From 46320cb3b9ead1a0ed18b4bb900c1a052fc54b9d Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Mon, 16 Jun 2025 18:00:40 -0700 Subject: [PATCH 01/54] Draft benchmarking module Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 345 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 345 insertions(+) create mode 100644 src/pyEQL/benchmark.py diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py new file mode 100644 index 00000000..68ea9eb3 --- /dev/null +++ b/src/pyEQL/benchmark.py @@ -0,0 +1,345 @@ +"""Solution model benchmarking utilities. + + +Usage: + + python pyeql.benchmark + +""" + +import json +import math +from collections.abc import Callable +from pathlib import Path + +import numpy as np + +from pyEQL import ureg +from pyEQL.solution import Solution + +# Maps solutes to property values dictionary +ReferenceData = dict[str, dict[str, float]] +# TODO: Select and validate data sources +SOURCES = [] +# TODO: revisit tolerance +# relative tolerance between experimental and computed properties for this test file +RTOL = 0.05 + +s1 = Solution(volume="2 L") +s2 = Solution([["Na+", "4 mol/L"], ["Cl-", "4 mol/L"]], volume="2 L") + + +# TODO: edit to save Solution objects and add conductivity data to reference data dictionary +def _create_conductivity_data() -> None: + """This method edits data in place.""" + data: list[tuple[Solution, ReferenceData]] = [] + DEST = Path(__file__).parent.joinpath("database") + + # per CRC handbook - "electrical conductiVity of Water" , conductivity of pure water + # at 25 and 100 C is 0.0550 and 0.765 uS/cm + assert np.isclose(s1.conductivity.to("uS/cm").magnitude, 0.055, atol=1e-3) + + # TODO - seems to be a possible bug related to setting temperature here + # s1.temperature = "100 degC" + # s2 = Solution(temperature='100 degC') + # assert np.isclose(s1.conductivity.to('uS/cm').magnitude, 0.765, atol=1e-3) + + # CRC handbook table - "equivalent conductivity of electrolytes in aqueous solution" + # nacl + for conc, cond in zip([0.001, 0.05, 0.1], [123.68, 111.01, 106.69], strict=False): + s1 = Solution({"Na+": f"{conc} mol/L", "Cl-": f"{conc} mol/L"}) + assert np.isclose( + s1.conductivity.to("S/m").magnitude, conc * cond / 10, atol=0.5 + ), f"Conductivity test failed for NaCl at {conc} mol/L. Result = {s1.conductivity.to('S/m').magnitude}" + + # higher concentration data points from Appelo, 2017 Figure 4. + s1 = Solution({"Na+": "2 mol/kg", "Cl-": "2 mol/kg"}) + assert np.isclose(s1.conductivity.to("mS/cm").magnitude, 145, atol=10) + + # MgCl2 + for conc, cond in zip([0.001, 0.05, 0.1], [124.15, 114.49, 97.05], strict=False): + s1 = Solution({"Mg+2": f"{conc} mol/L", "Cl-": f"{2 * conc} mol/L"}) + assert np.isclose( + s1.conductivity.to("S/m").magnitude, 2 * conc * cond / 10, atol=1 + ), f"Conductivity test failed for MgCl2 at {conc} mol/L. Result = {s1.conductivity.to('S/m').magnitude}" + + # per CRC handbook "standard KCl solutions for calibrating conductivity cells", 0.1m KCl has a conductivity of + # 12.824 mS/cm at 25 C + s_kcl = Solution({"K+": "0.1 mol/kg", "Cl-": "0.1 mol/kg"}) + assert np.isclose(s_kcl.conductivity.magnitude, 1.2824, atol=0.25) # conductivity is in S/m + + # TODO - expected failures due to limited temp adjustment of diffusion coeff + s_kcl.temperature = "5 degC" + assert np.isclose(s_kcl.conductivity.magnitude, 0.81837, atol=0.2) + + s_kcl.temperature = "50 degC" + assert np.isclose(s_kcl.conductivity.magnitude, 1.91809, atol=0.2) + + # TODO - conductivity model not very accurate at high conc. + s_kcl = Solution({"K+": "1 mol/kg", "Cl-": "1 mol/kg"}) + assert np.isclose(s_kcl.conductivity.magnitude, 10.862, atol=0.45) + + solutions = [s1, s2, s_kcl] + + for solution in solutions: + reference_data = {"conductivity": solution.conductivity} + data.append((solution, reference_data)) + + filename = DEST.joinpath("CRC_data.json") + with filename.open(mode="r", encoding="utf-8") as file: + json.dump(data, file, indent=4) + + +# TODO: edit to save Solution objects and add diffusion data to reference data dictionary +def _create_diffusion_data() -> None: + # test ionic strength adjustment + assert s1.get_diffusion_coefficient("H+") > s2.get_diffusion_coefficient("H+") + + # for Na+, d=122, a1=1.52, a2=3.7, A=1.173802/2.303 at 25 DegC, B = 3.2843078+10 + factor = np.exp( + -1.52 + * 1.173802 + / 2.303 + * 1 + * np.sqrt(s2.ionic_strength.magnitude) + / (1 + 3.2843078e10 * np.sqrt(s2.ionic_strength.magnitude) * 3.7 / (1 + s2.ionic_strength.magnitude**0.75)) + ) + assert np.isclose( + factor * s2.get_diffusion_coefficient("Na+").magnitude, + s2.get_diffusion_coefficient("Na+").magnitude, + atol=5e-11, + ) + s_dilute = Solution({"Na+": "1 mmol/L", "Cl-": "1 mmol/L"}) + assert np.isclose( + s_dilute.get_diffusion_coefficient("Na+", activity_correction=False).magnitude, 1.334e-9, atol=1e-12 + ) + assert np.isclose(s_dilute.get_transport_number("Na+"), 0.396, atol=1e-3) + assert np.isclose(s_dilute.get_transport_number("Cl-"), 0.604, atol=1e-3) + + # test setting a default value + s2.default_diffusion_coeff = 0 + assert s2.get_diffusion_coefficient("Cs+").magnitude == 0 + s2.default_diffusion_coeff = 1e-9 + assert s2.get_diffusion_coefficient("Cs+", activity_correction=False).magnitude == 1e-9 + s2.default_diffusion_coeff = 0 + assert s2.get_diffusion_coefficient("Cs+", activity_correction=True).magnitude < 1e-9 + d25 = s2.get_diffusion_coefficient("Na+", activity_correction=False).magnitude + nu25 = s2.water_substance.nu + s2.temperature = "40 degC" + d40 = s2.get_diffusion_coefficient("Na+", activity_correction=False).magnitude + nu40 = s2.water_substance.nu + assert np.isclose( + d40, + d25 * np.exp(122 / (273.15 + 40) - 122 / 298.15) * (nu25 / nu40), + atol=5e-11, + ) + + # test correction factors for concentration, as per Appelo 2017 Fig 5 + D1 = Solution({"Na+": "1 umol/L", "Cl-": "1 umol/L"}).get_diffusion_coefficient("Na+").magnitude + D2 = Solution({"Na+": "1.7 mol/kg", "Cl-": "1.7 mol/kg"}).get_diffusion_coefficient("Na+").magnitude + assert np.isclose(D2 / D1, 0.54, atol=1e-2) + + D1 = Solution({"K+": "1 umol/L", "Cl-": "1 umol/L"}).get_diffusion_coefficient("K+").magnitude + D2 = Solution({"K+": "0.5 mol/kg", "Cl-": "0.5 mol/kg"}).get_diffusion_coefficient("K+").magnitude + assert np.isclose(D2 / D1, 0.80, atol=1e-2) + + +def _create_activity_data() -> None: + # see test_activity.py & test_mixed_electrolyte_activity.py + pass + + +def _create_density_data() -> None: + # see test_density.py + pass + + +def _create_osmotic_coefficient_data() -> None: + # see test_osmotic_coeff.py + pass + + +# TODO: edit to save Solution objects and add molar conductivity data to reference data dictionary +def _create_molar_conductivity_data() -> None: + def test_molar_conductivity_potassium(self): + # K+ - 73.48 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["K+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("K+").to("m**2*S/mol").magnitude + expected = ureg.Quantity("73.48e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + def test_molar_conductivity_sodium(self): + # Na+ - 50.08 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["Na+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("Na+").to("m**2*S/mol").magnitude + expected = ureg.Quantity("50.08e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + def test_molar_conductivity_magnesium(self): + # Mg+2 - 106 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["Mg+2", "0.001 mol/L"], ["Cl-", "0.002 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("Mg+2").to("m**2*S/mol").magnitude + expected = ureg.Quantity("106e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, atol=0.005) + + def test_molar_conductivity_chloride(self): + # Cl- - 76.31 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["Na+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("Cl-").to("m**2*S/mol").magnitude + expected = ureg.Quantity("76.31e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + def test_molar_conductivity_fluoride(self): + # F- - 55.4 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["Na+", "0.001 mol/L"], ["F-", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("F-").to("m**2*S/mol").magnitude + expected = ureg.Quantity("55.4e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + def test_molar_conductivity_sulfate(self): + # SO4-2 - 160 x 10 ** -4 m ** 2 S / mol + s1 = Solution([["Na+", "0.002 mol/L"], ["SO4-2", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("SO4-2").to("m**2*S/mol").magnitude + expected = ureg.Quantity("160.0e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, atol=0.002) + + def test_molar_conductivity_hydroxide(self): + # OH- - 198 x 10 ** -4 m ** 2 S / mol + s1 = Solution(temperature="25 degC") + result = s1.get_molar_conductivity("OH-").to("m**2*S/mol").magnitude + expected = ureg.Quantity("198e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + def test_molar_conductivity_hydrogen(self): + # H+ - 349.65 x 10 ** -4 m ** 2 S / mol + s1 = Solution(temperature="25 degC") + result = s1.get_molar_conductivity("H+").to("m**2*S/mol").magnitude + expected = ureg.Quantity("349.65e-4 m**2 * S / mol").magnitude + + assert np.isclose(result, expected, rtol=RTOL) + + # molar conductivity of a neutral solute should be zero + def test_molar_conductivity_neutral(self): + s1 = Solution([["FeCl3", "0.001 mol/L"]], temperature="25 degC") + result = s1.get_molar_conductivity("FeCl3").to("m**2*S/mol").magnitude + expected = ureg.Quantity(0, "m**2 * S / mol").magnitude + + assert round(abs(result - expected), 5) == 0 + + # molar conductivity of water should be zero + def test_molar_conductivity_water(self): + s1 = Solution(temperature="25 degC") + result = s1.get_molar_conductivity("H2O").to("m**2*S/mol").magnitude + expected = ureg.Quantity(0, "m**2 * S / mol").magnitude + + assert round(abs(result - expected), 5) == 0 + + +# TODO: write database files and write loading function +def _load_database(source: str) -> list[tuple[Solution, dict[str, float]]]: + pass + + +def _get_reference(source: str) -> list[tuple[Solution, ReferenceData]]: + """Load reference data. + + Args: + source: One of "IDST" or "PHREEQC" or the path to a file containing reference data. If the latter, then the + path must point to a JSON which can be read into a list of Solution, Result pairs. Each Solution can only + contain the following keys: solutes, volume, temperature, pressure, pH, pE, balance_charge, and solvent. + The Result item must contain a dictionary mapping property names to their reference values for the + corresponding Solution. + + Returns: + A list of Solution, Result 2-tuples. + """ + match source: + case "IDST" | "PHREEQC": + reference = _load_database(source) + case _: + with Path(source).open(mode="r", encoding="utf-8") as file: + data = json.load(file) + + reference: list[tuple[Solution, dict[str, float]]] = [] + + for sol, values in data: + reference.append((Solution(**sol), values)) + + return reference + + +def benchmark_engine( + references: list[tuple[Solution, ReferenceData]], *, getter: Callable[[Solution, str, str], float] | None = None +) -> dict[str, float]: + """Calculate the RMSE for a set of solutions with respect to reference data. + + + Args: + references: A dictionary mapping solution properties to their reference values. + getter: A Callable that should accept three positional arguments: A Solution object, a solute string, and a + string indicating the name of a solvent property. The Callable should return the property value from the + Solution. Defaults to the Solution._get_property method. + + Returns: + A dictionary mapping each key in the reference to the cumulative root-mean-squared error across all solutions. + """ + + def _get_property(s: Solution, solute: str, name: str) -> float: + return s._get_property(solute, name) + + getter = getter or _get_property + + errors = {} + + for solution, data in references: + for solute, solute_data in data.items(): + for property, reference_value in solute_data.items(): + calculated = _get_property(solution, solute, property) + + if property not in errors: + errors[property] = [] + + errors[property].append(math.abs(calculated - reference_value)) + + return {k: np.std(values) for k, values in errors.items()} + + +# TODO: Decide on reporting method and metrics +def report_results(results: dict[tuple[str, str], float]) -> None: + """Report the results of the benchmarking. + + Args: + results: A dictionary mapping 2-tuples (engine, source) to the associated root-means-squared error across + all data points in the source for the given engine. + """ + + +def run_benchmark() -> None: + """Solution benchmarking function. + + This function works by reading in reference property values from a list of sources. The reference data is composed + of an identifying Solution object and a dictionary mapping properties to their reference values. The reference + values are checked against pyEQL-calculated values for a variety of engines. + """ + # TODO: create engines (e.g., Pitzer, PHREEQC) + # see test_phreeqc.py + engines = [] + references = [(s, _get_reference(s)) for s in SOURCES] + results: dict[tuple[str, str], float] = {} + + for eng in engines: + for source, ref in references: + results[(eng, source)] = benchmark_engine(ref) + + report_results(results) + + +if __name__ == "__main__": + run_benchmark() From 87620d94998dedbafecc1eef5a6212781f7641d9 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 02:51:25 -0700 Subject: [PATCH 02/54] Major refactor Replace ReferenceData with _BenchmarkEntry. This named tuple now separates solution and solute properties which enables the separate retrieval of each type of property. An analogous _get_solution_property method has been implemented. _get_reference is renamed to _get_dataset as the data structure returned by the method defines a general solution/solute property data set (reference data + Solution object which can be used for benchmarking). benchmark_engine functionality moved to report_results for simplicity. If more fine-tuned control over data set partitioning or result reporting is desired, this can be implemented quite readily by undoing this change. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 184 +++++++++++++++++++++++++++-------------- 1 file changed, 122 insertions(+), 62 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 68ea9eb3..08647b0a 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -8,19 +8,21 @@ """ import json -import math from collections.abc import Callable +from itertools import product from pathlib import Path +from typing import Any, NamedTuple import numpy as np from pyEQL import ureg from pyEQL.solution import Solution +from pyEQL.utils import FormulaDict -# Maps solutes to property values dictionary -ReferenceData = dict[str, dict[str, float]] # TODO: Select and validate data sources -SOURCES = [] +# If all solution reference data are generated from the same solutions, then solutions can be used as an input into +# source creation +SOURCES: list[str] = [] # TODO: revisit tolerance # relative tolerance between experimental and computed properties for this test file RTOL = 0.05 @@ -29,10 +31,63 @@ s2 = Solution([["Na+", "4 mol/L"], ["Cl-", "4 mol/L"]], volume="2 L") +class _BenchmarkEntry(NamedTuple): + solution: Solution + # dict[str, list[tuple[str, float]]]: solute, [(property, value)] + solute_data: FormulaDict = FormulaDict() + solution_data: list[tuple[str, float]] = [] + + +# TODO: check tests for missing property checks +def _create_crc_data(s) -> list[_BenchmarkEntry]: + datasets = [] + # list of concentrations to test, mol/kg + conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] + # TODO: replace with parametrization scheme which preserves charge neutrality + cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] + anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] + + for (cation, nu_cation), (anion, nu_anion) in product(cations, anions): + # list of published experimental activity coefficients + # TODO: archive as CSV + pub_activity_coeff = [ + 0.965, + 0.952, + 0.929, + 0.905, + 0.876, + 0.832, + 0.797, + 0.768, + 0.759, + 0.811, + 1.009, + 2.380, + ] + + for i, conc in enumerate(conc_list): + conc_c = str(conc * nu_cation) + "mol/kg" + conc_a = str(conc * nu_anion) + "mol/kg" + sol = Solution() + sol.add_solute(cation, conc_c) + sol.add_solute(anion, conc_a) + expected = pub_activity_coeff[i] + activities = FormulaDict(**{cation: expected, anion: expected}) + # TODO: read/calculate appropriately + osmo_coeff = None + volume = None + dataset = _BenchmarkEntry( + solution=sol, activities=activities, osmotic_coefficient=osmo_coeff, solute_volume=volume + ) + datasets.append(dataset) + + return datasets + + # TODO: edit to save Solution objects and add conductivity data to reference data dictionary def _create_conductivity_data() -> None: """This method edits data in place.""" - data: list[tuple[Solution, ReferenceData]] = [] + data: list[tuple[Solution, _BenchmarkEntry]] = [] DEST = Path(__file__).parent.joinpath("database") # per CRC handbook - "electrical conductiVity of Water" , conductivity of pure water @@ -90,7 +145,7 @@ def _create_conductivity_data() -> None: json.dump(data, file, indent=4) -# TODO: edit to save Solution objects and add diffusion data to reference data dictionary +# TODO: find equivalent reference sources and write replicate _create_crc_data logic def _create_diffusion_data() -> None: # test ionic strength adjustment assert s1.get_diffusion_coefficient("H+") > s2.get_diffusion_coefficient("H+") @@ -144,11 +199,6 @@ def _create_diffusion_data() -> None: assert np.isclose(D2 / D1, 0.80, atol=1e-2) -def _create_activity_data() -> None: - # see test_activity.py & test_mixed_electrolyte_activity.py - pass - - def _create_density_data() -> None: # see test_density.py pass @@ -247,21 +297,18 @@ def _load_database(source: str) -> list[tuple[Solution, dict[str, float]]]: pass -def _get_reference(source: str) -> list[tuple[Solution, ReferenceData]]: - """Load reference data. +def _get_dataset(source: str) -> list[_BenchmarkEntry]: + """Load reference dataset. Args: - source: One of "IDST" or "PHREEQC" or the path to a file containing reference data. If the latter, then the - path must point to a JSON which can be read into a list of Solution, Result pairs. Each Solution can only - contain the following keys: solutes, volume, temperature, pressure, pH, pE, balance_charge, and solvent. - The Result item must contain a dictionary mapping property names to their reference values for the - corresponding Solution. + source: One of "CRC", "IDST", or "May2011JCED" or the path to a file containing reference data. If the latter, + then the [path must point to a JSON which can be read into a _BenchmarkEntry object. Returns: - A list of Solution, Result 2-tuples. + A list of _BenchmarkEntry objects one for each data point in the data set. """ match source: - case "IDST" | "PHREEQC": + case "CRC" | "IDST" | "May2011JCED": reference = _load_database(source) case _: with Path(source).open(mode="r", encoding="utf-8") as file: @@ -275,54 +322,71 @@ def _get_reference(source: str) -> list[tuple[Solution, ReferenceData]]: return reference -def benchmark_engine( - references: list[tuple[Solution, ReferenceData]], *, getter: Callable[[Solution, str, str], float] | None = None -) -> dict[str, float]: - """Calculate the RMSE for a set of solutions with respect to reference data. - - - Args: - references: A dictionary mapping solution properties to their reference values. - getter: A Callable that should accept three positional arguments: A Solution object, a solute string, and a - string indicating the name of a solvent property. The Callable should return the property value from the - Solution. Defaults to the Solution._get_property method. - - Returns: - A dictionary mapping each key in the reference to the cumulative root-mean-squared error across all solutions. - """ +def _rmse(data: list[tuple[float, float]]) -> float: + return np.std([ref - calc for ref, calc in data]) - def _get_property(s: Solution, solute: str, name: str) -> float: - return s._get_property(solute, name) - getter = getter or _get_property +def _get_solute_property(solution: Solution, solute: str, name: str) -> Any | None: + return solution.get_property(solute, name) - errors = {} - for solution, data in references: - for solute, solute_data in data.items(): - for property, reference_value in solute_data.items(): - calculated = _get_property(solution, solute, property) +def _get_solution_property(solution: Solution, name: str) -> Any | None: + if hasattr(solution, name): + return getattr(solution, name) - if property not in errors: - errors[property] = [] + if hasattr(solution, f"get_{name}"): + return getattr(solution, f"get_{name}") - errors[property].append(math.abs(calculated - reference_value)) + msg = f"Property {name} is not supported" + raise NotImplementedError(msg) - return {k: np.std(values) for k, values in errors.items()} - -# TODO: Decide on reporting method and metrics -def report_results(results: dict[tuple[str, str], float]) -> None: +def report_results( + dataset: list[_BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None +) -> None: """Report the results of the benchmarking. Args: - results: A dictionary mapping 2-tuples (engine, source) to the associated root-means-squared error across + dataset: A dictionary mapping 2-tuples (engine, source) to the associated root-means-squared error across all data points in the source for the given engine. + metric: A function that acts on the list of 2-tuples (reference, calculated), which contains reference and + calculated values. This function should calculate a statistical metric for the list. Defaults to the root- + mean-squared error. """ + metric = metric or _rmse + + # Populate data structure for tracking activity/osmotic coefficient and solvent volume statistics + # property, (reference, calculated) + solute_data_pairs: dict[str, list[tuple[float, float]]] = {} + # property, (reference, calculated) + solution_data_pairs: dict[str, list[tuple[float, float]]] = {} + + for d in dataset: + for solute, solute_data in d.solute_data.items(): + for property, reference in solute_data: + if property not in solute_data_pairs: + solute_data_pairs[property] = [] + + solute_data_pairs[property].append((reference, _get_solute_property(d.solution, solute, property))) + + for property, reference in d.solution_data: + if property not in solution_data_pairs: + solution_data_pairs[property] = [] + solution_data_pairs[property].append((reference, _get_solution_property(d.solution, solute, property))) -def run_benchmark() -> None: - """Solution benchmarking function. + solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} + solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} + + for property, stat in solute_stats.items(): + print(f"{property} statistics: {stat}") + + for property, stat in solution_stats.items(): + print(f"{property} statistics: {stat}") + + +def main() -> None: + """Run solution benchmarking logic. This function works by reading in reference property values from a list of sources. The reference data is composed of an identifying Solution object and a dictionary mapping properties to their reference values. The reference @@ -330,16 +394,12 @@ def run_benchmark() -> None: """ # TODO: create engines (e.g., Pitzer, PHREEQC) # see test_phreeqc.py - engines = [] - references = [(s, _get_reference(s)) for s in SOURCES] - results: dict[tuple[str, str], float] = {} - - for eng in engines: - for source, ref in references: - results[(eng, source)] = benchmark_engine(ref) + datasets = [_get_dataset(s) for s in SOURCES] + results: dict[str, list[_BenchmarkEntry]] = {} - report_results(results) + for i, dataset in enumerate(datasets): + results[SOURCES[i]] = report_results(dataset) if __name__ == "__main__": - run_benchmark() + main() From 20e09739fd99ba887b6bd92bae5726c858356b37 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 04:13:31 -0700 Subject: [PATCH 03/54] Don't explicitly create soln; drafted CRC loader Solution creation is now handed when reference files are read. Benchmarking is parametrized by engine. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 323 +++++++---------------------------------- 1 file changed, 54 insertions(+), 269 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 08647b0a..90e23d99 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -9,26 +9,19 @@ import json from collections.abc import Callable -from itertools import product from pathlib import Path -from typing import Any, NamedTuple +from typing import Any, Literal, NamedTuple import numpy as np -from pyEQL import ureg +from pyEQL.engines import EOS, IdealEOS, NativeEOS, PhreeqcEOS from pyEQL.solution import Solution from pyEQL.utils import FormulaDict # TODO: Select and validate data sources # If all solution reference data are generated from the same solutions, then solutions can be used as an input into # source creation -SOURCES: list[str] = [] -# TODO: revisit tolerance -# relative tolerance between experimental and computed properties for this test file -RTOL = 0.05 - -s1 = Solution(volume="2 L") -s2 = Solution([["Na+", "4 mol/L"], ["Cl-", "4 mol/L"]], volume="2 L") +SOURCES: list[str] = ["CRC", "IDST", "May2011JCED"] class _BenchmarkEntry(NamedTuple): @@ -38,263 +31,41 @@ class _BenchmarkEntry(NamedTuple): solution_data: list[tuple[str, float]] = [] -# TODO: check tests for missing property checks -def _create_crc_data(s) -> list[_BenchmarkEntry]: - datasets = [] - # list of concentrations to test, mol/kg - conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] - # TODO: replace with parametrization scheme which preserves charge neutrality - cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] - anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] - - for (cation, nu_cation), (anion, nu_anion) in product(cations, anions): - # list of published experimental activity coefficients - # TODO: archive as CSV - pub_activity_coeff = [ - 0.965, - 0.952, - 0.929, - 0.905, - 0.876, - 0.832, - 0.797, - 0.768, - 0.759, - 0.811, - 1.009, - 2.380, - ] - - for i, conc in enumerate(conc_list): - conc_c = str(conc * nu_cation) + "mol/kg" - conc_a = str(conc * nu_anion) + "mol/kg" - sol = Solution() - sol.add_solute(cation, conc_c) - sol.add_solute(anion, conc_a) - expected = pub_activity_coeff[i] - activities = FormulaDict(**{cation: expected, anion: expected}) - # TODO: read/calculate appropriately - osmo_coeff = None - volume = None - dataset = _BenchmarkEntry( - solution=sol, activities=activities, osmotic_coefficient=osmo_coeff, solute_volume=volume - ) - datasets.append(dataset) - - return datasets - - -# TODO: edit to save Solution objects and add conductivity data to reference data dictionary -def _create_conductivity_data() -> None: - """This method edits data in place.""" - data: list[tuple[Solution, _BenchmarkEntry]] = [] - DEST = Path(__file__).parent.joinpath("database") - - # per CRC handbook - "electrical conductiVity of Water" , conductivity of pure water - # at 25 and 100 C is 0.0550 and 0.765 uS/cm - assert np.isclose(s1.conductivity.to("uS/cm").magnitude, 0.055, atol=1e-3) - - # TODO - seems to be a possible bug related to setting temperature here - # s1.temperature = "100 degC" - # s2 = Solution(temperature='100 degC') - # assert np.isclose(s1.conductivity.to('uS/cm').magnitude, 0.765, atol=1e-3) - - # CRC handbook table - "equivalent conductivity of electrolytes in aqueous solution" - # nacl - for conc, cond in zip([0.001, 0.05, 0.1], [123.68, 111.01, 106.69], strict=False): - s1 = Solution({"Na+": f"{conc} mol/L", "Cl-": f"{conc} mol/L"}) - assert np.isclose( - s1.conductivity.to("S/m").magnitude, conc * cond / 10, atol=0.5 - ), f"Conductivity test failed for NaCl at {conc} mol/L. Result = {s1.conductivity.to('S/m').magnitude}" - - # higher concentration data points from Appelo, 2017 Figure 4. - s1 = Solution({"Na+": "2 mol/kg", "Cl-": "2 mol/kg"}) - assert np.isclose(s1.conductivity.to("mS/cm").magnitude, 145, atol=10) - - # MgCl2 - for conc, cond in zip([0.001, 0.05, 0.1], [124.15, 114.49, 97.05], strict=False): - s1 = Solution({"Mg+2": f"{conc} mol/L", "Cl-": f"{2 * conc} mol/L"}) - assert np.isclose( - s1.conductivity.to("S/m").magnitude, 2 * conc * cond / 10, atol=1 - ), f"Conductivity test failed for MgCl2 at {conc} mol/L. Result = {s1.conductivity.to('S/m').magnitude}" - - # per CRC handbook "standard KCl solutions for calibrating conductivity cells", 0.1m KCl has a conductivity of - # 12.824 mS/cm at 25 C - s_kcl = Solution({"K+": "0.1 mol/kg", "Cl-": "0.1 mol/kg"}) - assert np.isclose(s_kcl.conductivity.magnitude, 1.2824, atol=0.25) # conductivity is in S/m - - # TODO - expected failures due to limited temp adjustment of diffusion coeff - s_kcl.temperature = "5 degC" - assert np.isclose(s_kcl.conductivity.magnitude, 0.81837, atol=0.2) - - s_kcl.temperature = "50 degC" - assert np.isclose(s_kcl.conductivity.magnitude, 1.91809, atol=0.2) - - # TODO - conductivity model not very accurate at high conc. - s_kcl = Solution({"K+": "1 mol/kg", "Cl-": "1 mol/kg"}) - assert np.isclose(s_kcl.conductivity.magnitude, 10.862, atol=0.45) - - solutions = [s1, s2, s_kcl] - - for solution in solutions: - reference_data = {"conductivity": solution.conductivity} - data.append((solution, reference_data)) - - filename = DEST.joinpath("CRC_data.json") - with filename.open(mode="r", encoding="utf-8") as file: - json.dump(data, file, indent=4) - - -# TODO: find equivalent reference sources and write replicate _create_crc_data logic -def _create_diffusion_data() -> None: - # test ionic strength adjustment - assert s1.get_diffusion_coefficient("H+") > s2.get_diffusion_coefficient("H+") - - # for Na+, d=122, a1=1.52, a2=3.7, A=1.173802/2.303 at 25 DegC, B = 3.2843078+10 - factor = np.exp( - -1.52 - * 1.173802 - / 2.303 - * 1 - * np.sqrt(s2.ionic_strength.magnitude) - / (1 + 3.2843078e10 * np.sqrt(s2.ionic_strength.magnitude) * 3.7 / (1 + s2.ionic_strength.magnitude**0.75)) - ) - assert np.isclose( - factor * s2.get_diffusion_coefficient("Na+").magnitude, - s2.get_diffusion_coefficient("Na+").magnitude, - atol=5e-11, - ) - s_dilute = Solution({"Na+": "1 mmol/L", "Cl-": "1 mmol/L"}) - assert np.isclose( - s_dilute.get_diffusion_coefficient("Na+", activity_correction=False).magnitude, 1.334e-9, atol=1e-12 - ) - assert np.isclose(s_dilute.get_transport_number("Na+"), 0.396, atol=1e-3) - assert np.isclose(s_dilute.get_transport_number("Cl-"), 0.604, atol=1e-3) - - # test setting a default value - s2.default_diffusion_coeff = 0 - assert s2.get_diffusion_coefficient("Cs+").magnitude == 0 - s2.default_diffusion_coeff = 1e-9 - assert s2.get_diffusion_coefficient("Cs+", activity_correction=False).magnitude == 1e-9 - s2.default_diffusion_coeff = 0 - assert s2.get_diffusion_coefficient("Cs+", activity_correction=True).magnitude < 1e-9 - d25 = s2.get_diffusion_coefficient("Na+", activity_correction=False).magnitude - nu25 = s2.water_substance.nu - s2.temperature = "40 degC" - d40 = s2.get_diffusion_coefficient("Na+", activity_correction=False).magnitude - nu40 = s2.water_substance.nu - assert np.isclose( - d40, - d25 * np.exp(122 / (273.15 + 40) - 122 / 298.15) * (nu25 / nu40), - atol=5e-11, - ) - - # test correction factors for concentration, as per Appelo 2017 Fig 5 - D1 = Solution({"Na+": "1 umol/L", "Cl-": "1 umol/L"}).get_diffusion_coefficient("Na+").magnitude - D2 = Solution({"Na+": "1.7 mol/kg", "Cl-": "1.7 mol/kg"}).get_diffusion_coefficient("Na+").magnitude - assert