Add BH9 benchmark

ml_peg/analysis/molecular_reactions/bh9/analyse_bh9.py

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+"""
+Analyse the BH9 reaction barriers dataset.
+
+Journal of Chemical Theory and Computation 2022 18 (1), 151-166
+DOI: 10.1021/acs.jctc.1c00694
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from ase import units
+from ase.io import read, write
+import pytest
+
+from ml_peg.analysis.utils.decorators import build_table, plot_parity
+from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.app import APP_ROOT
+from ml_peg.calcs import CALCS_ROOT
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+D3_MODEL_NAMES = build_d3_name_map(MODELS)
+
+KCAL_TO_EV = units.kcal / units.mol
+EV_TO_KCAL = 1 / KCAL_TO_EV
+CALC_PATH = CALCS_ROOT / "molecular_reactions" / "bh9" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "molecular_reactions" / "bh9"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+
+def get_system_names() -> list[str]:
+    """
+    Get list of reaction system names from the first available model.
+
+    Returns
+    -------
+    list[str]
+        List of system names (reaction identifiers).
+    """
+    for model_name in sorted(CALC_PATH.glob("*")):
+        if model_name.is_dir():
+            xyz_paths = sorted((CALC_PATH / model_name).glob("*TS.xyz"))
+            if xyz_paths:
+                return [path.stem.replace("TS", "") for path in xyz_paths]
+    return []
+
+
+def get_reaction_numbers() -> list[int]:
+    """
+    Get reaction numbers extracted from system names.
+
+    Returns
+    -------
+    list[int]
+        List of reaction numbers (e.g., [1, 2, 3, ...]).
+    """
+    system_names = get_system_names()
+    reaction_nums = []
+    for name in system_names:
+        # Extract reaction number from format like "01_1" -> 1
+        parts = name.split("_")
+        if len(parts) == 2:
+            reaction_nums.append(int(parts[0]))
+    return reaction_nums
+
+
+def get_structure_numbers() -> list[int]:
+    """
+    Get structure numbers (different geometries for same reaction).
+
+    Returns
+    -------
+    list[int]
+        List of structure numbers for each reaction.
+    """
+    system_names = get_system_names()
+    struct_nums = []
+    for name in system_names:
+        # Extract structure number from format like "01_1" -> 1
+        parts = name.split("_")
+        if len(parts) == 2:
+            struct_nums.append(int(parts[1]))
+    return struct_nums
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_bh9_barriers.json",
+    title="Reaction barriers",
+    x_label="Predicted barrier / eV",
+    y_label="Reference barrier / eV",
+    hoverdata={
+        "Reaction": get_reaction_numbers(),
+        "Structure": get_structure_numbers(),
+        "System ID": get_system_names(),
+    },
+)
+def barrier_heights() -> dict[str, list]:
+    """
+    Get barrier heights for all systems.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted barrier heights.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+    ref_stored = False
+
+    system_names = get_system_names()
+    for model_name in MODELS:
+        model_barriers = []
+        ref_barriers = []
+        model_dir = CALC_PATH / model_name
+        if not model_dir.exists():
+            results[model_name] = []
+            continue
+        for system_name in system_names:
+            model_forward_barrier = 0
+            ref_forward_barrier = 0
+
+            # Write structures for app
+            structs_dir = OUT_PATH / model_name
+            structs_dir.mkdir(parents=True, exist_ok=True)
+
+            for fname in model_dir.glob(f"{system_name}*"):
+                if "TS" in fname.stem:
+                    atoms = read(fname)
+                    model_forward_barrier += atoms.info["model_energy"]
+                    ref_forward_barrier = atoms.info["ref_forward_barrier"]
+                    write(structs_dir / f"{fname.stem}.xyz", atoms)
+
+                if "R" in fname.stem:
+                    atoms = read(fname)
+                    model_forward_barrier -= atoms.info["model_energy"]
+                    write(structs_dir / f"{fname.stem}.xyz", atoms)
+            model_barriers.append(model_forward_barrier)
+            ref_barriers.append(ref_forward_barrier)
+
+        results[model_name] = model_barriers
+        if not ref_stored:
+            results["ref"] = ref_barriers
+            ref_stored = True
+    return results
+
+
+@pytest.fixture
+def get_mae(barrier_heights) -> dict[str, float]:
+    """
+    Get mean absolute error for barrier heights.
+
+    Parameters
+    ----------
+    barrier_heights
+        Dictionary of reference and predicted barrier heights.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted barrier height errors for all models.
+    """
+    results = {}
+    for model_name in MODELS:
+        results[model_name] = mae(barrier_heights["ref"], barrier_heights[model_name])
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "bh9_barriers_metrics_table.json",
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    mlip_name_map=D3_MODEL_NAMES,
+)
+def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
+    """
+    Get all metrics.
+
+    Parameters
+    ----------
+    get_mae
+        Mean absolute errors for all models.
+
+    Returns
+    -------
+    dict[str, dict]
+        Metric names and values for all models.
+    """
+    return {
+        "MAE": get_mae,
+    }
+
+
+def test_bh9_barriers(metrics: dict[str, dict]) -> None:
+    """
+    Run bh9_barriers test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return

