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 kinect_problem_with_h2o_hcl_caco3_mgco3_co2_calcite():
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O HCl CaCO3 MgCO3")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Calcite")
calciteReaction = editor.addMineralReaction("Calcite")
calciteReaction.setEquation("Calcite = Ca++ + CO3--")
calciteReaction.addMechanism("logk = -5.81 mol/(m2*s); Ea = 23.5 kJ/mol")
calciteReaction.addMechanism(
"logk = -0.30 mol/(m2*s); Ea = 14.4 kJ/mol; a[H+] = 1.0"
)
calciteReaction.setSpecificSurfaceArea(10, "cm2/g")
system = ChemicalSystem(editor)
reactions = ReactionSystem(editor)
partition = Partition(system)
partition.setKineticPhases(["Calcite"])
problem = EquilibriumProblem(system)
problem.setPartition(partition)
problem.add("H2O", 1, "kg")
problem.add("HCl", 1, "mmol")
state = equilibrate(problem)
state.setSpeciesMass("Calcite", 100, "g")
return (state, reactions, partition)
def kinect_problem_with_h2o_nacl_caco3_mgco3_hcl_co2_calcite_magnesite_dolomite_halite():
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
editor.addAqueousPhase("H2O NaCl CaCO3 MgCO3 HCl")
editor.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor.addMineralPhase("Calcite")
editor.addMineralPhase("Magnesite")
editor.addMineralPhase("Dolomite")
editor.addMineralPhase("Halite")
calciteReaction = editor.addMineralReaction("Calcite")
calciteReaction.setEquation("Calcite = Ca++ + CO3--")
calciteReaction.addMechanism("logk = -5.81 mol/(m2*s); Ea = 23.5 kJ/mol")
calciteReaction.addMechanism(
"logk = -0.30 mol/(m2*s); Ea = 14.4 kJ/mol; a[H+] = 1.0"
)
calciteReaction.setSpecificSurfaceArea(10, "cm2/g")
magnesiteReaction = editor.addMineralReaction("Magnesite")
magnesiteReaction.setEquation("Magnesite = Mg++ + CO3--")
magnesiteReaction.addMechanism("logk = -9.34 mol/(m2*s); Ea = 23.5 kJ/mol")
magnesiteReaction.addMechanism(
"logk = -6.38 mol/(m2*s); Ea = 14.4 kJ/mol; a[H+] = 1.0"
)
magnesiteReaction.setSpecificSurfaceArea(10, "cm2/g")
dolomiteReaction = editor.addMineralReaction("Dolomite")
dolomiteReaction.setEquation("Dolomite = Ca++ + Mg++ + 2*CO3--")
dolomiteReaction.addMechanism("logk = -7.53 mol/(m2*s); Ea = 52.2 kJ/mol")
dolomiteReaction.addMechanism(
"logk = -3.19 mol/(m2*s); Ea = 36.1 kJ/mol; a[H+] = 0.5"
)
dolomiteReaction.setSpecificSurfaceArea(10, "cm2/g")
system = ChemicalSystem(editor)
reactions = ReactionSystem(editor)
partition = Partition(system)
partition.setKineticSpecies(["Calcite", "Magnesite", "Dolomite"])
problem = EquilibriumProblem(system)
problem.setPartition(partition)
problem.add("H2O", 1, "kg")
problem.add("NaCl", 1, "mol")
problem.add("CO2", 1, "mol")
state = equilibrate(problem)
state.setSpeciesMass("Calcite", 100, "g")
state.setSpeciesMass("Dolomite", 50, "g")
return (state, reactions, partition)
def equilibrium_problem_using_thermofun_aq17_database():
"""
Build a problem using ThermoFun database aq17
"""
database = thermofun.Database("databases/thermofun/aq17-thermofun.json")
editor = ChemicalEditor(database)
editor.setTemperatures([500.0], "celsius")
editor.setPressures([3000.0], "bar")
editor.addAqueousPhase([
"Al(OH)2+", "Al(OH)3@", "Al(OH)4-", "Al+3", "AlH3SiO4+2", "AlOH+2",
"Ca+2", "CaCO3@", "CaCl+", "CaCl2@", "CaHCO3+", "CaHSiO3+", "CaOH+",
"CaSiO3@", "K+", "KAlO2@", "KCl@", "KOH@", "KCO3-", "KHCO3@", "Mg+2",
"MgCO3@", "MgCl+", "MgCl2@", "MgHCO3+", "MgHSiO3+", "MgOH+", "MgSiO3@",
"Na+", "NaAl(OH)4@", "NaCO3-", "NaCl@", "NaHCO3@", "NaHSiO3@", "NaOH@",
"HSiO3-", "SiO2@", "CO@", "CO2@", "CO3-2", "HCO3-", "CH4@", "Cl-",
"HCl@", "H2@", "O2@", "OH-", "H+", "H2O@"
])
editor.addMineralPhase("Albite")
editor.addMineralPhase("Andalusite")
editor.addMineralPhase("Calcite")
editor.addMineralPhase("Corundum")
editor.addMineralPhase("Diopside")
editor.addMineralPhase("Dolomite")
editor.addMineralPhase("Enstatite")
editor.addMineralPhase("Grossular")
editor.addMineralPhase("Margarite")
editor.addMineralPhase("Microcline")
editor.addMineralPhase("Muscovite")
editor.addMineralPhase("Pargasite-Mg")
editor.addMineralPhase("Phlogopite")
editor.addMineralPhase("Quartz")
editor.addMineralPhase("Sanidine")
editor.addMineralPhase("Sillimanite")
editor.addMineralPhase("Zoisite")
system = ChemicalSystem(editor)
problem = EquilibriumProblem(system)
problem.add("H2O", 1000, "g")
problem.add("CO2", 0.001, "g")
problem.add("CaCO3", 1, "g")
problem.add("MgSiO3", 1, "g")
problem.add("NaCl", 5, "g")
problem.add("NaAlSi3O8", 37, "g")
problem.add("KAl3Si3O10(OH)2", 13, "g")
problem.add("SiO2", 30, "g")
problem.add("KAlSi3O8", 20, "g")
problem.setTemperature(500.0, "celsius")
problem.setPressure(3000.0, "bar")
return (system, problem)
def test_add_phases_right_use():
"""Test the normal use of addAqueousPhase, addGaseousPhase and addMineralPhase."""
