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} diff --git a/src/pyEQL/benchmark.py b/src/pyEQL/benchmark.py new file mode 100644 index 00000000..139e04b1 --- /dev/null +++ b/src/pyEQL/benchmark.py @@ -0,0 +1,474 @@ +"""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 pyEQL.engines import IdealEOS + +>>> engine = IdealEOS() +>>> stats = benchmark_engine(engine, sources=["crc"]) +>>> stats["crc"].solution_stats["mean_activity_coefficient"] +... + +Example: Benchmark one solution model against another + +>>> 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 + +# Create the solutions +>>> cations = ["H[+1]", "Na[+1]", "Ca[+2]"] +>>> anions = ["OH[-1]", "Cl[-1]", "SO4[-2]"] +>>> concs = ["0.1 mol/L", "25%"] +>>> ideal_solutions = [] +>>> native_solutions = [] + +>>> for ions for product(cations, anions): +... for conc in concs: +... solutes = {ion: conc for ion in ions} +... 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 = {} + +>>> 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] = native_entry + +>>> stats = calculate_stats(ideal_data, native_data) +""" + +import json +import logging +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 + +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 +from pyEQL.solution import Solution +from pyEQL.utils import standardize_formula + +logger = logging.getLogger(__name__) + +INTERNAL_SOURCES: list[str] = ["CRC", "IDST", "JPCRD", "May2011JCED"] + + +class BenchmarkEntry(NamedTuple): + """A set of data for a solution. + + Attributes: + 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``. + """ + + solution: Solution + solute_data: dict[str, dict[str, Quantity]] = {} + solution_data: dict[str, Quantity] = {} + + +class BenchmarkResults(NamedTuple): + """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] + + +# TODO: Admittedly, this is an ugly solution to enable Solutions to serve as dictionary keys to speed up the +# 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], ...], + # State: temperature, pressure + # ? should other state variables be checked (e.g., pH, pE)? + tuple[str, str], +] + + +def _create_solution_key(solution: Solution) -> SolutionKey: + vol = solution.volume.magnitude + 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 tuple(composition), state + + +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, +) -> dict[SolutionKey, BenchmarkEntry]: + """Load reference dataset. + + Args: + 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 ``source`` will be loaded. + solute_properties: list[tuple[str, str]], optional + 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 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 + its structure. + """ + match str(source).lower(): + case "crc" | "idst" | "jpcrd": + 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: dict[SolutionKey, BenchmarkEntry] = {} + solution_keys = [] if solutions is None else [_create_solution_key(s) for s in solutions] + + for raw_solution, raw_solute_data, raw_solution_data in data: + # TODO: handle weight % concentration data + solution = Solution(**raw_solution) + soln_key = _create_solution_key(solution) + + if solutions is not None and soln_key not in solution_keys: + continue + + solute_data: dict[str, dict[str, Quantity]] = {} + solution_data = {} + + for solute, values in raw_solute_data.items(): + standardized_solute = standardize_formula(solute) + solute_data[standardized_solute] = {} + for p, q in values.items(): + 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: + solution_data[p] = ureg.Quantity(q) + + reference[soln_key] = BenchmarkEntry( + solution=solution, + solute_data=solute_data, + solution_data=solution_data, + ) + + 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]], + solution_properties: list[str], +) -> BenchmarkEntry: + """Create a BenchmarkEntry from a Solution and specified properties. + + Args: + 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[str] + The solution properties to add to the entry. + """ + solute_data = {} + + for solute, solute_property in solute_properties: + 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 = {} + + for solution_property in solution_properties: + data = _get_solution_property(solution, solution_property) + solution_data[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"], + datasets: list[dict[SolutionKey, BenchmarkEntry]], +) -> dict[SolutionKey, BenchmarkEntry]: + """Create an engine-based dataset containing the properties contained within other datasets.""" + 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][0].extend((solute, prop) for prop in list(entry.solute_data[solute])) + mapper[key][1].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 calculate_stats( + reference: dict[SolutionKey, BenchmarkEntry], + calculated: dict[SolutionKey, BenchmarkEntry], + *, + metric: Callable[[list[tuple[Quantity, Quantity]]], float] | None = None, +) -> BenchmarkResults: + """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] + 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[Quantity, Quantity]]], float], optional + A function that acts on the list of 2-tuples (reference, calculated), which contains reference and + 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. 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([((ref - calc) ** 2).m for ref, calc in data])) + + metric = metric or _rmse + + # property: [(reference, calculated)] + 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] = [] + + 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] = [] + + 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()} + + return BenchmarkResults(solute_stats=solute_stats, solution_stats=solution_stats) + + +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: 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 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. + 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. + """ + sources = sources or INTERNAL_SOURCES + datasets = [ + load_dataset( + s, solutions=solutions, solute_properties=solute_properties, solution_properties=solution_properties + ) + for s in sources + ] + engine_dataset = _create_engine_dataset(engine, datasets) + return {sources[i]: calculate_stats(ref, engine_dataset) for i, ref in enumerate(datasets)} 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": { + "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" + }, + 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{ + "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" + } + ] +] diff --git a/tests/test_benchmark.py b/tests/test_benchmark.py new file mode 100644 index 00000000..7af22515 --- /dev/null +++ b/tests/test_benchmark.py @@ -0,0 +1,175 @@ +from itertools import product +from pathlib import Path + +import pytest + +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 + +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() + + +@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) + + +class TestLoadDataset: + @staticmethod + def test_should_load_dataset_from_file(source: str) -> None: + 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 = 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 + + @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: + return request.param + + +@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"]) +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", + # "viscosity_dynamic", + # "osmolality", + # "osmolarity", + # "chemical_potential_energy", + # "activity_coefficient_pitzer", + ], +) +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]: + 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(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()) + + +class TestBenchmarkEngine: + @staticmethod + @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 + + +class TestCreateEngineDataset: + pass + + +class TestCreateEntry: + pass diff --git a/tests/test_benchmark/conductivity.json b/tests/test_benchmark/conductivity.json new file mode 100644 index 00000000..5ab3f977 --- /dev/null +++ b/tests/test_benchmark/conductivity.json @@ -0,0 +1,3928 @@ +[ + [ + { + "solutes": { + "H[+1]": "1.5 %", + "N[-3]": "0.5 %" + }, + "temperature": "293.15 K" + }, + {}, + { + "conductivity": "0.00025 S/m" + } + ], + [ + { + "solutes": { + "H[+1]": "3.0 %", + "N[-3]": "1.0 %" + }, + "temperature": "293.15 K" + }, + {}, + { + "conductivity": "0.0007 S/m" + } + ], + [ + { + "solutes": { + "H[+1]": "6.0 %", + "N[-3]": "2.0 %" + }, + 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