np.isclose(D2 / D1, 0.54, atol=1e-2) - - D1 = Solution({"K+": "1 umol/L", "Cl-": "1 umol/L"}).get_diffusion_coefficient("K+").magnitude - D2 = Solution({"K+": "0.5 mol/kg", "Cl-": "0.5 mol/kg"}).get_diffusion_coefficient("K+").magnitude - assert np.isclose(D2 / D1, 0.80, atol=1e-2) - - -def _create_density_data() -> None: - # see test_density.py - pass - - -def _create_osmotic_coefficient_data() -> None: - # see test_osmotic_coeff.py - pass - - -# TODO: edit to save Solution objects and add molar conductivity data to reference data dictionary -def _create_molar_conductivity_data() -> None: - def test_molar_conductivity_potassium(self): - # K+ - 73.48 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["K+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("K+").to("m**2*S/mol").magnitude - expected = ureg.Quantity("73.48e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, rtol=RTOL) - - def test_molar_conductivity_sodium(self): - # Na+ - 50.08 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["Na+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("Na+").to("m**2*S/mol").magnitude - expected = ureg.Quantity("50.08e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, rtol=RTOL) - - def test_molar_conductivity_magnesium(self): - # Mg+2 - 106 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["Mg+2", "0.001 mol/L"], ["Cl-", "0.002 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("Mg+2").to("m**2*S/mol").magnitude - expected = ureg.Quantity("106e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, atol=0.005) - - def test_molar_conductivity_chloride(self): - # Cl- - 76.31 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["Na+", "0.001 mol/L"], ["Cl-", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("Cl-").to("m**2*S/mol").magnitude - expected = ureg.Quantity("76.31e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, rtol=RTOL) - - def test_molar_conductivity_fluoride(self): - # F- - 55.4 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["Na+", "0.001 mol/L"], ["F-", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("F-").to("m**2*S/mol").magnitude - expected = ureg.Quantity("55.4e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, rtol=RTOL) - - def test_molar_conductivity_sulfate(self): - # SO4-2 - 160 x 10 ** -4 m ** 2 S / mol - s1 = Solution([["Na+", "0.002 mol/L"], ["SO4-2", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("SO4-2").to("m**2*S/mol").magnitude - expected = ureg.Quantity("160.0e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, atol=0.002) - - def test_molar_conductivity_hydroxide(self): - # OH- - 198 x 10 ** -4 m ** 2 S / mol - s1 = Solution(temperature="25 degC") - result = s1.get_molar_conductivity("OH-").to("m**2*S/mol").magnitude - expected = ureg.Quantity("198e-4 m**2 * S / mol").magnitude - - assert np.isclose(result, expected, rtol=RTOL) +# TODO: check tests for missing property checks and values +# TODO: write sub-loaders for different CRC archive types +# TODO: consolidate data files +# TODO: identify/understand theoretical, reference, and package equivalences +# TODO: check tests for other reference databases +# TODO: find other reference databases +# TODO: write loading function for other reference databases +def _load_crc_data(s) -> list[_BenchmarkEntry]: + # datasets = [] + + # solute data + # load activity coefficient data + + # load molal electrical conductivity - def test_molar_conductivity_hydrogen(self): - # H+ - 349.65 x 10 ** -4 m ** 2 S / mol - s1 = Solution(temperature="25 degC") - result = s1.get_molar_conductivity("H+").to("m**2*S/mol").magnitude - expected = ureg.Quantity("349.65e-4 m**2 * S / mol").magnitude + # load diffusion coefficient data - assert np.isclose(result, expected, rtol=RTOL) + # merge solution.solute_data - # molar conductivity of a neutral solute should be zero - def test_molar_conductivity_neutral(self): - s1 = Solution([["FeCl3", "0.001 mol/L"]], temperature="25 degC") - result = s1.get_molar_conductivity("FeCl3").to("m**2*S/mol").magnitude - expected = ureg.Quantity(0, "m**2 * S / mol").magnitude + # solution data + # load density data - assert round(abs(result - expected), 5) == 0 + # load electrical conductivity - # molar conductivity of water should be zero - def test_molar_conductivity_water(self): - s1 = Solution(temperature="25 degC") - result = s1.get_molar_conductivity("H2O").to("m**2*S/mol").magnitude - expected = ureg.Quantity(0, "m**2 * S / mol").magnitude + # ? load osmotic coefficient data - assert round(abs(result - expected), 5) == 0 + # merge solution.solution_data + # previous parametrization of ion pairs + # cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] + # anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] + # previous list of concentrations to test, mol/kg + # conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] -# TODO: write database files and write loading function -def _load_database(source: str) -> list[tuple[Solution, dict[str, float]]]: - pass + return [] def _get_dataset(source: str) -> list[_BenchmarkEntry]: @@ -308,20 +79,33 @@ def _get_dataset(source: str) -> list[_BenchmarkEntry]: A list of _BenchmarkEntry objects one for each data point in the data set. """ match source: - case "CRC" | "IDST" | "May2011JCED": - reference = _load_database(source) + case "CRC": + reference = _load_crc_data(source) + case "IDST": + pass + case "May2011JCED": + pass case _: with Path(source).open(mode="r", encoding="utf-8") as file: data = json.load(file) - reference: list[tuple[Solution, dict[str, float]]] = [] + reference: list[_BenchmarkEntry] = [] - for sol, values in data: - reference.append((Solution(**sol), values)) + for solution, solute_data, solution_data in data: + reference.append( + _BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) + ) return reference +def _patch_dataset( + dataset: list[_BenchmarkEntry], *, engine: EOS | Literal["native", "ideal", "phreeqc"] = "native" +) -> None: + for data in dataset: + data.solution.engine = engine + + def _rmse(data: list[tuple[float, float]]) -> float: return np.std([ref - calc for ref, calc in data]) @@ -392,13 +176,14 @@ def main() -> None: of an identifying Solution object and a dictionary mapping properties to their reference values. The reference values are checked against pyEQL-calculated values for a variety of engines. """ - # TODO: create engines (e.g., Pitzer, PHREEQC) - # see test_phreeqc.py + engines: list[EOS] = [IdealEOS, NativeEOS, PhreeqcEOS] datasets = [_get_dataset(s) for s in SOURCES] - results: dict[str, list[_BenchmarkEntry]] = {} + results: dict[tuple[str, str], list[_BenchmarkEntry]] = {} - for i, dataset in enumerate(datasets): - results[SOURCES[i]] = report_results(dataset) + for engine in engines: + _patch_dataset(datasets, engine=engine) + for i, dataset in enumerate(datasets): + results[(engine.__name__, SOURCES[i])] = report_results(dataset) if __name__ == "__main__": From 61b03adff70bdb545c3ec472ae7b8807f5f095c2 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 04:15:03 -0700 Subject: [PATCH 04/54] Draft parsers for benchmarking data sources Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/parsers.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 src/pyEQL/parsers.py diff --git a/src/pyEQL/parsers.py b/src/pyEQL/parsers.py new file mode 100644 index 00000000..4837d070 --- /dev/null +++ b/src/pyEQL/parsers.py @@ -0,0 +1,21 @@ +"""Reference data source parsers.""" + +from typing import Any + +from pyEQL.benchmark import _BenchmarkEntry + + +def parse_crc(d: dict[str, Any]) -> _BenchmarkEntry: + """Parse data from CRC.""" + # read solution from "Mol. form" key + + # mean activity coefficient from gamma(0.1 m)-like keys + + # electrical conductivity from kappa(0.5%)-like keys + + # molar electrical conductivity from Λ/S cm2 mol-1
0.0001 M-like keys + + +def parse_idst(d: dict[str, Any]) -> _BenchmarkEntry: + # molal concentration, molal activity/osmotic coefficient + pass From 70b7b16044fde56ff6049bab1e08237b72ae7575 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 14:51:05 -0700 Subject: [PATCH 05/54] Implement function to calculate mean activity Although EOS subclasses define get_activity_coefficicient to return the activity coefficients of individual solutes, one can only measure the mean activity coefficient experimentally. As such, to benchmark against experimental data, we must use the definition of the mean activity coefficient in terms of the activity coefficients of the individual ions. Alternatively, this function could be implemented as a property (Solution.mean_activity) or a method (Solution.get_mean_activity). Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 90e23d99..c1915224 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -9,12 +9,14 @@ import json from collections.abc import Callable +from functools import reduce from pathlib import Path from typing import Any, Literal, NamedTuple import numpy as np from pyEQL.engines import EOS, IdealEOS, NativeEOS, PhreeqcEOS +from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution from pyEQL.utils import FormulaDict @@ -114,7 +116,23 @@ def _get_solute_property(solution: Solution, solute: str, name: str) -> Any | No return solution.get_property(solute, name) +def _get_mean_activity(solution: Solution) -> float: + activity_nu_pairs: list[tuple[float, int]] = [] + + for salt_dict in solution.get_salt_dict().values(): + salt = Salt.from_dict(salt_dict) + act_cat = solution.get_activity_coefficient(salt.cation) + act_an = solution.get_activity_coefficient(salt.anion) + activity_nu_pairs.extend([(act_an, salt.nu_anion), (act_cat, salt.nu_cation)]) + + factor = reduce(lambda x, y: x * y[0] ** y[1], activity_nu_pairs, initial=1.0) + exponent = 1 / sum(x[1] for x in activity_nu_pairs) + return factor**exponent + + def _get_solution_property(solution: Solution, name: str) -> Any | None: + if name == "mean_activity": + return _get_mean_activity(solution) if hasattr(solution, name): return getattr(solution, name) From c4965e490e139e3345ccaf65c8c54e48036ee6d1 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 17:02:01 -0700 Subject: [PATCH 06/54] Clean up functions; add docstrings Publicize functions/classes for processing input/output data models Return values from main function (renamed to benchmark_engine for clarity) and pass engine and source as arguments. Store results instead of printing to console. Parse Solution dictionary into Solution object when reading dataset from file. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 94 +++++++++++++++++++++++++----------------- 1 file changed, 56 insertions(+), 38 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index c1915224..1f1c31fa 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -1,10 +1,13 @@ """Solution model benchmarking utilities. - Usage: - python pyeql.benchmark +>>> from pyEQL.benchmark import benchmark_engine +>>> from pyEQL.engines import IdealEOS +>>> results = benchmark_engine(IdealEOS(), sources=["CRC"]) +>>> results["CRC"].solution_data["mean_activity"] +... """ import json @@ -15,7 +18,7 @@ import numpy as np -from pyEQL.engines import EOS, IdealEOS, NativeEOS, PhreeqcEOS +from pyEQL.engines import EOS from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution from pyEQL.utils import FormulaDict @@ -23,16 +26,30 @@ # TODO: Select and validate data sources # If all solution reference data are generated from the same solutions, then solutions can be used as an input into # source creation -SOURCES: list[str] = ["CRC", "IDST", "May2011JCED"] +INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "May2011JCED"] + +class BenchmarkEntry(NamedTuple): + """Solution reference data entry. + + Attributes: + solution: The Solution to which the reference data applies. + solute_data: A dictionary mapping solutes to a list of solute property-value 2-tuples. + solution_data: A list of solution property-value 2-tuples. + """ -class _BenchmarkEntry(NamedTuple): solution: Solution - # dict[str, list[tuple[str, float]]]: solute, [(property, value)] solute_data: FormulaDict = FormulaDict() solution_data: list[tuple[str, float]] = [] +class BenchmarkResults(NamedTuple): + """Solute and solution stats from :func:`pyEQL.benchmark.benchmark_engine`.""" + + solute_stats: dict[str, float] + solution_stats: dict[str, float] + + # TODO: check tests for missing property checks and values # TODO: write sub-loaders for different CRC archive types # TODO: consolidate data files @@ -40,7 +57,8 @@ class _BenchmarkEntry(NamedTuple): # TODO: check tests for other reference databases # TODO: find other reference databases # TODO: write loading function for other reference databases -def _load_crc_data(s) -> list[_BenchmarkEntry]: +def _load_crc_data(s) -> list[BenchmarkEntry]: + # Use JSONStore? # datasets = [] # solute data @@ -70,7 +88,7 @@ def _load_crc_data(s) -> list[_BenchmarkEntry]: return [] -def _get_dataset(source: str) -> list[_BenchmarkEntry]: +def get_dataset(source: str) -> list[BenchmarkEntry]: """Load reference dataset. Args: @@ -91,18 +109,20 @@ def _get_dataset(source: str) -> list[_BenchmarkEntry]: with Path(source).open(mode="r", encoding="utf-8") as file: data = json.load(file) - reference: list[_BenchmarkEntry] = [] + reference: list[BenchmarkEntry] = [] for solution, solute_data, solution_data in data: reference.append( - _BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) + BenchmarkEntry( + solution=Solution.from_dict(solution), solute_data=solute_data, solution_data=solution_data + ) ) return reference def _patch_dataset( - dataset: list[_BenchmarkEntry], *, engine: EOS | Literal["native", "ideal", "phreeqc"] = "native" + dataset: list[BenchmarkEntry], *, engine: EOS | Literal["native", "ideal", "phreeqc"] = "native" ) -> None: for data in dataset: data.solution.engine = engine @@ -144,23 +164,24 @@ def _get_solution_property(solution: Solution, name: str) -> Any | None: def report_results( - dataset: list[_BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None -) -> None: + dataset: list[BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None +) -> BenchmarkResults: """Report the results of the benchmarking. Args: - dataset: A dictionary mapping 2-tuples (engine, source) to the associated root-means-squared error across - all data points in the source for the given engine. + dataset: A list of _BenchmarkEntry objects metric: A function that acts on the list of 2-tuples (reference, calculated), which contains reference and calculated values. This function should calculate a statistical metric for the list. Defaults to the root- mean-squared error. + + Returns: + A 2-tuple (`solute_stats`, `solution_stats`) where `solute_stats` and `solution_stats` are dictionaries mapping + solute and solution properties, respectively, to their benchmark statistics. """ metric = metric or _rmse - # Populate data structure for tracking activity/osmotic coefficient and solvent volume statistics - # property, (reference, calculated) + # property: [(reference, calculated)] solute_data_pairs: dict[str, list[tuple[float, float]]] = {} - # property, (reference, calculated) solution_data_pairs: dict[str, list[tuple[float, float]]] = {} for d in dataset: @@ -175,34 +196,31 @@ def report_results( if property not in solution_data_pairs: solution_data_pairs[property] = [] - solution_data_pairs[property].append((reference, _get_solution_property(d.solution, solute, property))) + solution_data_pairs[property].append((reference, _get_solution_property(d.solution, property))) solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} - for property, stat in solute_stats.items(): - print(f"{property} statistics: {stat}") + return BenchmarkResults(solute_stats=solute_stats, solution_stats=solution_stats) - for property, stat in solution_stats.items(): - print(f"{property} statistics: {stat}") +def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> BenchmarkResults: + """Benchmark a modeling engine against reference data. -def main() -> None: - """Run solution benchmarking logic. + Args: + engine: The modeling engine to benchmark. + sources: One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of _BenchmarkEntry + objects. - This function works by reading in reference property values from a list of sources. The reference data is composed - of an identifying Solution object and a dictionary mapping properties to their reference values. The reference - values are checked against pyEQL-calculated values for a variety of engines. + Returns: + A dictionary mapping source names to the corresponding solute and solution statistical metrics. """ - engines: list[EOS] = [IdealEOS, NativeEOS, PhreeqcEOS] - datasets = [_get_dataset(s) for s in SOURCES] - results: dict[tuple[str, str], list[_BenchmarkEntry]] = {} - - for engine in engines: - _patch_dataset(datasets, engine=engine) - for i, dataset in enumerate(datasets): - results[(engine.__name__, SOURCES[i])] = report_results(dataset) + sources = sources or INTERNAL_SOURCES + datasets = [get_dataset(s) for s in sources] + results: BenchmarkResults = {} + for i, dataset in enumerate(datasets): + _patch_dataset(dataset, engine=engine) + results[sources[i]] = report_results(dataset) -if __name__ == "__main__": - main() + return results From abd1c045d94835762c524db463f20f8973ed7f0f Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 17:08:50 -0700 Subject: [PATCH 07/54] Fix type hints Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/parsers.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/pyEQL/parsers.py b/src/pyEQL/parsers.py index 4837d070..bd937963 100644 --- a/src/pyEQL/parsers.py +++ b/src/pyEQL/parsers.py @@ -2,10 +2,10 @@ from typing import Any -from pyEQL.benchmark import _BenchmarkEntry +from pyEQL.benchmark import BenchmarkEntry -def parse_crc(d: dict[str, Any]) -> _BenchmarkEntry: +def parse_crc(d: dict[str, Any]) -> list[BenchmarkEntry]: """Parse data from CRC.""" # read solution from "Mol. form" key @@ -16,6 +16,6 @@ def parse_crc(d: dict[str, Any]) -> _BenchmarkEntry: # molar electrical conductivity from Λ/S cm2 mol-1
0.0001 M-like keys -def parse_idst(d: dict[str, Any]) -> _BenchmarkEntry: +def parse_idst(d: dict[str, Any]) -> list[BenchmarkEntry]: + """Parse data from IDST.""" # molal concentration, molal activity/osmotic coefficient - pass From 248585dfbde9a420ec283796f37a43355a14b3e9 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 18:14:24 -0700 Subject: [PATCH 08/54] Fix docstrings and errors Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 1f1c31fa..4de23408 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -36,6 +36,9 @@ class BenchmarkEntry(NamedTuple): solution: The Solution to which the reference data applies. solute_data: A dictionary mapping solutes to a list of solute property-value 2-tuples. solution_data: A list of solution property-value 2-tuples. + + The property strings in the 2-tuples in `solute_data` and `solution_data` should correspond to properties that can + be retrieved using the formalisms outlined in `_get_solute_property` and `_get_solution_property`. """ solution: Solution @@ -93,10 +96,10 @@ def get_dataset(source: str) -> list[BenchmarkEntry]: Args: source: One of "CRC", "IDST", or "May2011JCED" or the path to a file containing reference data. If the latter, - then the [path must point to a JSON which can be read into a _BenchmarkEntry object. + then the [path must point to a JSON which can be read into a BenchmarkEntry object. Returns: - A list of _BenchmarkEntry objects one for each data point in the data set. + A list of BenchmarkEntry objects one for each data point in the data set. """ match source: case "CRC": @@ -132,8 +135,14 @@ def _rmse(data: list[tuple[float, float]]) -> float: return np.std([ref - calc for ref, calc in data]) -def _get_solute_property(solution: Solution, solute: str, name: str) -> Any | None: - return solution.get_property(solute, name) +def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: + value = solution.get_property(solute, name) + + if value is None: + msg = f"Solute property: {name} not supported" + raise ValueError(msg) + + return value def _get_mean_activity(solution: Solution) -> float: @@ -150,7 +159,7 @@ def _get_mean_activity(solution: Solution) -> float: return factor**exponent -def _get_solution_property(solution: Solution, name: str) -> Any | None: +def _get_solution_property(solution: Solution, name: str) -> Any: if name == "mean_activity": return _get_mean_activity(solution) if hasattr(solution, name): @@ -160,7 +169,7 @@ def _get_solution_property(solution: Solution, name: str) -> Any | None: return getattr(solution, f"get_{name}") msg = f"Property {name} is not supported" - raise NotImplementedError(msg) + raise ValueError(msg) def report_results( @@ -169,7 +178,7 @@ def report_results( """Report the results of the benchmarking. Args: - dataset: A list of _BenchmarkEntry objects + dataset: A list of BenchmarkEntry objects metric: A function that acts on the list of 2-tuples (reference, calculated), which contains reference and calculated values. This function should calculate a statistical metric for the list. Defaults to the root- mean-squared error. @@ -209,7 +218,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm Args: engine: The modeling engine to benchmark. - sources: One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of _BenchmarkEntry + sources: One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry objects. Returns: From 8d3b94344e62fff6ba463e7f7773b8390d231df4 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 20:05:47 -0700 Subject: [PATCH 09/54] Move reference data loading to own module Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 42 ++--------------- src/pyEQL/reference.py | 104 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 107 insertions(+), 39 deletions(-) create mode 100644 src/pyEQL/reference.py diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 4de23408..def51343 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -19,6 +19,7 @@ import numpy as np from pyEQL.engines import EOS +from pyEQL.reference import _load_crc_data from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution from pyEQL.utils import FormulaDict @@ -53,44 +54,7 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -# TODO: check tests for missing property checks and values -# TODO: write sub-loaders for different CRC archive types -# TODO: consolidate data files -# TODO: identify/understand theoretical, reference, and package equivalences -# TODO: check tests for other reference databases -# TODO: find other reference databases -# TODO: write loading function for other reference databases -def _load_crc_data(s) -> list[BenchmarkEntry]: - # Use JSONStore? - # datasets = [] - - # solute data - # load activity coefficient data - - # load molal electrical conductivity - - # load diffusion coefficient data - - # merge solution.solute_data - - # solution data - # load density data - - # load electrical conductivity - - # ? load osmotic coefficient data - - # merge solution.solution_data - - # previous parametrization of ion pairs - # cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] - # anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] - # previous list of concentrations to test, mol/kg - # conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] - - return [] - - +# TODO: optimize strategy-switching algorithm for source names def get_dataset(source: str) -> list[BenchmarkEntry]: """Load reference dataset. @@ -103,7 +67,7 @@ def get_dataset(source: str) -> list[BenchmarkEntry]: """ match source: case "CRC": - reference = _load_crc_data(source) + reference = _load_crc_data() case "IDST": pass case "May2011JCED": diff --git a/src/pyEQL/reference.py b/src/pyEQL/reference.py new file mode 100644 index 00000000..866df3db --- /dev/null +++ b/src/pyEQL/reference.py @@ -0,0 +1,104 @@ +"""Reference data for benchmarking.""" + +from pyEQL.benchmark import BenchmarkEntry + + +# TODO: search for each property in each reference database & sketch sub-loader block +# TODO: identify/understand theoretical, reference, and package equivalences (i.e., how do literature values translate +# TODO: to Python attributes) +# TODO: verify that _get_solute/ion_property framework will work for reference properties +# TODO: consolidate existing data files +# TODO: remove redundant sources +# TODO: write sub-loaders for different CRC archive types +# TODO: write loading function for other reference databases +def _load_crc_data() -> list[BenchmarkEntry]: + # Use JSONStore? + # datasets = [] + + # SOLUTE DATA + + # property: molar electrical conductivity + # Salts: KCl, NaCl, MgCl2, NaF, Na2SO4, OH-, FeCl3, H2O + # Concentrations: 0.001, 0.002 + # sources: molar_electrical_conductivity/ + + # SOLUTION DATA + # property: mean activity coefficient data + # Salts: HCl, CsI, BaCl2, LiCl, RbCl, MgCl2, KBr, K2SO4 + # Concentrations: 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5 + # TODO: compile data + # sources: activity_coefficients/ + + # load density data + + # load electrical conductivity + + # ? load osmotic coefficient data + + # merge solution.solution_data + + # previous parametrization of ion pairs + # cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] + # anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] + # previous list of concentrations to test, mol/kg + # conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] + + return [] + + +def _load_idst_data() -> list[BenchmarkEntry]: + pass + + +def _load_jpcrd_data() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: mean activity coefficient + # Salts: NaCl + # Concentrations: 0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6 + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) + # - Theoretical Mean Activity Coefficients of Strong Electrolytes in Aqueous Solutions from 0 to 100C - + # Walter J. Hamer. NSRDS-NBS 24, 271p. (1968). + + # Additional properties from Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R.. + # "Properties Index" (p. 94): + # density, diffusion coefficient, electrical resistivity/conductivity, osmotic coefficients, dielectric constants + # Debye length + pass + + +def _load_environ_sci_data() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: debye length + # Salts: NaCl, Na2SO4 + # Concentrations: 0.1, 10 + # source: doi:10.1021/es400571g + pass + + +def _load_fluid_phase_data() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: dielectric constant + # Salts: NaCl, KBr, LiCl, RbCl + # Concentrations: 0.5, 1, 2, 2.1, 3.4, 4.4, 5, 6.5, 12 + # source: doi:10.1016/j.fluid.2014.05.037 + pass + + +def _load_jchem_eng_data1() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: activity coefficient + # Salts: Na+/K+/NO3- + # Concentrations: 1:3, 1:1, 3:1 + # source: doi:10.1021/je9004432 + pass + + +def _load_jchem_eng_data2() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: osmotic coefficient + # Salts: NH4NO3, Cu(2)SO4 + # Concentrations: 0.25, 0.5, 0.75, 1, 1.5, 2 + # source: doi:10.1021/je2009329 + pass From 62c26e58f38fd722093e6c4b1f205b283c6e21a3 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 20:39:10 -0700 Subject: [PATCH 10/54] Sketch loading functions Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/reference.py | 84 ++++++++++++++++++++++++++++++++---------- 1 file changed, 64 insertions(+), 20 deletions(-) diff --git a/src/pyEQL/reference.py b/src/pyEQL/reference.py index 866df3db..1cc3039b 100644 --- a/src/pyEQL/reference.py +++ b/src/pyEQL/reference.py @@ -3,7 +3,6 @@ from pyEQL.benchmark import BenchmarkEntry -# TODO: search for each property in each reference database & sketch sub-loader block # TODO: identify/understand theoretical, reference, and package equivalences (i.e., how do literature values translate # TODO: to Python attributes) # TODO: verify that _get_solute/ion_property framework will work for reference properties @@ -20,51 +19,96 @@ def _load_crc_data() -> list[BenchmarkEntry]: # property: molar electrical conductivity # Salts: KCl, NaCl, MgCl2, NaF, Na2SO4, OH-, FeCl3, H2O # Concentrations: 0.001, 0.002 + # TODO: compile data # sources: molar_electrical_conductivity/ # SOLUTION DATA - # property: mean activity coefficient data + # property: mean activity coefficient # Salts: HCl, CsI, BaCl2, LiCl, RbCl, MgCl2, KBr, K2SO4 # Concentrations: 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5 # TODO: compile data # sources: activity_coefficients/ - # load density data - - # load electrical conductivity - - # ? load osmotic coefficient data - - # merge solution.solution_data + # property: density + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: density/ - # previous parametrization of ion pairs - # cations = [("H+", 1), ("Cs+", 1), ("Li+", 1), ("Rb+", 1), ("K+", 1), ("Na", 1), ("Mg", 2), ("Ba", 2)] - # anions = [("Cl-", 1), ("I-", 1), ("Br", 1), ("SO4-2", 2)] - # previous list of concentrations to test, mol/kg - # conc_list = [0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5] + # property: conductivity + # Salts: NaCl, KCl, MgCl2 + # Concentrations: 0.001, 0.05, 0.1 + # TODO: compile data + # sources: "Electrical Conductivity of Aqueous Solutions at 20C as a Function of Concentration" return [] def _load_idst_data() -> list[BenchmarkEntry]: + # SOLUTION DATA + # property: mean activity coefficient + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - https://idst.inl.gov + + # property: osmotic coefficients + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - https://idst.inl.gov pass def _load_jpcrd_data() -> list[BenchmarkEntry]: # SOLUTION DATA # property: mean activity coefficient - # Salts: NaCl - # Concentrations: 0.1, 0.25, 0.5, 0.75, 1, 2, 3, 4, 5, 6 + # Salts: ? + # Concentrations: ? # TODO: compile data # sources: # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) # - Theoretical Mean Activity Coefficients of Strong Electrolytes in Aqueous Solutions from 0 to 100C - # Walter J. Hamer. NSRDS-NBS 24, 271p. (1968). + # - Thermodynamic Properties of Aqueous Sodium Chloride Solutions — Kenneth S. Pitzer, J. Christopher Peiper, and + # R. H. Busey. J Phys Chem Ref Data 13, 1(1984). + + # property: density + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - # Additional properties from Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R.. - # "Properties Index" (p. 94): - # density, diffusion coefficient, electrical resistivity/conductivity, osmotic coefficients, dielectric constants - # Debye length + # property: dielectric constant + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) + + # property: electrical resistivity/conductivity + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) + + # property: osmotic coefficients + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) + + # property: dielectric constant + # Salts: ? + # Concentrations: ? + # TODO: compile data + # sources: + # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) pass From 32b74dfae5470af305ffb87a2e0a57768bceec24 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Tue, 17 Jun 2025 21:30:32 -0700 Subject: [PATCH 11/54] Remove parsers Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/parsers.py | 21 --------------------- 1 file changed, 21 deletions(-) delete mode 100644 src/pyEQL/parsers.py diff --git a/src/pyEQL/parsers.py b/src/pyEQL/parsers.py deleted file mode 100644 index bd937963..00000000 --- a/src/pyEQL/parsers.py +++ /dev/null @@ -1,21 +0,0 @@ -"""Reference data source parsers.""" - -from typing import Any - -from pyEQL.benchmark import BenchmarkEntry - - -def parse_crc(d: dict[str, Any]) -> list[BenchmarkEntry]: - """Parse data from CRC.""" - # read solution from "Mol. form" key - - # mean activity coefficient from gamma(0.1 m)-like keys - - # electrical conductivity from kappa(0.5%)-like keys - - # molar electrical conductivity from Λ/S cm2 mol-1