ml_peg/analysis/molecular_reactions/bh9/metrics.yml

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+metrics:
+  MAE:
+    good: 0.0
+    bad: 2.0
+    unit: eV
+    tooltip: Mean Absolute Error for all systems
+    level_of_theory: CCSD(T)

ml_peg/app/molecular_reactions/bh9/app_bh9.py

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+"""Run BH9 barriers app."""
+
+from __future__ import annotations
+
+from dash import Dash
+from dash.html import Div
+
+from ml_peg.app import APP_ROOT
+from ml_peg.app.base_app import BaseApp
+from ml_peg.app.utils.build_callbacks import (
+    plot_from_table_column,
+    struct_from_scatter,
+)
+from ml_peg.app.utils.load import read_plot
+from ml_peg.models.get_models import get_model_names
+from ml_peg.models.models import current_models
+
+MODELS = get_model_names(current_models)
+BENCHMARK_NAME = "BH9"
+DOCS_URL = (
+    "https://ddmms.github.io/ml-peg/user_guide/benchmarks/"
+    "molecular.html#bh9-reaction-barriers"
+)
+DATA_PATH = APP_ROOT / "data" / "molecular_reactions" / "bh9"
+
+
+class BH9App(BaseApp):
+    """BH9 benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_bh9_barriers.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        model_dir = DATA_PATH / MODELS[0]
+        if model_dir.exists():
+            ts_files = sorted(model_dir.glob("*TS.xyz"))
+            structs = [
+                f"assets/molecular_reactions/bh9/{MODELS[0]}/{ts_file.name}"
+                for ts_file in ts_files
+            ]
+        else:
+            structs = []
+
+        plot_from_table_column(
+            table_id=self.table_id,
+            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
+            column_to_plot={"MAE": scatter},
+        )
+
+        struct_from_scatter(
+            scatter_id=f"{BENCHMARK_NAME}-figure",
+            struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+            structs=structs,
+            mode="struct",
+        )
+
+
+def get_app() -> BH9App:
+    """
+    Get BH9 benchmark app layout and callback registration.
+
+    Returns
+    -------
+    BH9App
+        Benchmark layout and callback registration.
+    """
+    return BH9App(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting hydrolysis reaction barriers for the "
+            "BH9 dataset of nine aqueous reactions spanning multiple functional "
+            "groups. Reference data from CCSD(T) calculations."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "bh9_barriers_metrics_table.json",
+        extra_components=[
+            Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
+        ],
+    )
+
+
+if __name__ == "__main__":
+    full_app = Dash(__name__, assets_folder=DATA_PATH.parent.parent)
+    benchmark_app = get_app()
+    full_app.layout = benchmark_app.layout
+    benchmark_app.register_callbacks()
+    full_app.run(port=8071, debug=True)

ml_peg/calcs/molecular_reactions/bh9/.dvc/.gitignore

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+/config.local
+/tmp
+/cache

ml_peg/calcs/molecular_reactions/bh9/.dvcignore

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+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore