_co2_nacl_halite_dissolved_60C_300bar():
"""
Build a problem with H2O, H+, Na+, Cl-, HCO3-, CO2(aq), CO3-- and
Halite at 60 °C and 300 bar
"""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase(
["CO(aq)", "CO2(aq)", "CO3--", "Cl-", "ClO-", "ClO2-", "ClO3-", "ClO4-", "H+", "H2(aq)", "H2O(l)", "H2O2(aq)", "HCO3-", "HCl(aq)", "HClO(aq)", "HClO2(aq)", "HO2-", "Na+", "NaCl(aq)", "NaOH(aq)", "O2(aq)", "OH-"]
).setActivityModelDrummondCO2()
editor.addGaseousPhase(["H2O(g)", "CO2(g)"]).setChemicalModelSpycherPruessEnnis()
editor.addMineralPhase("Halite")
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.add("H2O", 1, "kg")
problem.add("CO2", 100, "g")
problem.add("NaCl", 1, "mol")
problem.setTemperature(60, "celsius")
problem.setPressure(300, "bar")
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))
def test_equilibrium_CH4_H2S_CO2_H2O_liq_gas_aq(temperature, pressure,
num_regression):
"""
This test checks the capability of solving a system that has CH4, H2S,
CO2, H2O with
@param Temperature
temperature in Kelvin which will be used to compute equilibrium
@param Pressure
pressure in bar which will be used to compute equilibrium
"""
db = Database("supcrt98.xml")
editor = ChemicalEditor(db)
eos_params = CubicEOSParams(
phase_identification_method=PhaseIdentificationMethod.
GibbsEnergyAndEquationOfStateMethod, )
editor.addAqueousPhase(["CO2(aq)", "H2S(aq)", "H2O(l)"])
editor.addGaseousPhase(["CH4(g)", "CO2(g)", "H2S(g)",
"H2O(g)"]).setChemicalModelCubicEOS(eos_params)
editor.addLiquidPhase(["CH4(liq)", "CO2(liq)", "H2S(liq)",
"H2O(liq)"]).setChemicalModelCubicEOS(eos_params)
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.setTemperature(temperature, "K")
problem.setPressure(pressure, "bar")
problem.add("H2O(g)", 0.50, "mol")
problem.add("CO2(g)", 0.05, "mol")
problem.add("H2S(g)", 0.40, "mol")
problem.add("CH4(g)", 0.05, "mol")
# This is a workaround to avoid an Eigen assertion when in Debug:
# `DenseBase::resize() does not actually allow to resize.`, triggered by `y(iee) = optimum_state.y * RT;`
problem.add("Z", 1e-15, "mol")
solver = EquilibriumSolver(problem.system())
options = EquilibriumOptions()
options.hessian = GibbsHessian.Exact
options.nonlinear.max_iterations = 100
options.optimum.max_iterations = 200
options.optimum.ipnewton.step = StepMode.Conservative
options.optimum.tolerance = 1e-14
solver.setOptions(options)
state = ChemicalState(system)
result = solver.solve(state, problem)
assert result.optimum.succeeded
species_amount = {
"CO2(aq)": np.asarray([state.speciesAmount("CO2(g)")]),
"H2S(aq)": np.asarray([state.speciesAmount("H2S(aq)")]),
"H2O(l)": np.asarray([state.speciesAmount("H2O(l)")]),
"CH4(g)": np.asarray([state.speciesAmount("CH4(g)")]),
"CO2(g)": np.asarray([state.speciesAmount("CO2(g)")]),
"H2S(g)": np.asarray([state.speciesAmount("H2S(g)")]),
"H2O(g)": np.asarray([state.speciesAmount("H2O(g)")]),
"CH4(liq)": np.asarray([state.speciesAmount("CH4(liq)")]),
"CO2(liq)": np.asarray([state.speciesAmount("CO2(liq)")]),
"H2S(liq)": np.asarray([state.speciesAmount("H2S(liq)")]),
"H2O(liq)": np.asarray([state.speciesAmount("H2O(liq)")]),
}
num_regression.check(species_amount)
def chemical_editor():
editor = ChemicalEditor()
editor.addAqueousPhase("H2O(l) H+ OH- HCO3- CO2(aq) CO3--".split())
editor.addGaseousPhase("H2O(g) CO2(g)".split())
editor.addMineralPhase("Graphite")
return editor
