From 559d50f9d505d5042df976f4d0f010f4e925850a Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Sun, 22 Feb 2026 01:44:12 +0000
Subject: [PATCH 01/27] Water densities analysis

---
 .../WaterDensity/analyse_WaterDensity.py      | 197 ++++++++++++++++++
 .../WaterDensity/metrics.yml                  |   8 +
 2 files changed, 205 insertions(+)
 create mode 100644 ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
 create mode 100644 ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml

diff --git a/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py b/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
new file mode 100644
index 000000000..511598e90
--- /dev/null
+++ b/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
@@ -0,0 +1,197 @@
+"""Analyse water densities."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from ase import units
+import numpy as np
+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.calcs.utils.utils import download_s3_data
+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)
+
+CALC_PATH = CALCS_ROOT / "molecular_dynamics" / "WaterDensity" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "molecular_dynamics" / "WaterDensity"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+EV_TO_KCAL = units.mol / units.kcal
+INFO = [270, 290, 300, 330]
+
+experimental_data = {
+    "temperature": np.array(
+        [
+            270,
+            273.15,
+            277,
+            280,
+            283,
+            286,
+            290,
+            293,
+            296,
+            300,
+            303,
+            306,
+            310,
+            313,
+            316,
+            320,
+            323,
+            326,
+            330,
+            333,
+            336,
+            340,
+        ]
+    ),
+    "density": np.array(
+        [
+            0.9998,
+            0.9999,
+            1.0000,
+            0.9999,
+            0.9998,
+            0.9997,
+            0.9991,
+            0.9985,
+            0.9978,
+            0.9970,
+            0.9957,
+            0.9944,
+            0.9927,
+            0.9910,
+            0.9893,
+            0.9871,
+            0.9849,
+            0.9827,
+            0.9802,
+            0.9777,
+            0.9752,
+            0.9723,
+        ]
+    ),  # g/cm³
+}
+
+DATA_PATH = (
+    download_s3_data(
+        filename="WaterDensities.zip",
+        key="inputs/molecular_dynamics/WaterDensities/WaterDensities.zip",
+    )
+    / "WaterDensities"
+)
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_WaterDensity.json",
+    title="Water density",
+    x_label="Predicted density / g/cm^3",
+    y_label="Reference density / g/cm^3",
+    hoverdata={"Labels": INFO},
+)
+def densities() -> dict[str, list]:
+    """
+    Get water density for all the teperatures.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted densities.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+
+    results["ref"] = [
+        density
+        for density, temp in zip(
+            experimental_data["density"], experimental_data["temperature"], strict=False
+        )
+        if temp in INFO
+    ]
+
+    for model_name in MODELS:
+        for temperature in INFO:
+            instantaneous_densities = []
+            with open(
+                DATA_PATH / model_name / f"water_T_{temperature:.1f}" / "water.log"
+            ) as lines:
+                skip_time_ps = 500
+                for line in lines:
+                    items = line.strip().split()
+                    time = float(items[1])
+                    if time < skip_time_ps:
+                        continue
+                    instantaneous_densities.append(float(items[13]))
+
+            results[model_name].append(np.mean(instantaneous_densities))
+    return results
+
+
+@pytest.fixture
+def get_mae(densities) -> dict[str, float]:
+    """
+    Get mean absolute error for densities for all temperatures.
+
+    Parameters
+    ----------
+    densities
+        Dictionary of reference and predicted densities.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted densities errors for all models.
+    """
+    results = {}
+    for model_name in MODELS:
+        results[model_name] = mae(densities["ref"], densities[model_name])
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "WaterDensity_metrics_table.json",
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    weights=DEFAULT_WEIGHTS,
+    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_water_density(metrics: dict[str, dict]) -> None:
+    """
+    Run water density test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return
diff --git a/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml b/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
new file mode 100644
index 000000000..0f5f5961e
--- /dev/null
+++ b/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
@@ -0,0 +1,8 @@
+metrics:
+   MAE:
+    good: 0.0
+    bad: 0.4
+    unit: g/cm^3
+    tooltip: Mean Absolute Error in density for all systems
+    level_of_theory: Experimental density
+    weight: 1

From 7fdbfab2f14f0003d8f715e1e655396342b23cd6 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Sun, 22 Feb 2026 01:44:39 +0000
Subject: [PATCH 02/27] change thresholds

---
 ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml b/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
index 0f5f5961e..0754e9a91 100644
--- a/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
+++ b/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
@@ -1,7 +1,7 @@
 metrics:
    MAE:
     good: 0.0
-    bad: 0.4
+    bad: 0.2
     unit: g/cm^3
     tooltip: Mean Absolute Error in density for all systems
     level_of_theory: Experimental density

From 18dc038f0c1c6ef2861ca39806c88599826c4b6d Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Sun, 22 Feb 2026 01:57:27 +0000
Subject: [PATCH 03/27] Water density app

---
 .../WaterDensity/app_WaterDensity.py          | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py

diff --git a/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py b/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py
new file mode 100644
index 000000000..74fee5f61
--- /dev/null
+++ b/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py
@@ -0,0 +1,69 @@
+"""Run water density 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,
+)
+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 = "WaterDensity"
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/molecular_dynamics.html#Water_Density"
+DATA_PATH = APP_ROOT / "data" / "molecular_dynamics" / "WaterDensity"
+
+
+class WaterDensityApp(BaseApp):
+    """Water density benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_water_density.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        plot_from_table_column(
+            table_id=self.table_id,
+            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
+            column_to_plot={"MAE": scatter},
+        )
+
+
+def get_app() -> WaterDensityApp:
+    """
+    Get water density benchmark app layout and callback registration.
+
+    Returns
+    -------
+    WaterDensityApp
+        Benchmark layout and callback registration.
+    """
+    return WaterDensityApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting water density at different temperatures."
+            "Reference data is experimental densities."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "water_density_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=8063, debug=True)

From 48f74eca02cc1d04d38ab53291df03fd24d57cd1 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Sun, 22 Feb 2026 02:02:16 +0000
Subject: [PATCH 04/27] Water density docs

---
 .../benchmarks/molecular_dynamics.rst         | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 docs/source/user_guide/benchmarks/molecular_dynamics.rst

diff --git a/docs/source/user_guide/benchmarks/molecular_dynamics.rst b/docs/source/user_guide/benchmarks/molecular_dynamics.rst
new file mode 100644
index 000000000..dcae3cfb1
--- /dev/null
+++ b/docs/source/user_guide/benchmarks/molecular_dynamics.rst
@@ -0,0 +1,38 @@
+
+==================
+Molecular dynamics
+==================
+
+Water density
+================
+
+Summary
+-------
+
+Performance in predicting the density of water at temperatures of 270, 290, 300, and 330 K.
+The water systems consist of 333 molecules.
+
+Metrics
+-------
+
+1. Density error
+
+For each system, the density is calculated by taking the average density of an NPT molecular
+dynamics run. The initial part of the simulation, here 500 ps, is omitted from the density
+calculation. This is compared to the reference density, obtained from experiment.
+
+Computational cost
+------------------
+
+Low: tests are likely to take several days to run on GPU.
+
+Data availability
+-----------------
+
+Input structures:
+
+*
+
+Reference data:
+
+* Experiment

From 2983367f54cc41e32da697edf62da85b6e0a644a Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <116088428+kuryla@users.noreply.github.com>
Date: Mon, 2 Mar 2026 12:32:34 +0000
Subject: [PATCH 05/27] 3dTMV benchmark (#380)

Co-authored-by: Domantas Kuryla <dk584@icepc16>
Co-authored-by: joehart2001 <jh2536@cam.ac.uk>
Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
---
 docs/source/user_guide/benchmarks/index.rst   |   1 +
 .../user_guide/benchmarks/tm_complexes.rst    |  42 +++
 .../tm_complexes/3dTMV/analyse_3dTMV.py       | 282 ++++++++++++++++++
 .../analysis/tm_complexes/3dTMV/metrics.yml   |  25 ++
 ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py    |  97 ++++++
 ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py | 157 ++++++++++
 6 files changed, 604 insertions(+)
 create mode 100644 docs/source/user_guide/benchmarks/tm_complexes.rst
 create mode 100644 ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
 create mode 100644 ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
 create mode 100644 ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
 create mode 100644 ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py

diff --git a/docs/source/user_guide/benchmarks/index.rst b/docs/source/user_guide/benchmarks/index.rst
index 83afd6ec5..63333e784 100644
--- a/docs/source/user_guide/benchmarks/index.rst
+++ b/docs/source/user_guide/benchmarks/index.rst
@@ -14,3 +14,4 @@ Benchmarks
     bulk_crystal
     lanthanides
     non_covalent_interactions
+    tm_complexes
diff --git a/docs/source/user_guide/benchmarks/tm_complexes.rst b/docs/source/user_guide/benchmarks/tm_complexes.rst
new file mode 100644
index 000000000..80f8a1a29
--- /dev/null
+++ b/docs/source/user_guide/benchmarks/tm_complexes.rst
@@ -0,0 +1,42 @@
+==========================
+Transition Metal Complexes
+==========================
+
+3dTMV
+=======
+
+Summary
+-------
+
+Performance in predicting vertical ionization energies for 28 transition metal
+complexes.
+
+Metrics
+-------
+
+1. Ionization energy error
+
+For each complex, the ionization energy is calculated by taking the difference in energy
+between the complex in its oxidized state and initial state, which differ by one electron
+and spin multiplicity. This is compared to the reference ionization energy, calculated in the same way.
+
+Computational cost
+------------------
+
+Low: tests are likely to take minutes to run on CPU.
+
+Data availability
+-----------------
+
+Input structures:
+
+* Toward Benchmark-Quality Ab Initio Predictions for 3d Transition Metal
+  Electrocatalysts: A Comparison of CCSD(T) and ph-AFQMC Hagen Neugebauer, Hung T.
+  Vuong, John L. Weber, Richard A. Friesner, James Shee, and Andreas Hansen Journal of
+  Chemical Theory and Computation 2023 19 (18), 6208-6225,
+  DOI: 10.1021/acs.jctc.3c00617
+
+Reference data:
+
+* Same as input data
+* ph-AFQMC level of theory: Auxiliary-Field Quantum Monte Carlo.
diff --git a/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
new file mode 100644
index 000000000..ddd6e2db8
--- /dev/null
+++ b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
@@ -0,0 +1,282 @@
+"""Analyse the 3dTMV benchmark."""
+
+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)
+
+EV_TO_KCAL = units.mol / units.kcal
+CALC_PATH = CALCS_ROOT / "tm_complexes" / "3dTMV" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "tm_complexes" / "3dTMV"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+SUBSETS = {
+    1: "SR",
+    2: "SR",
+    3: "SR",
+    4: "SR",
+    5: "SR",
+    6: "SR",
+    7: "SR",
+    8: "SR",
+    9: "SR",
+    10: "SR",
+    11: "SR",
+    12: "SR",
+    13: "SR/MR",
+    14: "SR/MR",
+    15: "SR/MR",
+    16: "SR/MR",
+    17: "SR/MR",
+    18: "SR/MR",
+    19: "SR/MR",
+    20: "SR/MR",
+    21: "SR/MR",
+    22: "SR/MR",
+    23: "MR",
+    24: "MR",
+    25: "MR",
+    26: "MR",
+    27: "MR",
+    28: "MR",
+}
+
+
+def labels():
+    """
+    Get complex ids.
+
+    Returns
+    -------
+    list
+        IDs of the complexes.
+    """
+    return list(range(1, 29))
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_3dtmv.json",
+    title="Ionization energies",
+    x_label="Predicted ionization energy / kcal/mol",
+    y_label="Reference ionization energy / kcal/mol",
+    hoverdata={
+        "Labels": labels(),
+    },
+)
+def ionization_energies() -> dict[str, list]:
+    """
+    Get ionization energies for all systems.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted energies.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+    ref_stored = False
+
+    for model_name in MODELS:
+        for complex_id in labels():
+            atoms = read(CALC_PATH / model_name / f"{complex_id}.xyz")
+            model_ion_energy = atoms.info["model_ionization_energy"]
+            ref_ion_energy = atoms.info["ref_ionization_energy"]
+            # Write structures for app
+            structs_dir = OUT_PATH / model_name
+            structs_dir.mkdir(parents=True, exist_ok=True)
+            write(structs_dir / f"{complex_id}.xyz", atoms)
+            results[model_name].append(model_ion_energy * EV_TO_KCAL)
+            if not ref_stored:
+                results["ref"].append(ref_ion_energy * EV_TO_KCAL)
+        ref_stored = True
+    return results
+
+
+@pytest.fixture
+def sr_mae(ionization_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for SR subset.
+
+    Parameters
+    ----------
+    ionization_energies
+        Dictionary of reference and predicted energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted energy errors for all models.
+    """
+    results = {}
+
+    for model_name in MODELS:
+        subsampled_ref_e = [
+            ionization_energies["ref"][i - 1] for i in labels() if SUBSETS[i] == "SR"
+        ]
+        subsampled_model_e = [
+            ionization_energies[model_name][i - 1]
+            for i in labels()
+            if SUBSETS[i] == "SR"
+        ]
+        results[model_name] = mae(subsampled_ref_e, subsampled_model_e)
+    return results
+
+
+@pytest.fixture
+def mr_mae(ionization_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for MR subset.
+
+    Parameters
+    ----------
+    ionization_energies
+        Dictionary of reference and predicted energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted energy errors for all models.
+    """
+    results = {}
+
+    for model_name in MODELS:
+        subsampled_ref_e = [
+            ionization_energies["ref"][i - 1] for i in labels() if SUBSETS[i] == "MR"
+        ]
+        subsampled_model_e = [
+            ionization_energies[model_name][i - 1]
+            for i in labels()
+            if SUBSETS[i] == "MR"
+        ]
+        results[model_name] = mae(subsampled_ref_e, subsampled_model_e)
+    return results
+
+
+@pytest.fixture
+def sr_mr_mae(ionization_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for SR/MR subset.
+
+    Parameters
+    ----------
+    ionization_energies
+        Dictionary of reference and predicted energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted energy errors for all models.
+    """
+    results = {}
+
+    for model_name in MODELS:
+        subsampled_ref_e = [
+            ionization_energies["ref"][i - 1] for i in labels() if SUBSETS[i] == "SR/MR"
+        ]
+        subsampled_model_e = [
+            ionization_energies[model_name][i - 1]
+            for i in labels()
+            if SUBSETS[i] == "SR/MR"
+        ]
+        results[model_name] = mae(subsampled_ref_e, subsampled_model_e)
+    return results
+
+
+@pytest.fixture
+def total_mae(ionization_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for all conmplexes.
+
+    Parameters
+    ----------
+    ionization_energies
+        Dictionary of reference and predicted energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted energy errors for all models.
+    """
+    results = {}
+
+    for model_name in MODELS:
+        results[model_name] = mae(
+            ionization_energies["ref"], ionization_energies[model_name]
+        )
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "3dtmv_metrics_table.json",
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    mlip_name_map=D3_MODEL_NAMES,
+)
+def metrics(
+    total_mae: dict[str, float],
+    sr_mae: dict[str, float],
+    mr_mae: dict[str, float],
+    sr_mr_mae: dict[str, float],
+) -> dict[str, dict]:
+    """
+    Get all metrics.
+
+    Parameters
+    ----------
+    total_mae
+        Mean absolute errors for all models, all complexes.
+    sr_mae
+        Mean absolute errors for all models, single-reference complexes.
+    mr_mae
+        Mean absolute errors for all models, multi-reference complexes.
+    sr_mr_mae
+        Mean absolute errors for all models, intermediate complexes.
+
+    Returns
+    -------
+    dict[str, dict]
+        Metric names and values for all models.
+    """
+    return {
+        "Overall MAE": total_mae,
+        "SR MAE": sr_mae,
+        "MR MAE": mr_mae,
+        "SR/MR MAE": sr_mr_mae,
+    }
+
+
+def test_3dtmv(metrics: dict[str, dict]) -> None:
+    """
+    Run 3dTMV test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return
diff --git a/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml b/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
new file mode 100644
index 000000000..c0fed546d
--- /dev/null
+++ b/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
@@ -0,0 +1,25 @@
+metrics:
+  Overall MAE:
+    good: 0.0
+    bad: 50
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for all systems
+    level_of_theory: ph-AFQMC
+  SR MAE:
+    good: 0.0
+    bad: 50
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for the single reference (SR) subset
+    level_of_theory: ph-AFQMC
+  MR MAE:
+    good: 0.0
+    bad: 50
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for the multireference (MR) subset
+    level_of_theory: ph-AFQMC
+  SR/MR MAE:
+    good: 0.0
+    bad: 50
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for the SR/MR (intermediate category) subset
+    level_of_theory: ph-AFQMC
diff --git a/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py b/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
new file mode 100644
index 000000000..af3290b4b
--- /dev/null
+++ b/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
@@ -0,0 +1,97 @@
+"""Run 3dTMV 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 = "3dTMV"
+DOCS_URL = (
+    "https://ddmms.github.io/ml-peg/user_guide/benchmarks/"
+    "molecular.html#3dTMV-tm-complexes"
+)
+DATA_PATH = APP_ROOT / "data" / "tm_complexes" / "3dTMV"
+
+
+class Benchmark3dTMVApp(BaseApp):
+    """3dTMV benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_3dtmv.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        model_dir = DATA_PATH / MODELS[0]
+        if model_dir.exists():
+            # Note: sorting different to rxn_count order in calc
+            ts_files = sorted(model_dir.glob("*.xyz"), key=lambda path: int(path.stem))
+            structs = [
+                f"assets/tm_complexes/3dTMV/{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={
+                "Overall MAE": scatter,
+                "SR MAE": scatter,
+                "MR MAE": scatter,
+                "SR/MR 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() -> Benchmark3dTMVApp:
+    """
+    Get 3dTMV benchmark app layout and callback registration.
+
+    Returns
+    -------
+    Benchmark3dTMVApp
+        Benchmark layout and callback registration.
+    """
+    return Benchmark3dTMVApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting vertical ionization energies for the "
+            "3dTMV dataset of 28 transition metal complexes."
+            "Reference data from ph-AFQMC calculations."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "3dtmv_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)
diff --git a/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
new file mode 100644
index 000000000..9c7e49413
--- /dev/null
+++ b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
@@ -0,0 +1,157 @@
+"""
+Compute the 3dTMV dataset for transition metal complex vertical ionization energies.
+
+Journal of Chemical Theory and Computation 2023 19 (18), 6208-6225
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from ase import units
+from ase.io import read, write
+import pytest
+from tqdm import tqdm
+
+from ml_peg.calcs.utils.utils import download_s3_data
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+KCAL_TO_EV = units.kcal / units.mol
+
+OUT_PATH = Path(__file__).parent / "outputs"
+
+# Molecular data from Main Paper Table 1
+MOLECULAR_DATA = {
+    1: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    2: {"charge_ox": 1, "charge_in": 0, "mult_ox": 1, "mult_in": 2, "subset": "SR"},
+    3: {"charge_ox": 1, "charge_in": 0, "mult_ox": 4, "mult_in": 3, "subset": "SR"},
+    4: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    5: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    6: {"charge_ox": 2, "charge_in": 1, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    7: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    8: {"charge_ox": 2, "charge_in": 1, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    9: {"charge_ox": 2, "charge_in": 1, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    10: {"charge_ox": 2, "charge_in": 1, "mult_ox": 2, "mult_in": 1, "subset": "SR"},
+    11: {"charge_ox": 2, "charge_in": 1, "mult_ox": 1, "mult_in": 2, "subset": "SR"},
+    12: {"charge_ox": 2, "charge_in": 1, "mult_ox": 1, "mult_in": 2, "subset": "SR"},
+    13: {"charge_ox": 1, "charge_in": 0, "mult_ox": 1, "mult_in": 2, "subset": "SR/MR"},
+    14: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 3, "subset": "SR/MR"},
+    15: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    16: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    17: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    18: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    19: {"charge_ox": 2, "charge_in": 1, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    20: {"charge_ox": 1, "charge_in": 0, "mult_ox": 3, "mult_in": 2, "subset": "SR/MR"},
+    21: {"charge_ox": 1, "charge_in": 0, "mult_ox": 3, "mult_in": 2, "subset": "SR/MR"},
+    22: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "SR/MR"},
+    23: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "MR"},
+    24: {"charge_ox": 1, "charge_in": 0, "mult_ox": 3, "mult_in": 4, "subset": "MR"},
+    25: {"charge_ox": 1, "charge_in": 0, "mult_ox": 3, "mult_in": 6, "subset": "MR"},
+    26: {"charge_ox": 1, "charge_in": 0, "mult_ox": 2, "mult_in": 1, "subset": "MR"},
+    27: {"charge_ox": 0, "charge_in": -1, "mult_ox": 2, "mult_in": 3, "subset": "MR"},
+    28: {"charge_ox": 0, "charge_in": -1, "mult_ox": 1, "mult_in": 2, "subset": "MR"},
+}
+
+# ph-AFQMC reference IPs from SM Table S9 (kcal/mol)
+REFERENCE_IES = {
+    # SR subset (1-12)
+    1: 188.4,
+    2: 158.3,
+    3: 119.6,
+    4: 152.3,
+    5: 142.2,
+    6: 315.9,
+    7: 191.1,
+    8: 259.6,
+    9: 276.2,
+    10: 284.1,
+    11: 198.5,
+    12: 230.3,
+    # SR/MR subset (13-22)
+    13: 120.9,
+    14: 148.1,
+    15: 140.4,
+    16: 164.1,
+    17: 130.9,
+    18: 136.3,
+    19: 300.7,
+    20: 186.4,
+    21: 125.3,
+    22: 161.2,
+    # MR subset (23-28)
+    23: 198.9,
+    24: 166.0,
+    25: 215.8,
+    26: 192.9,
+    27: 68.6,
+    28: 43.6,
+}
+
+
+def get_atoms(data_path, complex_id: int):
+    """
+    Get the atoms object with charge and spin.
+
+    Parameters
+    ----------
+    data_path
+        Path to the data.
+    complex_id
+        Identifier of the complex, from 1 to 28.
+
+    Returns
+    -------
+    Atoms
+        Atoms object of the system.
+    """
+    return read(data_path / str(complex_id) / "struc.xyz")
+
+
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_3dtmv(mlip: tuple[str, Any]) -> None:
+    """
+    Run 3dTMV benchmark.
+
+    Parameters
+    ----------
+    mlip
+        Name of model use and model to get calculator.
+    """
+    model_name, model = mlip
+
+    data_path = (
+        download_s3_data(
+            filename="3dTMV.zip",
+            key="inputs/tm_complexes/3dTMV/3dTMV.zip",
+        )
+        / "3dTMV"
+    )
+    for complex_id in tqdm(range(1, 29)):
+        atoms = get_atoms(data_path, complex_id)
+        atoms_ox = atoms.copy()
+        atoms_ox.info["charge"] = MOLECULAR_DATA[complex_id]["charge_ox"]
+        atoms_ox.info["spin"] = MOLECULAR_DATA[complex_id]["mult_ox"]
+        atoms_ox.calc = model.add_d3_calculator(model.get_calculator())
+        oxidized_energy = atoms_ox.get_potential_energy()
+
+        atoms_in = atoms.copy()
+        atoms_in.info["charge"] = MOLECULAR_DATA[complex_id]["charge_in"]
+        atoms_in.info["spin"] = MOLECULAR_DATA[complex_id]["mult_in"]
+        atoms_in.calc = model.add_d3_calculator(model.get_calculator())
+        initial_energy = atoms_in.get_potential_energy()
+
+        model_ion_energy = oxidized_energy - initial_energy
+
+        atoms.info.update(
+            {
+                "model_ionization_energy": model_ion_energy,
+                "ref_ionization_energy": REFERENCE_IES[complex_id] * KCAL_TO_EV,
+            }
+        )
+        write_dir = OUT_PATH / model_name
+        write_dir.mkdir(parents=True, exist_ok=True)
+        write(write_dir / f"{complex_id}.xyz", atoms)

From 9273e629227428287a1eebcd878a4c394e10bf16 Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Tue, 3 Mar 2026 22:43:48 +0000
Subject: [PATCH 06/27] Update MACE (#398)

---
 pyproject.toml | 2 +-
 uv.lock        | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b4dd09055..d9ff60e98 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ grace = [
     "tensorpotential == 0.5.1; python_version < '3.13'",
 ]
 mace = [
-    "mace-torch==0.3.14",
+    "mace-torch==0.3.15",
 ]
 
 mattersim = [
diff --git a/uv.lock b/uv.lock
index bff4c60b7..fe9123429 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4724,7 +4724,7 @@ wheels = [
 
 [[package]]
 name = "mace-torch"
-version = "0.3.14"
+version = "0.3.15"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "ase" },
@@ -4749,9 +4749,9 @@ dependencies = [
     { name = "torchmetrics" },
     { name = "tqdm" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/c2/c5/41fcb72b386e4b864501430ca2075f0797a5915adca3c0f3022a20427d1a/mace_torch-0.3.14.tar.gz", hash = "sha256:7e05372b50b5ee3da2973d7da860bde0facbc0934bb672af264af303d3596d05", size = 206925, upload-time = "2025-08-06T17:30:15.272Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/2c/a7/2a60120b15eca67d153e6b5a40cb4b70e4bbe00b9504df2c82a6cf38fda3/mace_torch-0.3.15.tar.gz", hash = "sha256:23f9bd7521db56ce91586c110089bdbd79ffd2475fec8fea2cae4780be495049", size = 230748, upload-time = "2026-02-22T23:35:03.411Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/c6/53/7d7b1de354a43e11cb19b370f81833f078f931aff4555b24e869013eea1a/mace_torch-0.3.14-py3-none-any.whl", hash = "sha256:9a7a00a79b3fa3448a13961e2a4af616ff10466fa193aeb4579dc83be9da1b00", size = 237087, upload-time = "2025-08-06T17:30:11.377Z" },
+    { url = "https://files.pythonhosted.org/packages/01/6d/d5b578dce5c995ce8c9cbeb53871331e575a09bf11ca4739fac770665b6e/mace_torch-0.3.15-py3-none-any.whl", hash = "sha256:9e38df131667f4abdb3c0ab7b77927f217886cbca68c417dcc985465c4b9a53c", size = 264276, upload-time = "2026-02-22T23:35:01.73Z" },
 ]
 
 [[package]]
@@ -6077,7 +6077,7 @@ requires-dist = [
     { name = "fairchem-core", marker = "extra == 'uma'", specifier = "==2.10.0" },
     { name = "janus-core", specifier = ">=0.8.2,<1.0.0" },
     { name = "kaleido", specifier = ">=1.0.0" },
-    { name = "mace-torch", marker = "extra == 'mace'", specifier = "==0.3.14" },
+    { name = "mace-torch", marker = "extra == 'mace'", specifier = "==0.3.15" },
     { name = "matcalc" },
     { name = "matminer" },
     { name = "mattersim", marker = "extra == 'mattersim'", specifier = "==1.2.0" },

From 64a07baaa82de6451230cfe218cc5bf7cd101d5d Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Tue, 3 Mar 2026 22:44:20 +0000
Subject: [PATCH 07/27] Tidy 3dTMV benchmark (#399)

---
 ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py | 1 +
 ml_peg/analysis/tm_complexes/3dTMV/metrics.yml      | 4 ++++
 ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py          | 5 +----
 ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py       | 8 ++++++--
 4 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
index ddd6e2db8..304d488f8 100644
--- a/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
+++ b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
@@ -236,6 +236,7 @@ def total_mae(ionization_energies) -> dict[str, float]:
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     mlip_name_map=D3_MODEL_NAMES,
+    weights=DEFAULT_WEIGHTS,
 )
 def metrics(
     total_mae: dict[str, float],
diff --git a/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml b/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
index c0fed546d..0d7ba50b3 100644
--- a/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
+++ b/ml_peg/analysis/tm_complexes/3dTMV/metrics.yml
@@ -5,21 +5,25 @@ metrics:
     unit: kcal/mol
     tooltip: Mean Absolute Error for all systems
     level_of_theory: ph-AFQMC
+    weight: 1
   SR MAE:
     good: 0.0
     bad: 50
     unit: kcal/mol
     tooltip: Mean Absolute Error for the single reference (SR) subset
     level_of_theory: ph-AFQMC
+    weight: 0
   MR MAE:
     good: 0.0
     bad: 50
     unit: kcal/mol
     tooltip: Mean Absolute Error for the multireference (MR) subset
     level_of_theory: ph-AFQMC
+    weight: 0
   SR/MR MAE:
     good: 0.0
     bad: 50
     unit: kcal/mol
     tooltip: Mean Absolute Error for the SR/MR (intermediate category) subset
     level_of_theory: ph-AFQMC
+    weight: 0
diff --git a/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py b/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
index af3290b4b..2ac3a0fb8 100644
--- a/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
+++ b/ml_peg/app/tm_complexes/3dTMV/app_3dTMV.py
@@ -17,10 +17,7 @@
 