database = Database("supcrt98.xml")
# Check adding phase by giving an string with all species
list_of_aqueous_species_expected = r"H2O\(l\)\s*H\+\s*OH-\s*HCO3-\s*CO2\(aq\)\s*CO3--\s*"
list_of_gaseous_species_expected = r"H2O\(g\)\s*CO2\(g\)\s*"
list_of_liquid_species_expected = r"H2O\(liq\)\s*CO2\(liq\)\s*"
list_of_mineral_species_expected = r"Graphite\s*"
editor1 = ChemicalEditor(database)
editor1.addAqueousPhase("H2O(l) H+ OH- HCO3- CO2(aq) CO3--")
editor1.addGaseousPhase("H2O(g) CO2(g)")
editor1.addLiquidPhase("H2O(liq) CO2(liq)")
editor1.addMineralPhase("Graphite")
aqueous_phase_1 = editor1.aqueousPhase()
gaseous_phase_1 = editor1.gaseousPhase()
liquid_phase_1 = editor1.liquidPhase()
mineral_phases_1 = editor1.mineralPhases()
aqueous_species_added_1 = _getting_species_names(aqueous_phase_1)
gaseous_species_added_1 = _getting_species_names(gaseous_phase_1)
liquid_species_added_1 = _getting_species_names(liquid_phase_1)
mineral_species_added_1 = _getting_species_names(mineral_phases_1[0])
assert re.match(list_of_aqueous_species_expected, aqueous_species_added_1)
assert re.match(list_of_gaseous_species_expected, gaseous_species_added_1)
assert re.match(list_of_liquid_species_expected, liquid_species_added_1)
assert re.match(list_of_mineral_species_expected, mineral_species_added_1)
# Check adding phase by giving a list of string with all species
editor2 = ChemicalEditor(database)
editor2.addAqueousPhase(
["H2O(l)", "H+", "OH-", "HCO3-", "CO2(aq)", "CO3--"])
editor2.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor2.addLiquidPhase(["H2O(liq)", "CO2(liq)"])
editor2.addMineralPhase(["Graphite"])
aqueous_phase_2 = editor2.aqueousPhase()
gaseous_phase_2 = editor2.gaseousPhase()
liquid_phase_2 = editor2.liquidPhase()
mineral_phases_2 = editor2.mineralPhases()
aqueous_species_added_2 = _getting_species_names(aqueous_phase_2)
gaseous_species_added_2 = _getting_species_names(gaseous_phase_2)
liquid_species_added_2 = _getting_species_names(liquid_phase_2)
mineral_species_added_2 = _getting_species_names(mineral_phases_2[0])
assert re.match(list_of_aqueous_species_expected, aqueous_species_added_2)
assert re.match(list_of_gaseous_species_expected, gaseous_species_added_2)
assert re.match(list_of_liquid_species_expected, liquid_species_added_2)
assert re.match(list_of_mineral_species_expected, mineral_species_added_2)
def test_equilibrium_path(num_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.addAqueousPhase("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.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,
)
pathDict = convert_dataframe_to_dict(pathTable)
num_regression.check(pathDict)
def test_add_phases_right_use():
"""Test the normal use of addAqueousPhase, addGaseousPhase and addMineralPhase."""
editor1 = ChemicalEditor()
editor1.addAqueousPhase("H2O(l) H+ OH- HCO3- CO2(aq) CO3--")
editor1.addGaseousPhase("H2O(g) CO2(g)")
editor1.addMineralPhase("Graphite")
editor2 = ChemicalEditor()
editor2.addAqueousPhase(
["H2O(l)", "H+", "OH-", "HCO3-", "CO2(aq)", "CO3--"])
editor2.addGaseousPhase(["H2O(g)", "CO2(g)"])
editor2.addMineralPhase(["Graphite"])
system1 = ChemicalSystem(editor1)
system2 = ChemicalSystem(editor2)
_check_equivalent_chemical_systems(system1, system2)
def test_add_phases_wrong_use():
"""Test the wrong usage of addAqueousPhase, addGaseousPhase and addMineralPhase."""
database = Database("supcrt98.xml")
editor = ChemicalEditor(database)
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.addMineralPhase("Siderite C")
with pytest.raises(RuntimeError):
editor.addMineralPhase(["CaCO3"])
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_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.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")
problem.alkalinity(25.0, "meq/L", "Cl")
return (system, problem)
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.addAqueousPhase("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.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_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 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
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)