0.0001 M-like keys - - -def parse_idst(d: dict[str, Any]) -> list[BenchmarkEntry]: - """Parse data from IDST.""" - # molal concentration, molal activity/osmotic coefficient From 4cc1b5ec9c95979bc4a7ce6f841c1448611314ca Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Wed, 18 Jun 2025 00:15:55 -0700 Subject: [PATCH 12/54] Remove todos Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/reference.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/pyEQL/reference.py b/src/pyEQL/reference.py index 1cc3039b..05f448da 100644 --- a/src/pyEQL/reference.py +++ b/src/pyEQL/reference.py @@ -3,9 +3,6 @@ from pyEQL.benchmark import BenchmarkEntry -# TODO: identify/understand theoretical, reference, and package equivalences (i.e., how do literature values translate -# TODO: to Python attributes) -# TODO: verify that _get_solute/ion_property framework will work for reference properties # TODO: consolidate existing data files # TODO: remove redundant sources # TODO: write sub-loaders for different CRC archive types From 1862e003ffb2d6db6752211818ef18d3359cb796 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Wed, 18 Jun 2025 02:21:03 -0700 Subject: [PATCH 13/54] Optimized strategy-switching algorithm for sources Passing a string corresponding to an internal source name retrieves the Path to the data file (distributed with package). All files are loaded in the same way. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 36 +++++++++++++++--------------------- 1 file changed, 15 insertions(+), 21 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index def51343..4368a100 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -19,7 +19,6 @@ import numpy as np from pyEQL.engines import EOS -from pyEQL.reference import _load_crc_data from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution from pyEQL.utils import FormulaDict @@ -27,7 +26,7 @@ # TODO: Select and validate data sources # If all solution reference data are generated from the same solutions, then solutions can be used as an input into # source creation -INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "May2011JCED"] +INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "JPCRD", "May2011JCED"] class BenchmarkEntry(NamedTuple): @@ -54,36 +53,31 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -# TODO: optimize strategy-switching algorithm for source names -def get_dataset(source: str) -> list[BenchmarkEntry]: +def get_dataset(source: str | Path) -> list[BenchmarkEntry]: """Load reference dataset. Args: - source: One of "CRC", "IDST", or "May2011JCED" or the path to a file containing reference data. If the latter, + source: One of "CRC", "IDST", "JPCRD", or "May2011JCED" or the path to a file containing reference data. If the latter, then the [path must point to a JSON which can be read into a BenchmarkEntry object. Returns: A list of BenchmarkEntry objects one for each data point in the data set. """ match source: - case "CRC": - reference = _load_crc_data() - case "IDST": - pass - case "May2011JCED": - pass + case "CRC" | "IDST" | "JPCRD": + source = Path(__file__).parent.joinpath("database", f"{source}.json") case _: - with Path(source).open(mode="r", encoding="utf-8") as file: - data = json.load(file) + source = Path(source) - reference: list[BenchmarkEntry] = [] + with source.open(mode="r", encoding="utf-8") as file: + data = json.load(file) - for solution, solute_data, solution_data in data: - reference.append( - BenchmarkEntry( - solution=Solution.from_dict(solution), solute_data=solute_data, solution_data=solution_data - ) - ) + reference: list[BenchmarkEntry] = [] + + for solution, solute_data, solution_data in data: + reference.append( + BenchmarkEntry(solution=Solution.from_dict(solution), solute_data=solute_data, solution_data=solution_data) + ) return reference @@ -183,7 +177,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm Args: engine: The modeling engine to benchmark. sources: One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry - objects. + objects. Defaults to INTERNAL_SOURCES. Returns: A dictionary mapping source names to the corresponding solute and solution statistical metrics. From 39679fa2c520f370ff6a998014b0b39abe0e1221 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Wed, 18 Jun 2025 17:56:35 -0700 Subject: [PATCH 14/54] Parse dataset values into Quantity objects Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 4368a100..317d8946 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -17,7 +17,9 @@ from typing import Any, Literal, NamedTuple import numpy as np +from pint import Quantity +from pyEQL import ureg from pyEQL.engines import EOS from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution @@ -35,7 +37,7 @@ class BenchmarkEntry(NamedTuple): Attributes: solution: The Solution to which the reference data applies. solute_data: A dictionary mapping solutes to a list of solute property-value 2-tuples. - solution_data: A list of solution property-value 2-tuples. + solution_data: A list of solution property-quantity 2-tuples. The property strings in the 2-tuples in `solute_data` and `solution_data` should correspond to properties that can be retrieved using the formalisms outlined in `_get_solute_property` and `_get_solution_property`. @@ -43,7 +45,7 @@ class BenchmarkEntry(NamedTuple): solution: Solution solute_data: FormulaDict = FormulaDict() - solution_data: list[tuple[str, float]] = [] + solution_data: list[tuple[str, Quantity]] = [] class BenchmarkResults(NamedTuple): @@ -70,11 +72,17 @@ def get_dataset(source: str | Path) -> list[BenchmarkEntry]: source = Path(source) with source.open(mode="r", encoding="utf-8") as file: - data = json.load(file) + data: list[tuple[dict, dict[str, list], list[tuple]]] = json.load(file) reference: list[BenchmarkEntry] = [] for solution, solute_data, solution_data in data: + for k, values in solute_data.items(): + solute_data[k] = [ureg.Quantity(float(x), y) for x, y in values] + + for i, (x, y) in solution_data: + solution_data[i] = ureg.Quantity(float(x), y) + reference.append( BenchmarkEntry(solution=Solution.from_dict(solution), solute_data=solute_data, solution_data=solution_data) ) From f26ec0e289c6c735ae3dffb0d3a4c7048573e22b Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Wed, 18 Jun 2025 19:27:40 -0700 Subject: [PATCH 15/54] Draft benchmark tests Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 tests/test_benchmark.py diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py new file mode 100644 index 00000000..709eee16 --- /dev/null +++ b/tests/test_benchmark.py @@ -0,0 +1,10 @@ +class TestDataset: + pass + + +class TestReportResults: + pass + + +class TestBenchmarkEngine: + pass From 526ec7101ecf6af8592ad72401e1fd21996ff0ae Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Wed, 18 Jun 2025 21:43:43 -0700 Subject: [PATCH 16/54] Convert solute and solution data values ...to list[tuple[str, Quantity]] Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 317d8946..f552628a 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -78,13 +78,17 @@ def get_dataset(source: str | Path) -> list[BenchmarkEntry]: for solution, solute_data, solution_data in data: for k, values in solute_data.items(): - solute_data[k] = [ureg.Quantity(float(x), y) for x, y in values] + solute_data[k] = [(prop, ureg.Quantity(q)) for prop, q in values] - for i, (x, y) in solution_data: - solution_data[i] = ureg.Quantity(float(x), y) + for i, (prop, q) in solution_data: + solution_data[i] = prop, ureg.Quantity(q) reference.append( - BenchmarkEntry(solution=Solution.from_dict(solution), solute_data=solute_data, solution_data=solution_data) + BenchmarkEntry( + solution=Solution.from_dict(solution), + solute_data=FormulaDict(**solute_data), + solution_data=solution_data, + ) ) return reference From 5cb88435e2f5264200a39629fbe5af353722ee95 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 02:45:46 -0700 Subject: [PATCH 17/54] Rename property to match conventional name Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index f552628a..2ee45898 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -115,7 +115,7 @@ def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: return value -def _get_mean_activity(solution: Solution) -> float: +def _get_mean_activity_coefficient(solution: Solution) -> float: activity_nu_pairs: list[tuple[float, int]] = [] for salt_dict in solution.get_salt_dict().values(): @@ -130,8 +130,8 @@ def _get_mean_activity(solution: Solution) -> float: def _get_solution_property(solution: Solution, name: str) -> Any: - if name == "mean_activity": - return _get_mean_activity(solution) + if name == "mean_activity_coefficient": + return _get_mean_activity_coefficient(solution) if hasattr(solution, name): return getattr(solution, name) From 2d113d6d07d5ba1d6a9d54f4af4bd9468479c5b9 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 04:50:33 -0700 Subject: [PATCH 18/54] Expand benchmark unit tests Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 108 ++++++++++++++++++++++++++++++++++++++-- 1 file changed, 104 insertions(+), 4 deletions(-) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index 709eee16..7cf815f2 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -1,10 +1,110 @@ -class TestDataset: - pass +from pathlib import Path + +import pytest + +from pyEQL.benchmark import ( + BenchmarkEntry, + _get_solute_property, + _get_solution_property, + benchmark_engine, + get_dataset, + report_results, +) +from pyEQL.engines import EOS, IdealEOS, NativeEOS +from pyEQL.solution import Solution +from pyEQL.utils import FormulaDict + +datadir = Path(__file__).parent.joinpath(Path(__file__).stem) + + +@pytest.fixture( + name="engine", + params=[ + IdealEOS, + NativeEOS, + # PhreeqcEOS - hide for now + ], +) +def fixture_engine(request: pytest.FixtureRequest) -> EOS: + engine: type[EOS] = request.param + return engine() + + +class TestGetDataset: + @staticmethod + @pytest.mark.parametrize("source", ["molar_conductivity.json"]) + def test_should_load_dataset_from_file(source: str) -> None: + dataset = get_dataset(datadir.joinpath(source)) + assert dataset + + +@pytest.fixture(name="cation", params=["Na[+1]", "NH4[+1]"]) +def fixture_cation(request: pytest.FixtureRequest) -> str: + return request.param + + +@pytest.fixture(name="anion", params=["Cl[-1]", "SO4[-2]"]) +def fixture_anion(request: pytest.FixtureRequest) -> str: + return request.param + + +@pytest.fixture(name="conc", params=["0.1 mol/L", "25%"]) +def fixture_conc(request: pytest.FixtureRequest) -> str: + return request.param + + +@pytest.fixture( + name="solutes", +) +def fixture_solutes(cation: str, anion: str, conc: str) -> dict[str, str]: + return {cation: conc, anion: conc} + + +@pytest.fixture(name="solution") +def fixture_solution(solutes: dict[str, str], engine: EOS) -> Solution: + return Solution(solutes=solutes, engine=engine) + + +@pytest.fixture(name="solute_property", params=["activity_coefficient", "molar_conductivity"]) +def fixture_solute_property(request: pytest.FixtureRequest) -> str: + return request.param + + +@pytest.fixture( + name="solution_property", + params=["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"], +) +def fixture_solution_property(request: pytest.FixtureRequest) -> str: + return request.param + + +@pytest.fixture( + name="dataset", +) +def fixture_dataset(solution: Solution, solute_property: str, solution_property: str) -> list[BenchmarkEntry]: + solute_data = FormulaDict() + + for solute in solution.components: + data = _get_solute_property(solution, solute, solute_property) + solute_data[solute] = [(solute_property, data)] + + data = _get_solution_property(solution, solution_property) + solution_data = [(solution_property, data)] + + dataset = BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) + return [dataset] class TestReportResults: - pass + @staticmethod + def test_should_report_zero_rmse_with_engine_dataset(dataset: list[BenchmarkEntry]) -> None: + results = report_results(dataset) + assert all(err == 0 for err in results.solute_stats.values()) + assert all(err == 0 for err in results.solution_stats.values()) class TestBenchmarkEngine: - pass + @staticmethod + def test_should_benchmark_all_engines(engine: EOS) -> None: + benchmark_results = benchmark_engine(engine, sources=[datadir.joinpath("molar_conductivity.json")]) + assert benchmark_results From cf247ceba8004cdf9fe31426c0ae362a8c813b59 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 04:51:36 -0700 Subject: [PATCH 19/54] Fix property retrieval, RMSE calc; rename vars The new RMSE is more robust in the case that property values are Python primitives. Property getters are now called to retrieve properties. This fixes a bug where the getter was returned instead of the value. Variables are renamed (from property) to avoid shadowing a Python built-in. Enumerating solution data (in get_dataset) yields the right number of items to unpack. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 51 +++++++++++++++++++++++++++--------------- 1 file changed, 33 insertions(+), 18 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 2ee45898..1a918ab1 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -77,15 +77,15 @@ def get_dataset(source: str | Path) -> list[BenchmarkEntry]: reference: list[BenchmarkEntry] = [] for solution, solute_data, solution_data in data: - for k, values in solute_data.items(): - solute_data[k] = [(prop, ureg.Quantity(q)) for prop, q in values] + for solute, values in solute_data.items(): + solute_data[solute] = [(prop, ureg.Quantity(q)) for prop, q in values] - for i, (prop, q) in solution_data: + for i, (prop, q) in enumerate(solution_data): solution_data[i] = prop, ureg.Quantity(q) reference.append( BenchmarkEntry( - solution=Solution.from_dict(solution), + solution=Solution(**solution), solute_data=FormulaDict(**solute_data), solution_data=solution_data, ) @@ -101,16 +101,30 @@ def _patch_dataset( data.solution.engine = engine -def _rmse(data: list[tuple[float, float]]) -> float: - return np.std([ref - calc for ref, calc in data]) +def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: + reduced = [] + + for ref, calc in data: + val = ref - calc + + if hasattr(val, "m"): + val = val.m + + reduced.append(val) + return np.std(reduced) def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: value = solution.get_property(solute, name) if value is None: - msg = f"Solute property: {name} not supported" - raise ValueError(msg) + if hasattr(solution, name): + value = getattr(solution, name) + elif hasattr(solution, f"get_{name}"): + value = getattr(solution, f"get_{name}")(solute) + else: + msg = f"Solute property: {name} not supported" + raise ValueError(msg) return value @@ -136,7 +150,7 @@ def _get_solution_property(solution: Solution, name: str) -> Any: return getattr(solution, name) if hasattr(solution, f"get_{name}"): - return getattr(solution, f"get_{name}") + return getattr(solution, f"get_{name}")() msg = f"Property {name} is not supported" raise ValueError(msg) @@ -165,17 +179,17 @@ def report_results( for d in dataset: for solute, solute_data in d.solute_data.items(): - for property, reference in solute_data: - if property not in solute_data_pairs: - solute_data_pairs[property] = [] + for prop, reference in solute_data: + if prop not in solute_data_pairs: + solute_data_pairs[prop] = [] - solute_data_pairs[property].append((reference, _get_solute_property(d.solution, solute, property))) + solute_data_pairs[prop].append((reference, _get_solute_property(d.solution, solute, prop))) - for property, reference in d.solution_data: - if property not in solution_data_pairs: - solution_data_pairs[property] = [] + for prop, reference in d.solution_data: + if prop not in solution_data_pairs: + solution_data_pairs[prop] = [] - solution_data_pairs[property].append((reference, _get_solution_property(d.solution, property))) + solution_data_pairs[prop].append((reference, _get_solution_property(d.solution, prop))) solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} @@ -200,6 +214,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm for i, dataset in enumerate(datasets): _patch_dataset(dataset, engine=engine) - results[sources[i]] = report_results(dataset) + key = Path(sources[i]).name + results[key] = report_results(dataset) return results From 8743883014ef934edb6c861f24c8aa74e7c1768f Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 05:21:11 -0700 Subject: [PATCH 20/54] Fix implementation of RMSE Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 1a918ab1..a57cbcb7 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -11,6 +11,7 @@ """ import json +import math from collections.abc import Callable from functools import reduce from pathlib import Path @@ -105,13 +106,13 @@ def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: reduced = [] for ref, calc in data: - val = ref - calc + val = (ref - calc) ** 2 if hasattr(val, "m"): val = val.m reduced.append(val) - return np.std(reduced) + return math.sqrt(np.mean(reduced)) def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: From d8aeaa01ec25662b981327195ee425c1a02f17ae Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 05:23:20 -0700 Subject: [PATCH 21/54] Add molar conductivity reference data Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark/molar_conductivity.json | 8610 ++++++++++++++++++ 1 file changed, 8610 insertions(+) create mode 100644 tests/test_benchmark/molar_conductivity.json diff --git a/tests/test_benchmark/molar_conductivity.json b/tests/test_benchmark/molar_conductivity.json new file mode 100644 index 00000000..d009b5be --- /dev/null +++ b/tests/test_benchmark/molar_conductivity.json @@ -0,0 +1,8610 @@ +[ + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "12.045 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "14.794999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "17.349999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "19.944999999999997 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "22.68 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "24.84 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "22.959999999999997 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "27.599999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "32.9 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "38.03999999999999 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "41.86 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "46.519999999999996 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "31.424999999999997 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "38.235 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "44.834999999999994 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "51.089999999999996 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "57.27 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.5 mol/l", + "H[+1]": "1.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "63.20999999999999 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "283.15 K" + }, + {}, + [ + [ + "conductivity", + "30.16 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "37.72 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "46.26 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "54.36 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "62.82 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "70.1 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.0 mol/l", + "H[+1]": "2.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "77.47999999999999 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.5 mol/l", + "H[+1]": "2.5 mol/l" + }, + "temperature": "283.15 K" + }, + {}, + [ + [ + "conductivity", + "34.199999999999996 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.5 mol/l", + "H[+1]": "2.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "42.925 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "2.5 mol/l", + "H[+1]": 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+ "0.08486999999999999 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.02 mol/l", + "Zn[+2]": "0.02 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "conductivity", + "0.14839999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.05 mol/l", + "Zn[+2]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "conductivity", + "0.30585 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.1 mol/l", + "Zn[+2]": "0.1 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "conductivity", + "0.5261 S/m" + ] + ] + ] +] From 66dee23c8528ce388b6af831a87b1ecc00fc1ac7 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 05:32:27 -0700 Subject: [PATCH 22/54] Rename function for clarity Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 6 +++--- tests/test_benchmark.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index a57cbcb7..2d7d13bf 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -157,10 +157,10 @@ def _get_solution_property(solution: Solution, name: str) -> Any: raise ValueError(msg) -def report_results( +def calculate_stats( dataset: list[BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None ) -> BenchmarkResults: - """Report the results of the benchmarking. + """Calculate benchmarking statistics. Args: dataset: A list of BenchmarkEntry objects @@ -216,6 +216,6 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm for i, dataset in enumerate(datasets): _patch_dataset(dataset, engine=engine) key = Path(sources[i]).name - results[key] = report_results(dataset) + results[key] = calculate_stats(dataset) return results diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index 7cf815f2..66b6611f 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -7,8 +7,8 @@ _get_solute_property, _get_solution_property, benchmark_engine, + calculate_stats, get_dataset, - report_results, ) from pyEQL.engines import EOS, IdealEOS, NativeEOS from pyEQL.solution import Solution @@ -95,10 +95,10 @@ def fixture_dataset(solution: Solution, solute_property: str, solution_property: return [dataset] -class TestReportResults: +class TestCalculateStats: @staticmethod - def test_should_report_zero_rmse_with_engine_dataset(dataset: list[BenchmarkEntry]) -> None: - results = report_results(dataset) + def test_should_calculate_zero_rmse_with_engine_dataset(dataset: list[BenchmarkEntry]) -> None: + results = calculate_stats(dataset) assert all(err == 0 for err in results.solute_stats.values()) assert all(err == 0 for err in results.solution_stats.values()) From ffbd84f3deb3c52b2d063a9f0a95d57e0abd052e Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 05:59:30 -0700 Subject: [PATCH 23/54] Add utility to create BenchmarkEntry Improve docstrings Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 62 ++++++++++++++++++++++++++++++++++++++--- tests/test_benchmark.py | 22 ++------------- 2 files changed, 60 insertions(+), 24 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 2d7d13bf..683aedaa 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -1,6 +1,6 @@ """Solution model benchmarking utilities. -Usage: +Example: Benchmark a solution model against reference data >>> from pyEQL.benchmark import benchmark_engine >>> from pyEQL.engines import IdealEOS @@ -8,6 +8,37 @@ >>> results = benchmark_engine(IdealEOS(), sources=["CRC"]) >>> results["CRC"].solution_data["mean_activity"] ... + +Example: Generate a reference dataset from a solution model + +>>> from pyEQL import Solution +>>> from pyEQL.benchmark import calculate_stats +>>> from pyEQL.benchmark import create_entry +>>> from pyEQL.engines import IdealEOS +>>> from pyEQL.engines import NativeEOS + +>>> cations = ["H[+1]", "Na[+1]", "Ca[+2]"] +>>> anions = ["OH[-1]", "Cl[-1]", "SO4[-2]"] +>>> concs = ["0.1 mol/L", "25%"] +>>> solutions = [] + +>>> for ions for product(cations, anions): +... for conc in concs: +... solutes = {ion: conc for ion in ions} +... solutions.append(Solution(solutes=solutes, engine=IdealEOS())) + +>>> solute_properties = ["activity_coefficient", "molar_conductivity"] +>>> solution_properties = ["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"] +>>> dataset = [] + +>>> for solution in solutions: +... entry = create_entry(solution, solute_properties, solution_properties) +... dataset.append(entry) + +>>> for data in dataset: +... data.solution.engine = NativeEOS() + +>>> stats = calculate_stats(dataset) """ import json @@ -26,9 +57,6 @@ from pyEQL.solution import Solution from pyEQL.utils import FormulaDict -# TODO: Select and validate data sources -# If all solution reference data are generated from the same solutions, then solutions can be used as an input into -# source creation INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "JPCRD", "May2011JCED"] @@ -157,6 +185,32 @@ def _get_solution_property(solution: Solution, name: str) -> Any: raise ValueError(msg) +def create_entry(solution: Solution, solute_properties: list[str], solution_properties: list[str]) -> BenchmarkEntry: + """Create a BenchmarkEntry from a Solution and specified properties. + + Args: + solution: The Solution from which to create the entry. + solute_properties: The solute properties to add to the entry. + solution_properties: The solution properties to add to the entry. + """ + solute_data = FormulaDict() + + for solute in solution.components: + solute_data[solute] = [] + + for solute_property in solute_properties: + data = _get_solute_property(solution, solute, solute_property) + solute_data[solute].append((solute_property, data)) + + solution_data = [] + + for solution_property in solution_properties: + data = _get_solution_property(solution, solution_property) + solution_data.append((solution_property, data)) + + return BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) + + def calculate_stats( dataset: list[BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None ) -> BenchmarkResults: diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index 66b6611f..c580fc00 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -2,17 +2,9 @@ import pytest -from pyEQL.benchmark import ( - BenchmarkEntry, - _get_solute_property, - _get_solution_property, - benchmark_engine, - calculate_stats, - get_dataset, -) +from pyEQL.benchmark import BenchmarkEntry, benchmark_engine, calculate_stats, create_entry, get_dataset from pyEQL.engines import EOS, IdealEOS, NativeEOS from pyEQL.solution import Solution -from pyEQL.utils import FormulaDict datadir = Path(__file__).parent.joinpath(Path(__file__).stem) @@ -82,17 +74,7 @@ def fixture_solution_property(request: pytest.FixtureRequest) -> str: name="dataset", ) def fixture_dataset(solution: Solution, solute_property: str, solution_property: str) -> list[BenchmarkEntry]: - solute_data = FormulaDict() - - for solute in solution.components: - data = _get_solute_property(solution, solute, solute_property) - solute_data[solute] = [(solute_property, data)] - - data = _get_solution_property(solution, solution_property) - solution_data = [(solution_property, data)] - - dataset = BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) - return [dataset] + return [create_entry(solution, [solute_property], [solution_property])] class TestCalculateStats: From e0002c875938ffbd89d7dd764f517ccbf5d10a97 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 06:33:39 -0700 Subject: [PATCH 24/54] Remove extra Salt key; fix reduce signature Salt takes no extra kwargs. reduce takes no kwargs. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 683aedaa..49d84d6f 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -88,8 +88,8 @@ def get_dataset(source: str | Path) -> list[BenchmarkEntry]: """Load reference dataset. Args: - source: One of "CRC", "IDST", "JPCRD", or "May2011JCED" or the path to a file containing reference data. If the latter, - then the [path must point to a JSON which can be read into a BenchmarkEntry object. + source: One of "CRC", "IDST", "JPCRD", or "May2011JCED" or the path to a file containing reference data. If the + latter, then the [path must point to a JSON which can be read into a BenchmarkEntry object. Returns: A list of BenchmarkEntry objects one for each data point in the data set. @@ -162,12 +162,13 @@ def _get_mean_activity_coefficient(solution: Solution) -> float: activity_nu_pairs: list[tuple[float, int]] = [] for salt_dict in solution.get_salt_dict().values(): + _ = salt_dict.pop("mol") salt = Salt.from_dict(salt_dict) act_cat = solution.get_activity_coefficient(salt.cation) act_an = solution.get_activity_coefficient(salt.anion) activity_nu_pairs.extend([(act_an, salt.nu_anion), (act_cat, salt.nu_cation)]) - factor = reduce(lambda x, y: x * y[0] ** y[1], activity_nu_pairs, initial=1.0) + factor = reduce(lambda x, y: x * y[0] ** y[1], activity_nu_pairs, 1.0) exponent = 1 / sum(x[1] for x in activity_nu_pairs) return factor**exponent From 85277fd8a0016c8b0f9a4d8e8b39519c3c9b9b28 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 06:34:32 -0700 Subject: [PATCH 25/54] Create source fixture Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index c580fc00..de6773fd 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -85,8 +85,13 @@ def test_should_calculate_zero_rmse_with_engine_dataset(dataset: list[BenchmarkE assert all(err == 0 for err in results.solution_stats.values()) +@pytest.fixture(name="source", params=["molar_conductivity.json", "mean_activity_coefficient.json"]) +def fixture_source(request: pytest.FixtureRequest) -> list[Path]: + return datadir.joinpath(request.param) + + class TestBenchmarkEngine: @staticmethod - def test_should_benchmark_all_engines(engine: EOS) -> None: - benchmark_results = benchmark_engine(engine, sources=[datadir.joinpath("molar_conductivity.json")]) + def test_should_benchmark_all_engines(engine: EOS, source: Path) -> None: + benchmark_results = benchmark_engine(engine, sources=[source]) assert benchmark_results From fd05cebd0ab7a1f26fd4c1bffb7c81795cc038fc Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 07:31:04 -0700 Subject: [PATCH 26/54] Add more properties Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 36 +++++++++++++++++++++++++++++++++--- tests/test_benchmark.py | 30 ++++++++++++++++++++---------- 2 files changed, 53 insertions(+), 13 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 49d84d6f..5efaf6e8 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -51,6 +51,7 @@ import numpy as np from pint import Quantity +import pyEQL from pyEQL import ureg from pyEQL.engines import EOS from pyEQL.salt_ion_match import Salt @@ -61,11 +62,11 @@ class BenchmarkEntry(NamedTuple): - """Solution reference data entry. + """A set of data for a solution. Attributes: solution: The Solution to which the reference data applies. - solute_data: A dictionary mapping solutes to a list of solute property-value 2-tuples. + solute_data: A dictionary mapping solutes to a list of solute property-quantity 2-tuples. solution_data: A list of solution property-quantity 2-tuples. The property strings in the 2-tuples in `solute_data` and `solution_data` should correspond to properties that can @@ -78,7 +79,7 @@ class BenchmarkEntry(NamedTuple): class BenchmarkResults(NamedTuple): - """Solute and solution stats from :func:`pyEQL.benchmark.benchmark_engine`.""" + """Solute and solution stats from :func:`pyEQL.benchmark.calculate_stats`.""" solute_stats: dict[str, float] solution_stats: dict[str, float] @@ -173,9 +174,38 @@ def _get_mean_activity_coefficient(solution: Solution) -> float: return factor**exponent +def _get_activity_coefficient_pitzer(solution: Solution) -> float: + salt = solution.get_salt() + param = solution.get_property(salt.formula, "model_parameters.activity_pitzer") + alpha1 = 2 + alpha2 = 0 + molality = salt.get_effective_molality(solution.ionic_strength) + temperature = str(solution.temperature) + + return pyEQL.activity_correction.get_activity_coefficient_pitzer( + solution.ionic_strength, + molality, + alpha1, + alpha2, + ureg.Quantity(param["Beta0"]["value"]).magnitude, + ureg.Quantity(param["Beta1"]["value"]).magnitude, + ureg.Quantity(param["Beta2"]["value"]).magnitude, + ureg.Quantity(param["Cphi"]["value"]).magnitude, + salt.z_cation, + salt.z_anion, + salt.nu_cation, + salt.nu_anion, + temperature, + ) + + def _get_solution_property(solution: Solution, name: str) -> Any: if name == "mean_activity_coefficient": return _get_mean_activity_coefficient(solution) + + if name == "activity_coefficient_pitzer": + return _get_activity_coefficient_pitzer(solution) + if hasattr(solution, name): return getattr(solution, name) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index de6773fd..f6dc9e70 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -22,25 +22,29 @@ def fixture_engine(request: pytest.FixtureRequest) -> EOS: return engine() +@pytest.fixture(name="source", params=["molar_conductivity.json", "mean_activity_coefficient.json"]) +def fixture_source(request: pytest.FixtureRequest) -> list[Path]: + return datadir.joinpath(request.param) + + class TestGetDataset: @staticmethod - @pytest.mark.parametrize("source", ["molar_conductivity.json"]) def test_should_load_dataset_from_file(source: str) -> None: dataset = get_dataset(datadir.joinpath(source)) assert dataset -@pytest.fixture(name="cation", params=["Na[+1]", "NH4[+1]"]) +@pytest.fixture(name="cation", params=["Na[+1]"]) def fixture_cation(request: pytest.FixtureRequest) -> str: return request.param -@pytest.fixture(name="anion", params=["Cl[-1]", "SO4[-2]"]) +@pytest.fixture(name="anion", params=["Cl[-1]"]) def fixture_anion(request: pytest.FixtureRequest) -> str: return request.param -@pytest.fixture(name="conc", params=["0.1 mol/L", "25%"]) +@pytest.fixture(name="conc", params=["0.1 mol/L"]) def fixture_conc(request: pytest.FixtureRequest) -> str: return request.param @@ -64,7 +68,18 @@ def fixture_solute_property(request: pytest.FixtureRequest) -> str: @pytest.fixture( name="solution_property", - params=["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"], + params=[ + "dielectric_constant", + "debye_length", + "conductivity", + "osmotic_coefficient", + "density", + "viscosity_dynamic", + "osmolality", + "osmolarity", + "chemical_potential_energy", + "activity_coefficient_pitzer", + ], ) def fixture_solution_property(request: pytest.FixtureRequest) -> str: return request.param @@ -85,11 +100,6 @@ def test_should_calculate_zero_rmse_with_engine_dataset(dataset: list[BenchmarkE assert all(err == 0 for err in results.solution_stats.values()) -@pytest.fixture(name="source", params=["molar_conductivity.json", "mean_activity_coefficient.json"]) -def fixture_source(request: pytest.FixtureRequest) -> list[Path]: - return datadir.joinpath(request.param) - - class TestBenchmarkEngine: @staticmethod def test_should_benchmark_all_engines(engine: EOS, source: Path) -> None: From ce7b4c0dd75e3f45b293997670912d963352247a Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 07:35:38 -0700 Subject: [PATCH 27/54] Add CRC DB files Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/database/CRC.json | 16242 ++++++++++++++++ tests/test_benchmark.py | 6 + tests/test_benchmark/conductivity.json | 4834 +++++ .../mean_activity_coefficient.json | 16242 ++++++++++++++++ 4 files changed, 37324 insertions(+) create mode 100644 src/pyEQL/database/CRC.json create mode 100644 tests/test_benchmark/conductivity.json create mode 100644 tests/test_benchmark/mean_activity_coefficient.json diff --git a/src/pyEQL/database/CRC.json b/src/pyEQL/database/CRC.json new file mode 100644 index 00000000..fdce59fc --- /dev/null +++ b/src/pyEQL/database/CRC.json @@ -0,0 +1,16242 @@ +[ + [ + { + "solutes": { + "Ag[+1]": "0.1 mol/kg", + "NO3[-1]": "0.1 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.734 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.2 mol/kg", + "NO3[-1]": "0.2 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.657 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.3 mol/kg", + "NO3[-1]": "0.3 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.606 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.4 mol/kg", + "NO3[-1]": "0.4 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.567 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.5 mol/kg", + "NO3[-1]": "0.5 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.536 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.6 mol/kg", + "NO3[-1]": "0.6 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.509 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.7 mol/kg", + "NO3[-1]": "0.7 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.485 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.8 mol/kg", + "NO3[-1]": "0.8 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.464 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "0.9 mol/kg", + "NO3[-1]": "0.9 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.446 " + ] + ] + ], + [ + { + "solutes": { + "Ag[+1]": "1.0 mol/kg", + "NO3[-1]": "1.0 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.429 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.1 mol/kg", + "Cl[-1]": "0.30000000000000004 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.337 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.2 mol/kg", + "Cl[-1]": "0.6000000000000001 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.305 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.3 mol/kg", + "Cl[-1]": "0.8999999999999999 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.302 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.4 mol/kg", + "Cl[-1]": "1.2000000000000002 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.313 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.5 mol/kg", + "Cl[-1]": "1.5 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.331 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.6 mol/kg", + "Cl[-1]": "1.7999999999999998 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.356 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.7 mol/kg", + "Cl[-1]": "2.0999999999999996 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.388 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.8 mol/kg", + "Cl[-1]": "2.4000000000000004 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.429 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.9 mol/kg", + "Cl[-1]": "2.7 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.479 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "1.0 mol/kg", + "Cl[-1]": "3.0 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.539 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.2 mol/kg", + "SO4[-2]": "0.30000000000000004 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.035 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.4 mol/kg", + "SO4[-2]": "0.6000000000000001 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "0.0225 " + ] + ] + ], + [ + { + "solutes": { + "Al[+3]": "0.6 mol/kg", + "SO4[-2]": "0.8999999999999999 mol/kg" + }, + 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a/tests/test_benchmark/conductivity.json b/tests/test_benchmark/conductivity.json new file mode 100644 index 00000000..a77e6dfa --- /dev/null +++ b/tests/test_benchmark/conductivity.json @@ -0,0 +1,4834 @@ +[ + [ + { + "solutes": { + "H[+1]": "0.01507537688442211 %", + "N[-3]": "0.005025125628140704 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "2.512562814070352e-06 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.030303030303030304 %", + "N[-3]": "0.010101010101010102 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "7.070707070707071e-06 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.061224489795918366 %", + "N[-3]": "0.02040816326530612 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "2.0408163265306123e-05 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.15789473684210525 %", + "N[-3]": "0.05263157894736842 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + 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{ + "solutes": { + "I[-1]": "20.0 mol/kg", + "Zn[+2]": "10.0 mol/kg" + }, + "temperature": "298.15 K" + }, + {}, + [ + [ + "mean_activity_coefficient", + "4.698 " + ] + ] + ] +] From fa9fad7966ff56197af1d937645376fc990ece63 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 07:58:23 -0700 Subject: [PATCH 28/54] Rename function Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 6 +++--- tests/test_benchmark.py | 8 ++++---- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 5efaf6e8..9145f7fb 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -85,7 +85,7 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -def get_dataset(source: str | Path) -> list[BenchmarkEntry]: +def load_dataset(source: str | Path) -> list[BenchmarkEntry]: """Load reference dataset. Args: @@ -93,7 +93,7 @@ def get_dataset(source: str | Path) -> list[BenchmarkEntry]: latter, then the [path must point to a JSON which can be read into a BenchmarkEntry object. Returns: - A list of BenchmarkEntry objects one for each data point in the data set. + A list of BenchmarkEntry objects, one for each data point in the dataset. """ match source: case "CRC" | "IDST" | "JPCRD": @@ -295,7 +295,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm A dictionary mapping source names to the corresponding solute and solution statistical metrics. """ sources = sources or INTERNAL_SOURCES - datasets = [get_dataset(s) for s in sources] + datasets = [load_dataset(s) for s in sources] results: BenchmarkResults = {} for i, dataset in enumerate(datasets): diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index ac571f4a..d586b787 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -2,7 +2,7 @@ import pytest -from pyEQL.benchmark import BenchmarkEntry, benchmark_engine, calculate_stats, create_entry, get_dataset +from pyEQL.benchmark import BenchmarkEntry, benchmark_engine, calculate_stats, create_entry, load_dataset from pyEQL.engines import EOS, IdealEOS, NativeEOS from pyEQL.solution import Solution @@ -27,16 +27,16 @@ def fixture_source(request: pytest.FixtureRequest) -> list[Path]: return datadir.joinpath(request.param) -class TestGetDataset: +class TestLoadDataset: @staticmethod def test_should_load_dataset_from_file(source: str) -> None: - dataset = get_dataset(datadir.joinpath(source)) + dataset = load_dataset(datadir.joinpath(source)) assert dataset @staticmethod @pytest.mark.parametrize("source", ["CRC"]) def test_should_load_dataset_from_internal_source(source: str) -> None: - dataset = get_dataset(source) + dataset = load_dataset(source) assert dataset From 78981412d0ef9a952aa9b567f53cf2ee9cb1458e Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 10:50:13 -0700 Subject: [PATCH 29/54] Update CRC data Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 12 +- src/pyEQL/database/CRC.json | 13440 ++++++++++++++++++++++++++++++++++ 2 files changed, 13446 insertions(+), 6 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 9145f7fb..a41e3ce7 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -5,8 +5,8 @@ >>> from pyEQL.benchmark import benchmark_engine >>> from pyEQL.engines import IdealEOS ->>> results = benchmark_engine(IdealEOS(), sources=["CRC"]) ->>> results["CRC"].solution_data["mean_activity"] +>>> results = benchmark_engine(IdealEOS(), sources=["crc"]) +>>> results["crc"].solution_stats["mean_activity_coefficient"] ... Example: Generate a reference dataset from a solution model @@ -95,9 +95,9 @@ def load_dataset(source: str | Path) -> list[BenchmarkEntry]: Returns: A list of BenchmarkEntry objects, one for each data point in the dataset. """ - match source: - case "CRC" | "IDST" | "JPCRD": - source = Path(__file__).parent.joinpath("database", f"{source}.json") + match str(source).lower(): + case "crc" | "idst" | "jpcrd": + source = Path(__file__).parent.joinpath("database", f"{source.lower()}.json") case _: source = Path(source) @@ -300,7 +300,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm for i, dataset in enumerate(datasets): _patch_dataset(dataset, engine=engine) - key = Path(sources[i]).name + key = Path(sources[i]).stem results[key] = calculate_stats(dataset) return results diff --git a/src/pyEQL/database/CRC.json b/src/pyEQL/database/CRC.json index fdce59fc..4d407da1 100644 --- a/src/pyEQL/database/CRC.json +++ b/src/pyEQL/database/CRC.json @@ -1,4 +1,13444 @@ [ + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "12.045 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "14.794999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "17.349999999999998 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "19.944999999999997 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "22.68 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "24.84 S/m" + ] + ] + ], + [ + { + "solutes": { + "Br[-1]": "1.0 mol/l", + "H[+1]": "1.0 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + [ + [ + "conductivity", + "22.959999999999997 S/m" + 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"0.35294117647058826 %", + "SO4[-2]": "0.17647058823529413 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.016076470588235296 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.5 %", + "SO4[-2]": "0.25 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.02725 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.010050251256281407 %", + "S2O3[-2]": "0.005025125628140704 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "2.864321608040201e-05 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.020202020202020204 %", + "S2O3[-2]": "0.010101010101010102 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.00010808080808080809 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.04081632653061224 %", + "S2O3[-2]": "0.02040816326530612 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0003979591836734693 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.10526315789473684 %", + "S2O3[-2]": "0.05263157894736842 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0022789473684210523 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.2222222222222222 %", + "S2O3[-2]": "0.1111111111111111 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.008522222222222223 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.35294117647058826 %", + "S2O3[-2]": "0.17647058823529413 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.01835294117647059 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.5 %", + "S2O3[-2]": "0.25 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.03075 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.6666666666666666 %", + "S2O3[-2]": "0.3333333333333333 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.04466666666666667 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "0.8571428571428571 %", + "S2O3[-2]": "0.42857142857142855 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.05828571428571429 S/m" + ] + ] + ], + [ + { + "solutes": { + "Na[+1]": "1.3333333333333333 %", + "S2O3[-2]": "0.6666666666666666 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.07866666666666666 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.010050251256281407 %", + "Sr[+2]": "0.005025125628140704 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "2.9648241206030153e-05 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.020202020202020204 %", + "Sr[+2]": "0.010101010101010102 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.00011515151515151518 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.04081632653061224 %", + "Sr[+2]": "0.02040816326530612 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.00044897959183673463 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.10526315789473684 %", + "Sr[+2]": "0.05263157894736842 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0025842105263157895 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.2222222222222222 %", + "Sr[+2]": "0.1111111111111111 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.010166666666666666 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.35294117647058826 %", + "Sr[+2]": "0.17647058823529413 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.022411764705882357 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.5 %", + "Sr[+2]": "0.25 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.03825 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.6666666666666666 %", + "Sr[+2]": "0.3333333333333333 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.056 S/m" + ] + ] + ], + [ + { + "solutes": { + "Cl[-1]": "0.8571428571428571 %", + "Sr[+2]": "0.42857142857142855 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.07628571428571428 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.010050251256281407 %", + "SO4[-2]": "0.005025125628140704 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0001221105527638191 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.020202020202020204 %", + "SO4[-2]": "0.010101010101010102 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.00048282828282828285 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.04081632653061224 %", + "SO4[-2]": "0.02040816326530612 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.001877551020408163 S/m" + ] + ] + ], + [ + { + "solutes": { + "H[+1]": "0.10526315789473684 %", + "SO4[-2]": "0.05263157894736842 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.011105263157894736 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.005025125628140704 %", + "Zn[+2]": "0.005025125628140704 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "1.4070351758793969e-05 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.010101010101010102 %", + "Zn[+2]": "0.010101010101010102 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "5.454545454545456e-05 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.02040816326530612 %", + "Zn[+2]": "0.02040816326530612 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0002040816326530612 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.05263157894736842 %", + "Zn[+2]": "0.05263157894736842 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0010789473684210526 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.1111111111111111 %", + "Zn[+2]": "0.1111111111111111 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0037444444444444443 S/m" + ] + ] + ], + [ + { + "solutes": { + "SO4[-2]": "0.17647058823529413 %", + "Zn[+2]": "0.17647058823529413 %" + }, + "temperature": "293.15 K" + }, + {}, + [ + [ + "conductivity", + "0.0076411764705882354 S/m" + ] + ] + ], [ { "solutes": { From 3f6b4687fb882d62c922264188eb9cf7bebd9b75 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 11:13:20 -0700 Subject: [PATCH 30/54] Remove empty file Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/reference.py | 145 ----------------------------------------- 1 file changed, 145 deletions(-) delete mode 100644 src/pyEQL/reference.py diff --git a/src/pyEQL/reference.py b/src/pyEQL/reference.py deleted file mode 100644 index 05f448da..00000000 --- a/src/pyEQL/reference.py +++ /dev/null @@ -1,145 +0,0 @@ -"""Reference data for benchmarking.""" - -from pyEQL.benchmark import BenchmarkEntry - - -# TODO: consolidate existing data files -# TODO: remove redundant sources -# TODO: write sub-loaders for different CRC archive types -# TODO: write loading function for other reference databases -def _load_crc_data() -> list[BenchmarkEntry]: - # Use JSONStore? - # datasets = [] - - # SOLUTE DATA - - # property: molar electrical conductivity - # Salts: KCl, NaCl, MgCl2, NaF, Na2SO4, OH-, FeCl3, H2O - # Concentrations: 0.001, 0.002 - # TODO: compile data - # sources: molar_electrical_conductivity/ - - # SOLUTION DATA - # property: mean activity coefficient - # Salts: HCl, CsI, BaCl2, LiCl, RbCl, MgCl2, KBr, K2SO4 - # Concentrations: 0.001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, 1, 2, 5 - # TODO: compile data - # sources: activity_coefficients/ - - # property: density - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: density/ - - # property: conductivity - # Salts: NaCl, KCl, MgCl2 - # Concentrations: 0.001, 0.05, 0.1 - # TODO: compile data - # sources: "Electrical Conductivity of Aqueous Solutions at 20C as a Function of Concentration" - - return [] - - -def _load_idst_data() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: mean activity coefficient - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - https://idst.inl.gov - - # property: osmotic coefficients - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - https://idst.inl.gov - pass - - -def _load_jpcrd_data() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: mean activity coefficient - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - # - Theoretical Mean Activity Coefficients of Strong Electrolytes in Aqueous Solutions from 0 to 100C - - # Walter J. Hamer. NSRDS-NBS 24, 271p. (1968). - # - Thermodynamic Properties of Aqueous Sodium Chloride Solutions — Kenneth S. Pitzer, J. Christopher Peiper, and - # R. H. Busey. J Phys Chem Ref Data 13, 1(1984). - - # property: density - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - - # property: dielectric constant - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - - # property: electrical resistivity/conductivity - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - - # property: osmotic coefficients - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - - # property: dielectric constant - # Salts: ? - # Concentrations: ? - # TODO: compile data - # sources: - # - Standard Reference Data Publications 1964-1984, NBS, Sauerwein J. C., Dalton, G. R. "Properties Index" (p. 94) - pass - - -def _load_environ_sci_data() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: debye length - # Salts: NaCl, Na2SO4 - # Concentrations: 0.1, 10 - # source: doi:10.1021/es400571g - pass - - -def _load_fluid_phase_data() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: dielectric constant - # Salts: NaCl, KBr, LiCl, RbCl - # Concentrations: 0.5, 1, 2, 2.1, 3.4, 4.4, 5, 6.5, 12 - # source: doi:10.1016/j.fluid.2014.05.037 - pass - - -def _load_jchem_eng_data1() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: activity coefficient - # Salts: Na+/K+/NO3- - # Concentrations: 1:3, 1:1, 3:1 - # source: doi:10.1021/je9004432 - pass - - -def _load_jchem_eng_data2() -> list[BenchmarkEntry]: - # SOLUTION DATA - # property: osmotic coefficient - # Salts: NH4NO3, Cu(2)SO4 - # Concentrations: 0.25, 0.5, 0.75, 1, 1.5, 2 - # source: doi:10.1021/je2009329 - pass From 8c5747c79f20c32cc68b24e3e5dc9708a0d8b7e0 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Thu, 19 Jun 2025 11:16:51 -0700 Subject: [PATCH 31/54] Fix type hints Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index a41e3ce7..b9bd6c85 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -97,7 +97,7 @@ def load_dataset(source: str | Path) -> list[BenchmarkEntry]: """ match str(source).lower(): case "crc" | "idst" | "jpcrd": - source = Path(__file__).parent.joinpath("database", f"{source.lower()}.json") + source = Path(__file__).parent.joinpath("database", f"{str(source).lower()}.json") case _: source = Path(source) @@ -296,7 +296,7 @@ def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> Benchm """ sources = sources or INTERNAL_SOURCES datasets = [load_dataset(s) for s in sources] - results: BenchmarkResults = {} + results: dict[str, BenchmarkResults] = {} for i, dataset in enumerate(datasets): _patch_dataset(dataset, engine=engine) From b5e7f628a9f9c90e38f04aec2eeb777ea2b1bb86 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Fri, 20 Jun 2025 19:29:19 -0700 Subject: [PATCH 32/54] Write new signature for benchmark_engine Users should be able to select which properties as well as which solutions (compositions, thermodynamic state) to benchmark against. This will also enable speed-ups in testing. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 26 +++++++++++++++++++++++--- 1 file changed, 23 insertions(+), 3 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index b9bd6c85..4067b832 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -283,13 +283,33 @@ def calculate_stats( return BenchmarkResults(solute_stats=solute_stats, solution_stats=solution_stats) -def benchmark_engine(engine: EOS, *, sources: list[str] | None = None) -> BenchmarkResults: +def benchmark_engine( + engine: EOS, + *, + sources: list[str] | None = None, + solutions: list[Solution] | None = None, + solute_properties: list[tuple[str, str]] | None = None, + solution_properties: list[str] | None = None, +) -> BenchmarkResults: """Benchmark a modeling engine against reference data. Args: - engine: The modeling engine to benchmark. - sources: One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry + engine: EOS + The modeling engine to benchmark. + sources: list[str], optional + One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry objects. Defaults to INTERNAL_SOURCES. + solutions: list[Solution], optional + The solutions against which the engine will be benchmarked. If omitted, all compositions and conditions in + the reference data contained in ``sources`` will be used for the benchmarking. + solute_properties: list[tuple[str, str]], optional + The solute properties to include in the benchmarking, specified as ``(solute, property)``. The engine will + only be benchmarked against those solute properties listed here. If omitted, the engine will be benchmarked + against all solute properties in ``sources``. + solution_properties: list[str], optional + The solution properties to include in the benchmarking. The engine will only be benchmarked against those + solution properties listed here. Defaults to None in which case the engine will be benchmarked against all + solute properties in ``sources``. Returns: A dictionary mapping source names to the corresponding solute and solution statistical metrics. From a1ac0b538b51f3250d98323b8c40996c6385f547 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 06:10:00 -0700 Subject: [PATCH 33/54] Add solns/props in load_dataset/BenchmarkEntry Implementing BenchmarkEntry.solute_properties/solution_properties in this way will enable speed-ups in testing when calculating error statistics between calculated and reference datasets (list[BenchmarkEntry]) as data lookup from a dictionary by key has O(1) time complexity (one will have the name of the property when calculating error) while finding a specific item in a list has O(N) time complexity. Accordingly, load_dataset now expects solute/solution properties within data files to be structured as dictionaries instead of prperty-value 2-tuples and accepts solutions, solute_properties, and solution_properties as keyword-only arguments. That data for a solution is included is determined by its components, molar concentration, temperature, and pressure. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 88 +++++++++++++++++++++++++++++++++++------- 1 file changed, 74 insertions(+), 14 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 4067b832..890b5f01 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -74,8 +74,8 @@ class BenchmarkEntry(NamedTuple): """ solution: Solution - solute_data: FormulaDict = FormulaDict() - solution_data: list[tuple[str, Quantity]] = [] + solute_data: FormulaDict[str, dict[str, Quantity]] = FormulaDict() + solution_data: dict[str, Quantity] = {} class BenchmarkResults(NamedTuple): @@ -85,12 +85,52 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -def load_dataset(source: str | Path) -> list[BenchmarkEntry]: +def _equivalent_solutions(soln1: Solution, soln2: Solution) -> bool: + same_components = sorted(soln1.components) == sorted(soln2.components) + + if not same_components: + return False + + vol1 = soln1.volume + vol2 = soln2.volume + for comp, mol in soln1.components.items(): + conc1 = mol / vol1 + + # TODO: relative tolerance needed? + same_compositions = (soln2.components[comp] / vol2) == conc1 + if not same_compositions: + return False + + # TODO: should other state variables be checked (e.g., pH, pE)? + return soln1.temperature == soln2.temperature and soln1.pressure == soln2.pressure + + +def load_dataset( + source: str | Path, + *, + solutions: list[Solution] | None = None, + solute_properties: list[tuple[str, str]] | None = None, + solution_properties: list[str] | None = None, +) -> list[BenchmarkEntry]: """Load reference dataset. Args: - source: One of "CRC", "IDST", "JPCRD", or "May2011JCED" or the path to a file containing reference data. If the + source: str | Path + One of "CRC", "IDST", "JPCRD", or "May2011JCED" or the path to a file containing reference data. If the latter, then the [path must point to a JSON which can be read into a BenchmarkEntry object. + solutions: list[Solution], optional + The solutions for which data will be loaded from the dataset. If provided, only data corresponding to + solutions with the same composition, temperature, and pressure will be loaded. If omitted, all + compositions and conditions in the reference data contained in ``sources`` will be used for the + benchmarking. + solute_properties: list[tuple[str, str]], optional + The solute properties to include in the benchmarking, specified as ``(solute, property)``. The engine will + only be benchmarked against those solute properties listed here. If omitted, the engine will be benchmarked + against all solute properties in ``sources``. + solution_properties: list[str], optional + The solution properties to include in the benchmarking. The engine will only be benchmarked against those + solution properties listed here. Defaults to None in which case the engine will be benchmarked against all + solute properties in ``sources``. Returns: A list of BenchmarkEntry objects, one for each data point in the dataset. @@ -106,17 +146,30 @@ def load_dataset(source: str | Path) -> list[BenchmarkEntry]: reference: list[BenchmarkEntry] = [] - for solution, solute_data, solution_data in data: - for solute, values in solute_data.items(): - solute_data[solute] = [(prop, ureg.Quantity(q)) for prop, q in values] + for solution, raw_solute_data, raw_solution_data in data: + # TODO: handle weight % concentration data + soln = Solution(**solution) + + if not any(_equivalent_solutions(s, soln) for s in solutions): + continue + + solute_data = FormulaDict[str, dict[str, Quantity]] = FormulaDict() + solution_data = {} - for i, (prop, q) in enumerate(solution_data): - solution_data[i] = prop, ureg.Quantity(q) + for solute, values in raw_solute_data.items(): + solute_data[solute] = {} + for p, q in values.items(): + if solute_properties is None or (solute, p) in solute_properties: + solute_data[solute][p] = ureg.Quantity(q) + + for p, q in raw_solution_data.items(): + if solution_properties is None or p in solution_properties: + solution_data[p] = ureg.Quantity(q) reference.append( BenchmarkEntry( - solution=Solution(**solution), - solute_data=FormulaDict(**solute_data), + solution=soln, + solute_data=solute_data, solution_data=solution_data, ) ) @@ -300,8 +353,10 @@ def benchmark_engine( One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry objects. Defaults to INTERNAL_SOURCES. solutions: list[Solution], optional - The solutions against which the engine will be benchmarked. If omitted, all compositions and conditions in - the reference data contained in ``sources`` will be used for the benchmarking. + The solutions for which data will be loaded from the dataset. If provided, only data corresponding to + solutions with the same components, concentrations, and conditions (temperature, pressure) will be loaded. + If omitted, reference data for all components, concentrations, and conditions (temperature, pressure) + contained in ``sources`` will be used for the benchmarking. solute_properties: list[tuple[str, str]], optional The solute properties to include in the benchmarking, specified as ``(solute, property)``. The engine will only be benchmarked against those solute properties listed here. If omitted, the engine will be benchmarked @@ -315,7 +370,12 @@ def benchmark_engine( A dictionary mapping source names to the corresponding solute and solution statistical metrics. """ sources = sources or INTERNAL_SOURCES - datasets = [load_dataset(s) for s in sources] + datasets = [ + load_dataset( + s, solutions=solutions, solute_properties=solute_properties, solution_properties=solution_properties + ) + for s in sources + ] results: dict[str, BenchmarkResults] = {} for i, dataset in enumerate(datasets): From a613aaa69a81f2e8de6fbeb48a328fd639f260ab Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 13:08:18 -0700 Subject: [PATCH 34/54] Defer decision on key structure Encapsulating the logic for creating dictionary keys in a function and creating a type alias for its type should minimize the amount of refactor required if the format is changed and appease mypy. This also makes comparison of Solutions for the purpose of benchmarking considerably more simple. load_dataset now returns a dictionary with keys indicating the Solution for which the data applies as generated by _create_solution_key. Internal data sources are now opened more reliably using resources.files. Generating the list of SolutionKeys corresponding to the `solutions` parameter in advance simplifies the logic required to check for the Solution in `solutions`. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 61 +++++++++++++++++++++++------------------- 1 file changed, 33 insertions(+), 28 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 890b5f01..8f59b06a 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -45,6 +45,7 @@ import math from collections.abc import Callable from functools import reduce +from importlib.resources import files from pathlib import Path from typing import Any, Literal, NamedTuple @@ -85,24 +86,27 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -def _equivalent_solutions(soln1: Solution, soln2: Solution) -> bool: - same_components = sorted(soln1.components) == sorted(soln2.components) +# TODO: Admittedly, this is an ugly solution to enable Solutions to serve as dictionary keys to speed up # the +# calculation of benchmarking stats. For now, we wrap the decision on the final key format in a function +# _create_solution_key that produces hashable values from a Solution and abstract the key format with a type alias +# (SolutionKey). +# Composition +SolutionKey = tuple[ + # Composition: (ion, concentration) + tuple[tuple[str, str], ...], + # State: temperature, pressure + tuple[str, str], +] - if not same_components: - return False - - vol1 = soln1.volume - vol2 = soln2.volume - for comp, mol in soln1.components.items(): - conc1 = mol / vol1 - - # TODO: relative tolerance needed? - same_compositions = (soln2.components[comp] / vol2) == conc1 - if not same_compositions: - return False +def _create_solution_key(solution: Solution) -> SolutionKey: + vol = solution.volume.magnitude + components = sorted(solution.components) + composition = tuple((component, solution.components[component] / vol) for component in components) # TODO: should other state variables be checked (e.g., pH, pE)? - return soln1.temperature == soln2.temperature and soln1.pressure == soln2.pressure + state = solution.temperature, solution.pressure + + return composition, state def load_dataset( @@ -111,7 +115,7 @@ def load_dataset( solutions: list[Solution] | None = None, solute_properties: list[tuple[str, str]] | None = None, solution_properties: list[str] | None = None, -) -> list[BenchmarkEntry]: +) -> dict[str, BenchmarkEntry]: """Load reference dataset. Args: @@ -133,24 +137,27 @@ def load_dataset( solute properties in ``sources``. Returns: - A list of BenchmarkEntry objects, one for each data point in the dataset. + A dictionary mapping SolutionKey to BenchmarkEntry objects. See the comment over SolutionKey for details about + its structure. """ match str(source).lower(): case "crc" | "idst" | "jpcrd": - source = Path(__file__).parent.joinpath("database", f"{str(source).lower()}.json") + source = files("pyEQL").joinpath("database", f"{str(source).lower()}.json") case _: source = Path(source) with source.open(mode="r", encoding="utf-8") as file: data: list[tuple[dict, dict[str, list], list[tuple]]] = json.load(file) - reference: list[BenchmarkEntry] = [] + reference: dict[SolutionKey, BenchmarkEntry] = {} + solution_keys = [] if solutions is None else [_create_solution_key(s) for s in solutions] - for solution, raw_solute_data, raw_solution_data in data: + for raw_solution, raw_solute_data, raw_solution_data in data: # TODO: handle weight % concentration data - soln = Solution(**solution) + solution = Solution(**raw_solution) + soln_key = _create_solution_key(solution) - if not any(_equivalent_solutions(s, soln) for s in solutions): + if solutions is not None and soln_key not in solution_keys: continue solute_data = FormulaDict[str, dict[str, Quantity]] = FormulaDict() @@ -166,12 +173,10 @@ def load_dataset( if solution_properties is None or p in solution_properties: solution_data[p] = ureg.Quantity(q) - reference.append( - BenchmarkEntry( - solution=soln, - solute_data=solute_data, - solution_data=solution_data, - ) + reference[soln_key] = BenchmarkEntry( + solution=solution, + solute_data=solute_data, + solution_data=solution_data, ) return reference From dc3eab1cc4b63ad905cfba730b9fe39a9d79b85a Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 15:38:49 -0700 Subject: [PATCH 35/54] Use same data structures for engine/reference data Using the same data structures for engine and reference data is desired because it will separate the logic for retrieving properties and calculating stats and simplify the retrieval of corresponding items in calculate_stats. This implementation ensures that only one Solution object is created for each Solution across all benchmark datasets and that each BenchmarkEntry object is associated with a unique Solution. In this way, a single dataset can be generated for the engine, which can then be benchmarked against each reference dataset. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 99 ++++++++++++++++++++++++++++-------------- 1 file changed, 66 insertions(+), 33 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 8f59b06a..79a545e7 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -182,11 +182,71 @@ def load_dataset( return reference -def _patch_dataset( - dataset: list[BenchmarkEntry], *, engine: EOS | Literal["native", "ideal", "phreeqc"] = "native" -) -> None: - for data in dataset: - data.solution.engine = engine +def create_entry( + solution: Solution, + solute_properties: list[tuple[str, str]], + solution_properties: list[str], +) -> BenchmarkEntry: + """Create a BenchmarkEntry from a Solution and specified properties. + + Args: + solution: The Solution from which to create the entry. + solute_properties: The solute properties to add to the entry. + solution_properties: The solution properties to add to the entry. + """ + solute_data = FormulaDict() + + for solute, solute_property in solute_properties: + if solute not in solute_data: + solute_data[solute] = [] + data = _get_solute_property(solution, solute, solute_property) + solute_data[solute].append((solute_property, data)) + + solution_data = [] + + for solution_property in solution_properties: + data = _get_solution_property(solution, solution_property) + solution_data.append((solution_property, data)) + + return BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) + + +def _create_engine_dataset( + engine: EOS | Literal["native", "ideal", "phreeqc"] = "native", + datasets: list[dict[SolutionKey, BenchmarkEntry]] | None = None, +) -> dict[SolutionKey, BenchmarkEntry]: + mapper: dict[ + SolutionKey, + tuple[ + # solute_properties + list[tuple[str, str]], + # solution_properties + list[str], + ], + ] = [] + + for dataset in datasets: + for key, entry in dataset.items(): + if key not in mapper: + mapper[key] = [], [] + + for solute in entry.solute_data: + mapper[key][1].extend((solute, prop) for prop in list(entry.solute_data[solute])) + mapper[key][2].extend(entry.solution_data) + + engine_dataset = {} + + for solution_key, (solute_properties, solution_properties) in mapper.items(): + temperature, pressure = solution_key[1] + solution = Solution(solutes=dict(solution_key[0]), temperature=temperature, pressure=pressure, engine=engine) + entry = create_entry( + solution=solution, + solute_properties=sorted(set(solute_properties)), + solution_properties=sorted(set(solution_properties)), + ) + engine_dataset[key] = entry + + return engine_dataset def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: @@ -274,32 +334,6 @@ def _get_solution_property(solution: Solution, name: str) -> Any: raise ValueError(msg) -def create_entry(solution: Solution, solute_properties: list[str], solution_properties: list[str]) -> BenchmarkEntry: - """Create a BenchmarkEntry from a Solution and specified properties. - - Args: - solution: The Solution from which to create the entry. - solute_properties: The solute properties to add to the entry. - solution_properties: The solution properties to add to the entry. - """ - solute_data = FormulaDict() - - for solute in solution.components: - solute_data[solute] = [] - - for solute_property in solute_properties: - data = _get_solute_property(solution, solute, solute_property) - solute_data[solute].append((solute_property, data)) - - solution_data = [] - - for solution_property in solution_properties: - data = _get_solution_property(solution, solution_property) - solution_data.append((solution_property, data)) - - return BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) - - def calculate_stats( dataset: list[BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None ) -> BenchmarkResults: @@ -382,9 +416,8 @@ def benchmark_engine( for s in sources ] results: dict[str, BenchmarkResults] = {} - + _ = _create_engine_dataset(engine, datasets) for i, dataset in enumerate(datasets): - _patch_dataset(dataset, engine=engine) key = Path(sources[i]).stem results[key] = calculate_stats(dataset) From 178f49e2b934508fc8403e328fda4b0b9dc6e60c Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 16:36:56 -0700 Subject: [PATCH 36/54] Implement reference/calculated for calculate_stats Accepting two identical data structures generalizes calculate_stats for all combinations of sources of data (e.g., reference-reference, engine-engine, engine-reference). An additional benefit is that now, from the signature, it is more clear to users how to organize the two sets of data to be compared. Previously, engine data was implicitly generated using the Solution objects in each BenchmarkEntry. As mentioned previously, this now removes the logic for retrieving solute and solution properties. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 41 ++++++++++++++++++----------------------- 1 file changed, 18 insertions(+), 23 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 79a545e7..0acbf75b 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -335,19 +335,23 @@ def _get_solution_property(solution: Solution, name: str) -> Any: def calculate_stats( - dataset: list[BenchmarkEntry], *, metric: Callable[[list[tuple[float, float]]], float] | None = None + reference: dict[SolutionKey, BenchmarkEntry], + calculated: dict[SolutionKey, BenchmarkEntry], + *, + metric: Callable[[list[tuple[float, float]]], float] | None = None, ) -> BenchmarkResults: """Calculate benchmarking statistics. Args: - dataset: A list of BenchmarkEntry objects + reference: A dictionary mapping SolutionKeys to BenchmarkEntry object. + calculated: A dictionary mapping SolutionKeys to BenchmarkEntry object. metric: A function that acts on the list of 2-tuples (reference, calculated), which contains reference and calculated values. This function should calculate a statistical metric for the list. Defaults to the root- mean-squared error. Returns: - A 2-tuple (`solute_stats`, `solution_stats`) where `solute_stats` and `solution_stats` are dictionaries mapping - solute and solution properties, respectively, to their benchmark statistics. + A 2-tuple (``solute_stats``, ``solution_stats``) where ``solute_stats`` and ``solution_stats`` are dictionaries + mapping solute and solution properties, respectively, to their benchmark statistics. """ metric = metric or _rmse @@ -355,19 +359,15 @@ def calculate_stats( solute_data_pairs: dict[str, list[tuple[float, float]]] = {} solution_data_pairs: dict[str, list[tuple[float, float]]] = {} - for d in dataset: - for solute, solute_data in d.solute_data.items(): - for prop, reference in solute_data: - if prop not in solute_data_pairs: - solute_data_pairs[prop] = [] - - solute_data_pairs[prop].append((reference, _get_solute_property(d.solution, solute, prop))) + for key, entry in reference.items(): + for solute in entry.solute_data: + for prop, value in entry.solute_data[solute].items(): + calculated_value = calculated[key].solute_data[solute][prop] + solute_data_pairs[prop].append((value, calculated_value)) - for prop, reference in d.solution_data: - if prop not in solution_data_pairs: - solution_data_pairs[prop] = [] - - solution_data_pairs[prop].append((reference, _get_solution_property(d.solution, prop))) + for prop, value in entry.solution_data.items(): + calculated_value = calculated[key].solution_data[prop] + solute_data_pairs[prop].append((value, calculated_value)) solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} @@ -415,10 +415,5 @@ def benchmark_engine( ) for s in sources ] - results: dict[str, BenchmarkResults] = {} - _ = _create_engine_dataset(engine, datasets) - for i, dataset in enumerate(datasets): - key = Path(sources[i]).stem - results[key] = calculate_stats(dataset) - - return results + engine_dataset = _create_engine_dataset(engine, datasets) + return {sources[i]: calculate_stats(ref, engine_dataset) for i, ref in enumerate(datasets)} From eaff9a9b88bda57e2b3cd0d581398e9c673e341c Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 17:02:37 -0700 Subject: [PATCH 37/54] Reorder functions in order or use Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 163 +++++++++++++++++++++-------------------- 1 file changed, 85 insertions(+), 78 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 0acbf75b..502e11dc 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -182,6 +182,78 @@ def load_dataset( return reference +def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: + value = solution.get_property(solute, name) + + if value is None: + if hasattr(solution, name): + value = getattr(solution, name) + elif hasattr(solution, f"get_{name}"): + value = getattr(solution, f"get_{name}")(solute) + else: + msg = f"Solute property: {name} not supported" + raise ValueError(msg) + + return value + + +def _get_mean_activity_coefficient(solution: Solution) -> float: + activity_nu_pairs: list[tuple[float, int]] = [] + + for salt_dict in solution.get_salt_dict().values(): + _ = salt_dict.pop("mol") + salt = Salt.from_dict(salt_dict) + act_cat = solution.get_activity_coefficient(salt.cation) + act_an = solution.get_activity_coefficient(salt.anion) + activity_nu_pairs.extend([(act_an, salt.nu_anion), (act_cat, salt.nu_cation)]) + + factor = reduce(lambda x, y: x * y[0] ** y[1], activity_nu_pairs, 1.0) + exponent = 1 / sum(x[1] for x in activity_nu_pairs) + return factor**exponent + + +def _get_activity_coefficient_pitzer(solution: Solution) -> float: + salt = solution.get_salt() + param = solution.get_property(salt.formula, "model_parameters.activity_pitzer") + alpha1 = 2 + alpha2 = 0 + molality = salt.get_effective_molality(solution.ionic_strength) + temperature = str(solution.temperature) + + return pyEQL.activity_correction.get_activity_coefficient_pitzer( + solution.ionic_strength, + molality, + alpha1, + alpha2, + ureg.Quantity(param["Beta0"]["value"]).magnitude, + ureg.Quantity(param["Beta1"]["value"]).magnitude, + ureg.Quantity(param["Beta2"]["value"]).magnitude, + ureg.Quantity(param["Cphi"]["value"]).magnitude, + salt.z_cation, + salt.z_anion, + salt.nu_cation, + salt.nu_anion, + temperature, + ) + + +def _get_solution_property(solution: Solution, name: str) -> Any: + if name == "mean_activity_coefficient": + return _get_mean_activity_coefficient(solution) + + if name == "activity_coefficient_pitzer": + return _get_activity_coefficient_pitzer(solution) + + if hasattr(solution, name): + return getattr(solution, name) + + if hasattr(solution, f"get_{name}"): + return getattr(solution, f"get_{name}")() + + msg = f"Property {name} is not supported" + raise ValueError(msg) + + def create_entry( solution: Solution, solute_properties: list[tuple[str, str]], @@ -190,9 +262,12 @@ def create_entry( """Create a BenchmarkEntry from a Solution and specified properties. Args: - solution: The Solution from which to create the entry. - solute_properties: The solute properties to add to the entry. - solution_properties: The solution properties to add to the entry. + solution: Solution + The Solution from which to create the entry. + solute_properties: list[tuple[str, str]] + The solute properties to add to the entry. + solution_properties: list[tuple[str, str]] + The solution properties to add to the entry. """ solute_data = FormulaDict() @@ -262,78 +337,6 @@ def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: return math.sqrt(np.mean(reduced)) -def _get_solute_property(solution: Solution, solute: str, name: str) -> Any: - value = solution.get_property(solute, name) - - if value is None: - if hasattr(solution, name): - value = getattr(solution, name) - elif hasattr(solution, f"get_{name}"): - value = getattr(solution, f"get_{name}")(solute) - else: - msg = f"Solute property: {name} not supported" - raise ValueError(msg) - - return value - - -def _get_mean_activity_coefficient(solution: Solution) -> float: - activity_nu_pairs: list[tuple[float, int]] = [] - - for salt_dict in solution.get_salt_dict().values(): - _ = salt_dict.pop("mol") - salt = Salt.from_dict(salt_dict) - act_cat = solution.get_activity_coefficient(salt.cation) - act_an = solution.get_activity_coefficient(salt.anion) - activity_nu_pairs.extend([(act_an, salt.nu_anion), (act_cat, salt.nu_cation)]) - - factor = reduce(lambda x, y: x * y[0] ** y[1], activity_nu_pairs, 1.0) - exponent = 1 / sum(x[1] for x in activity_nu_pairs) - return factor**exponent - - -def _get_activity_coefficient_pitzer(solution: Solution) -> float: - salt = solution.get_salt() - param = solution.get_property(salt.formula, "model_parameters.activity_pitzer") - alpha1 = 2 - alpha2 = 0 - molality = salt.get_effective_molality(solution.ionic_strength) - temperature = str(solution.temperature) - - return pyEQL.activity_correction.get_activity_coefficient_pitzer( - solution.ionic_strength, - molality, - alpha1, - alpha2, - ureg.Quantity(param["Beta0"]["value"]).magnitude, - ureg.Quantity(param["Beta1"]["value"]).magnitude, - ureg.Quantity(param["Beta2"]["value"]).magnitude, - ureg.Quantity(param["Cphi"]["value"]).magnitude, - salt.z_cation, - salt.z_anion, - salt.nu_cation, - salt.nu_anion, - temperature, - ) - - -def _get_solution_property(solution: Solution, name: str) -> Any: - if name == "mean_activity_coefficient": - return _get_mean_activity_coefficient(solution) - - if name == "activity_coefficient_pitzer": - return _get_activity_coefficient_pitzer(solution) - - if hasattr(solution, name): - return getattr(solution, name) - - if hasattr(solution, f"get_{name}"): - return getattr(solution, f"get_{name}")() - - msg = f"Property {name} is not supported" - raise ValueError(msg) - - def calculate_stats( reference: dict[SolutionKey, BenchmarkEntry], calculated: dict[SolutionKey, BenchmarkEntry], @@ -343,9 +346,13 @@ def calculate_stats( """Calculate benchmarking statistics. Args: - reference: A dictionary mapping SolutionKeys to BenchmarkEntry object. - calculated: A dictionary mapping SolutionKeys to BenchmarkEntry object. - metric: A function that acts on the list of 2-tuples (reference, calculated), which contains reference and + reference: dict[SolutionKey, BenchmarkEntry] + The reference data, a dictionary mapping SolutionKeys to BenchmarkEntry object. + calculated: dict[SolutionKey, BenchmarkEntry] + The data to be benchmarked against the reference data, dictionary mapping SolutionKeys to + BenchmarkEntry object. + metric: Callable[[list[tuple[float, float]]], float], optional + A function that acts on the list of 2-tuples (reference, calculated), which contains reference and calculated values. This function should calculate a statistical metric for the list. Defaults to the root- mean-squared error. From 11329f0b9a7d2b2c082738652b7dd7320905f984 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 17:46:18 -0700 Subject: [PATCH 38/54] Update docstrings; remove unneeded func Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 37 +++++++++++++------------------------ 1 file changed, 13 insertions(+), 24 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 502e11dc..baee3e76 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -67,11 +67,11 @@ class BenchmarkEntry(NamedTuple): Attributes: solution: The Solution to which the reference data applies. - solute_data: A dictionary mapping solutes to a list of solute property-quantity 2-tuples. - solution_data: A list of solution property-quantity 2-tuples. + solute_data: A dictionary mapping solutes to a dictionary mapping solute properties to a Quantity. + solution_data: A dictionary mapping solution properties to a Quantity. - The property strings in the 2-tuples in `solute_data` and `solution_data` should correspond to properties that can - be retrieved using the formalisms outlined in `_get_solute_property` and `_get_solution_property`. + The property strings that serve as keys in ``solute_data`` and ``solution_data`` should correspond to properties + that can be retrieved using the formalisms outlined in ``_get_solute_property`` and ``_get_solution_property``. """ solution: Solution @@ -86,15 +86,15 @@ class BenchmarkResults(NamedTuple): solution_stats: dict[str, float] -# TODO: Admittedly, this is an ugly solution to enable Solutions to serve as dictionary keys to speed up # the +# TODO: Admittedly, this is an ugly solution to enable Solutions to serve as dictionary keys to speed up the # calculation of benchmarking stats. For now, we wrap the decision on the final key format in a function -# _create_solution_key that produces hashable values from a Solution and abstract the key format with a type alias -# (SolutionKey). -# Composition +# (_create_solution_key) that produces hashable values from a Solution, and we abstract the key format with a type +# alias (SolutionKey). SolutionKey = tuple[ # Composition: (ion, concentration) tuple[tuple[str, str], ...], # State: temperature, pressure + # ? should other state variables be checked (e.g., pH, pE)? tuple[str, str], ] @@ -103,9 +103,7 @@ def _create_solution_key(solution: Solution) -> SolutionKey: vol = solution.volume.magnitude components = sorted(solution.components) composition = tuple((component, solution.components[component] / vol) for component in components) - # TODO: should other state variables be checked (e.g., pH, pE)? state = solution.temperature, solution.pressure - return composition, state @@ -266,7 +264,7 @@ def create_entry( The Solution from which to create the entry. solute_properties: list[tuple[str, str]] The solute properties to add to the entry. - solution_properties: list[tuple[str, str]] + solution_properties: list[str] The solution properties to add to the entry. """ solute_data = FormulaDict() @@ -324,19 +322,6 @@ def _create_engine_dataset( return engine_dataset -def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: - reduced = [] - - for ref, calc in data: - val = (ref - calc) ** 2 - - if hasattr(val, "m"): - val = val.m - - reduced.append(val) - return math.sqrt(np.mean(reduced)) - - def calculate_stats( reference: dict[SolutionKey, BenchmarkEntry], calculated: dict[SolutionKey, BenchmarkEntry], @@ -360,6 +345,10 @@ def calculate_stats( A 2-tuple (``solute_stats``, ``solution_stats``) where ``solute_stats`` and ``solution_stats`` are dictionaries mapping solute and solution properties, respectively, to their benchmark statistics. """ + + def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: + return math.sqrt(np.mean([(ref - calc) ** 2 for ref, calc in data])) + metric = metric or _rmse # property: [(reference, calculated)] From f129c93eb7cb753b4a21d54e59e000ea192ae2a4 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 18:03:15 -0700 Subject: [PATCH 39/54] Remove database file Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/database/CRC.json | 29682 ---------------------------------- 1 file changed, 29682 deletions(-) delete mode 100644 src/pyEQL/database/CRC.json diff --git a/src/pyEQL/database/CRC.json b/src/pyEQL/database/CRC.json deleted file mode 100644 index 4d407da1..00000000 --- a/src/pyEQL/database/CRC.json +++ /dev/null @@ -1,29682 +0,0 @@ -[ - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "12.045 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "14.794999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "17.349999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "19.944999999999997 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "22.68 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "0.5 mol/l", - "H[+1]": "0.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "24.84 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "22.959999999999997 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "27.599999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "32.9 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "38.03999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "41.86 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.0 mol/l", - "H[+1]": "1.0 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - "conductivity", - "46.519999999999996 S/m" - ] - ] - ], - [ - { - "solutes": { - "Br[-1]": "1.5 mol/l", - "H[+1]": "1.5 mol/l" - }, - "temperature": "273.15 K" - }, - {}, - [ - [ - 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Ugochukwu Nwosu Date: Sat, 21 Jun 2025 18:03:50 -0700 Subject: [PATCH 40/54] Update database files Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/database/crc.json | 6944 +++++++ tests/test_benchmark/conductivity.json | 2718 +-- .../mean_activity_coefficient.json | 16231 +--------------- tests/test_benchmark/molar_conductivity.json | 8599 +------- 4 files changed, 7854 insertions(+), 26638 deletions(-) create mode 100644 src/pyEQL/database/crc.json diff --git a/src/pyEQL/database/crc.json b/src/pyEQL/database/crc.json new file mode 100644 index 00000000..25dba155 --- /dev/null +++ b/src/pyEQL/database/crc.json @@ -0,0 +1,6944 @@ +[ + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + { + "conductivity": "12.045 S/m" + } + ], + [ + { + "solutes": { + "Br[-1]": "0.5 mol/l", + "H[+1]": "0.5 mol/l" + }, + "temperature": "273.15 K" + }, + {}, + { + "conductivity": "14.794999999999998 S/m" + } + ], + [ + { + "solutes": { + 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{}, + { + "conductivity": "0.04772 S/m" + } + ] +] diff --git a/tests/test_benchmark/conductivity.json b/tests/test_benchmark/conductivity.json index a77e6dfa..3141577d 100644 --- a/tests/test_benchmark/conductivity.json +++ b/tests/test_benchmark/conductivity.json @@ -8,12 +8,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.512562814070352e-06 S/m" - ] - ] + { + "conductivity": "2.512562814070352e-06 S/m" + } ], [ { @@ -24,12 +21,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.070707070707071e-06 S/m" - ] - ] + { + "conductivity": "7.070707070707071e-06 S/m" + } ], [ { @@ -40,12 +34,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.0408163265306123e-05 S/m" - ] - ] + { + "conductivity": "2.0408163265306123e-05 S/m" + } ], [ { @@ -56,12 +47,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.789473684210527e-05 S/m" - ] - ] + { + "conductivity": "5.789473684210527e-05 S/m" + } ], [ { @@ -72,12 +60,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001111111111111111 S/m" - ] - ] + { + "conductivity": "0.0001111111111111111 S/m" + } ], [ { @@ -88,12 +73,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001235294117647059 S/m" - ] - ] + { + "conductivity": "0.0001235294117647059 S/m" + } ], [ { @@ -104,12 +86,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.000125 S/m" - ] - ] + { + "conductivity": "0.000125 S/m" + } ], [ { @@ -120,12 +99,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00013333333333333334 S/m" - ] - ] + { + "conductivity": "0.00013333333333333334 S/m" + } ], [ { @@ -136,12 +112,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.276381909547739e-05 S/m" - ] - ] + { + "conductivity": "5.276381909547739e-05 S/m" + } ], [ { @@ -152,12 +125,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00020606060606060607 S/m" - ] - ] + { + "conductivity": "0.00020606060606060607 S/m" + } ], [ { @@ -168,12 +138,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0008224489795918366 S/m" - ] - ] + { + "conductivity": "0.0008224489795918366 S/m" + } ], [ { @@ -184,12 +151,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0050157894736842104 S/m" - ] - ] + { + "conductivity": "0.0050157894736842104 S/m" + } ], [ { @@ -200,12 +164,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.02 S/m" - ] - ] + { + "conductivity": "0.02 S/m" + } ], [ { @@ -216,12 +177,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "3.718592964824121e-05 S/m" - ] - ] + { + "conductivity": "3.718592964824121e-05 S/m" + } ], [ { @@ -232,12 +190,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00014343434343434345 S/m" - ] - ] + { + "conductivity": "0.00014343434343434345 S/m" + } ], [ { @@ -248,12 +203,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0005244897959183673 S/m" - ] - ] + { + "conductivity": "0.0005244897959183673 S/m" + } ], [ { @@ -264,12 +216,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003021052631578947 S/m" - ] - ] + { + "conductivity": "0.003021052631578947 S/m" + } ], [ { @@ -280,12 +229,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.011666666666666665 S/m" - ] - ] + { + "conductivity": "0.011666666666666665 S/m" + } ], [ { @@ -296,12 +242,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.025941176470588235 S/m" - ] - ] + { + "conductivity": "0.025941176470588235 S/m" + } ], [ { @@ -312,12 +255,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.04625 S/m" - ] - ] + { + "conductivity": "0.04625 S/m" + } ], [ { @@ -328,12 +268,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07166666666666666 S/m" - ] - ] + { + "conductivity": "0.07166666666666666 S/m" + } ], [ { @@ -344,12 +281,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.3618090452261305e-05 S/m" - ] - ] + { + "conductivity": "2.3618090452261305e-05 S/m" + } ], [ { @@ -360,12 +294,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "9.191919191919194e-05 S/m" - ] - ] + { + "conductivity": "9.191919191919194e-05 S/m" + } ], [ { @@ -376,12 +307,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003551020408163265 S/m" - ] - ] + { + "conductivity": "0.0003551020408163265 S/m" + } ], [ { @@ -392,12 +320,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002126315789473684 S/m" - ] - ] + { + "conductivity": "0.002126315789473684 S/m" + } ], [ { @@ -408,12 +333,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.008522222222222223 S/m" - ] - ] + { + "conductivity": "0.008522222222222223 S/m" + } ], [ { @@ -424,12 +346,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.019235294117647062 S/m" - ] - ] + { + "conductivity": "0.019235294117647062 S/m" + } ], [ { @@ -440,12 +359,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03425 S/m" - ] - ] + { + "conductivity": "0.03425 S/m" + } ], [ { @@ -456,12 +372,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "4.07035175879397e-05 S/m" - ] - ] + { + "conductivity": "4.07035175879397e-05 S/m" + } ], [ { @@ -472,12 +385,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001585858585858586 S/m" - ] - ] + { + "conductivity": "0.0001585858585858586 S/m" + } ], [ { @@ -488,12 +398,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0006 S/m" - ] - ] + { + "conductivity": "0.0006 S/m" + } ], [ { @@ -504,12 +411,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0035263157894736843 S/m" - ] - ] + { + "conductivity": "0.0035263157894736843 S/m" + } ], [ { @@ -520,12 +424,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.013000000000000001 S/m" - ] - ] + { + "conductivity": "0.013000000000000001 S/m" + } ], [ { @@ -536,12 +437,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.027705882352941177 S/m" - ] - ] + { + "conductivity": "0.027705882352941177 S/m" + } ], [ { @@ -552,12 +450,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.04425 S/m" - ] - ] + { + "conductivity": "0.04425 S/m" + } ], [ { @@ -568,12 +463,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.061 S/m" - ] - ] + { + "conductivity": "0.061 S/m" + } ], [ { @@ -584,12 +476,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0737142857142857 S/m" - ] - ] + { + "conductivity": "0.0737142857142857 S/m" + } ], [ { @@ -600,12 +489,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07066666666666666 S/m" - ] - ] + { + "conductivity": "0.07066666666666666 S/m" + } ], [ { @@ -616,12 +502,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.9095477386934673e-05 S/m" - ] - ] + { + "conductivity": "1.9095477386934673e-05 S/m" + } ], [ { @@ -632,12 +515,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.474747474747475e-05 S/m" - ] - ] + { + "conductivity": "7.474747474747475e-05 S/m" + } ], [ { @@ -648,12 +528,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002816326530612245 S/m" - ] - ] + { + "conductivity": "0.0002816326530612245 S/m" + } ], [ { @@ -664,12 +541,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.001731578947368421 S/m" - ] - ] + { + "conductivity": "0.001731578947368421 S/m" + } ], [ { @@ -680,12 +554,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00731111111111111 S/m" - ] - ] + { + "conductivity": "0.00731111111111111 S/m" + } ], [ { @@ -696,12 +567,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.018000000000000002 S/m" - ] - ] + { + "conductivity": "0.018000000000000002 S/m" + } ], [ { @@ -712,12 +580,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.035500000000000004 S/m" - ] - ] + { + "conductivity": "0.035500000000000004 S/m" + } ], [ { @@ -728,12 +593,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "6.030150753768844e-06 S/m" - ] - ] + { + "conductivity": "6.030150753768844e-06 S/m" + } ], [ { @@ -744,12 +606,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.1212121212121215e-05 S/m" - ] - ] + { + "conductivity": "2.1212121212121215e-05 S/m" + } ], [ { @@ -760,12 +619,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "6.122448979591836e-05 S/m" - ] - ] + { + "conductivity": "6.122448979591836e-05 S/m" + } ], [ { @@ -776,12 +632,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002473684210526316 S/m" - ] - ] + { + "conductivity": "0.0002473684210526316 S/m" + } ], [ { @@ -792,12 +645,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.000688888888888889 S/m" - ] - ] + { + "conductivity": "0.000688888888888889 S/m" + } ], [ { @@ -808,12 +658,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0012352941176470588 S/m" - ] - ] + { + "conductivity": "0.0012352941176470588 S/m" + } ], [ { @@ -824,12 +671,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0018000000000000002 S/m" - ] - ] + { + "conductivity": "0.0018000000000000002 S/m" + } ], [ { @@ -840,12 +684,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0023666666666666662 S/m" - ] - ] + { + "conductivity": "0.0023666666666666662 S/m" + } ], [ { @@ -856,12 +697,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.4572864321608041e-05 S/m" - ] - ] + { + "conductivity": "1.4572864321608041e-05 S/m" + } ], [ { @@ -872,12 +710,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.454545454545456e-05 S/m" - ] - ] + { + "conductivity": "5.454545454545456e-05 S/m" + } ], [ { @@ -888,12 +723,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00018979591836734694 S/m" - ] - ] + { + "conductivity": "0.00018979591836734694 S/m" + } ], [ { @@ -904,12 +736,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.001 S/m" - ] - ] + { + "conductivity": "0.001 S/m" + } ], [ { @@ -920,12 +749,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003577777777777778 S/m" - ] - ] + { + "conductivity": "0.003577777777777778 S/m" + } ], [ { @@ -936,12 +762,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.007464705882352942 S/m" - ] - ] + { + "conductivity": "0.007464705882352942 S/m" + } ], [ { @@ -952,12 +775,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.035175879396984e-06 S/m" - ] - ] + { + "conductivity": "7.035175879396984e-06 S/m" + } ], [ { @@ -968,12 +788,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.4242424242424244e-05 S/m" - ] - ] + { + "conductivity": "2.4242424242424244e-05 S/m" + } ], [ { @@ -984,12 +801,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.142857142857142e-05 S/m" - ] - ] + { + "conductivity": "7.142857142857142e-05 S/m" + } ], [ { @@ -1000,12 +814,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00029473684210526316 S/m" - ] - ] + { + "conductivity": "0.00029473684210526316 S/m" + } ], [ { @@ -1016,12 +827,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0008666666666666666 S/m" - ] - ] + { + "conductivity": "0.0008666666666666666 S/m" + } ], [ { @@ -1032,12 +840,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0015882352941176472 S/m" - ] - ] + { + "conductivity": "0.0015882352941176472 S/m" + } ], [ { @@ -1048,12 +853,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002475 S/m" - ] - ] + { + "conductivity": "0.002475 S/m" + } ], [ { @@ -1064,12 +866,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003466666666666667 S/m" - ] - ] + { + "conductivity": "0.003466666666666667 S/m" + } ], [ { @@ -1080,12 +879,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0045000000000000005 S/m" - ] - ] + { + "conductivity": "0.0045000000000000005 S/m" + } ], [ { @@ -1096,12 +892,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0066 S/m" - ] - ] + { + "conductivity": "0.0066 S/m" + } ], [ { @@ -1112,12 +905,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0086 S/m" - ] - ] + { + "conductivity": "0.0086 S/m" + } ], [ { @@ -1128,12 +918,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00022663316582914575 S/m" - ] - ] + { + "conductivity": "0.00022663316582914575 S/m" + } ], [ { @@ -1144,12 +931,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0009383838383838386 S/m" - ] - ] + { + "conductivity": "0.0009383838383838386 S/m" + } ], [ { @@ -1160,12 +944,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00373469387755102 S/m" - ] - ] + { + "conductivity": "0.00373469387755102 S/m" + } ], [ { @@ -1176,12 +957,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.075376884422111e-05 S/m" - ] - ] + { + "conductivity": "5.075376884422111e-05 S/m" + } ], [ { @@ -1192,12 +970,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00019191919191919194 S/m" - ] - ] + { + "conductivity": "0.00019191919191919194 S/m" + } ], [ { @@ -1208,12 +983,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0007122448979591836 S/m" - ] - ] + { + "conductivity": "0.0007122448979591836 S/m" + } ], [ { @@ -1224,12 +996,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.004021052631578948 S/m" - ] - ] + { + "conductivity": "0.004021052631578948 S/m" + } ], [ { @@ -1240,12 +1009,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.01411111111111111 S/m" - ] - ] + { + "conductivity": "0.01411111111111111 S/m" + } ], [ { @@ -1256,12 +1022,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.02735294117647059 S/m" - ] - ] + { + "conductivity": "0.02735294117647059 S/m" + } ], [ { @@ -1272,12 +1035,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0425 S/m" - ] - ] + { + "conductivity": "0.0425 S/m" + } ], [ { @@ -1288,12 +1048,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.055 S/m" - ] - ] + { + "conductivity": "0.055 S/m" + } ], [ { @@ -1304,12 +1061,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.06257142857142857 S/m" - ] - ] + { + "conductivity": "0.06257142857142857 S/m" + } ], [ { @@ -1320,12 +1074,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "4.321608040201005e-05 S/m" - ] - ] + { + "conductivity": "4.321608040201005e-05 S/m" + } ], [ { @@ -1336,12 +1087,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001676767676767677 S/m" - ] - ] + { + "conductivity": "0.0001676767676767677 S/m" + } ], [ { @@ -1352,12 +1100,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.000636734693877551 S/m" - ] - ] + { + "conductivity": "0.000636734693877551 S/m" + } ], [ { @@ -1368,12 +1113,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0035210526315789473 S/m" - ] - ] + { + "conductivity": "0.0035210526315789473 S/m" + } ], [ { @@ -1384,12 +1126,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.012 S/m" - ] - ] + { + "conductivity": "0.012 S/m" + } ], [ { @@ -1400,12 +1139,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.022764705882352944 S/m" - ] - ] + { + "conductivity": "0.022764705882352944 S/m" + } ], [ { @@ -1416,12 +1152,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0335 S/m" - ] - ] + { + "conductivity": "0.0335 S/m" + } ], [ { @@ -1432,12 +1165,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.04066666666666666 S/m" - ] - ] + { + "conductivity": "0.04066666666666666 S/m" + } ], [ { @@ -1448,12 +1178,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.042 S/m" - ] - ] + { + "conductivity": "0.042 S/m" + } ], [ { @@ -1464,12 +1191,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.0603015075376886e-05 S/m" - ] - ] + { + "conductivity": "2.0603015075376886e-05 S/m" + } ], [ { @@ -1480,12 +1204,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.676767676767678e-05 S/m" - ] - ] + { + "conductivity": "7.676767676767678e-05 S/m" + } ], [ { @@ -1496,12 +1217,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002714285714285714 S/m" - ] - ] + { + "conductivity": "0.0002714285714285714 S/m" + } ], [ { @@ -1512,12 +1230,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0014421052631578945 S/m" - ] - ] + { + "conductivity": "0.0014421052631578945 S/m" + } ], [ { @@ -1528,12 +1243,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.004744444444444444 S/m" - ] - ] + { + "conductivity": "0.004744444444444444 S/m" + } ], [ { @@ -1544,12 +1256,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.009564705882352942 S/m" - ] - ] + { + "conductivity": "0.009564705882352942 S/m" + } ], [ { @@ -1560,12 +1269,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.012775 S/m" - ] - ] + { + "conductivity": "0.012775 S/m" + } ], [ { @@ -1576,12 +1282,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0147 S/m" - ] - ] + { + "conductivity": "0.0147 S/m" + } ], [ { @@ -1592,12 +1295,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "6.262626262626262e-05 S/m" - ] - ] + { + "conductivity": "6.262626262626262e-05 S/m" + } ], [ { @@ -1608,12 +1308,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002163265306122449 S/m" - ] - ] + { + "conductivity": "0.0002163265306122449 S/m" + } ], [ { @@ -1624,12 +1321,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0011368421052631579 S/m" - ] - ] + { + "conductivity": "0.0011368421052631579 S/m" + } ], [ { @@ -1640,12 +1334,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003833333333333333 S/m" - ] - ] + { + "conductivity": "0.003833333333333333 S/m" + } ], [ { @@ -1656,12 +1347,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.007711764705882354 S/m" - ] - ] + { + "conductivity": "0.007711764705882354 S/m" + } ], [ { @@ -1672,12 +1360,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0119 S/m" - ] - ] + { + "conductivity": "0.0119 S/m" + } ], [ { @@ -1688,12 +1373,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00014271356783919598 S/m" - ] - ] + { + "conductivity": "0.00014271356783919598 S/m" + } ], [ { @@ -1704,12 +1386,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0005666666666666668 S/m" - ] - ] + { + "conductivity": "0.0005666666666666668 S/m" + } ], [ { @@ -1720,12 +1399,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002204081632653061 S/m" - ] - ] + { + "conductivity": "0.002204081632653061 S/m" + } ], [ { @@ -1736,12 +1412,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.035175879396985e-05 S/m" - ] - ] + { + "conductivity": "7.035175879396985e-05 S/m" + } ], [ { @@ -1752,12 +1425,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00022020202020202025 S/m" - ] - ] + { + "conductivity": "0.00022020202020202025 S/m" + } ], [ { @@ -1768,12 +1438,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.000720408163265306 S/m" - ] - ] + { + "conductivity": "0.000720408163265306 S/m" + } ], [ { @@ -1784,12 +1451,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003452631578947368 S/m" - ] - ] + { + "conductivity": "0.003452631578947368 S/m" + } ], [ { @@ -1800,12 +1464,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.7638190954773873e-05 S/m" - ] - ] + { + "conductivity": "2.7638190954773873e-05 S/m" + } ], [ { @@ -1816,12 +1477,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010202020202020203 S/m" - ] - ] + { + "conductivity": "0.00010202020202020203 S/m" + } ], [ { @@ -1832,12 +1490,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00033061224489795916 S/m" - ] - ] + { + "conductivity": "0.00033061224489795916 S/m" + } ], [ { @@ -1848,12 +1503,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0016578947368421052 S/m" - ] - ] + { + "conductivity": "0.0016578947368421052 S/m" + } ], [ { @@ -1864,12 +1516,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0066 S/m" - ] - ] + { + "conductivity": "0.0066 S/m" + } ], [ { @@ -1880,12 +1529,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.015600000000000001 S/m" - ] - ] + { + "conductivity": "0.015600000000000001 S/m" + } ], [ { @@ -1896,12 +1542,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.029500000000000002 S/m" - ] - ] + { + "conductivity": "0.029500000000000002 S/m" + } ], [ { @@ -1912,12 +1555,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.048666666666666664 S/m" - ] - ] + { + "conductivity": "0.048666666666666664 S/m" + } ], [ { @@ -1928,12 +1568,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07414285714285714 S/m" - ] - ] + { + "conductivity": "0.07414285714285714 S/m" + } ], [ { @@ -1944,12 +1581,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.1393333333333333 S/m" - ] - ] + { + "conductivity": "0.1393333333333333 S/m" + } ], [ { @@ -1960,12 +1594,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.613065326633166e-05 S/m" - ] - ] + { + "conductivity": "2.613065326633166e-05 S/m" + } ], [ { @@ -1976,12 +1607,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010303030303030303 S/m" - ] - ] + { + "conductivity": "0.00010303030303030303 S/m" + } ], [ { @@ -1992,12 +1620,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003979591836734693 S/m" - ] - ] + { + "conductivity": "0.0003979591836734693 S/m" + } ], [ { @@ -2008,12 +1633,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002510526315789474 S/m" - ] - ] + { + "conductivity": "0.002510526315789474 S/m" + } ], [ { @@ -2024,12 +1646,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.010622222222222222 S/m" - ] - ] + { + "conductivity": "0.010622222222222222 S/m" + } ], [ { @@ -2040,12 +1659,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.025411764705882356 S/m" - ] - ] + { + "conductivity": "0.025411764705882356 S/m" + } ], [ { @@ -2056,12 +1672,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0485 S/m" - ] - ] + { + "conductivity": "0.0485 S/m" + } ], [ { @@ -2072,12 +1685,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "3.517587939698493e-05 S/m" - ] - ] + { + "conductivity": "3.517587939698493e-05 S/m" + } ], [ { @@ -2088,12 +1698,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00013737373737373736 S/m" - ] - ] + { + "conductivity": "0.00013737373737373736 S/m" + } ], [ { @@ -2104,12 +1711,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0005183673469387754 S/m" - ] - ] + { + "conductivity": "0.0005183673469387754 S/m" + } ], [ { @@ -2120,12 +1724,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003052631578947368 S/m" - ] - ] + { + "conductivity": "0.003052631578947368 S/m" + } ], [ { @@ -2136,12 +1737,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.01211111111111111 S/m" - ] - ] + { + "conductivity": "0.01211111111111111 S/m" + } ], [ { @@ -2152,12 +1750,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.026823529411764708 S/m" - ] - ] + { + "conductivity": "0.026823529411764708 S/m" + } ], [ { @@ -2168,12 +1763,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.047 S/m" - ] - ] + { + "conductivity": "0.047 S/m" + } ], [ { @@ -2184,12 +1776,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07433333333333333 S/m" - ] - ] + { + "conductivity": "0.07433333333333333 S/m" + } ], [ { @@ -2200,12 +1789,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "4.120603015075377e-05 S/m" - ] - ] + { + "conductivity": "4.120603015075377e-05 S/m" + } ], [ { @@ -2216,12 +1802,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001585858585858586 S/m" - ] - ] + { + "conductivity": "0.0001585858585858586 S/m" + } ], [ { @@ -2232,12 +1815,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0006020408163265307 S/m" - ] - ] + { + "conductivity": "0.0006020408163265307 S/m" + } ], [ { @@ -2248,12 +1828,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0037842105263157897 S/m" - ] - ] + { + "conductivity": "0.0037842105263157897 S/m" + } ], [ { @@ -2264,12 +1841,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.015888888888888886 S/m" - ] - ] + { + "conductivity": "0.015888888888888886 S/m" + } ], [ { @@ -2280,12 +1854,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03670588235294118 S/m" - ] - ] + { + "conductivity": "0.03670588235294118 S/m" + } ], [ { @@ -2296,12 +1867,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.507537688442211e-05 S/m" - ] - ] + { + "conductivity": "1.507537688442211e-05 S/m" + } ], [ { @@ -2312,12 +1880,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.9595959595959606e-05 S/m" - ] - ] + { + "conductivity": "5.9595959595959606e-05 S/m" + } ], [ { @@ -2328,12 +1893,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00022448979591836732 S/m" - ] - ] + { + "conductivity": "0.00022448979591836732 S/m" + } ], [ { @@ -2344,12 +1906,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0013157894736842105 S/m" - ] - ] + { + "conductivity": "0.0013157894736842105 S/m" + } ], [ { @@ -2360,12 +1919,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.004955555555555556 S/m" - ] - ] + { + "conductivity": "0.004955555555555556 S/m" + } ], [ { @@ -2376,12 +1932,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.3115577889447238e-05 S/m" - ] - ] + { + "conductivity": "2.3115577889447238e-05 S/m" + } ], [ { @@ -2392,12 +1945,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "8.989898989898991e-05 S/m" - ] - ] + { + "conductivity": "8.989898989898991e-05 S/m" + } ], [ { @@ -2408,12 +1958,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003469387755102041 S/m" - ] - ] + { + "conductivity": "0.0003469387755102041 S/m" + } ], [ { @@ -2424,12 +1971,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0020421052631578946 S/m" - ] - ] + { + "conductivity": "0.0020421052631578946 S/m" + } ], [ { @@ -2440,12 +1984,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.008044444444444444 S/m" - ] - ] + { + "conductivity": "0.008044444444444444 S/m" + } ], [ { @@ -2456,12 +1997,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.017823529411764707 S/m" - ] - ] + { + "conductivity": "0.017823529411764707 S/m" + } ], [ { @@ -2472,12 +2010,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.032 S/m" - ] - ] + { + "conductivity": "0.032 S/m" + } ], [ { @@ -2488,12 +2023,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.613065326633166e-05 S/m" - ] - ] + { + "conductivity": "2.613065326633166e-05 S/m" + } ], [ { @@ -2504,12 +2036,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001 S/m" - ] - ] + { + "conductivity": "0.0001 S/m" + } ], [ { @@ -2520,12 +2049,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00037346938775510203 S/m" - ] - ] + { + "conductivity": "0.00037346938775510203 S/m" + } ], [ { @@ -2536,12 +2062,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002121052631578947 S/m" - ] - ] + { + "conductivity": "0.002121052631578947 S/m" + } ], [ { @@ -2552,12 +2075,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010050251256281407 S/m" - ] - ] + { + "conductivity": "0.00010050251256281407 S/m" + } ], [ { @@ -2568,12 +2088,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003888888888888889 S/m" - ] - ] + { + "conductivity": "0.0003888888888888889 S/m" + } ], [ { @@ -2584,12 +2101,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.001530612244897959 S/m" - ] - ] + { + "conductivity": "0.001530612244897959 S/m" + } ], [ { @@ -2600,12 +2114,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00936842105263158 S/m" - ] - ] + { + "conductivity": "0.00936842105263158 S/m" + } ], [ { @@ -2616,12 +2127,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.9095477386934673e-05 S/m" - ] - ] + { + "conductivity": "1.9095477386934673e-05 S/m" + } ], [ { @@ -2632,12 +2140,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.575757575757576e-05 S/m" - ] - ] + { + "conductivity": "7.575757575757576e-05 S/m" + } ], [ { @@ -2648,12 +2153,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00028979591836734693 S/m" - ] - ] + { + "conductivity": "0.00028979591836734693 S/m" + } ], [ { @@ -2664,12 +2166,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0018526315789473685 S/m" - ] - ] + { + "conductivity": "0.0018526315789473685 S/m" + } ], [ { @@ -2680,12 +2179,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.007977777777777776 S/m" - ] - ] + { + "conductivity": "0.007977777777777776 S/m" + } ], [ { @@ -2696,12 +2192,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.019411764705882354 S/m" - ] - ] + { + "conductivity": "0.019411764705882354 S/m" + } ], [ { @@ -2712,12 +2205,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.047 S/m" - ] - ] + { + "conductivity": "0.047 S/m" + } ], [ { @@ -2728,12 +2218,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07466666666666666 S/m" - ] - ] + { + "conductivity": "0.07466666666666666 S/m" + } ], [ { @@ -2744,12 +2231,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.7638190954773873e-05 S/m" - ] - ] + { + "conductivity": "2.7638190954773873e-05 S/m" + } ], [ { @@ -2760,12 +2244,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010808080808080809 S/m" - ] - ] + { + "conductivity": "0.00010808080808080809 S/m" + } ], [ { @@ -2776,12 +2257,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00041020408163265306 S/m" - ] - ] + { + "conductivity": "0.00041020408163265306 S/m" + } ], [ { @@ -2792,12 +2270,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0024736842105263154 S/m" - ] - ] + { + "conductivity": "0.0024736842105263154 S/m" + } ], [ { @@ -2808,12 +2283,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0097 S/m" - ] - ] + { + "conductivity": "0.0097 S/m" + } ], [ { @@ -2824,12 +2296,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.02188235294117647 S/m" - ] - ] + { + "conductivity": "0.02188235294117647 S/m" + } ], [ { @@ -2840,12 +2309,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03925 S/m" - ] - ] + { + "conductivity": "0.03925 S/m" + } ], [ { @@ -2856,12 +2322,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.06066666666666667 S/m" - ] - ] + { + "conductivity": "0.06066666666666667 S/m" + } ], [ { @@ -2872,12 +2335,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.7587939698492464e-05 S/m" - ] - ] + { + "conductivity": "1.7587939698492464e-05 S/m" + } ], [ { @@ -2888,12 +2348,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "6.96969696969697e-05 S/m" - ] - ] + { + "conductivity": "6.96969696969697e-05 S/m" + } ], [ { @@ -2904,12 +2361,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00026530612244897954 S/m" - ] - ] + { + "conductivity": "0.00026530612244897954 S/m" + } ], [ { @@ -2920,12 +2374,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0016052631578947368 S/m" - ] - ] + { + "conductivity": "0.0016052631578947368 S/m" + } ], [ { @@ -2936,12 +2387,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.9145728643216082e-05 S/m" - ] - ] + { + "conductivity": "2.9145728643216082e-05 S/m" + } ], [ { @@ -2952,12 +2400,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00011313131313131314 S/m" - ] - ] + { + "conductivity": "0.00011313131313131314 S/m" + } ], [ { @@ -2968,12 +2413,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00042857142857142855 S/m" - ] - ] + { + "conductivity": "0.00042857142857142855 S/m" + } ], [ { @@ -2984,12 +2426,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0025263157894736842 S/m" - ] - ] + { + "conductivity": "0.0025263157894736842 S/m" + } ], [ { @@ -3000,12 +2439,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.009844444444444444 S/m" - ] - ] + { + "conductivity": "0.009844444444444444 S/m" + } ], [ { @@ -3016,12 +2452,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.5577889447236183e-05 S/m" - ] - ] + { + "conductivity": "1.5577889447236183e-05 S/m" + } ], [ { @@ -3032,12 +2465,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "6.161616161616162e-05 S/m" - ] - ] + { + "conductivity": "6.161616161616162e-05 S/m" + } ], [ { @@ -3048,12 +2478,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00024489795918367346 S/m" - ] - ] + { + "conductivity": "0.00024489795918367346 S/m" + } ], [ { @@ -3064,12 +2491,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0014052631578947367 S/m" - ] - ] + { + "conductivity": "0.0014052631578947367 S/m" + } ], [ { @@ -3080,12 +2504,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.005533333333333333 S/m" - ] - ] + { + "conductivity": "0.005533333333333333 S/m" + } ], [ { @@ -3096,12 +2517,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.012705882352941178 S/m" - ] - ] + { + "conductivity": "0.012705882352941178 S/m" + } ], [ { @@ -3112,12 +2530,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0232 S/m" - ] - ] + { + "conductivity": "0.0232 S/m" + } ], [ { @@ -3128,12 +2543,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03733333333333333 S/m" - ] - ] + { + "conductivity": "0.03733333333333333 S/m" + } ], [ { @@ -3144,12 +2556,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.055285714285714285 S/m" - ] - ] + { + "conductivity": "0.055285714285714285 S/m" + } ], [ { @@ -3160,12 +2569,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.108 S/m" - ] - ] + { + "conductivity": "0.108 S/m" + } ], [ { @@ -3176,12 +2582,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.9597989949748744e-05 S/m" - ] - ] + { + "conductivity": "1.9597989949748744e-05 S/m" + } ], [ { @@ -3192,12 +2595,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "7.676767676767678e-05 S/m" - ] - ] + { + "conductivity": "7.676767676767678e-05 S/m" + } ], [ { @@ -3208,12 +2608,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002938775510204081 S/m" - ] - ] + { + "conductivity": "0.0002938775510204081 S/m" + } ], [ { @@ -3224,12 +2621,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.001626315789473684 S/m" - ] - ] + { + "conductivity": "0.001626315789473684 S/m" + } ], [ { @@ -3240,12 +2634,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.005933333333333333 S/m" - ] - ] + { + "conductivity": "0.005933333333333333 S/m" + } ], [ { @@ -3256,12 +2647,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.011311764705882353 S/m" - ] - ] + { + "conductivity": "0.011311764705882353 S/m" + } ], [ { @@ -3272,12 +2660,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.017325 S/m" - ] - ] + { + "conductivity": "0.017325 S/m" + } ], [ { @@ -3288,12 +2673,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.023066666666666666 S/m" - ] - ] + { + "conductivity": "0.023066666666666666 S/m" + } ], [ { @@ -3304,12 +2686,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.027557142857142853 S/m" - ] - ] + { + "conductivity": "0.027557142857142853 S/m" + } ], [ { @@ -3320,12 +2699,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.5125628140703518e-05 S/m" - ] - ] + { + "conductivity": "2.5125628140703518e-05 S/m" + } ], [ { @@ -3336,12 +2712,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "9.7979797979798e-05 S/m" - ] - ] + { + "conductivity": "9.7979797979798e-05 S/m" + } ], [ { @@ -3352,12 +2725,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00037551020408163263 S/m" - ] - ] + { + "conductivity": "0.00037551020408163263 S/m" + } ], [ { @@ -3368,12 +2738,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0023157894736842107 S/m" - ] - ] + { + "conductivity": "0.0023157894736842107 S/m" + } ], [ { @@ -3384,12 +2751,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.009399999999999999 S/m" - ] - ] + { + "conductivity": "0.009399999999999999 S/m" + } ], [ { @@ -3400,12 +2764,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.021529411764705884 S/m" - ] - ] + { + "conductivity": "0.021529411764705884 S/m" + } ], [ { @@ -3416,12 +2777,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03925 S/m" - ] - ] + { + "conductivity": "0.03925 S/m" + } ], [ { @@ -3432,12 +2790,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.06366666666666666 S/m" - ] - ] + { + "conductivity": "0.06366666666666666 S/m" + } ], [ { @@ -3448,12 +2803,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.09257142857142857 S/m" - ] - ] + { + "conductivity": "0.09257142857142857 S/m" + } ], [ { @@ -3464,12 +2816,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "3.517587939698493e-05 S/m" - ] - ] + { + "conductivity": "3.517587939698493e-05 S/m" + } ], [ { @@ -3480,12 +2829,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00013232323232323235 S/m" - ] - ] + { + "conductivity": "0.00013232323232323235 S/m" + } ], [ { @@ -3496,12 +2842,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0004755102040816326 S/m" - ] - ] + { + "conductivity": "0.0004755102040816326 S/m" + } ], [ { @@ -3512,12 +2855,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0024736842105263154 S/m" - ] - ] + { + "conductivity": "0.0024736842105263154 S/m" + } ], [ { @@ -3528,12 +2868,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.008266666666666667 S/m" - ] - ] + { + "conductivity": "0.008266666666666667 S/m" + } ], [ { @@ -3544,12 +2881,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.01563529411764706 S/m" - ] - ] + { + "conductivity": "0.01563529411764706 S/m" + } ], [ { @@ -3560,12 +2894,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "4.120603015075377e-05 S/m" - ] - ] + { + "conductivity": "4.120603015075377e-05 S/m" + } ], [ { @@ -3576,12 +2907,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00016161616161616162 S/m" - ] - ] + { + "conductivity": "0.00016161616161616162 S/m" + } ], [ { @@ -3592,12 +2920,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0006163265306122448 S/m" - ] - ] + { + "conductivity": "0.0006163265306122448 S/m" + } ], [ { @@ -3608,12 +2933,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003689473684210526 S/m" - ] - ] + { + "conductivity": "0.003689473684210526 S/m" + } ], [ { @@ -3624,12 +2946,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.014 S/m" - ] - ] + { + "conductivity": "0.014 S/m" + } ], [ { @@ -3640,12 +2959,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.030176470588235298 S/m" - ] - ] + { + "conductivity": "0.030176470588235298 S/m" + } ], [ { @@ -3656,12 +2972,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.051000000000000004 S/m" - ] - ] + { + "conductivity": "0.051000000000000004 S/m" + } ], [ { @@ -3672,12 +2985,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.074 S/m" - ] - ] + { + "conductivity": "0.074 S/m" + } ], [ { @@ -3688,12 +2998,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.1055276381909548e-05 S/m" - ] - ] + { + "conductivity": "1.1055276381909548e-05 S/m" + } ], [ { @@ -3704,12 +3011,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "4.444444444444445e-05 S/m" - ] - ] + { + "conductivity": "4.444444444444445e-05 S/m" + } ], [ { @@ -3720,12 +3024,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001857142857142857 S/m" - ] - ] + { + "conductivity": "0.0001857142857142857 S/m" + } ], [ { @@ -3736,12 +3037,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0011052631578947368 S/m" - ] - ] + { + "conductivity": "0.0011052631578947368 S/m" + } ], [ { @@ -3752,12 +3050,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.003688888888888889 S/m" - ] - ] + { + "conductivity": "0.003688888888888889 S/m" + } ], [ { @@ -3768,12 +3063,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0076411764705882354 S/m" - ] - ] + { + "conductivity": "0.0076411764705882354 S/m" + } ], [ { @@ -3784,12 +3076,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.012400000000000001 S/m" - ] - ] + { + "conductivity": "0.012400000000000001 S/m" + } ], [ { @@ -3800,12 +3089,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0177 S/m" - ] - ] + { + "conductivity": "0.0177 S/m" + } ], [ { @@ -3816,12 +3102,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.023142857142857142 S/m" - ] - ] + { + "conductivity": "0.023142857142857142 S/m" + } ], [ { @@ -3832,12 +3115,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.030733333333333335 S/m" - ] - ] + { + "conductivity": "0.030733333333333335 S/m" + } ], [ { @@ -3848,12 +3128,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.1105527638190957e-05 S/m" - ] - ] + { + "conductivity": "2.1105527638190957e-05 S/m" + } ], [ { @@ -3864,12 +3141,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "8.282828282828283e-05 S/m" - ] - ] + { + "conductivity": "8.282828282828283e-05 S/m" + } ], [ { @@ -3880,12 +3154,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003061224489795918 S/m" - ] - ] + { + "conductivity": "0.0003061224489795918 S/m" + } ], [ { @@ -3896,12 +3167,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0016526315789473682 S/m" - ] - ] + { + "conductivity": "0.0016526315789473682 S/m" + } ], [ { @@ -3912,12 +3180,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.3115577889447238e-05 S/m" - ] - ] + { + "conductivity": "2.3115577889447238e-05 S/m" + } ], [ { @@ -3928,12 +3193,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "8.787878787878787e-05 S/m" - ] - ] + { + "conductivity": "8.787878787878787e-05 S/m" + } ], [ { @@ -3944,12 +3206,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003183673469387755 S/m" - ] - ] + { + "conductivity": "0.0003183673469387755 S/m" + } ], [ { @@ -3960,12 +3219,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0016526315789473682 S/m" - ] - ] + { + "conductivity": "0.0016526315789473682 S/m" + } ], [ { @@ -3976,12 +3232,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00012462311557788947 S/m" - ] - ] + { + "conductivity": "0.00012462311557788947 S/m" + } ], [ { @@ -3992,12 +3245,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.000490909090909091 S/m" - ] - ] + { + "conductivity": "0.000490909090909091 S/m" + } ], [ { @@ -4008,12 +3258,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0018999999999999998 S/m" - ] - ] + { + "conductivity": "0.0018999999999999998 S/m" + } ], [ { @@ -4024,12 +3271,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.010842105263157894 S/m" - ] - ] + { + "conductivity": "0.010842105263157894 S/m" + } ], [ { @@ -4040,12 +3284,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.7135678391959802e-05 S/m" - ] - ] + { + "conductivity": "2.7135678391959802e-05 S/m" + } ], [ { @@ -4056,12 +3297,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010707070707070708 S/m" - ] - ] + { + "conductivity": "0.00010707070707070708 S/m" + } ], [ { @@ -4072,12 +3310,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00041632653061224485 S/m" - ] - ] + { + "conductivity": "0.00041632653061224485 S/m" + } ], [ { @@ -4088,12 +3323,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002431578947368421 S/m" - ] - ] + { + "conductivity": "0.002431578947368421 S/m" + } ], [ { @@ -4104,12 +3336,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.009177777777777778 S/m" - ] - ] + { + "conductivity": "0.009177777777777778 S/m" + } ], [ { @@ -4120,12 +3349,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.01958823529411765 S/m" - ] - ] + { + "conductivity": "0.01958823529411765 S/m" + } ], [ { @@ -4136,12 +3362,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0335 S/m" - ] - ] + { + "conductivity": "0.0335 S/m" + } ], [ { @@ -4152,12 +3375,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.050666666666666665 S/m" - ] - ] + { + "conductivity": "0.050666666666666665 S/m" + } ], [ { @@ -4168,12 +3388,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07071428571428572 S/m" - ] - ] + { + "conductivity": "0.07071428571428572 S/m" + } ], [ { @@ -4184,12 +3401,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.11866666666666666 S/m" - ] - ] + { + "conductivity": "0.11866666666666666 S/m" + } ], [ { @@ -4200,12 +3414,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "3.668341708542714e-05 S/m" - ] - ] + { + "conductivity": "3.668341708542714e-05 S/m" + } ], [ { @@ -4216,12 +3427,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00014242424242424243 S/m" - ] - ] + { + "conductivity": "0.00014242424242424243 S/m" + } ], [ { @@ -4232,12 +3440,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0004632653061224489 S/m" - ] - ] + { + "conductivity": "0.0004632653061224489 S/m" + } ], [ { @@ -4248,12 +3453,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.002289473684210526 S/m" - ] - ] + { + "conductivity": "0.002289473684210526 S/m" + } ], [ { @@ -4264,12 +3466,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.9648241206030153e-05 S/m" - ] - ] + { + "conductivity": "2.9648241206030153e-05 S/m" + } ], [ { @@ -4280,12 +3479,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00011313131313131314 S/m" - ] - ] + { + "conductivity": "0.00011313131313131314 S/m" + } ], [ { @@ -4296,12 +3492,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0004040816326530612 S/m" - ] - ] + { + "conductivity": "0.0004040816326530612 S/m" + } ], [ { @@ -4312,12 +3505,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0022473684210526316 S/m" - ] - ] + { + "conductivity": "0.0022473684210526316 S/m" + } ], [ { @@ -4328,12 +3518,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.007922222222222221 S/m" - ] - ] + { + "conductivity": "0.007922222222222221 S/m" + } ], [ { @@ -4344,12 +3531,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.016076470588235296 S/m" - ] - ] + { + "conductivity": "0.016076470588235296 S/m" + } ], [ { @@ -4360,12 +3544,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.02725 S/m" - ] - ] + { + "conductivity": "0.02725 S/m" + } ], [ { @@ -4376,12 +3557,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.864321608040201e-05 S/m" - ] - ] + { + "conductivity": "2.864321608040201e-05 S/m" + } ], [ { @@ -4392,12 +3570,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00010808080808080809 S/m" - ] - ] + { + "conductivity": "0.00010808080808080809 S/m" + } ], [ { @@ -4408,12 +3583,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0003979591836734693 S/m" - ] - ] + { + "conductivity": "0.0003979591836734693 S/m" + } ], [ { @@ -4424,12 +3596,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0022789473684210523 S/m" - ] - ] + { + "conductivity": "0.0022789473684210523 S/m" + } ], [ { @@ -4440,12 +3609,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.008522222222222223 S/m" - ] - ] + { + "conductivity": "0.008522222222222223 S/m" + } ], [ { @@ -4456,12 +3622,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.01835294117647059 S/m" - ] - ] + { + "conductivity": "0.01835294117647059 S/m" + } ], [ { @@ -4472,12 +3635,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03075 S/m" - ] - ] + { + "conductivity": "0.03075 S/m" + } ], [ { @@ -4488,12 +3648,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.04466666666666667 S/m" - ] - ] + { + "conductivity": "0.04466666666666667 S/m" + } ], [ { @@ -4504,12 +3661,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.05828571428571429 S/m" - ] - ] + { + "conductivity": "0.05828571428571429 S/m" + } ], [ { @@ -4520,12 +3674,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07866666666666666 S/m" - ] - ] + { + "conductivity": "0.07866666666666666 S/m" + } ], [ { @@ -4536,12 +3687,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "2.9648241206030153e-05 S/m" - ] - ] + { + "conductivity": "2.9648241206030153e-05 S/m" + } ], [ { @@ -4552,12 +3700,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00011515151515151518 S/m" - ] - ] + { + "conductivity": "0.00011515151515151518 S/m" + } ], [ { @@ -4568,12 +3713,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00044897959183673463 S/m" - ] - ] + { + "conductivity": "0.00044897959183673463 S/m" + } ], [ { @@ -4584,12 +3726,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0025842105263157895 S/m" - ] - ] + { + "conductivity": "0.0025842105263157895 S/m" + } ], [ { @@ -4600,12 +3739,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.010166666666666666 S/m" - ] - ] + { + "conductivity": "0.010166666666666666 S/m" + } ], [ { @@ -4616,12 +3752,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.022411764705882357 S/m" - ] - ] + { + "conductivity": "0.022411764705882357 S/m" + } ], [ { @@ -4632,12 +3765,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.03825 S/m" - ] - ] + { + "conductivity": "0.03825 S/m" + } ], [ { @@ -4648,12 +3778,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.056 S/m" - ] - ] + { + "conductivity": "0.056 S/m" + } ], [ { @@ -4664,12 +3791,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.07628571428571428 S/m" - ] - ] + { + "conductivity": "0.07628571428571428 S/m" + } ], [ { @@ -4680,12 +3804,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0001221105527638191 S/m" - ] - ] + { + "conductivity": "0.0001221105527638191 S/m" + } ], [ { @@ -4696,12 +3817,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.00048282828282828285 S/m" - ] - ] + { + "conductivity": "0.00048282828282828285 S/m" + } ], [ { @@ -4712,12 +3830,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.001877551020408163 S/m" - ] - ] + { + "conductivity": "0.001877551020408163 S/m" + } ], [ { @@ -4728,12 +3843,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.011105263157894736 S/m" - ] - ] + { + "conductivity": "0.011105263157894736 S/m" + } ], [ { @@ -4744,12 +3856,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "1.4070351758793969e-05 S/m" - ] - ] + { + "conductivity": "1.4070351758793969e-05 S/m" + } ], [ { @@ -4760,12 +3869,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "5.454545454545456e-05 S/m" - ] - ] + { + "conductivity": "5.454545454545456e-05 S/m" + } ], [ { @@ -4776,12 +3882,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0002040816326530612 S/m" - ] - ] + { + "conductivity": "0.0002040816326530612 S/m" + } ], [ { @@ -4792,12 +3895,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0010789473684210526 S/m" - ] - ] + { + "conductivity": "0.0010789473684210526 S/m" + } ], [ { @@ -4808,12 +3908,9 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0037444444444444443 S/m" - ] - ] + { + "conductivity": "0.0037444444444444443 S/m" + } ], [ { @@ -4824,11 +3921,8 @@ "temperature": "293.15 K" }, {}, - [ - [ - "conductivity", - "0.0076411764705882354 S/m" - ] - ] + { + "conductivity": "0.0076411764705882354 S/m" + } ] ] diff --git a/tests/test_benchmark/mean_activity_coefficient.json b/tests/test_benchmark/mean_activity_coefficient.json index fdce59fc..1839f689 100644 --- a/tests/test_benchmark/mean_activity_coefficient.json +++ b/tests/test_benchmark/mean_activity_coefficient.json @@ 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"conductivity", - "0.7276 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.0005 mol/l", - "Na[+1]": "0.0005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.006221999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.005 mol/l", - "Na[+1]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.060294999999999994 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.01 mol/l", - "Na[+1]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.11845 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.02 mol/l", - "Na[+1]": "0.02 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.2314 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.05 mol/l", - "Na[+1]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.55505 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.1 mol/l", - "Na[+1]": "0.1 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "1.0669 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.0005 mol/l", - "Na[+1]": "0.0005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.005778999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.005 mol/l", - "Na[+1]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.05585 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.01 mol/l", - "Na[+1]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.10954000000000001 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.02 mol/l", - "Na[+1]": "0.02 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.21381999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.05 mol/l", - "Na[+1]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.5117499999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "ClO4[-1]": "0.1 mol/l", - "Na[+1]": "0.1 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.9838 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.0005 mol/l", - "Na[+1]": "0.0005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.006264999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.005 mol/l", - "Na[+1]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.060594999999999996 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.01 mol/l", - "Na[+1]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.11918000000000001 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.02 mol/l", - "Na[+1]": "0.02 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.23328000000000002 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.05 mol/l", - "Na[+1]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.56365 S/m" - ] - ] - ], - [ - { - "solutes": { - "I[-1]": "0.1 mol/l", - "Na[+1]": "0.1 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "1.0873 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.0005 mol/l", - "OH[-1]": "0.0005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.012275 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.005 mol/l", - "OH[-1]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.12034999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.01 mol/l", - "OH[-1]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.23789999999999997 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.0005 mol/l", - "SO4[-2]": "0.00025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.0031420000000000003 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.005 mol/l", - "SO4[-2]": "0.0025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.0292725 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.01 mol/l", - "SO4[-2]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.05618999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.02 mol/l", - "SO4[-2]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.10673 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.05 mol/l", - "SO4[-2]": "0.025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.24425000000000002 S/m" - ] - ] - ], - [ - { - "solutes": { - "Na[+1]": "0.1 mol/l", - "SO4[-2]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.44969999999999993 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.0005 mol/l", - "Sr[+2]": "0.00025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.003296 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.005 mol/l", - "Sr[+2]": "0.0025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.031044999999999996 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.01 mol/l", - "Sr[+2]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.060115 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.02 mol/l", - "Sr[+2]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.11548 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.05 mol/l", - "Sr[+2]": "0.025 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.27049999999999996 S/m" - ] - ] - ], - [ - { - "solutes": { - "Cl[-1]": "0.1 mol/l", - "Sr[+2]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.5106999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.0005 mol/l", - "Zn[+2]": "0.0005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.006065 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.005 mol/l", - "Zn[+2]": "0.005 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.04772 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.01 mol/l", - "Zn[+2]": "0.01 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.08486999999999999 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.02 mol/l", - "Zn[+2]": "0.02 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.14839999999999998 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.05 mol/l", - "Zn[+2]": "0.05 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.30585 S/m" - ] - ] - ], - [ - { - "solutes": { - "SO4[-2]": "0.1 mol/l", - "Zn[+2]": "0.1 mol/l" - }, - "temperature": "298.15 K" - }, - {}, - [ - [ - "conductivity", - "0.5261 S/m" - ] - ] + "conductivity": "12.045 S/m" + } ] ] From 6092c0b506d17fdf41a70ea8ad3ff5225ecc5c8c Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 19:11:18 -0700 Subject: [PATCH 41/54] Update tests; shrink solution properties tested Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 36 ++++++++++++++++++++++++------------ 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index d586b787..2c115ee7 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -2,7 +2,15 @@ import pytest -from pyEQL.benchmark import BenchmarkEntry, benchmark_engine, calculate_stats, create_entry, load_dataset +from pyEQL.benchmark import ( + BenchmarkEntry, + _create_engine_dataset, + _create_solution_key, + benchmark_engine, + calculate_stats, + create_entry, + load_dataset, +) from pyEQL.engines import EOS, IdealEOS, NativeEOS from pyEQL.solution import Solution @@ -34,7 +42,7 @@ def test_should_load_dataset_from_file(source: str) -> None: assert dataset @staticmethod - @pytest.mark.parametrize("source", ["CRC"]) + @pytest.mark.parametrize("source", ["crc"]) def test_should_load_dataset_from_internal_source(source: str) -> None: dataset = load_dataset(source) assert dataset @@ -75,16 +83,16 @@ def fixture_solute_property(request: pytest.FixtureRequest) -> str: @pytest.fixture( name="solution_property", params=[ - "dielectric_constant", - "debye_length", + # "dielectric_constant", + # "debye_length", "conductivity", "osmotic_coefficient", "density", - "viscosity_dynamic", - "osmolality", - "osmolarity", - "chemical_potential_energy", - "activity_coefficient_pitzer", + # "viscosity_dynamic", + # "osmolality", + # "osmolarity", + # "chemical_potential_energy", + # "activity_coefficient_pitzer", ], ) def fixture_solution_property(request: pytest.FixtureRequest) -> str: @@ -95,13 +103,17 @@ def fixture_solution_property(request: pytest.FixtureRequest) -> str: name="dataset", ) def fixture_dataset(solution: Solution, solute_property: str, solution_property: str) -> list[BenchmarkEntry]: - return [create_entry(solution, [solute_property], [solution_property])] + key = _create_solution_key(solution) + return { + key: create_entry(solution, [(solute, solute_property) for solute in solution.components], [solution_property]) + } class TestCalculateStats: @staticmethod - def test_should_calculate_zero_rmse_with_engine_dataset(dataset: list[BenchmarkEntry]) -> None: - results = calculate_stats(dataset) + def test_should_calculate_zero_rmse_with_engine_dataset(engine: EOS, dataset: list[BenchmarkEntry]) -> None: + engine_dataset = _create_engine_dataset(engine, [dataset]) + results = calculate_stats(engine_dataset, engine_dataset) assert all(err == 0 for err in results.solute_stats.values()) assert all(err == 0 for err in results.solution_stats.values()) From 48f80bbe22cb6070da86e7f5b9e40065fccd4b08 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 20:26:04 -0700 Subject: [PATCH 42/54] Remove use of FormulaDict; fix bugs FormulaDict was initially used in order to automatically standardize how solutes appear in solution compositions and solute property lists. However, in addition to standardizing ion formulas, FormulaDict also sorts its internal copy of the dictionary by its values. This led to an error in the previous implementation because the values are dictionaries, and dictionaries don't implement the required methods for comparison with '<' and '>'. Instead, we manually call standardize_formula in the public functions where malformatted formulas are likely. This is when loading datasets and when creating a BenchmarkEntry from a Solution. Bugs: initialize property data as dictionaries in create_entry; fix indices and data type in _create_engine_dataset; initialize data pair lists in calculate_stats. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 44 ++++++++++++++++++++++++------------------ 1 file changed, 25 insertions(+), 19 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index baee3e76..db42c8fa 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -57,7 +57,7 @@ from pyEQL.engines import EOS from pyEQL.salt_ion_match import Salt from pyEQL.solution import Solution -from pyEQL.utils import FormulaDict +from pyEQL.utils import standardize_formula INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "JPCRD", "May2011JCED"] @@ -75,7 +75,7 @@ class BenchmarkEntry(NamedTuple): """ solution: Solution - solute_data: FormulaDict[str, dict[str, Quantity]] = FormulaDict() + solute_data: dict[str, dict[str, Quantity]] = {} solution_data: dict[str, Quantity] = {} @@ -113,7 +113,7 @@ def load_dataset( solutions: list[Solution] | None = None, solute_properties: list[tuple[str, str]] | None = None, solution_properties: list[str] | None = None, -) -> dict[str, BenchmarkEntry]: +) -> dict[SolutionKey, BenchmarkEntry]: """Load reference dataset. Args: @@ -158,14 +158,15 @@ def load_dataset( if solutions is not None and soln_key not in solution_keys: continue - solute_data = FormulaDict[str, dict[str, Quantity]] = FormulaDict() + solute_data: dict[str, dict[str, Quantity]] = {} solution_data = {} for solute, values in raw_solute_data.items(): - solute_data[solute] = {} + standardized_solute = standardize_formula(solute) + solute_data[standardized_solute] = {} for p, q in values.items(): - if solute_properties is None or (solute, p) in solute_properties: - solute_data[solute][p] = ureg.Quantity(q) + if solute_properties is None or (standardized_solute, p) in solute_properties: + solute_data[standardized_solute][p] = ureg.Quantity(q) for p, q in raw_solution_data.items(): if solution_properties is None or p in solution_properties: @@ -267,19 +268,20 @@ def create_entry( solution_properties: list[str] The solution properties to add to the entry. """ - solute_data = FormulaDict() + solute_data = {} for solute, solute_property in solute_properties: - if solute not in solute_data: - solute_data[solute] = [] - data = _get_solute_property(solution, solute, solute_property) - solute_data[solute].append((solute_property, data)) + standardized_solute = standardize_formula(solute) + if standardized_solute not in solute_data: + solute_data[standardized_solute] = {} + data = _get_solute_property(solution, standardized_solute, solute_property) + solute_data[standardized_solute][solute_property] = data - solution_data = [] + solution_data = {} for solution_property in solution_properties: data = _get_solution_property(solution, solution_property) - solution_data.append((solution_property, data)) + solution_data[solution_property] = data return BenchmarkEntry(solution=solution, solute_data=solute_data, solution_data=solution_data) @@ -296,7 +298,7 @@ def _create_engine_dataset( # solution_properties list[str], ], - ] = [] + ] = {} for dataset in datasets: for key, entry in dataset.items(): @@ -304,8 +306,8 @@ def _create_engine_dataset( mapper[key] = [], [] for solute in entry.solute_data: - mapper[key][1].extend((solute, prop) for prop in list(entry.solute_data[solute])) - mapper[key][2].extend(entry.solution_data) + mapper[key][0].extend((solute, prop) for prop in list(entry.solute_data[solute])) + mapper[key][1].extend(entry.solution_data) engine_dataset = {} @@ -347,7 +349,7 @@ def calculate_stats( """ def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: - return math.sqrt(np.mean([(ref - calc) ** 2 for ref, calc in data])) + return math.sqrt(np.mean([Quantity(ref - calc).m ** 2 for ref, calc in data])) metric = metric or _rmse @@ -358,12 +360,16 @@ def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: for key, entry in reference.items(): for solute in entry.solute_data: for prop, value in entry.solute_data[solute].items(): + if prop not in solute_data_pairs: + solute_data_pairs[prop] = [] calculated_value = calculated[key].solute_data[solute][prop] solute_data_pairs[prop].append((value, calculated_value)) for prop, value in entry.solution_data.items(): + if prop not in solution_data_pairs: + solution_data_pairs[prop] = [] calculated_value = calculated[key].solution_data[prop] - solute_data_pairs[prop].append((value, calculated_value)) + solution_data_pairs[prop].append((value, calculated_value)) solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} From 6160eb0039683b0483bad281fc1dfd0a6fac83c2 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 21:07:18 -0700 Subject: [PATCH 43/54] Polish docstrings Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index db42c8fa..ff764ddb 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -66,9 +66,12 @@ class BenchmarkEntry(NamedTuple): """A set of data for a solution. Attributes: - solution: The Solution to which the reference data applies. - solute_data: A dictionary mapping solutes to a dictionary mapping solute properties to a Quantity. - solution_data: A dictionary mapping solution properties to a Quantity. + solution: Solution + The Solution to which the reference data applies. + solute_data: dict[str, dict[str, Quantity]] + A dictionary mapping solutes to a dictionary mapping solute properties to a Quantity. + solution_data: dict[str, Quantity] + A dictionary mapping solution properties to a Quantity. The property strings that serve as keys in ``solute_data`` and ``solution_data`` should correspond to properties that can be retrieved using the formalisms outlined in ``_get_solute_property`` and ``_get_solution_property``. @@ -80,7 +83,14 @@ class BenchmarkEntry(NamedTuple): class BenchmarkResults(NamedTuple): - """Solute and solution stats from :func:`pyEQL.benchmark.calculate_stats`.""" + """Solute and solution stats from :func:`pyEQL.benchmark.calculate_stats`. + + Attributes: + solute_stats: dict[str, float] + Benchmarking statistics for solute properties. + solution_stats: dict[str, float] + Benchmarking statistics for solution properties. + """ solute_stats: dict[str, float] solution_stats: dict[str, float] From df0063a9c18b56aaafc0eab4d1d0bce3be41badb Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 22:20:40 -0700 Subject: [PATCH 44/54] Add units for concentration in SolutionKey The concentration for Solution objects that are created in _create_engine_dataset is determined from the SolutionKey. Without units, the amounts are not interpreted as concentrations and the Solution does not have the correct composition. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index ff764ddb..c7d23faf 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -112,7 +112,7 @@ class BenchmarkResults(NamedTuple): def _create_solution_key(solution: Solution) -> SolutionKey: vol = solution.volume.magnitude components = sorted(solution.components) - composition = tuple((component, solution.components[component] / vol) for component in components) + composition = tuple((component, f"{solution.components[component] / vol} mol/L") for component in components) state = solution.temperature, solution.pressure return composition, state From a6f867892594a686107d0de1e2e063ff33d40ffd Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 22:41:15 -0700 Subject: [PATCH 45/54] Add more unit tests The three load_dataset unit tests are just outlines and are expected to fail. The explicit test cases for test_should_benchmark_all_engines are intended to eventually overlap with those in test_conductivity and eventually replace them. Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 36 +- tests/test_benchmark/conductivity.json | 1812 +-- .../mean_activity_coefficient.json | 13182 ++++++++++++++++ tests/test_benchmark/molar_conductivity.json | 6981 ++++++++ 4 files changed, 21102 insertions(+), 909 deletions(-) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index 2c115ee7..cc14183a 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -1,3 +1,4 @@ +from itertools import product from pathlib import Path import pytest @@ -30,7 +31,9 @@ def fixture_engine(request: pytest.FixtureRequest) -> EOS: return engine() -@pytest.fixture(name="source", params=["molar_conductivity.json", "mean_activity_coefficient.json"]) +@pytest.fixture( + name="source", params=["conductivity.json", "molar_conductivity.json", "mean_activity_coefficient.json"] +) def fixture_source(request: pytest.FixtureRequest) -> list[Path]: return datadir.joinpath(request.param) @@ -47,6 +50,24 @@ def test_should_load_dataset_from_internal_source(source: str) -> None: dataset = load_dataset(source) assert dataset + @staticmethod + @pytest.mark.xfail + def test_should_only_load_data_for_specified_solutions() -> None: + only_load_data_for_specified_solutions = False + assert only_load_data_for_specified_solutions + + @staticmethod + @pytest.mark.xfail + def test_should_only_load_data_for_specified_solute_properties() -> None: + only_load_data_for_specified_solutions = False + assert only_load_data_for_specified_solutions + + @staticmethod + @pytest.mark.xfail + def test_should_only_load_data_for_specified_solution_properties() -> None: + only_load_data_for_specified_solutions = False + assert only_load_data_for_specified_solutions + @pytest.fixture(name="cation", params=["Na[+1]"]) def fixture_cation(request: pytest.FixtureRequest) -> str: @@ -120,6 +141,15 @@ def test_should_calculate_zero_rmse_with_engine_dataset(engine: EOS, dataset: li class TestBenchmarkEngine: @staticmethod - def test_should_benchmark_all_engines(engine: EOS, source: Path) -> None: - benchmark_results = benchmark_engine(engine, sources=[source]) + @pytest.fixture(name="source", params=["molar_conductivity.json"]) + def fixture_source(request: pytest.FixtureRequest) -> list[Path]: + return datadir.joinpath(request.param) + + @staticmethod + @pytest.mark.parametrize( + ("conc", "cation"), + list(product(["0.0005 mol/L", "0.001 mol/L", "0.01 mol/L", "0.05 mol/L", "0.1 mol/L"], ["Na[+1]", "K[+1]"])), + ) + def test_should_benchmark_all_engines(engine: EOS, source: Path, solution: Solution) -> None: + benchmark_results = benchmark_engine(engine, sources=[source], solutions=[solution]) assert benchmark_results diff --git a/tests/test_benchmark/conductivity.json b/tests/test_benchmark/conductivity.json index 3141577d..5ab3f977 100644 --- a/tests/test_benchmark/conductivity.json +++ b/tests/test_benchmark/conductivity.json @@ -2,3927 +2,3927 @@ [ { "solutes": { - "H[+1]": "0.01507537688442211 %", - "N[-3]": "0.005025125628140704 %" + "H[+1]": "1.5 %", + "N[-3]": "0.5 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "2.512562814070352e-06 S/m" + "conductivity": "0.00025 S/m" } ], [ { "solutes": { - "H[+1]": "0.030303030303030304 %", - "N[-3]": "0.010101010101010102 %" + "H[+1]": "3.0 %", + "N[-3]": "1.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "7.070707070707071e-06 S/m" + "conductivity": "0.0007 S/m" } ], [ { "solutes": { - "H[+1]": "0.061224489795918366 %", - "N[-3]": "0.02040816326530612 %" + "H[+1]": "6.0 %", + "N[-3]": "2.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "2.0408163265306123e-05 S/m" + "conductivity": "0.002 S/m" } ], [ { "solutes": { - "H[+1]": "0.15789473684210525 %", - "N[-3]": "0.05263157894736842 %" + "H[+1]": "15.0 %", + "N[-3]": "5.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "5.789473684210527e-05 S/m" + "conductivity": "0.0055 S/m" } ], [ { "solutes": { - "H[+1]": "0.3333333333333333 %", - "N[-3]": "0.1111111111111111 %" + "H[+1]": "30.0 %", + "N[-3]": "10.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.0001111111111111111 S/m" + "conductivity": "0.01 S/m" } ], [ { "solutes": { - "H[+1]": "0.5294117647058824 %", - "N[-3]": "0.17647058823529413 %" + "H[+1]": "45.0 %", + "N[-3]": "15.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.0001235294117647059 S/m" + "conductivity": "0.0105 S/m" } ], [ { "solutes": { - "H[+1]": "0.75 %", - "N[-3]": "0.25 %" + "H[+1]": "60.0 %", + "N[-3]": "20.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.000125 S/m" + "conductivity": "0.01 S/m" } ], [ { "solutes": { - "H[+1]": "1.0 %", - "N[-3]": "0.3333333333333333 %" + "H[+1]": "75.0 %", + "N[-3]": "25.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.00013333333333333334 S/m" + "conductivity": "0.01 S/m" } ], [ { "solutes": { - "Cl[-1]": "0.005025125628140704 %", - "NH4[+1]": "0.005025125628140704 %" + "Cl[-1]": "0.5 %", + "NH4[+1]": "0.5 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "5.276381909547739e-05 S/m" + "conductivity": "0.00525 S/m" } ], [ { "solutes": { - "Cl[-1]": "0.010101010101010102 %", - "NH4[+1]": "0.010101010101010102 %" + "Cl[-1]": "1.0 %", + "NH4[+1]": "1.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.00020606060606060607 S/m" + "conductivity": "0.020399999999999998 S/m" } ], [ { "solutes": { - "Cl[-1]": "0.02040816326530612 %", - "NH4[+1]": "0.02040816326530612 %" + "Cl[-1]": "2.0 %", + "NH4[+1]": "2.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.0008224489795918366 S/m" + "conductivity": "0.08059999999999999 S/m" } ], [ { "solutes": { - "Cl[-1]": "0.05263157894736842 %", - "NH4[+1]": "0.05263157894736842 %" + "Cl[-1]": "5.0 %", + "NH4[+1]": "5.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.0050157894736842104 S/m" + "conductivity": "0.47650000000000003 S/m" } ], [ { "solutes": { - "Cl[-1]": "0.1111111111111111 %", - "NH4[+1]": "0.1111111111111111 %" + "Cl[-1]": "10.0 %", + "NH4[+1]": "10.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.02 S/m" + "conductivity": "1.8 S/m" } ], [ { "solutes": { - "NH4[+1]": "0.010050251256281407 %", - "SO4[-2]": "0.005025125628140704 %" + "NH4[+1]": "1.0 %", + "SO4[-2]": "0.5 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "3.718592964824121e-05 S/m" + "conductivity": "0.0037 S/m" } ], [ { "solutes": { - "NH4[+1]": "0.020202020202020204 %", - "SO4[-2]": "0.010101010101010102 %" + "NH4[+1]": "2.0 %", + "SO4[-2]": "1.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.00014343434343434345 S/m" + "conductivity": "0.014199999999999999 S/m" } ], [ { "solutes": { - "NH4[+1]": "0.04081632653061224 %", - "SO4[-2]": "0.02040816326530612 %" + "NH4[+1]": "4.0 %", + "SO4[-2]": "2.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "0.0005244897959183673 S/m" + "conductivity": "0.0514 S/m" } ], [ { "solutes": { - "NH4[+1]": 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"temperature": "293.15 K" }, {}, { - "conductivity": "0.035500000000000004 S/m" + "conductivity": "2.84 S/m" } ], [ { "solutes": { - "C[+1]": "0.005025125628140704 %", - "OH[-1]": "0.005025125628140704 %" + "C[+1]": "0.5 %", + "OH[-1]": "0.5 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "6.030150753768844e-06 S/m" + "conductivity": "0.0006 S/m" } ], [ { "solutes": { - "C[+1]": "0.010101010101010102 %", - "OH[-1]": "0.010101010101010102 %" + "C[+1]": "1.0 %", + "OH[-1]": "1.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "2.1212121212121215e-05 S/m" + "conductivity": "0.0021000000000000003 S/m" } ], [ { "solutes": { - "C[+1]": "0.02040816326530612 %", - "OH[-1]": "0.02040816326530612 %" + "C[+1]": "2.0 %", + "OH[-1]": "2.0 %" }, "temperature": "293.15 K" }, {}, { - "conductivity": "6.122448979591836e-05 S/m" + "conductivity": "0.006 S/m" } ], [ { "solutes": { - "C[+1]": "0.05263157894736842 %", - "OH[-1]": "0.05263157894736842 %" + "C[+1]": "5.0 %", + "OH[-1]": 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"solutes": { + "ClO4[-1]": "0.0005 mol/l", + "Na[+1]": "0.0005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.005778999999999999 S/m" + } + ], + [ + { + "solutes": { + "ClO4[-1]": "0.005 mol/l", + "Na[+1]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.05585 S/m" + } + ], + [ + { + "solutes": { + "ClO4[-1]": "0.01 mol/l", + "Na[+1]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.10954000000000001 S/m" + } + ], + [ + { + "solutes": { + "ClO4[-1]": "0.02 mol/l", + "Na[+1]": "0.02 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.21381999999999998 S/m" + } + ], + [ + { + "solutes": { + "ClO4[-1]": "0.05 mol/l", + "Na[+1]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.5117499999999999 S/m" + } + ], + [ + { + "solutes": { + "ClO4[-1]": "0.1 mol/l", + "Na[+1]": "0.1 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.9838 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.0005 mol/l", + "Na[+1]": "0.0005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.006264999999999999 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.005 mol/l", + "Na[+1]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.060594999999999996 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.01 mol/l", + "Na[+1]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.11918000000000001 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.02 mol/l", + "Na[+1]": "0.02 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.23328000000000002 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.05 mol/l", + "Na[+1]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.56365 S/m" + } + ], + [ + { + "solutes": { + "I[-1]": "0.1 mol/l", + "Na[+1]": "0.1 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "1.0873 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.0005 mol/l", + "OH[-1]": "0.0005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.012275 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.005 mol/l", + "OH[-1]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.12034999999999998 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.01 mol/l", + "OH[-1]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.23789999999999997 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.0005 mol/l", + "SO4[-2]": "0.00025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.0031420000000000003 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.005 mol/l", + "SO4[-2]": "0.0025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.0292725 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.01 mol/l", + "SO4[-2]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.05618999999999999 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.02 mol/l", + "SO4[-2]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.10673 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.05 mol/l", + "SO4[-2]": "0.025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.24425000000000002 S/m" + } + ], + [ + { + "solutes": { + "Na[+1]": "0.1 mol/l", + "SO4[-2]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.44969999999999993 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.0005 mol/l", + "Sr[+2]": "0.00025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.003296 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.005 mol/l", + "Sr[+2]": "0.0025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.031044999999999996 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.01 mol/l", + "Sr[+2]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.060115 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.02 mol/l", + "Sr[+2]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.11548 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.05 mol/l", + "Sr[+2]": "0.025 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.27049999999999996 S/m" + } + ], + [ + { + "solutes": { + "Cl[-1]": "0.1 mol/l", + "Sr[+2]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.5106999999999999 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.0005 mol/l", + "Zn[+2]": "0.0005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.006065 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.005 mol/l", + "Zn[+2]": "0.005 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.04772 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.01 mol/l", + "Zn[+2]": "0.01 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.08486999999999999 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.02 mol/l", + "Zn[+2]": "0.02 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.14839999999999998 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.05 mol/l", + "Zn[+2]": "0.05 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.30585 S/m" + } + ], + [ + { + "solutes": { + "SO4[-2]": "0.1 mol/l", + "Zn[+2]": "0.1 mol/l" + }, + "temperature": "298.15 K" + }, + {}, + { + "conductivity": "0.5261 S/m" + } ] ] From 5a025b23ac826b8c5441b3a913340d025836f791 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sat, 21 Jun 2025 23:57:10 -0700 Subject: [PATCH 46/54] Update module docstring Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 30 +++++++++++++++++------------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index c7d23faf..7a045e33 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -9,36 +9,40 @@ >>> results["crc"].solution_stats["mean_activity_coefficient"] ... -Example: Generate a reference dataset from a solution model +Example: Generate a reference dataset from a solution model engine >>> from pyEQL import Solution >>> from pyEQL.benchmark import calculate_stats >>> from pyEQL.benchmark import create_entry +>>> from pyEQL.benchmark import _create_solution_key >>> from pyEQL.engines import IdealEOS >>> from pyEQL.engines import NativeEOS >>> cations = ["H[+1]", "Na[+1]", "Ca[+2]"] >>> anions = ["OH[-1]", "Cl[-1]", "SO4[-2]"] >>> concs = ["0.1 mol/L", "25%"] ->>> solutions = [] +>>> solute_properties = ["activity_coefficient", "molar_conductivity"] +>>> solution_properties = ["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"] +>>> ideal_solutions = [] +>>> native_solutions = [] >>> for ions for product(cations, anions): ... for conc in concs: ... solutes = {ion: conc for ion in ions} -... solutions.append(Solution(solutes=solutes, engine=IdealEOS())) - ->>> solute_properties = ["activity_coefficient", "molar_conductivity"] ->>> solution_properties = ["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"] ->>> dataset = [] +... ideal_solutions.append(Solution(solutes=solutes, engine=IdealEOS())) +... native_solutions.append(Solution(solutes=solutes, engine=NativeEOS())) ->>> for solution in solutions: -... entry = create_entry(solution, solute_properties, solution_properties) -... dataset.append(entry) +>>> ideal_data = {} +>>> native_data = {} ->>> for data in dataset: -... data.solution.engine = NativeEOS() +>>> for ideal_solution, native_solution in zip(ideal_solutions, native_solutions, strict=True): +... ideal_entry = create_entry(ideal_solution, solute_properties, solution_properties) +... native_entry = create_entry(native_solution, solute_properties, solution_properties) +... key = _create_solution_key(ideal_solution) +... ideal_data[key] = ideal_entry +... native_data[key] = ideal_entry ->>> stats = calculate_stats(dataset) +>>> stats = calculate_stats(ideal_data, native_data) """ import json From c0dc6fb3e0dffbd11b4d324306c81199261a2e38 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 00:25:38 -0700 Subject: [PATCH 47/54] Exclude the solvent from the solution key The number of moles of solvent is dependent on the engine, but in the capacity that SolutionKey will be used, two Solutions with the same concentrations of their solutes with differing engines (and thus differing moles of solvent) should be considered identical if they are at the same state (temperature and pressure). Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 7a045e33..202fc217 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -115,10 +115,13 @@ class BenchmarkResults(NamedTuple): def _create_solution_key(solution: Solution) -> SolutionKey: vol = solution.volume.magnitude - components = sorted(solution.components) - composition = tuple((component, f"{solution.components[component] / vol} mol/L") for component in components) + composition = [] + for component in sorted(solution.components): + if component != solution.solvent: + amount = f"{solution.components[component] / vol} mol/L" + composition.append((component, amount)) state = solution.temperature, solution.pressure - return composition, state + return tuple(composition), state def load_dataset( From e72d68b75ed90f20b6f87390e82f3437e95e3046 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 00:40:36 -0700 Subject: [PATCH 48/54] Outline additional unit tests Signed-off-by: Ugochukwu Nwosu --- tests/test_benchmark.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py index cc14183a..7af22515 100644 --- a/tests/test_benchmark.py +++ b/tests/test_benchmark.py @@ -68,6 +68,18 @@ def test_should_only_load_data_for_specified_solution_properties() -> None: only_load_data_for_specified_solutions = False assert only_load_data_for_specified_solutions + @staticmethod + @pytest.mark.xfail + def test_should_load_data_values_as_quantities() -> None: + load_data_values_as_quantities = False + assert load_data_values_as_quantities + + @staticmethod + @pytest.mark.xfail + def test_should_standardize_the_chemical_formulas_in_solute_data() -> None: + standardize_the_chemical_formulas_in_solute_data = False + assert standardize_the_chemical_formulas_in_solute_data + @pytest.fixture(name="cation", params=["Na[+1]"]) def fixture_cation(request: pytest.FixtureRequest) -> str: @@ -153,3 +165,11 @@ def fixture_source(request: pytest.FixtureRequest) -> list[Path]: def test_should_benchmark_all_engines(engine: EOS, source: Path, solution: Solution) -> None: benchmark_results = benchmark_engine(engine, sources=[source], solutions=[solution]) assert benchmark_results + + +class TestCreateEngineDataset: + pass + + +class TestCreateEntry: + pass From bbb1b021c12bb057f0cbd4ca59fe0e7f3a6a515d Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 12:45:18 -0700 Subject: [PATCH 49/54] Fix language in docstrings Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 202fc217..f5bc3a48 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -140,16 +140,15 @@ def load_dataset( solutions: list[Solution], optional The solutions for which data will be loaded from the dataset. If provided, only data corresponding to solutions with the same composition, temperature, and pressure will be loaded. If omitted, all - compositions and conditions in the reference data contained in ``sources`` will be used for the - benchmarking. + compositions and conditions in the reference data contained in ``source`` will be loaded. solute_properties: list[tuple[str, str]], optional - The solute properties to include in the benchmarking, specified as ``(solute, property)``. The engine will - only be benchmarked against those solute properties listed here. If omitted, the engine will be benchmarked - against all solute properties in ``sources``. + The solute properties to loaded from the dataset, specified as ``(solute, property)``. If provided, only + data for the specified solute properties will be loaded. If omitted, all solute properties in the reference + data contained in ``source`` will be loaded. solution_properties: list[str], optional - The solution properties to include in the benchmarking. The engine will only be benchmarked against those - solution properties listed here. Defaults to None in which case the engine will be benchmarked against all - solute properties in ``sources``. + The solution properties to loaded from the dataset. If provided, only data for the specified solution + properties will be loaded. If omitted, all solution properties in the reference data contained in ``source`` + will be loaded. Returns: A dictionary mapping SolutionKey to BenchmarkEntry objects. See the comment over SolutionKey for details about @@ -411,8 +410,8 @@ def benchmark_engine( One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry objects. Defaults to INTERNAL_SOURCES. solutions: list[Solution], optional - The solutions for which data will be loaded from the dataset. If provided, only data corresponding to - solutions with the same components, concentrations, and conditions (temperature, pressure) will be loaded. + The solutions to include n the benchmarking. If provided, only data corresponding to + solutions with the same components, concentrations, and conditions (temperature, pressure) will be used. If omitted, reference data for all components, concentrations, and conditions (temperature, pressure) contained in ``sources`` will be used for the benchmarking. solute_properties: list[tuple[str, str]], optional From 5d17d08ea629c9f8598e7cda5ff4880819aa9189 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 14:20:09 -0700 Subject: [PATCH 50/54] Revise docstrings Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index f5bc3a48..632c4f93 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -1,15 +1,16 @@ """Solution model benchmarking utilities. -Example: Benchmark a solution model against reference data +Example: Benchmark the IdealEOS solution model against CRC reference data >>> from pyEQL.benchmark import benchmark_engine >>> from pyEQL.engines import IdealEOS ->>> results = benchmark_engine(IdealEOS(), sources=["crc"]) +>>> engine = IdealEOS() +>>> results = benchmark_engine(engine, sources=["crc"]) >>> results["crc"].solution_stats["mean_activity_coefficient"] ... -Example: Generate a reference dataset from a solution model engine +Example: Benchmark one solution model against another >>> from pyEQL import Solution >>> from pyEQL.benchmark import calculate_stats @@ -101,9 +102,10 @@ class BenchmarkResults(NamedTuple): # TODO: Admittedly, this is an ugly solution to enable Solutions to serve as dictionary keys to speed up the -# calculation of benchmarking stats. For now, we wrap the decision on the final key format in a function -# (_create_solution_key) that produces hashable values from a Solution, and we abstract the key format with a type -# alias (SolutionKey). +# calculation of benchmarking stats. Ideally, this key is cheap to generate and can be generated from the Solution +# alone in the functions that need it (e.g., load_dataset, calculate_stats, _create_engine_dataset). For now, we wrap +# the decision on the final key format in a function (_create_solution_key) that produces hashable values from a +# Solution, and we abstract the key format with a type alias (SolutionKey). SolutionKey = tuple[ # Composition: (ion, concentration) tuple[tuple[str, str], ...], From ced1b682fa48623bd8fa6529c644e6a0741e60fe Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 16:27:23 -0700 Subject: [PATCH 51/54] Update docstrings; Fix metric args Updated module docstring variable for consistency. Require both _create_engine_dataset arguments. For now, only require that the metric argument to calculate_stats can handle Quantity arguments, so that we can ensure that units are handled correctly. Note that the property values in BenchmarkEntry.solute_data and BenchmarkEntry.solution_data are expected to be Quantity objects. Also, the additional conditional statements in calculate_stats serve to handle the edge cases of when the return values of _get_solute_property and _get_solution_property are None and when there does not exist data in `calculated` corresponding to `reference`. Because this may be of intereste to the user, the event is logged at the INFO level. Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 63 ++++++++++++++++++++++++++++-------------- 1 file changed, 43 insertions(+), 20 deletions(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 632c4f93..03173784 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -6,8 +6,8 @@ >>> from pyEQL.engines import IdealEOS >>> engine = IdealEOS() ->>> results = benchmark_engine(engine, sources=["crc"]) ->>> results["crc"].solution_stats["mean_activity_coefficient"] +>>> stats = benchmark_engine(engine, sources=["crc"]) +>>> stats["crc"].solution_stats["mean_activity_coefficient"] ... Example: Benchmark one solution model against another @@ -19,11 +19,10 @@ >>> from pyEQL.engines import IdealEOS >>> from pyEQL.engines import NativeEOS +# Create the solutions >>> cations = ["H[+1]", "Na[+1]", "Ca[+2]"] >>> anions = ["OH[-1]", "Cl[-1]", "SO4[-2]"] >>> concs = ["0.1 mol/L", "25%"] ->>> solute_properties = ["activity_coefficient", "molar_conductivity"] ->>> solution_properties = ["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"] >>> ideal_solutions = [] >>> native_solutions = [] @@ -33,6 +32,9 @@ ... ideal_solutions.append(Solution(solutes=solutes, engine=IdealEOS())) ... native_solutions.append(Solution(solutes=solutes, engine=NativeEOS())) +# Create the datasets +>>> solute_properties = ["activity_coefficient", "molar_conductivity"] +>>> solution_properties = ["dielectric_constant", "debye_length", "conductivity", "osmotic_coefficient", "density"] >>> ideal_data = {} >>> native_data = {} @@ -41,12 +43,13 @@ ... native_entry = create_entry(native_solution, solute_properties, solution_properties) ... key = _create_solution_key(ideal_solution) ... ideal_data[key] = ideal_entry -... native_data[key] = ideal_entry +... native_data[key] = native_entry >>> stats = calculate_stats(ideal_data, native_data) """ import json +import logging import math from collections.abc import Callable from functools import reduce @@ -64,6 +67,8 @@ from pyEQL.solution import Solution from pyEQL.utils import standardize_formula +logger = logging.getLogger(__name__) + INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "JPCRD", "May2011JCED"] @@ -305,9 +310,10 @@ def create_entry( def _create_engine_dataset( - engine: EOS | Literal["native", "ideal", "phreeqc"] = "native", - datasets: list[dict[SolutionKey, BenchmarkEntry]] | None = None, + engine: EOS | Literal["native", "ideal", "phreeqc"], + datasets: list[dict[SolutionKey, BenchmarkEntry]], ) -> dict[SolutionKey, BenchmarkEntry]: + """Create an engine-based dataset containing the properties contained within other datasets.""" mapper: dict[ SolutionKey, tuple[ @@ -346,9 +352,11 @@ def calculate_stats( reference: dict[SolutionKey, BenchmarkEntry], calculated: dict[SolutionKey, BenchmarkEntry], *, - metric: Callable[[list[tuple[float, float]]], float] | None = None, + metric: Callable[[list[tuple[Quantity, Quantity]]], float] | None = None, ) -> BenchmarkResults: - """Calculate benchmarking statistics. + """Calculate benchmarking statistics for one dataset relative to another. + + Statistics will be calculated for each solute and solvent property in ``reference`` that appears in ``calculated``. Args: reference: dict[SolutionKey, BenchmarkEntry] @@ -356,38 +364,53 @@ def calculate_stats( calculated: dict[SolutionKey, BenchmarkEntry] The data to be benchmarked against the reference data, dictionary mapping SolutionKeys to BenchmarkEntry object. - metric: Callable[[list[tuple[float, float]]], float], optional + metric: Callable[[list[tuple[Quantity, Quantity]]], float], optional A function that acts on the list of 2-tuples (reference, calculated), which contains reference and - calculated values. This function should calculate a statistical metric for the list. Defaults to the root- - mean-squared error. + calculated values as Quantity objects. This function should calculate a statistical metric for the list. + Defaults to the root-mean-squared error. Returns: A 2-tuple (``solute_stats``, ``solution_stats``) where ``solute_stats`` and ``solution_stats`` are dictionaries - mapping solute and solution properties, respectively, to their benchmark statistics. + mapping solute and solution properties, respectively, to their benchmark statistics. The keys in + ``solute_stats`` are 2-tuples of strings (``solute``, ``prop``). The keys in ``solution_stats`` are strings. """ def _rmse(data: list[tuple[Quantity, Quantity]]) -> float: - return math.sqrt(np.mean([Quantity(ref - calc).m ** 2 for ref, calc in data])) + return math.sqrt(np.mean([((ref - calc) ** 2).m for ref, calc in data])) metric = metric or _rmse # property: [(reference, calculated)] - solute_data_pairs: dict[str, list[tuple[float, float]]] = {} - solution_data_pairs: dict[str, list[tuple[float, float]]] = {} + solute_data_pairs: dict[str, list[tuple[Quantity, Quantity]]] = {} + solution_data_pairs: dict[str, list[tuple[Quantity, Quantity]]] = {} for key, entry in reference.items(): for solute in entry.solute_data: for prop, value in entry.solute_data[solute].items(): if prop not in solute_data_pairs: solute_data_pairs[prop] = [] - calculated_value = calculated[key].solute_data[solute][prop] - solute_data_pairs[prop].append((value, calculated_value)) + + if ( + key in calculated + and solute in calculated[key].solute_data + and calculated[key].solute_data[solute].get(prop) is not None + ): + calculated_value = calculated[key].solute_data[solute][prop] + solute_data_pairs[prop].append((value, calculated_value)) + else: + logger.info( + "Unable to find data for key: %s, solute: %s, and solute property: %s", str(key), solute, prop + ) for prop, value in entry.solution_data.items(): if prop not in solution_data_pairs: solution_data_pairs[prop] = [] - calculated_value = calculated[key].solution_data[prop] - solution_data_pairs[prop].append((value, calculated_value)) + + if key in calculated and calculated[key].solution_data.get(prop) is not None: + calculated_value = calculated[key].solution_data[prop] + solution_data_pairs[prop].append((value, calculated_value)) + else: + logger.info("Unable to find data for key: %s and solution property: %s", str(key), prop) solute_stats = {k: metric(v) for k, v in solute_data_pairs.items()} solution_stats = {k: metric(v) for k, v in solution_data_pairs.items()} From 1d041e70f38b4ca3b81d4049749bfcc24c2d2c69 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 16:42:24 -0700 Subject: [PATCH 52/54] Fix typo Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 03173784..424a5638 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -435,7 +435,7 @@ def benchmark_engine( One of INTERNAL_SOURCES or the path to a JSON file that can be read into a list of BenchmarkEntry objects. Defaults to INTERNAL_SOURCES. solutions: list[Solution], optional - The solutions to include n the benchmarking. If provided, only data corresponding to + The solutions to include in the benchmarking. If provided, only data corresponding to solutions with the same components, concentrations, and conditions (temperature, pressure) will be used. If omitted, reference data for all components, concentrations, and conditions (temperature, pressure) contained in ``sources`` will be used for the benchmarking. From cc94ea803bb79e9e0993d11404e8d70a2c318329 Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 16:57:12 -0700 Subject: [PATCH 53/54] Add example for load_dataset Signed-off-by: Ugochukwu Nwosu --- src/pyEQL/benchmark.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py index 424a5638..139e04b1 100644 --- a/src/pyEQL/benchmark.py +++ b/src/pyEQL/benchmark.py @@ -1,5 +1,17 @@ """Solution model benchmarking utilities. +Example: Load CRC reference data + +>>> from pyEQL import Solution +>>> from pyEQL.benchmark import _create_solution_key +>>> from pyEQL.benchmark import load_dataset + +>>> soln = Solution(solutes={"Na[+1]": "0.1 mol/L", "Cl[-1]": "0.1 mol/L"}, temperature="298.15 K", pressure="1 atm") +>>> data = load_dataset("crc", solutions=[soln]) +>>> key = _create_solution_key(soln) +>>> data[key] +... + Example: Benchmark the IdealEOS solution model against CRC reference data >>> from pyEQL.benchmark import benchmark_engine From 82e06df4a2883e32b071d2587d351363e132729c Mon Sep 17 00:00:00 2001 From: Ugochukwu Nwosu Date: Sun, 22 Jun 2025 23:49:57 -0700 Subject: [PATCH 54/54] Add benchmarking to docs Signed-off-by: Ugochukwu Nwosu --- docs/internal.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docs/internal.md b/docs/internal.md index 42aefdee..e00258e5 100644 --- a/docs/internal.md +++ b/docs/internal.md @@ -19,6 +19,13 @@ These internal modules are used by `Solution` but typically are not directly acc :members: ``` +## Engine Benchmarking module + +```{eval-rst} +.. automodule:: pyEQL.benchmark + :members: +``` + ## Activity Correction functions ```{eval-rst}