 MODELS = get_model_names(current_models)
 BENCHMARK_NAME = "3dTMV"
-DOCS_URL = (
-    "https://ddmms.github.io/ml-peg/user_guide/benchmarks/"
-    "molecular.html#3dTMV-tm-complexes"
-)
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/tm_complexes.html#dtmv"
 DATA_PATH = APP_ROOT / "data" / "tm_complexes" / "3dTMV"
 
 
diff --git a/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
index 9c7e49413..88c8d34a7 100644
--- a/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
+++ b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
@@ -6,6 +6,7 @@
 
 from __future__ import annotations
 
+from copy import copy
 from pathlib import Path
 from typing import Any
 
@@ -122,6 +123,9 @@ def test_3dtmv(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -135,13 +139,13 @@ def test_3dtmv(mlip: tuple[str, Any]) -> None:
         atoms_ox = atoms.copy()
         atoms_ox.info["charge"] = MOLECULAR_DATA[complex_id]["charge_ox"]
         atoms_ox.info["spin"] = MOLECULAR_DATA[complex_id]["mult_ox"]
-        atoms_ox.calc = model.add_d3_calculator(model.get_calculator())
+        atoms_ox.calc = copy(calc)
         oxidized_energy = atoms_ox.get_potential_energy()
 
         atoms_in = atoms.copy()
         atoms_in.info["charge"] = MOLECULAR_DATA[complex_id]["charge_in"]
         atoms_in.info["spin"] = MOLECULAR_DATA[complex_id]["mult_in"]
-        atoms_in.calc = model.add_d3_calculator(model.get_calculator())
+        atoms_in.calc = copy(calc)
         initial_energy = atoms_in.get_potential_energy()
 
         model_ion_energy = oxidized_energy - initial_energy

From cb849a59f3585108ba3dacdcbe80d10d1e676413 Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Tue, 3 Mar 2026 22:44:35 +0000
Subject: [PATCH 08/27] Fix setting MACE default dtype (#400)

---
 ml_peg/models/get_models.py | 97 +++++++++++++++++++------------------
 1 file changed, 49 insertions(+), 48 deletions(-)

diff --git a/ml_peg/models/get_models.py b/ml_peg/models/get_models.py
index 523fa7aaf..a2c441eac 100644
--- a/ml_peg/models/get_models.py
+++ b/ml_peg/models/get_models.py
@@ -108,54 +108,55 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
     for name, cfg in get_subset(all_models, models).items():
         print(f"Loading model from models.yml: {name}")
 
-        if cfg["class_name"] == "FAIRChemCalculator":
-            kwargs = cfg.get("kwargs", {})
-            loaded_models[name] = FairChemCalc(
-                model_name=kwargs["model_name"],
-                task_name=kwargs.get("task_name", "omat"),
-                device=cfg.get("device", "cpu"),
-                overrides=kwargs.get("overrides", {}),
-                trained_on_d3=cfg.get("trained_on_d3", False),
-                d3_kwargs=cfg.get("d3_kwargs", {}),
-            )
-        elif cfg["class_name"] == "OrbCalc":
-            kwargs = cfg.get("kwargs", {})
-            loaded_models[name] = OrbCalc(
-                name=kwargs["name"],
-                device=cfg.get("device", "cpu"),
-                default_dtype=cfg.get("default_dtype", "float32"),
-                trained_on_d3=cfg.get("trained_on_d3", False),
-                d3_kwargs=cfg.get("d3_kwargs", {}),
-            )
-        elif cfg["class_name"] == "mace_mp":
-            loaded_models[name] = GenericASECalc(
-                module=cfg["module"],
-                class_name=cfg["class_name"],
-                device=cfg.get("device", "auto"),
-                default_dtype=cfg.get("default_dtype", "float32"),
-                kwargs=cfg.get("kwargs", {}),
-                trained_on_d3=cfg.get("trained_on_d3", False),
-                d3_kwargs=cfg.get("d3_kwargs", {}),
-            )
-        elif cfg["class_name"] == "PETMADCalculator":
-            loaded_models[name] = PetMadCalc(
-                module=cfg["module"],
-                class_name=cfg["class_name"],
-                device=cfg.get("device", "cpu"),
-                default_dtype=cfg.get("default_dtype", "float32"),
-                kwargs=cfg.get("kwargs", {}),
-                trained_on_d3=cfg.get("trained_on_d3", False),
-                d3_kwargs=cfg.get("d3_kwargs", {}),
-            )
-        else:
-            loaded_models[name] = GenericASECalc(
-                module=cfg["module"],
-                class_name=cfg["class_name"],
-                device=cfg.get("device", "auto"),
-                kwargs=cfg.get("kwargs", {}),
-                trained_on_d3=cfg.get("trained_on_d3", False),
-                d3_kwargs=cfg.get("d3_kwargs", {}),
-            )
+        match cfg["class_name"]:
+            case "FAIRChemCalculator":
+                kwargs = cfg.get("kwargs", {})
+                loaded_models[name] = FairChemCalc(
+                    model_name=kwargs["model_name"],
+                    task_name=kwargs.get("task_name", "omat"),
+                    device=cfg.get("device", "cpu"),
+                    overrides=kwargs.get("overrides", {}),
+                    trained_on_d3=cfg.get("trained_on_d3", False),
+                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                )
+            case "OrbCalc":
+                kwargs = cfg.get("kwargs", {})
+                loaded_models[name] = OrbCalc(
+                    name=kwargs["name"],
+                    device=cfg.get("device", "cpu"),
+                    default_dtype=cfg.get("default_dtype", "float32"),
+                    trained_on_d3=cfg.get("trained_on_d3", False),
+                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                )
+            case "mace" | "mace_mp" | "mace_off" | "mace_omol" | "mace_polar":
+                loaded_models[name] = GenericASECalc(
+                    module=cfg["module"],
+                    class_name=cfg["class_name"],
+                    device=cfg.get("device", "auto"),
+                    default_dtype=cfg.get("default_dtype", "float32"),
+                    kwargs=cfg.get("kwargs", {}),
+                    trained_on_d3=cfg.get("trained_on_d3", False),
+                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                )
+            case "PETMADCalculator":
+                loaded_models[name] = PetMadCalc(
+                    module=cfg["module"],
+                    class_name=cfg["class_name"],
+                    device=cfg.get("device", "cpu"),
+                    default_dtype=cfg.get("default_dtype", "float32"),
+                    kwargs=cfg.get("kwargs", {}),
+                    trained_on_d3=cfg.get("trained_on_d3", False),
+                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                )
+            case _:
+                loaded_models[name] = GenericASECalc(
+                    module=cfg["module"],
+                    class_name=cfg["class_name"],
+                    device=cfg.get("device", "auto"),
+                    kwargs=cfg.get("kwargs", {}),
+                    trained_on_d3=cfg.get("trained_on_d3", False),
+                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                )
 
     return loaded_models
 

From 58c07d9c841d3d50f3f31038aac32b181255ef6c Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Tue, 3 Mar 2026 22:45:05 +0000
Subject: [PATCH 09/27] Add mace-polar models (#401)

---
 ml_peg/models/models.yml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml
index c230bbee5..ce83dd31f 100644
--- a/ml_peg/models/models.yml
+++ b/ml_peg/models/models.yml
@@ -180,3 +180,33 @@ pet-mad:
     version: "v1.0.2"
   d3_kwargs:
     xc: pbesol
+
+# mace-polar-1-s:
+#   module: mace.calculators
+#   class_name: mace_polar
+#   device: "cpu"
+#   default_dtype: float32
+#   trained_on_d3: true
+#   level_of_theory: ωB97M-V
+#   kwargs:
+#     model: "polar-1-s"
+
+# mace-polar-1-m:
+#   module: mace.calculators
+#   class_name: mace_polar
+#   device: "cpu"
+#   default_dtype: float32
+#   trained_on_d3: true
+#   level_of_theory: ωB97M-V
+#   kwargs:
+#     model: "polar-1-m"
+
+# mace-polar-1-l:
+#   module: mace.calculators
+#   class_name: mace_polar
+#   device: "cpu"
+#   default_dtype: float32
+#   trained_on_d3: true
+#   level_of_theory: ωB97M-V
+#   kwargs:
+#     model: "polar-1-l"

From 1e97659d098f230749f65fe03b4a5606de036838 Mon Sep 17 00:00:00 2001
From: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Wed, 4 Mar 2026 01:25:05 +0000
Subject: [PATCH 10/27] Bump version for release 0.3.1

---
 pyproject.toml | 2 +-
 uv.lock        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d9ff60e98..48e5e6ae8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "ml-peg"
-version = "0.3.0"
+version = "0.3.1"
 description = "ML Performance and Extrapolation Guide"
 authors = [
     { name = "Elliott Kasoar" },
diff --git a/uv.lock b/uv.lock
index fe9123429..b7f7f422a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -5989,7 +5989,7 @@ wheels = [
 
 [[package]]
 name = "ml-peg"
-version = "0.3.0"
+version = "0.3.1"
 source = { editable = "." }
 dependencies = [
     { name = "boto3" },

From ee54957e2da776d5c54b6c5beaf40c64b64f6d57 Mon Sep 17 00:00:00 2001
From: Fabian Zills <46721498+PythonFZ@users.noreply.github.com>
Date: Wed, 4 Mar 2026 17:25:40 +0100
Subject: [PATCH 11/27] Add BMIM Cl bond formation benchmark (#334)

---
 .../user_guide/benchmarks/molecular.rst       |  50 +++
 .../BMIMCl_RDF/analyse_BMIMCl_RDF.py          | 199 +++++++++
 .../analysis/molecular/BMIMCl_RDF/metrics.yml |   7 +
 .../molecular/BMIMCl_RDF/app_BMIMCl_RDF.py    |  66 +++
 .../molecular/BMIMCl_RDF/calc_BMIMCl_RDF.py   |  82 ++++
 pyproject.toml                                |   1 +
 uv.lock                                       | 394 +++++++++++-------
 7 files changed, 645 insertions(+), 154 deletions(-)
 create mode 100644 ml_peg/analysis/molecular/BMIMCl_RDF/analyse_BMIMCl_RDF.py
 create mode 100644 ml_peg/analysis/molecular/BMIMCl_RDF/metrics.yml
 create mode 100644 ml_peg/app/molecular/BMIMCl_RDF/app_BMIMCl_RDF.py
 create mode 100644 ml_peg/calcs/molecular/BMIMCl_RDF/calc_BMIMCl_RDF.py

diff --git a/docs/source/user_guide/benchmarks/molecular.rst b/docs/source/user_guide/benchmarks/molecular.rst
index 21460d29c..7b1857d9e 100644
--- a/docs/source/user_guide/benchmarks/molecular.rst
+++ b/docs/source/user_guide/benchmarks/molecular.rst
@@ -124,3 +124,53 @@ Reference data:
 
 * Same as input data
 * DLPNO-CCSD(T)/CBS
+
+
+BMIM Cl RDF
+===========
+
+Summary
+-------
+
+Tests whether MLIPs incorrectly predict covalent bond formation between chloride
+anions (Cl⁻) and carbon atoms in 1-butyl-3-methylimidazolium (BMIM⁺) cations.
+Such Cl-C bonds should NOT form in the ionic liquid under normal conditions.
+
+This benchmark runs NVT molecular dynamics simulations of BMIM Cl at
+353.15 K and analyses the Cl-C RDF to detect any unphysical bond formation.
+
+
+Metrics
+-------
+
+1. Cl-C Bonds Formed
+
+Binary metric indicating whether unphysical Cl-C bonds formed during the MD simulation.
+
+The Cl-C RDF is computed from the MD trajectory. If the RDF shows a peak (g(r) > 0.1)
+at distances below 2.5 Å, this indicates bond formation and the model fails the test.
+
+* 0 = no bonds formed (correct physical behaviour)
+* 1 = bonds formed (unphysical, model failure)
+
+
+Computational cost
+------------------
+
+Medium: tests require running 10,000 steps of Langevin MD for a system of 10 ion
+pairs, which may take tens of minutes on GPU.
+
+
+Data availability
+-----------------
+
+Input structures:
+
+* Generated using molify from SMILES representations of BMIM⁺ (CCCCN1C=C[N+](=C1)C)
+  and Cl⁻ ions, packed to experimental density of 1052 kg/m³ at 353.15 K.
+* Zills, F. molify: Molecular Structure Interface. Journal of Open Source Software
+  10, 8829 (2025). https://doi.org/10.21105/joss.08829
+* Density from: Yang, F., Wang, D., Wang, X. & Liu, Z. Volumetric Properties of
+  Binary and Ternary Mixtures of Bis(2-hydroxyethyl)ammonium Acetate with Methanol,
+  N,N-Dimethylformamide, and Water at Several Temperatures. J. Chem. Eng. Data 62,
+  3958-3966 (2017). https://doi.org/10.1021/acs.jced.7b00654
diff --git a/ml_peg/analysis/molecular/BMIMCl_RDF/analyse_BMIMCl_RDF.py b/ml_peg/analysis/molecular/BMIMCl_RDF/analyse_BMIMCl_RDF.py
new file mode 100644
index 000000000..1831dcad5
--- /dev/null
+++ b/ml_peg/analysis/molecular/BMIMCl_RDF/analyse_BMIMCl_RDF.py
@@ -0,0 +1,199 @@
+"""Analyse BMIMCl RDF benchmark for unphysical Cl-C bond formation."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from ase.data import atomic_numbers
+from ase.geometry.rdf import get_rdf
+import ase.io as aio
+import numpy as np
+import pytest
+from tqdm import tqdm
+
+from ml_peg.analysis.utils.decorators import build_table, plot_scatter
+from ml_peg.analysis.utils.utils import load_metrics_config
+from ml_peg.app import APP_ROOT
+from ml_peg.calcs import CALCS_ROOT
+from ml_peg.models.get_models import get_model_names
+from ml_peg.models.models import current_models
+
+MODELS = get_model_names(current_models)
+CALC_PATH = CALCS_ROOT / "molecular" / "BMIMCl_RDF" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "molecular" / "BMIMCl_RDF"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+# RDF parameters
+ELEMENT1 = "Cl"
+ELEMENT2 = "C"
+Z1 = atomic_numbers[ELEMENT1]
+Z2 = atomic_numbers[ELEMENT2]
+BINS_PER_ANG = 50
+UNPHYSICAL_CUTOFF = 2.5
+# Angstrom - any Cl-C closer than this indicates
+# a bond which should not be there
+PEAK_THRESHOLD = 0.1  # g(r) threshold for bond detection
+
+
+def compute_rdf_from_trajectory(traj_path: Path) -> tuple[np.ndarray, np.ndarray]:
+    """
+    Compute Cl-C RDF from MD trajectory.
+
+    Parameters
+    ----------
+    traj_path
+        Path to trajectory xyz file.
+
+    Returns
+    -------
+    tuple[np.ndarray, np.ndarray]
+        (r, rdf) arrays - distances and averaged g(r) values.
+    """
+    images = aio.read(traj_path, index=":")
+
+    # Infer rmax from cell (NVT)
+    cell_lengths = images[0].cell.lengths()
+    rmax = min(cell_lengths) / 2 - 0.01
+    nbins = int(rmax * BINS_PER_ANG)
+
+    # Compute RDFs with progress bar
+    rdfs = []
+    r = None
+    for atoms in tqdm(images, desc="Computing RDF"):
+        rdf_frame, distances = get_rdf(
+            atoms, rmax, nbins, elements=(Z1, Z2), no_dists=False
+        )
+        rdfs.append(rdf_frame)
+        if r is None:
+            r = distances
+
+    rdf = np.mean(rdfs, axis=0)
+
+    return r, rdf
+
+
+def check_bond_formation(r: np.ndarray, rdf: np.ndarray) -> int:
+    """
+    Check if Cl-C bonds formed based on RDF.
+
+    Parameters
+    ----------
+    r
+        Distance array.
+    rdf
+        The g(r) values.
+
+    Returns
+    -------
+    int
+        1 if bonds formed (bad), 0 if no bonds (good).
+    """
+    mask = r < UNPHYSICAL_CUTOFF
+    max_gr = rdf[mask].max() if mask.any() else 0.0
+    return 1 if max_gr > PEAK_THRESHOLD else 0
+
+
+@pytest.fixture
+@plot_scatter(
+    title="Cl-C Radial Distribution Function",
+    x_label="r / Å",
+    y_label="g(r)",
+    show_line=True,
+    filename=str(OUT_PATH / "figure_rdf.json"),
+)
+def rdf_data() -> dict[str, list]:
+    """
+    Compute RDF for all models.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary mapping model names to [r, g(r)] arrays.
+    """
+    results = {}
+
+    OUT_PATH.mkdir(parents=True, exist_ok=True)
+
+    for model_name in MODELS:
+        traj_path = CALC_PATH / model_name / "md.xyz"
+        if not traj_path.exists():
+            continue
+
+        r, rdf = compute_rdf_from_trajectory(traj_path)
+        results[model_name] = [r.tolist(), rdf.tolist()]
+
+        rdf_out = OUT_PATH / model_name
+        rdf_out.mkdir(parents=True, exist_ok=True)
+        np.savetxt(
+            rdf_out / "rdf.dat",
+            np.column_stack([r, rdf]),
+            header="r/A g(r)",
+            fmt="%.6f",
+        )
+
+    return results
+
+
+@pytest.fixture
+def bond_formation(rdf_data: dict[str, list]) -> dict[str, int]:
+    """
+    Check bond formation for all models.
+
+    Parameters
+    ----------
+    rdf_data
+        Dictionary of RDF data per model.
+
+    Returns
+    -------
+    dict[str, int]
+        Dictionary mapping model names to bond formation flag (0 or 1).
+    """
+    results = {}
+    for model_name, (r, rdf) in rdf_data.items():
+        r_arr = np.array(r)
+        rdf_arr = np.array(rdf)
+        results[model_name] = check_bond_formation(r_arr, rdf_arr)
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=str(OUT_PATH / "bmimcl_metrics_table.json"),
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    weights=DEFAULT_WEIGHTS,
+)
+def metrics(bond_formation: dict[str, int]) -> dict[str, dict]:
+    """
+    Build metrics table.
+
+    Parameters
+    ----------
+    bond_formation
+        Bond formation flags per model.
+
+    Returns
+    -------
+    dict[str, dict]
+        Metrics dictionary for table building.
+    """
+    return {
+        "Cl-C Bonds Formed": bond_formation,
+    }
+
+
+def test_bmimcl_rdf(metrics: dict[str, dict]) -> None:
+    """
+    Run BMIMCl RDF analysis.
+
+    Parameters
+    ----------
+    metrics
+        Benchmark metrics generated by fixtures.
+    """
+    return
diff --git a/ml_peg/analysis/molecular/BMIMCl_RDF/metrics.yml b/ml_peg/analysis/molecular/BMIMCl_RDF/metrics.yml
new file mode 100644
index 000000000..75df3aab6
--- /dev/null
+++ b/ml_peg/analysis/molecular/BMIMCl_RDF/metrics.yml
@@ -0,0 +1,7 @@
+metrics:
+  Cl-C Bonds Formed:
+    good: 0.0
+    bad: 1.0
+    unit: null
+    tooltip: "Whether Cl-C bonds formed (g(r) > 0.1 for r < 2.5 A). 0 = no bonds (correct), 1 = bonds formed (wrong)."
+    weight: 1.0
diff --git a/ml_peg/app/molecular/BMIMCl_RDF/app_BMIMCl_RDF.py b/ml_peg/app/molecular/BMIMCl_RDF/app_BMIMCl_RDF.py
new file mode 100644
index 000000000..c8dbc5c06
--- /dev/null
+++ b/ml_peg/app/molecular/BMIMCl_RDF/app_BMIMCl_RDF.py
@@ -0,0 +1,66 @@
+"""Run BMIMCl RDF benchmark 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
+from ml_peg.app.utils.load import read_plot
+
+BENCHMARK_NAME = "BMIMCl Cl-C RDF"
+DOCS_URL = (
+    "https://ddmms.github.io/ml-peg/user_guide/benchmarks/molecular.html#bmimcl-rdf"
+)
+DATA_PATH = APP_ROOT / "data" / "molecular" / "BMIMCl_RDF"
+
+
+class BMIMClRDFApp(BaseApp):
+    """BMIMCl RDF benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        rdf_plot = read_plot(
+            DATA_PATH / "figure_rdf.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        plot_from_table_column(
+            table_id=self.table_id,
+            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
+            column_to_plot={"Cl-C Bonds Formed": rdf_plot},
+        )
+
+
+def get_app() -> BMIMClRDFApp:
+    """
+    Get BMIMCl RDF benchmark app layout and callback registration.
+
+    Returns
+    -------
+    BMIMClRDFApp
+        Benchmark layout and callback registration.
+    """
+    return BMIMClRDFApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Tests whether MLIPs incorrectly predict Cl-C bond formation "
+            "in BMIMCl ionic liquid. Bonds should NOT form."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "bmimcl_metrics_table.json",
+        extra_components=[
+            Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+        ],
+    )
+
+
+if __name__ == "__main__":
+    full_app = Dash(__name__, assets_folder=DATA_PATH.parent.parent)
+    bmimcl_app = get_app()
+    full_app.layout = bmimcl_app.layout
+    bmimcl_app.register_callbacks()
+
+    full_app.run(port=8054, debug=True)
diff --git a/ml_peg/calcs/molecular/BMIMCl_RDF/calc_BMIMCl_RDF.py b/ml_peg/calcs/molecular/BMIMCl_RDF/calc_BMIMCl_RDF.py
new file mode 100644
index 000000000..3bffef75c
--- /dev/null
+++ b/ml_peg/calcs/molecular/BMIMCl_RDF/calc_BMIMCl_RDF.py
@@ -0,0 +1,82 @@
+"""
+Run MD simulation of BMIMCl ionic liquid to test for unphysical Cl-C bond formation.
+
+This benchmark tests whether MLIPs incorrectly predict covalent bond formation
+between chloride anions and carbon atoms in BMIM cations. Such bonds should NOT
+form in ionic liquids at normal conditions.
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from ase import units
+from ase.io import write
+from ase.md.langevin import Langevin
+from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
+from ase.optimize import LBFGS
+import molify
+import pytest
+from tqdm import tqdm
+
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+OUT_PATH = Path(__file__).parent / "outputs"
+
+# MD parameters
+# Density from https://pubs.acs.org/doi/full/10.1021/acs.jced.7b00654 at 353.15 K
+TEMPERATURE = 353.15
+STEPS = 10_000
+TIMESTEP = 0.5  # fs
+FRICTION = 0.01
+N_ION_PAIRS = 10
+DENSITY = 1052  # kg/m³ at 353.15 K
+
+
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_bmimcl_md(mlip: tuple[str, Any]) -> None:
+    """
+    Run NVT MD simulation of BMIMCl ionic liquid.
+
+    Parameters
+    ----------
+    mlip
+        Name of model and model to get calculator.
+    """
+    model_name, model = mlip
+    calc = model.get_calculator()
+
+    bmim = molify.smiles2atoms("CCCCN1C=C[N+](=C1)C")
+    cl = molify.smiles2atoms("[Cl-]")
+    ion_pair = molify.pack(data=[[bmim], [cl]], counts=[1, 1], density=900)
+    box = molify.pack(data=[[ion_pair]], counts=[N_ION_PAIRS], density=DENSITY)
+    box.info["charge"] = 0
+    box.info["spin"] = 1
+    box.calc = calc
+
+    opt = LBFGS(box)
+    opt.run(fmax=0.1)
+
+    MaxwellBoltzmannDistribution(box, temperature_K=TEMPERATURE)
+
+    dyn = Langevin(
+        box,
+        timestep=TIMESTEP * units.fs,
+        temperature_K=TEMPERATURE,
+        friction=FRICTION / units.fs,
+    )
+
+    write_dir = OUT_PATH / model_name
+    write_dir.mkdir(parents=True, exist_ok=True)
+    traj_file = write_dir / "md.xyz"
+
+    if traj_file.exists():
+        traj_file.unlink()
+
+    for _ in tqdm(range(STEPS), desc=f"{model_name} MD"):
+        dyn.run(1)
+        write(traj_file, box, append=True)
diff --git a/pyproject.toml b/pyproject.toml
index 48e5e6ae8..e631180c0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,6 +37,7 @@ dependencies = [
     "MDAnalysis",
     "openpyxl",
     "tqdm",
+    "molify>=0.2.2",
 ]
 
 [project.optional-dependencies]
diff --git a/uv.lock b/uv.lock
index b7f7f422a..4324ccaac 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1828,62 +1828,67 @@ toml = [
 
 [[package]]
 name = "cryptography"
-version = "46.0.5"
+version = "46.0.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "cffi", marker = "platform_python_implementation != 'PyPy' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
     { name = "typing-extensions", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
 ]
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 [[package]]

From e366e1ad6526d3437c0bc4d400d7a9b9ed1dafb3 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <116088428+kuryla@users.noreply.github.com>
Date: Wed, 4 Mar 2026 17:21:36 +0000
Subject: [PATCH 12/27] Add QUID benchmark (#402)

Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
---
 .../QUID/analyse_QUID.py                      | 241 ++++++++++++++++++
 .../QUID/metrics.yml                          |  22 ++
 .../QUID/app_QUID.py                          |  92 +++++++
 .../QUID/calc_QUID.py                         | 175 +++++++++++++
 4 files changed, 530 insertions(+)
 create mode 100644 ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
 create mode 100644 ml_peg/analysis/non_covalent_interactions/QUID/metrics.yml
 create mode 100644 ml_peg/app/non_covalent_interactions/QUID/app_QUID.py
 create mode 100644 ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py

diff --git a/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py b/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
new file mode 100644
index 000000000..4c3b7c460
--- /dev/null
+++ b/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
@@ -0,0 +1,241 @@
+"""
+Analyse the QUID benchmark for ligand-pocket interactions.
+
+Puleva, M., Medrano Sandonas, L., Lőrincz, B.D. et al,
+Extending quantum-mechanical benchmark accuracy to biological ligand-pocket
+interactions,
+Nat Commun 16, 8583 (2025). https://doi.org/10.1038/s41467-025-63587-9
+"""
+
+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)
+
+CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "QUID" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "non_covalent_interactions" / "QUID"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+EV_TO_KCAL = units.mol / units.kcal
+
+
+def labels() -> dict[str, list[int]]:
+    """
+    Get dictionary of info for QUID structures.
+
+    Returns
+    -------
+    dict[str, list[int]]
+        Dictionary of system indices, complex atom counts, and complex charges.
+    """
+    info = {"all": [], "equilibrium": [], "dissociation": []}
+
+    for model_name in MODELS:
+        model_dir = CALC_PATH / model_name
+        if model_dir.exists():
+            xyz_files = sorted(model_dir.glob("*.xyz"))
+
+            info["all"] = [path.stem for path in xyz_files]
+            info["equilibrium"] = [label for label in info["all"] if "_" not in label]
+            info["dissociation"] = [label for label in info["all"] if "_" in label]
+
+    return info
+
+
+LABELS = labels()
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_quid.json",
+    title="Interaction energies",
+    x_label="Predicted energy / kcal/mol",
+    y_label="Reference energy / kcal/mol",
+    hoverdata={"Labels": LABELS["all"]},
+)
+def interaction_energies() -> dict[str, list]:
+    """
+    Get interaction energies for all systems.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted interaction energies.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+
+    ref_stored = False
+
+    for model_name in MODELS:
+        for label in LABELS["all"]:
+            atoms = read(CALC_PATH / model_name / f"{label}.xyz", index=0)
+
+            if not ref_stored:
+                results["ref"].append(atoms.info["ref_int_energy"][()] * EV_TO_KCAL)
+
+            results[model_name].append(atoms.info["model_int_energy"][()] * EV_TO_KCAL)
+
+            # Write structures for app
+            structs_dir = OUT_PATH / model_name
+            structs_dir.mkdir(parents=True, exist_ok=True)
+            write(structs_dir / f"{label}.xyz", atoms)
+
+        ref_stored = True
+    return results
+
+
+@pytest.fixture
+def total_mae(interaction_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for energies for all systems.
+
+    Parameters
+    ----------
+    interaction_energies
+        Dictionary of reference and predicted energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted energy errors for all models.
+    """
+    results = {}
+    for model_name in MODELS:
+        results[model_name] = mae(
+            interaction_energies["ref"], interaction_energies[model_name]
+        )
+    return results
+
+
+@pytest.fixture
+def equilibrium_mae(interaction_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for charged systems only.
+
+    Parameters
+    ----------
+    interaction_energies
+        Dictionary of reference and predicted interaction energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted interaction energy errors for charged systems.
+    """
+    equilibrium_indices = [
+        i for i, label in enumerate(LABELS["all"]) if label in LABELS["equilibrium"]
+    ]
+
+    results = {}
+    for model_name in MODELS:
+        if interaction_energies[model_name]:
+            ref_equilibrium = [
+                interaction_energies["ref"][i] for i in equilibrium_indices
+            ]
+            pred_equilibrium = [
+                interaction_energies[model_name][i] for i in equilibrium_indices
+            ]
+            results[model_name] = mae(ref_equilibrium, pred_equilibrium)
+        else:
+            results[model_name] = None
+    return results
+
+
+@pytest.fixture
+def dissociation_mae(interaction_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for dissociation systems only.
+
+    Parameters
+    ----------
+    interaction_energies
+        Dictionary of reference and predicted interaction energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted interaction energy errors for dissociation systems.
+    """
+    dissociation_indices = [
+        i for i, label in enumerate(LABELS["all"]) if label in LABELS["dissociation"]
+    ]
+
+    results = {}
+    for model_name in MODELS:
+        if interaction_energies[model_name]:
+            ref_dissociation = [
+                interaction_energies["ref"][i] for i in dissociation_indices
+            ]
+            pred_dissociation = [
+                interaction_energies[model_name][i] for i in dissociation_indices
+            ]
+            results[model_name] = mae(ref_dissociation, pred_dissociation)
+        else:
+            results[model_name] = None
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "quid_metrics_table.json",
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    weights=DEFAULT_WEIGHTS,
+    mlip_name_map=D3_MODEL_NAMES,
+)
+def metrics(
+    total_mae: dict[str, float],
+    equilibrium_mae: dict[str, float],
+    dissociation_mae: dict[str, float],
+) -> dict[str, dict]:
+    """
+    Get all metrics.
+
+    Parameters
+    ----------
+    total_mae
+        Mean absolute errors for all models.
+    equilibrium_mae
+        Mean absolute errors for all models for equilibrium systems.
+    dissociation_mae
+        Mean absolute errors for all models for dissociation systems.
+
+    Returns
+    -------
+    dict[str, dict]
+        Metric names and values for all models.
+    """
+    return {
+        "Equilibrium MAE": equilibrium_mae,
+        "Dissociation MAE": dissociation_mae,
+        "Overall MAE": total_mae,
+    }
+
+
+def test_quid(metrics: dict[str, dict]) -> None:
+    """
+    Run QUID test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return
diff --git a/ml_peg/analysis/non_covalent_interactions/QUID/metrics.yml b/ml_peg/analysis/non_covalent_interactions/QUID/metrics.yml
new file mode 100644
index 000000000..f1aed47a1
--- /dev/null
+++ b/ml_peg/analysis/non_covalent_interactions/QUID/metrics.yml
@@ -0,0 +1,22 @@
+metrics:
+  Overall MAE:
+    good: 0.3
+    bad: 2.0
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for all systems
+    level_of_theory: CCSD(T)
+    weight: 1
+  Equilibrium MAE:
+    good: 0.3
+    bad: 2.0
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for neutral systems
+    level_of_theory: CCSD(T)
+    weight: 0
+  Dissociation MAE:
+    good: 0.3
+    bad: 2.0
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for charged systems
+    level_of_theory: CCSD(T)
+    weight: 0
diff --git a/ml_peg/app/non_covalent_interactions/QUID/app_QUID.py b/ml_peg/app/non_covalent_interactions/QUID/app_QUID.py
new file mode 100644
index 000000000..c8947295d
--- /dev/null
+++ b/ml_peg/app/non_covalent_interactions/QUID/app_QUID.py
@@ -0,0 +1,92 @@
+"""Run QUID 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 = "QUID"
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/non_covalent_interactions.html#quid"
+DATA_PATH = APP_ROOT / "data" / "non_covalent_interactions" / "QUID"
+
+
+class QUIDApp(BaseApp):
+    """QUID benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_quid.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        model_dir = DATA_PATH / MODELS[0]
+        if model_dir.exists():
+            # Note: sorting different to rxn_count order in calc
+            ts_files = sorted(model_dir.glob("*.xyz"))
+            structs = [
+                f"assets/non_covalent_interactions/QUID/{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={
+                "Overall MAE": scatter,
+                "Equilibrium MAE": scatter,
+                "Dissociation 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() -> QUIDApp:
+    """
+    Get QUID benchmark app layout and callback registration.
+
+    Returns
+    -------
+    QUIDApp
+        Benchmark layout and callback registration.
+    """
+    return QUIDApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting ligand-pocket interaction energies "
+            "for the QUID dataset."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "quid_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)
diff --git a/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py b/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py
new file mode 100644
index 000000000..785cfa11f
--- /dev/null
+++ b/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py
@@ -0,0 +1,175 @@
+"""
+Compute the QUID benchmark for ligand-pocket interactions.
+
+Puleva, M., Medrano Sandonas, L., Lőrincz, B.D. et al,
+Extending quantum-mechanical benchmark accuracy to biological ligand-pocket
+interactions,
+Nat Commun 16, 8583 (2025). https://doi.org/10.1038/s41467-025-63587-9
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from ase import Atoms
+from ase.io import write
+import h5py
+import numpy as np
+import pytest
+from tqdm import tqdm
+
+from ml_peg.calcs.utils.utils import download_s3_data
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+OUT_PATH = Path(__file__).parent / "outputs"
+
+REF_PRIORITY = [
+    "CCSDT",
+    "LNO-CCSD(T)",
+    "CCSD(T)",
+]
+
+
+def choose_best_reference(
+    eint: dict[str, float] | None, force_key: str | None = None
+) -> tuple[str, float] | None:
+    """
+    Choose the best reference method and energy, given a dataset energies.
+
+    Parameters
+    ----------
+    eint
+        Dictionary of reference methods and interaction energies.
+    force_key
+        Whether to force one particular reference method key.
+
+    Returns
+    -------
+    Tuple[str, float]
+        Tuple containing the best method key and the interaction energy.
+    """
+    if not eint:
+        return None
+    # Force a specific reference key if provided
+    if force_key is not None:
+        # accept case-insensitive match and substring
+        fk = None
+        for k in eint.keys():
+            if force_key.lower() in k.lower():
+                fk = k
+                break
+        if fk is None:
+            return None
+        return fk, float(eint[fk][()])
+    # case-insensitive scoring
+    best_key = None
+    for pref in REF_PRIORITY:
+        for k in eint.keys():
+            if pref.lower() in k.lower():
+                # Prefer the first appearance following priority list
+                best_key = k
+                break
+        if best_key is not None:
+            break
+    if best_key is None:
+        return "", np.nan
+    return best_key, float(eint[best_key][()])
+
+
+def compute_interaction_energy(dataset, label, calc):
+    """
+    Compute and return the energy of the complex with given label and calc.
+
+    Parameters
+    ----------
+    dataset
+        HDF5 dataset containing the systems.
+    label
+        Label of the system within the dataset.
+    calc
+        Calculator to use.
+
+    Returns
+    -------
+    list
+        List containing the dimer and monomer ASE Atoms objects.
+    """
+    best_reference, ref_int_energy = choose_best_reference(dataset[label]["Eint"])
+    if np.isnan(ref_int_energy):
+        return []
+    # List to store dimer and monomers.
+    atoms_list = []
+    model_int_energy = 0
+    for atoms_name, stoich in zip(
+        ["dimer", "small_monomer", "big_monomer"], [1, -1, -1], strict=False
+    ):
+        atomic_numbers = dataset[label]["atoms"][atoms_name][:]
+        positions = dataset[label]["positions"][atoms_name][:]
+        atoms = Atoms(numbers=atomic_numbers, positions=positions)
+        atoms.info.update({"charge": 0, "spin": 1})
+        atoms.calc = calc
+        model_int_energy += atoms.get_potential_energy() * stoich
+        atoms.calc = None
+        atoms_list.append(atoms)
+    atoms_list[0].info.update(
+        {
+            "ref_int_energy": ref_int_energy,
+            "model_int_energy": model_int_energy,
+            "reference_used": best_reference,
+        }
+    )
+    return atoms_list
+
+
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_quid(mlip: tuple[str, Any]) -> None:
+    """
+    Run QUID protein ligand-pocket test.
+
+    Parameters
+    ----------
+    mlip
+        Name of model use and model to get calculator.
+    """
+    model_name, model = mlip
+    calc = model.get_calculator()
+
+    data_path = (
+        download_s3_data(
+            filename="QUID.zip",
+            key="inputs/non_covalent_interactions/QUID/QUID.zip",
+        )
+        / "QUID"
+    )
+
+    # Use double precision
+    model.default_dtype = "float64"
+    calc = model.get_calculator()
+    # Add D3 calculator for this test.
+    calc = model.add_d3_calculator(calc)
+
+    dataset = h5py.File(data_path / "QUID.h5")
+    for eq_label in tqdm(dataset.keys(), "Equilibrium"):
+        # Get equilibrium config.
+        atoms_list = compute_interaction_energy(dataset, eq_label, calc)
+        if len(atoms_list) == 0:
+            raise ValueError("No structures found")
+        write_dir = OUT_PATH / model_name
+        write_dir.mkdir(parents=True, exist_ok=True)
+        write(write_dir / f"{eq_label}.xyz", atoms_list)
+
+        if "dissociation" not in dataset[eq_label]:
+            continue
+        dissoc_dataset = dataset[eq_label]["dissociation"]
+        for dissoc_label in tqdm(dissoc_dataset.keys(), "Dissociation"):
+            # Get dissociation config.
+            atoms_list = compute_interaction_energy(dissoc_dataset, dissoc_label, calc)
+            if len(atoms_list) == 0:
+                continue
+            write_dir = OUT_PATH / model_name
+            write_dir.mkdir(parents=True, exist_ok=True)
+            write(write_dir / f"{dissoc_label}.xyz", atoms_list)

From 4766cf605128230d8cad4da8ce0d7a4e2bcd006f Mon Sep 17 00:00:00 2001
From: zwei-beiner <86890234+zwei-beiner@users.noreply.github.com>
Date: Wed, 4 Mar 2026 17:22:40 +0000
Subject: [PATCH 13/27] Add silicon interstitial NEBs benchmark (#326)

Co-authored-by: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
---
 docs/source/user_guide/benchmarks/nebs.rst    |  57 ++++
 .../nebs/si_defects/analyse_si_defects.py     | 294 ++++++++++++++++++
 ml_peg/analysis/nebs/si_defects/metrics.yml   |  37 +++
 ml_peg/app/nebs/si_defects/app_si_defects.py  | 123 ++++++++
 .../calcs/nebs/si_defects/calc_si_defects.py  | 160 ++++++++++
 5 files changed, 671 insertions(+)
 create mode 100644 ml_peg/analysis/nebs/si_defects/analyse_si_defects.py
 create mode 100644 ml_peg/analysis/nebs/si_defects/metrics.yml
 create mode 100644 ml_peg/app/nebs/si_defects/app_si_defects.py
 create mode 100644 ml_peg/calcs/nebs/si_defects/calc_si_defects.py

diff --git a/docs/source/user_guide/benchmarks/nebs.rst b/docs/source/user_guide/benchmarks/nebs.rst
index e081babf1..9a741711e 100644
--- a/docs/source/user_guide/benchmarks/nebs.rst
+++ b/docs/source/user_guide/benchmarks/nebs.rst
@@ -46,3 +46,60 @@ Reference data:
 
 * Manually taken from https://doi.org/10.1149/1.1633511.
 * Meta-GGA (Perdew-Wang) exchange correlation functional
+
+
+Si defects
+==========
+
+Summary
+-------
+
+Performance in predicting DFT singlepoint energies and forces along fixed nudged-elastic-band
+(NEB) images for a silicon interstitial migration pathway.
+
+Metrics
+-------
+
+For each of the three NEB datasets (64 atoms, 216 atoms, and 216 atoms di-to-single), MLIPs are
+evaluated on the same ordered NEB images as the reference.
+
+1. Energy MAE
+
+Mean absolute error (MAE) of *relative* energies along the NEB, shifting image 0 to 0 eV
+for both the DFT reference and the MLIP predictions.
+
+2. Force MAE
+
+Mean absolute error (MAE) of forces across all atoms and images along the NEB.
+
+Computational cost
+------------------
+
+Medium: tests are likely to take several minutes to run on CPU.
+
+Data availability
+-----------------
+
+Input/reference data:
+
+* Reference extxyz trajectories (including per-image DFT energies and forces) are distributed as a
+  separate zip archive and downloaded on-demand from the ML-PEG data store.
+  The calculation script uses the public ML-PEG S3 bucket to retrieve these inputs.
+* The reference DFT energies/forces come from Quantum ESPRESSO (PWscf) single-point calculations
+  with:
+
+  - Code/version: Quantum ESPRESSO PWSCF v.7.0
+  - XC functional: ``input_dft='PBE'``
+  - Cutoffs: ``ecutwfc=30.0`` Ry, ``ecutrho=240.0`` Ry
+  - Smearing: ``occupations='smearing'``, ``smearing='mv'``, ``degauss=0.01`` Ry
+  - SCF convergence/mixing: ``conv_thr=1.0d-6``, ``electron_maxstep=250``, ``mixing_beta=0.2``,
+    ``mixing_mode='local-TF'``
+  - Diagonalization: ``diagonalization='david'``
+  - Symmetry: ``nosym=.false.``, ``noinv=.false.`` (symmetry enabled)
+  - Pseudopotential: ``Si.pbe-n-kjpaw_psl.1.0.0.UPF`` (PSLibrary)
+
+  K-points by case:
+
+  - 64 atoms: Γ-only (``K_POINTS automatic 1 1 1 0 0 0``)
+  - 216 atoms: Γ-only (``K_POINTS gamma``)
+  - 216 atoms di-to-single: Γ-only (``K_POINTS gamma``)
diff --git a/ml_peg/analysis/nebs/si_defects/analyse_si_defects.py b/ml_peg/analysis/nebs/si_defects/analyse_si_defects.py
new file mode 100644
index 000000000..43ea77029
--- /dev/null
+++ b/ml_peg/analysis/nebs/si_defects/analyse_si_defects.py
@@ -0,0 +1,294 @@
+"""Analyse Si defects DFT singlepoints (energies + forces)."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+from ase.atoms import Atoms
+from ase.io import read, write
+import numpy as np
+import pandas as pd
+import pytest
+
+from ml_peg.analysis.utils.decorators import build_table, plot_scatter
+from ml_peg.analysis.utils.utils import 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 get_model_names
+from ml_peg.models.models import current_models
+
+MODELS = get_model_names(current_models)
+
+BENCHMARK_DIR = "si_defects"
+CALC_PATH = CALCS_ROOT / "nebs" / BENCHMARK_DIR / "outputs"
+OUT_PATH = APP_ROOT / "data" / "nebs" / BENCHMARK_DIR
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+
+@dataclass(frozen=True)
+class _Case:
+    """Definition of a single Si defects NEB dataset."""
+
+    key: str
+    label: str
+
+
+CASES: tuple[_Case, ...] = (
+    _Case(key="64_atoms", label="64"),
+    _Case(key="216_atoms", label="216"),
+    _Case(key="216_atoms_di_to_single", label="216 di-to-single"),
+)
+
+
+@dataclass(frozen=True)
+class _Results:
+    """Computed errors and assets for one (case, model) pair."""
+
+    energy_mae: float
+    force_mae: float
+    x: list[float]
+    energy_error: list[float]
+    force_rms: list[float]
+    structs: list[Atoms]
+
+
+def _load_structs(case_key: str, model: str) -> list[Atoms] | None:
+    """
+    Load MLIP-evaluated NEB frames (with DFT reference stored).
+
+    Parameters
+    ----------
+    case_key
+        Case key.
+    model
+        Model name.
+
+    Returns
+    -------
+    list[ase.atoms.Atoms] | None
+        Frames if the calculation output exists, otherwise ``None``.
+    """
+    path = CALC_PATH / case_key / model / f"{BENCHMARK_DIR}.extxyz"
+    if not path.exists():
+        return None
+    structs = read(path, index=":")
+    if not isinstance(structs, list) or not structs:
+        raise ValueError(f"Unexpected output content: {path}")
+    return structs
+
+
+def _compute(structs: list[Atoms]) -> _Results:
+    """
+    Compute per-image errors and global MAEs.
+
+    Parameters
+    ----------
+    structs
+        Ordered NEB frames with ``ref_energy_ev``, ``ref_forces``, ``pred_energy_ev``,
+        and ``pred_forces``.
+
+    Returns
+    -------
+    _Results
+        Computed errors and frames for downstream plotting/app.
+    """
+    ref_e = np.asarray([float(s.info["ref_energy_ev"]) for s in structs])
+    pred_e = np.asarray([float(s.info["pred_energy_ev"]) for s in structs])
+    # Compare *relative* energies along the NEB (shift image 0 to 0 eV for both
+    # reference and predictions). This removes any constant energy offset.
+    ref_e_rel = ref_e - ref_e[0]
+    pred_e_rel = pred_e - pred_e[0]
+    energy_error = pred_e_rel - ref_e_rel
+
+    ref_f = np.asarray([s.arrays["ref_forces"] for s in structs], dtype=float)
+    pred_f = np.asarray([s.arrays["pred_forces"] for s in structs], dtype=float)
+    force_error = pred_f - ref_f
+
+    x = [float(s.info.get("image_index", idx)) for idx, s in enumerate(structs)]
+    return _Results(
+        energy_mae=mae(ref_e_rel, pred_e_rel),
+        force_mae=mae(ref_f.reshape(-1), pred_f.reshape(-1)),
+        x=x,
+        energy_error=[float(v) for v in energy_error],
+        force_rms=[float(v) for v in np.sqrt(np.mean(force_error**2, axis=(1, 2)))],
+        structs=structs,
+    )
+
+
+def _write_assets(case_key: str, model: str, results: _Results) -> None:
+    """
+    Write structure trajectory and per-image CSV for the app.
+
+    Parameters
+    ----------
+    case_key
+        Case key.
+    model
+        Model name.
+    results
+        Computed errors and frames.
+    """
+    out_dir = OUT_PATH / case_key / model
+    out_dir.mkdir(parents=True, exist_ok=True)
+    write(out_dir / f"{model}-neb-band.extxyz", results.structs)
+    pd.DataFrame(
+        {
+            "image": results.x,
+            "energy_error_ev": results.energy_error,
+            "force_rms_ev_per_ang": results.force_rms,
+        }
+    ).to_csv(out_dir / f"{model}-per_image_errors.csv", index=False)
+
+
+def _write_plots(case_key: str, case_label: str, model: str, results: _Results) -> None:
+    """
+    Write Dash/Plotly JSON plots for one (case, model) pair.
+
+    Parameters
+    ----------
+    case_key
+        Case key.
+    case_label
+        Human-friendly case label.
+    model
+        Model name.
+    results
+        Computed errors and frames.
+    """
+    OUT_PATH.mkdir(parents=True, exist_ok=True)
+
+    @plot_scatter(
+        filename=OUT_PATH / f"figure_{model}_{case_key}_energy_error.json",
+        title=f"Energy error along NEB ({case_label})",
+        x_label="Image",
+        y_label="Energy error / eV",
+        show_line=True,
+    )
+    def plot_energy() -> dict[str, tuple[list[float], list[float]]]:
+        """
+        Plot per-image energy errors for a single model and case.
+
+        Returns
+        -------
+        dict[str, tuple[list[float], list[float]]]
+            Mapping of model name to x/y arrays.
+        """
+        return {model: [results.x, results.energy_error]}
+
+    @plot_scatter(
+        filename=OUT_PATH / f"figure_{model}_{case_key}_force_rms.json",
+        title=f"Force RMS error along NEB ({case_label})",
+        x_label="Image",
+        y_label="Force RMS error / (eV/Å)",
+        show_line=True,
+    )
+    def plot_forces() -> dict[str, tuple[list[float], list[float]]]:
+        """
+        Plot per-image force RMS errors for a single model and case.
+
+        Returns
+        -------
+        dict[str, tuple[list[float], list[float]]]
+            Mapping of model name to x/y arrays.
+        """
+        return {model: [results.x, results.force_rms]}
+
+    plot_energy()
+    plot_forces()
+
+
+@pytest.fixture
+def case_results() -> dict[tuple[str, str], _Results]:
+    """
+    Compute results for all available (case, model) combinations.
+
+    Returns
+    -------
+    dict[tuple[str, str], _Results]
+        Results indexed by ``(case_key, model_name)``.
+    """
+    OUT_PATH.mkdir(parents=True, exist_ok=True)
+    results: dict[tuple[str, str], _Results] = {}
+    for case in CASES:
+        for model in MODELS:
+            structs = _load_structs(case.key, model)
+            if structs is None:
+                continue
+            computed = _compute(structs)
+            _write_assets(case.key, model, computed)
+            _write_plots(case.key, case.label, model, computed)
+            results[(case.key, model)] = computed
+    return results
+
+
+@pytest.fixture
+def metrics_dict(
+    case_results: dict[tuple[str, str], _Results],
+) -> dict[str, dict[str, float]]:
+    """
+    Build raw metric dict for the benchmark table.
+
+    Parameters
+    ----------
+    case_results
+        Results indexed by ``(case_key, model_name)``.
+
+    Returns
+    -------
+    dict[str, dict[str, float]]
+        Metric values for all models.
+    """
+    metrics: dict[str, dict[str, float]] = {}
+    for case in CASES:
+        energy_key = f"Energy MAE ({case.label})"
+        force_key = f"Force MAE ({case.label})"
+        metrics[energy_key] = {}
+        metrics[force_key] = {}
+        for model in MODELS:
+            result = case_results.get((case.key, model))
+            if result is None:
+                continue
+            metrics[energy_key][model] = result.energy_mae
+            metrics[force_key][model] = result.force_mae
+    return metrics
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / f"{BENCHMARK_DIR}_metrics_table.json",
+    metric_tooltips=DEFAULT_TOOLTIPS,
+    thresholds=DEFAULT_THRESHOLDS,
+    weights=DEFAULT_WEIGHTS,
+)
+def metrics(metrics_dict: dict[str, dict[str, float]]) -> dict[str, dict]:
+    """
+    Build the benchmark table JSON.
+
+    Parameters
+    ----------
+    metrics_dict
+        Metric values for all models.
+
+    Returns
+    -------
+    dict[str, dict]
+        Metric names and values for all models.
+    """
+    return metrics_dict
+
+
+def test_si_defects(metrics: dict[str, dict]) -> None:
+    """
+    Run analysis for Si defects DFT singlepoints.
+
+    Parameters
+    ----------
+    metrics
+        Benchmark metrics table.
+    """
+    return
diff --git a/ml_peg/analysis/nebs/si_defects/metrics.yml b/ml_peg/analysis/nebs/si_defects/metrics.yml
new file mode 100644
index 000000000..fdd5cb755
--- /dev/null
+++ b/ml_peg/analysis/nebs/si_defects/metrics.yml
@@ -0,0 +1,37 @@
+metrics:
+  Energy MAE (64):
+    good: 0.02
+    bad: 0.2
+    unit: eV
+    tooltip: "MAE between MLIP and DFT (PBE) relative single-point energies along the NEB (image 0 shifted to 0 eV)."
+    level_of_theory: PBE
+  Force MAE (64):
+    good: 0.05
+    bad: 0.5
+    unit: eV/Å
+    tooltip: "MAE between MLIP and DFT (PBE) single-point forces across all atoms and images along the NEB."
+    level_of_theory: PBE
+  Energy MAE (216):
+    good: 0.02
+    bad: 0.2
+    unit: eV
+    tooltip: "MAE between MLIP and DFT (PBE) relative single-point energies along the NEB (image 0 shifted to 0 eV)."
+    level_of_theory: PBE
+  Force MAE (216):
+    good: 0.05
+    bad: 0.5
+    unit: eV/Å
+    tooltip: "MAE between MLIP and DFT (PBE) single-point forces across all atoms and images along the NEB."
+    level_of_theory: PBE
+  Energy MAE (216 di-to-single):
+    good: 0.02
+    bad: 0.2
+    unit: eV
+    tooltip: "MAE between MLIP and DFT (PBE) relative single-point energies along the NEB (image 0 shifted to 0 eV)."
+    level_of_theory: PBE
+  Force MAE (216 di-to-single):
+    good: 0.05
+    bad: 0.5
+    unit: eV/Å
+    tooltip: "MAE between MLIP and DFT (PBE) single-point forces across all atoms and images along the NEB."
+    level_of_theory: PBE
diff --git a/ml_peg/app/nebs/si_defects/app_si_defects.py b/ml_peg/app/nebs/si_defects/app_si_defects.py
new file mode 100644
index 000000000..a15a6936c
--- /dev/null
+++ b/ml_peg/app/nebs/si_defects/app_si_defects.py
@@ -0,0 +1,123 @@
+"""Run app for Si defects benchmark."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+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_cell, 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 = "Si defects"
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/nebs.html#si-defects"
+DATA_PATH = APP_ROOT / "data" / "nebs" / "si_defects"
+
+
+@dataclass(frozen=True)
+class _Case:
+    """Definition of a single Si defects NEB dataset."""
+
+    key: str
+    label: str
+
+
+CASES: tuple[_Case, ...] = (
+    _Case(key="64_atoms", label="64"),
+    _Case(key="216_atoms", label="216"),
+    _Case(key="216_atoms_di_to_single", label="216 di-to-single"),
+)
+
+
+class SiDefectNebSinglepointsApp(BaseApp):
+    """Si defects benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register interactive callbacks for plot and structure viewing."""
+        scatter_plots: dict[str, dict] = {}
+
+        for model in MODELS:
+            model_plots: dict[str, object] = {}
+            for case in CASES:
+                energy_plot_path = (
+                    DATA_PATH / f"figure_{model}_{case.key}_energy_error.json"
+                )
+                force_plot_path = (
+                    DATA_PATH / f"figure_{model}_{case.key}_force_rms.json"
+                )
+                if energy_plot_path.exists():
+                    model_plots[f"Energy MAE ({case.label})"] = read_plot(
+                        energy_plot_path,
+                        id=f"{BENCHMARK_NAME}-{model}-{case.key}-energy-figure",
+                    )
+                if force_plot_path.exists():
+                    model_plots[f"Force MAE ({case.label})"] = read_plot(
+                        force_plot_path,
+                        id=f"{BENCHMARK_NAME}-{model}-{case.key}-force-figure",
+                    )
+            if model_plots:
+                scatter_plots[model] = model_plots
+
+        plot_from_table_cell(
+            table_id=self.table_id,
+            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
+            cell_to_plot=scatter_plots,
+        )
+
+        for model in scatter_plots:
+            for case in CASES:
+                structs = (
+                    f"assets/nebs/si_defects/{case.key}/{model}/{model}-neb-band.extxyz"
+                )
+                struct_from_scatter(
+                    scatter_id=f"{BENCHMARK_NAME}-{model}-{case.key}-energy-figure",
+                    struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                    structs=structs,
+                    mode="traj",
+                )
+                struct_from_scatter(
+                    scatter_id=f"{BENCHMARK_NAME}-{model}-{case.key}-force-figure",
+                    struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                    structs=structs,
+                    mode="traj",
+                )
+
+
+def get_app() -> SiDefectNebSinglepointsApp:
+    """
+    Get Si defects app.
+
+    Returns
+    -------
+    SiDefectNebSinglepointsApp
+        App instance.
+    """
+    return SiDefectNebSinglepointsApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Energy/force MAE of MLIPs on fixed Si interstitial migration NEB images, "
+            "referenced to DFT singlepoints."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "si_defects_metrics_table.json",
+        extra_components=[
+            Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
+        ],
+    )
+
+
+if __name__ == "__main__":
+    # Use APP_ROOT/data as assets root so `assets/nebs/...` resolves correctly.
+    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=8060, debug=True)
diff --git a/ml_peg/calcs/nebs/si_defects/calc_si_defects.py b/ml_peg/calcs/nebs/si_defects/calc_si_defects.py
new file mode 100644
index 000000000..7180b6187
--- /dev/null
+++ b/ml_peg/calcs/nebs/si_defects/calc_si_defects.py
@@ -0,0 +1,160 @@
+"""Evaluate MLIPs on Si defects DFT singlepoints (energies + forces)."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+import sys
+from typing import Any
+
+from ase.atoms import Atoms
+from ase.io import read, write
+import numpy as np
+import pytest
+from tqdm.auto import tqdm
+
+from ml_peg.calcs.utils.utils import download_s3_data
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+DATA_PATH = Path(__file__).parent / "data"
+OUT_PATH = Path(__file__).parent / "outputs"
+S3_KEY = "inputs/nebs/si_defects/si_defects.zip"
+S3_FILENAME = "si_defects.zip"
+
+
+@dataclass(frozen=True)
+class _Case:
+    """Definition of a single Si defects NEB dataset."""
+
+    key: str
+    ref_file: str
+
+
+CASES: tuple[_Case, ...] = (
+    _Case(key="64_atoms", ref_file="64_atoms.extxyz"),
+    _Case(key="216_atoms", ref_file="216_atoms.extxyz"),
+    _Case(key="216_atoms_di_to_single", ref_file="216_atoms_di_to_single.extxyz"),
+)
+
+
+def _read_frames(path: Path) -> list[Atoms]:
+    """
+    Read all frames from an extxyz trajectory.
+
+    Parameters
+    ----------
+    path
+        Path to extxyz trajectory.
+
+    Returns
+    -------
+    list[ase.atoms.Atoms]
+        Frames as ASE atoms objects.
+    """
+    frames = read(path, index=":")
+    if not isinstance(frames, list) or not frames:
+        raise ValueError(f"No frames found in {path}")
+    return frames
+
+
+def _ref_energy_ev(atoms: Atoms) -> float:
+    """
+    Extract reference (DFT) energy in eV from a frame.
+
+    Parameters
+    ----------
+    atoms
+        Frame with ``ref_energy_ev`` in ``atoms.info``.
+
+    Returns
+    -------
+    float
+        Reference energy in eV.
+    """
+    if "ref_energy_ev" not in atoms.info:
+        raise KeyError("Missing ref_energy_ev in reference trajectory.")
+    return float(atoms.info["ref_energy_ev"])
+
+
+def _ref_forces(atoms: Atoms) -> np.ndarray:
+    """
+    Extract reference (DFT) forces in eV/Å from a frame.
+
+    Parameters
+    ----------
+    atoms
+        Frame with ``ref_forces`` in ``atoms.arrays``.
+
+    Returns
+    -------
+    numpy.ndarray
+        Reference forces array with shape ``(n_atoms, 3)``.
+    """
+    if "ref_forces" not in atoms.arrays:
+        raise KeyError("Missing ref_forces in reference trajectory.")
+    return np.asarray(atoms.arrays["ref_forces"], dtype=float)
+
+
+@pytest.mark.slow
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_si_defects(mlip: tuple[str, Any]) -> None:
+    """
+    Compare MLIP energies/forces to DFT along fixed NEB images.
+
+    Outputs per-case trajectories containing:
+    - ref_energy_ev, ref_forces
+    - pred_energy_ev, pred_forces
+
+    Parameters
+    ----------
+    mlip
+        Tuple of ``(model_name, model)`` as provided by ``MODELS.items()``.
+    """
+    model_name, model = mlip
+    calc = model.get_calculator()
+
+    local_files_present = all((DATA_PATH / case.ref_file).exists() for case in CASES)
+    if local_files_present:
+        data_dir = DATA_PATH
+    else:
+        data_dir = download_s3_data(key=S3_KEY, filename=S3_FILENAME) / "si_defects"
+
+    for case in CASES:
+        frames = _read_frames(data_dir / case.ref_file)
+        out_dir = OUT_PATH / case.key / model_name
+        out_dir.mkdir(parents=True, exist_ok=True)
+
+        results: list[Atoms] = []
+        it = frames
+        # Only show tqdm progress bars in an interactive terminal; otherwise the
+        # carriage-return updates tend to spam CI/log outputs.
+        if sys.stderr.isatty():
+            it = tqdm(
+                frames,
+                desc=f"{model_name} {case.key}",
+                unit="img",
+                leave=False,
+            )
+        for atoms in it:
+            ref_energy_ev = _ref_energy_ev(atoms)
+            ref_forces = _ref_forces(atoms)
+
+            atoms_pred = atoms.copy()
+            atoms_pred.calc = calc
+            # Set default charge and spin
+            atoms_pred.info.setdefault("charge", 0)
+            atoms_pred.info.setdefault("spin", 1)
+
+            out_atoms = atoms.copy()
+            out_atoms.info["ref_energy_ev"] = ref_energy_ev
+            out_atoms.arrays["ref_forces"] = ref_forces
+            out_atoms.info["pred_energy_ev"] = float(atoms_pred.get_potential_energy())
+            out_atoms.arrays["pred_forces"] = np.asarray(
+                atoms_pred.get_forces(), dtype=float
+            )
+            results.append(out_atoms)
+
+        write(out_dir / "si_defects.extxyz", results)

From f7b2bf2df1bbfc3d743e1a6cd584080c58cc6e0e Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <116088428+kuryla@users.noreply.github.com>
Date: Thu, 5 Mar 2026 16:49:50 +0000
Subject: [PATCH 14/27] Float64 precision for static tests (#408)

Co-authored-by: Domantas Kuryla <dk584@icepc16>
Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
Co-authored-by: Joseph Hart <92541539+joehart2001@users.noreply.github.com>
---
 .../lattice_constants/calc_lattice_constants.py       |  2 ++
 ml_peg/calcs/conformers/37Conf8/calc_37Conf8.py       |  7 ++++---
 ml_peg/calcs/conformers/DipCONFS/calc_DipCONFS.py     | 11 +++++------
 ml_peg/calcs/conformers/Glucose205/calc_Glucose205.py |  9 ++++-----
 ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py   |  8 ++++----
 ml_peg/calcs/conformers/Maltose222/calc_Maltose222.py |  9 ++++-----
 .../calcs/conformers/OpenFF_Tors/calc_OpenFF_Tors.py  |  9 +++++----
 ml_peg/calcs/conformers/UpU46/calc_UpU46.py           |  8 ++++----
 .../conformers/solvMPCONF196/calc_solvMPCONF196.py    |  9 ++++-----
 .../isomer_complexes/calc_isomer_complexes.py         |  2 ++
 ml_peg/calcs/molecular/GMTKN55/calc_GMTKN55.py        |  2 ++
 ml_peg/calcs/molecular/Wiggle150/calc_Wiggle150.py    |  2 ++
 .../calcs/molecular_crystal/CPOSS209/calc_CPOSS209.py |  2 ++
 .../molecular_crystal/DMC_ICE13/calc_DMC_ICE13.py     |  2 ++
 ml_peg/calcs/molecular_crystal/X23/calc_X23.py        |  2 ++
 .../calcs/molecular_reactions/BH2O_36/calc_BH2O_36.py | 10 +++++-----
 ml_peg/calcs/molecular_reactions/BH9/calc_BH9.py      |  9 +++++----
 .../calcs/molecular_reactions/CYCLO70/calc_CYCLO70.py | 10 +++++-----
 .../molecular_reactions/Criegee22/calc_Criegee22.py   | 10 +++++-----
 ml_peg/calcs/molecular_reactions/RDB7/calc_RDB7.py    |  9 ++++-----
 .../non_covalent_interactions/IONPI19/calc_IONPI19.py |  9 ++++-----
 .../NCIA_D1200/calc_NCIA_D1200.py                     | 10 +++++-----
 .../NCIA_D442x10/calc_NCIA_D442x10.py                 |  8 ++++----
 .../NCIA_HB300SPXx10/calc_NCIA_HB300SPXx10.py         | 10 +++++-----
 .../NCIA_HB375x10/calc_NCIA_HB375x10.py               | 10 +++++-----
 .../NCIA_IHB100x10/calc_NCIA_IHB100x10.py             |  9 ++++-----
 .../NCIA_R739x5/calc_NCIA_R739x5.py                   |  8 ++++----
 .../NCIA_SH250x10/calc_NCIA_SH250x10.py               |  8 ++++----
 .../calcs/non_covalent_interactions/QUID/calc_QUID.py | 10 ++++------
 ml_peg/calcs/supramolecular/LNCI16/calc_LNCI16.py     |  2 ++
 ml_peg/calcs/supramolecular/S30L/calc_S30L.py         |  2 ++
 ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py         |  2 ++
 ml_peg/calcs/utils/gscdb138.py                        |  7 ++++---
 33 files changed, 121 insertions(+), 106 deletions(-)

diff --git a/ml_peg/calcs/bulk_crystal/lattice_constants/calc_lattice_constants.py b/ml_peg/calcs/bulk_crystal/lattice_constants/calc_lattice_constants.py
index bb753693e..aa5433f0e 100644
--- a/ml_peg/calcs/bulk_crystal/lattice_constants/calc_lattice_constants.py
+++ b/ml_peg/calcs/bulk_crystal/lattice_constants/calc_lattice_constants.py
@@ -84,6 +84,8 @@ def test_lattice_consts(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     data_dir = (
diff --git a/ml_peg/calcs/conformers/37Conf8/calc_37Conf8.py b/ml_peg/calcs/conformers/37Conf8/calc_37Conf8.py
index c02aaa9bc..c000fdc92 100644
--- a/ml_peg/calcs/conformers/37Conf8/calc_37Conf8.py
+++ b/ml_peg/calcs/conformers/37Conf8/calc_37Conf8.py
@@ -37,7 +37,11 @@ def test_37conf8_conformer_energies(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -50,9 +54,6 @@ def test_37conf8_conformer_energies(mlip: tuple[str, Any]) -> None:
     df = pd.read_excel(
         data_path / "37Conf8_data.xlsx", sheet_name="Rel_Energy_SP", header=2
     )
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
 
     write_dir = OUT_PATH / model_name
     write_dir.mkdir(parents=True, exist_ok=True)
diff --git a/ml_peg/calcs/conformers/DipCONFS/calc_DipCONFS.py b/ml_peg/calcs/conformers/DipCONFS/calc_DipCONFS.py
index ba3aaff79..fc5997afe 100644
--- a/ml_peg/calcs/conformers/DipCONFS/calc_DipCONFS.py
+++ b/ml_peg/calcs/conformers/DipCONFS/calc_DipCONFS.py
@@ -62,9 +62,13 @@ def test_dipconfs(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
+    # Download data
     data_path = (
         download_s3_data(
             filename="DipCONFS.zip",
@@ -73,11 +77,6 @@ def test_dipconfs(mlip: tuple[str, Any]) -> None:
         / "DipCONFS"
     )
 
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     df = pd.read_excel(
         data_path / "ct4c00801_si_004.xlsx",
         sheet_name="Conformational Energies in kcal",
diff --git a/ml_peg/calcs/conformers/Glucose205/calc_Glucose205.py b/ml_peg/calcs/conformers/Glucose205/calc_Glucose205.py
index da2cf5ef9..e87a69723 100644
--- a/ml_peg/calcs/conformers/Glucose205/calc_Glucose205.py
+++ b/ml_peg/calcs/conformers/Glucose205/calc_Glucose205.py
@@ -103,7 +103,11 @@ def test_glucose205(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -114,11 +118,6 @@ def test_glucose205(mlip: tuple[str, Any]) -> None:
     )
 
     ref_energies = get_ref_energies(data_path)
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     lowest_conf_label = "alpha_002"
 
     conf_lowest = get_atoms(
diff --git a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py
index 6bdb054c8..eb42f80bb 100644
--- a/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py
+++ b/ml_peg/calcs/conformers/MPCONF196/calc_MPCONF196.py
@@ -103,7 +103,11 @@ def test_mpconf196(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -114,10 +118,6 @@ def test_mpconf196(mlip: tuple[str, Any]) -> None:
     )
 
     ref_energies = get_ref_energies(data_path)
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
 
     for molecule in tqdm(MOLECULES):
         model_abs_energies = []
diff --git a/ml_peg/calcs/conformers/Maltose222/calc_Maltose222.py b/ml_peg/calcs/conformers/Maltose222/calc_Maltose222.py
index 45395b4a6..cbe868304 100644
--- a/ml_peg/calcs/conformers/Maltose222/calc_Maltose222.py
+++ b/ml_peg/calcs/conformers/Maltose222/calc_Maltose222.py
@@ -103,7 +103,11 @@ def test_maltose222(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -114,11 +118,6 @@ def test_maltose222(mlip: tuple[str, Any]) -> None:
     )
 
     ref_energies = get_ref_energies(data_path)
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     lowest_conf_label = "maltose_001"
 
     conf_lowest = get_atoms(
diff --git a/ml_peg/calcs/conformers/OpenFF_Tors/calc_OpenFF_Tors.py b/ml_peg/calcs/conformers/OpenFF_Tors/calc_OpenFF_Tors.py
index a403fb7f6..511fad2db 100644
--- a/ml_peg/calcs/conformers/OpenFF_Tors/calc_OpenFF_Tors.py
+++ b/ml_peg/calcs/conformers/OpenFF_Tors/calc_OpenFF_Tors.py
@@ -38,7 +38,11 @@ def test_openff_tors(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -47,10 +51,7 @@ def test_openff_tors(mlip: tuple[str, Any]) -> None:
         )
         / "OpenFF-Tors"
     )
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
+
     with open(data_path / "MP2_heavy-aug-cc-pVTZ_torsiondrive_data.json") as file:
         data = json.load(file)
 
diff --git a/ml_peg/calcs/conformers/UpU46/calc_UpU46.py b/ml_peg/calcs/conformers/UpU46/calc_UpU46.py
index ba7b7b3b4..01e7130df 100644
--- a/ml_peg/calcs/conformers/UpU46/calc_UpU46.py
+++ b/ml_peg/calcs/conformers/UpU46/calc_UpU46.py
@@ -88,7 +88,11 @@ def test_upu46(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -99,10 +103,6 @@ def test_upu46(mlip: tuple[str, Any]) -> None:
     )
     zero_conf_label = "2p"
     ref_energies = get_ref_energies(data_path)
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
 
     conf_lowest = get_atoms(data_path / f"{zero_conf_label}.xyz")
     conf_lowest.calc = calc
diff --git a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py
index fbea775bb..65ff7bf73 100644
--- a/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py
+++ b/ml_peg/calcs/conformers/solvMPCONF196/calc_solvMPCONF196.py
@@ -102,7 +102,11 @@ def test_solvmpconf196(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -114,11 +118,6 @@ def test_solvmpconf196(mlip: tuple[str, Any]) -> None:
 
     ref_energies = get_ref_energies(data_path)
 
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for molecule in tqdm(MOLECULES):
         model_abs_energies = []
         ref_abs_energies = []
diff --git a/ml_peg/calcs/lanthanides/isomer_complexes/calc_isomer_complexes.py b/ml_peg/calcs/lanthanides/isomer_complexes/calc_isomer_complexes.py
index f3eb70fc2..82083cb41 100644
--- a/ml_peg/calcs/lanthanides/isomer_complexes/calc_isomer_complexes.py
+++ b/ml_peg/calcs/lanthanides/isomer_complexes/calc_isomer_complexes.py
@@ -111,6 +111,8 @@ def test_isomer_complexes(mlip: tuple[str, Any]) -> None:
         pytest.skip(f"No isomer structures found under {isomer_complexes_dir}.")
 
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     for entry in tqdm(entries, desc=f"Calculating energies for {model_name}"):
diff --git a/ml_peg/calcs/molecular/GMTKN55/calc_GMTKN55.py b/ml_peg/calcs/molecular/GMTKN55/calc_GMTKN55.py
index 085d3fcc6..070cd7471 100644
--- a/ml_peg/calcs/molecular/GMTKN55/calc_GMTKN55.py
+++ b/ml_peg/calcs/molecular/GMTKN55/calc_GMTKN55.py
@@ -41,6 +41,8 @@ def test_gmtkn55(mlip: tuple[str, Any]) -> None:
     """
     model_name, model = mlip
     print(f"\nEvaluating with model: {model_name}")
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     # Add D3 calculator for this test
diff --git a/ml_peg/calcs/molecular/Wiggle150/calc_Wiggle150.py b/ml_peg/calcs/molecular/Wiggle150/calc_Wiggle150.py
index 7117e1fff..66c03d2c1 100644
--- a/ml_peg/calcs/molecular/Wiggle150/calc_Wiggle150.py
+++ b/ml_peg/calcs/molecular/Wiggle150/calc_Wiggle150.py
@@ -185,6 +185,8 @@ def test_wiggle150(mlip: tuple[str, Any]) -> None:
     """
     model_name, model = mlip
     print(f"\nEvaluating with model: {model_name}")
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     # Add D3 calculator for this test
diff --git a/ml_peg/calcs/molecular_crystal/CPOSS209/calc_CPOSS209.py b/ml_peg/calcs/molecular_crystal/CPOSS209/calc_CPOSS209.py
index ef08e406a..b95547a75 100644
--- a/ml_peg/calcs/molecular_crystal/CPOSS209/calc_CPOSS209.py
+++ b/ml_peg/calcs/molecular_crystal/CPOSS209/calc_CPOSS209.py
@@ -31,6 +31,8 @@ def test_lattice_energy(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     # Add D3 calculator for this test
diff --git a/ml_peg/calcs/molecular_crystal/DMC_ICE13/calc_DMC_ICE13.py b/ml_peg/calcs/molecular_crystal/DMC_ICE13/calc_DMC_ICE13.py
index 3b5da9481..c5bf920c1 100644
--- a/ml_peg/calcs/molecular_crystal/DMC_ICE13/calc_DMC_ICE13.py
+++ b/ml_peg/calcs/molecular_crystal/DMC_ICE13/calc_DMC_ICE13.py
@@ -31,6 +31,8 @@ def test_lattice_energy(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     # Add D3 calculator for this test
diff --git a/ml_peg/calcs/molecular_crystal/X23/calc_X23.py b/ml_peg/calcs/molecular_crystal/X23/calc_X23.py
index 5b665de6d..511dce56a 100644
--- a/ml_peg/calcs/molecular_crystal/X23/calc_X23.py
+++ b/ml_peg/calcs/molecular_crystal/X23/calc_X23.py
@@ -35,6 +35,8 @@ def test_lattice_energy(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
 
     # Add D3 calculator for this test
diff --git a/ml_peg/calcs/molecular_reactions/BH2O_36/calc_BH2O_36.py b/ml_peg/calcs/molecular_reactions/BH2O_36/calc_BH2O_36.py
index d1dc8e738..20cf55927 100644
--- a/ml_peg/calcs/molecular_reactions/BH2O_36/calc_BH2O_36.py
+++ b/ml_peg/calcs/molecular_reactions/BH2O_36/calc_BH2O_36.py
@@ -86,7 +86,11 @@ def test_bh2o_36(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -95,13 +99,9 @@ def test_bh2o_36(mlip: tuple[str, Any]) -> None:
         )
         / "BH2O-36"
     )
-    # Read in data and attach calculator
+    # Read in data
     systems = get_systems(data_path / "mp2_super.json", data_path / "molecules/for_sp")
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for identifier, system in tqdm(systems.items()):
         atoms_rct = read(system["rct"]["xyz_path"])
         atoms_rct.info["charge"] = int(system["rct"]["charge"])
diff --git a/ml_peg/calcs/molecular_reactions/BH9/calc_BH9.py b/ml_peg/calcs/molecular_reactions/BH9/calc_BH9.py
index b51aad89c..dd78d8d10 100644
--- a/ml_peg/calcs/molecular_reactions/BH9/calc_BH9.py
+++ b/ml_peg/calcs/molecular_reactions/BH9/calc_BH9.py
@@ -144,7 +144,11 @@ def test_bh9(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -153,11 +157,8 @@ def test_bh9(mlip: tuple[str, Any]) -> None:
         )
         / "BH9"
     )
-    # Read in data and attach calculator
+    # Read in data
     ref_energies = get_ref_energies(data_path)
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
 
     xyz_path = data_path / "BH9_SI" / "XYZ_files"
     for label in tqdm(ref_energies):
diff --git a/ml_peg/calcs/molecular_reactions/CYCLO70/calc_CYCLO70.py b/ml_peg/calcs/molecular_reactions/CYCLO70/calc_CYCLO70.py
index 730fdb238..b1329f940 100644
--- a/ml_peg/calcs/molecular_reactions/CYCLO70/calc_CYCLO70.py
+++ b/ml_peg/calcs/molecular_reactions/CYCLO70/calc_CYCLO70.py
@@ -40,9 +40,13 @@ def test_cyclo70(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
+    # Download data
     data_path = (
         download_s3_data(
             filename="CYCLO70.zip",
@@ -51,10 +55,6 @@ def test_cyclo70(mlip: tuple[str, Any]) -> None:
         / "CYCLO70"
     )
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     with open(data_path / "dlpno-ccsdt-34.dat") as lines:
         # Skip header
         next(lines)
diff --git a/ml_peg/calcs/molecular_reactions/Criegee22/calc_Criegee22.py b/ml_peg/calcs/molecular_reactions/Criegee22/calc_Criegee22.py
index f82cf5a27..2c69a8541 100644
--- a/ml_peg/calcs/molecular_reactions/Criegee22/calc_Criegee22.py
+++ b/ml_peg/calcs/molecular_reactions/Criegee22/calc_Criegee22.py
@@ -37,7 +37,11 @@ def test_criegee22(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -47,11 +51,7 @@ def test_criegee22(mlip: tuple[str, Any]) -> None:
         / "Criegee22"
     )
 
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
+    # Read in data
     with open(data_path / "reference.txt") as lines:
         # Skip header
         next(lines)
diff --git a/ml_peg/calcs/molecular_reactions/RDB7/calc_RDB7.py b/ml_peg/calcs/molecular_reactions/RDB7/calc_RDB7.py
index 5495dce16..13f95e732 100644
--- a/ml_peg/calcs/molecular_reactions/RDB7/calc_RDB7.py
+++ b/ml_peg/calcs/molecular_reactions/RDB7/calc_RDB7.py
@@ -98,7 +98,11 @@ def test_rdb87(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -108,11 +112,6 @@ def test_rdb87(mlip: tuple[str, Any]) -> None:
         / "RDB7"
     )
 
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for i in tqdm(range(0, 11961)):
         bh_forward_ref = 0
         bh_forward_model = 0
diff --git a/ml_peg/calcs/non_covalent_interactions/IONPI19/calc_IONPI19.py b/ml_peg/calcs/non_covalent_interactions/IONPI19/calc_IONPI19.py
index cb946ef86..0f495aff2 100644
--- a/ml_peg/calcs/non_covalent_interactions/IONPI19/calc_IONPI19.py
+++ b/ml_peg/calcs/non_covalent_interactions/IONPI19/calc_IONPI19.py
@@ -116,7 +116,11 @@ def test_ionpi19(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -126,11 +130,6 @@ def test_ionpi19(mlip: tuple[str, Any]) -> None:
         / "ionpi19"
     )
     ref_energies = get_ref_energies(data_path)
-    # Read in data and attach calculator
-    calc = model.get_calculator()
-
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
 
     for system_id in tqdm(range(1, 20)):
         for config in SPECIES[system_id]:
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_D1200/calc_NCIA_D1200.py b/ml_peg/calcs/non_covalent_interactions/NCIA_D1200/calc_NCIA_D1200.py
index 5ff722708..03551e489 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_D1200/calc_NCIA_D1200.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_D1200/calc_NCIA_D1200.py
@@ -105,9 +105,13 @@ def test_ncia_d1200(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
+    # Download data
     data_path = (
         download_s3_data(
             filename="NCIA_D1200.zip",
@@ -117,10 +121,6 @@ def test_ncia_d1200(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}_100.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_D442x10/calc_NCIA_D442x10.py b/ml_peg/calcs/non_covalent_interactions/NCIA_D442x10/calc_NCIA_D442x10.py
index 4ef6054b9..7ab29c2b8 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_D442x10/calc_NCIA_D442x10.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_D442x10/calc_NCIA_D442x10.py
@@ -104,7 +104,11 @@ def test_ncia_d442x10(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -115,10 +119,6 @@ def test_ncia_d442x10(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label[:-3] + label[-2:]}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_HB300SPXx10/calc_NCIA_HB300SPXx10.py b/ml_peg/calcs/non_covalent_interactions/NCIA_HB300SPXx10/calc_NCIA_HB300SPXx10.py
index 13ae44b02..f51a9b63a 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_HB300SPXx10/calc_NCIA_HB300SPXx10.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_HB300SPXx10/calc_NCIA_HB300SPXx10.py
@@ -102,9 +102,13 @@ def test_ncia_hb300spxx10(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
+    # Download data
     data_path = (
         download_s3_data(
             filename="NCIA_HB300SPXx10.zip",
@@ -114,10 +118,6 @@ def test_ncia_hb300spxx10(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_HB375x10/calc_NCIA_HB375x10.py b/ml_peg/calcs/non_covalent_interactions/NCIA_HB375x10/calc_NCIA_HB375x10.py
index 21e355e57..52fec1f9f 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_HB375x10/calc_NCIA_HB375x10.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_HB375x10/calc_NCIA_HB375x10.py
@@ -108,9 +108,13 @@ def test_ncia_hb375x10(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
+    # Download data
     data_path = (
         download_s3_data(
             filename="NCIA_HB375x10.zip",
@@ -120,10 +124,6 @@ def test_ncia_hb375x10(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_IHB100x10/calc_NCIA_IHB100x10.py b/ml_peg/calcs/non_covalent_interactions/NCIA_IHB100x10/calc_NCIA_IHB100x10.py
index 1cdd7d41b..9b1907f07 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_IHB100x10/calc_NCIA_IHB100x10.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_IHB100x10/calc_NCIA_IHB100x10.py
@@ -106,9 +106,12 @@ def test_ncia_ihb100x10(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
-    # Read in data and attach calculator
     data_path = (
         download_s3_data(
             filename="NCIA_IHB100x10.zip",
@@ -118,10 +121,6 @@ def test_ncia_ihb100x10(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_R739x5/calc_NCIA_R739x5.py b/ml_peg/calcs/non_covalent_interactions/NCIA_R739x5/calc_NCIA_R739x5.py
index 98aa7c363..c8acdac6f 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_R739x5/calc_NCIA_R739x5.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_R739x5/calc_NCIA_R739x5.py
@@ -104,7 +104,11 @@ def test_ncia_r739x5(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -115,10 +119,6 @@ def test_ncia_r739x5(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/NCIA_SH250x10/calc_NCIA_SH250x10.py b/ml_peg/calcs/non_covalent_interactions/NCIA_SH250x10/calc_NCIA_SH250x10.py
index 5419c5a52..bce89e24c 100644
--- a/ml_peg/calcs/non_covalent_interactions/NCIA_SH250x10/calc_NCIA_SH250x10.py
+++ b/ml_peg/calcs/non_covalent_interactions/NCIA_SH250x10/calc_NCIA_SH250x10.py
@@ -103,7 +103,11 @@ def test_lattice_energy(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -114,10 +118,6 @@ def test_lattice_energy(mlip: tuple[str, Any]) -> None:
     )
     ref_energies = get_ref_energies(data_path)
 
-    calc = model.get_calculator()
-    # Add D3 calculator for this test
-    calc = model.add_d3_calculator(calc)
-
     for label, ref_energy in tqdm(ref_energies.items()):
         xyz_fname = f"{label}.xyz"
         atoms = read(data_path / "geometries" / xyz_fname)
diff --git a/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py b/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py
index 785cfa11f..09f80618f 100644
--- a/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py
+++ b/ml_peg/calcs/non_covalent_interactions/QUID/calc_QUID.py
@@ -136,7 +136,11 @@ def test_quid(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -146,12 +150,6 @@ def test_quid(mlip: tuple[str, Any]) -> None:
         / "QUID"
     )
 
-    # Use double precision
-    model.default_dtype = "float64"
-    calc = model.get_calculator()
-    # Add D3 calculator for this test.
-    calc = model.add_d3_calculator(calc)
-
     dataset = h5py.File(data_path / "QUID.h5")
     for eq_label in tqdm(dataset.keys(), "Equilibrium"):
         # Get equilibrium config.
diff --git a/ml_peg/calcs/supramolecular/LNCI16/calc_LNCI16.py b/ml_peg/calcs/supramolecular/LNCI16/calc_LNCI16.py
index 95b3569a5..98c1e0253 100644
--- a/ml_peg/calcs/supramolecular/LNCI16/calc_LNCI16.py
+++ b/ml_peg/calcs/supramolecular/LNCI16/calc_LNCI16.py
@@ -260,6 +260,8 @@ def benchmark_lnci16(
 
     def run(self):
         """Run LNCI16 benchmark calculations."""
+        # Use double precision
+        self.model.default_dtype = "float64"
         calc = self.model.get_calculator()
 
         # Get benchmark data
diff --git a/ml_peg/calcs/supramolecular/S30L/calc_S30L.py b/ml_peg/calcs/supramolecular/S30L/calc_S30L.py
index 76c7a503f..062254d52 100644
--- a/ml_peg/calcs/supramolecular/S30L/calc_S30L.py
+++ b/ml_peg/calcs/supramolecular/S30L/calc_S30L.py
@@ -226,6 +226,8 @@ def benchmark_s30l(
 
     def run(self):
         """Run S30L benchmark calculations."""
+        # Use double precision
+        self.model.default_dtype = "float64"
         calc = self.model.get_calculator()
 
         # Add D3 calculator for this test
diff --git a/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
index 88c8d34a7..c439f5c68 100644
--- a/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
+++ b/ml_peg/calcs/tm_complexes/3dTMV/calc_3dTMV.py
@@ -123,6 +123,8 @@ def test_3dtmv(mlip: tuple[str, Any]) -> None:
         Name of model use and model to get calculator.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
     # Add D3 calculator for this test
     calc = model.add_d3_calculator(calc)
diff --git a/ml_peg/calcs/utils/gscdb138.py b/ml_peg/calcs/utils/gscdb138.py
index 44722c018..6881c8267 100644
--- a/ml_peg/calcs/utils/gscdb138.py
+++ b/ml_peg/calcs/utils/gscdb138.py
@@ -80,7 +80,11 @@ def run_gscdb138(
         Elements to exclude from calculations. Default is all elements.
     """
     model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
     calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
 
     data_path = (
         download_s3_data(
@@ -93,9 +97,6 @@ def run_gscdb138(
     xyz_dir = data_path / "xyz_files"
     write_dir = out_path / model_name
     write_dir.mkdir(exist_ok=True, parents=True)
-    calc = model.get_calculator()
-    # Add D3 calculator for this test.
-    calc = model.add_d3_calculator(calc)
 
     for dataset in datasets:
         # Load dataset information.

From 7df6ce6459f5cc63c12be5d725d36c7d682ff9bf Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <116088428+kuryla@users.noreply.github.com>
Date: Thu, 5 Mar 2026 17:37:00 +0000
Subject: [PATCH 15/27] ACONFL (#389)

Co-authored-by: ElliottKasoar <45317199+ElliottKasoar@users.noreply.github.com>
---
 .../user_guide/benchmarks/conformers.rst      |  42 +++++
 docs/source/user_guide/benchmarks/index.rst   |   1 +
 .../conformers/ACONFL/analyse_ACONFL.py       | 149 ++++++++++++++++++
 ml_peg/analysis/conformers/ACONFL/metrics.yml |   7 +
 ml_peg/app/conformers/ACONFL/app_ACONFL.py    |  87 ++++++++++
 ml_peg/calcs/conformers/ACONFL/calc_ACONFL.py |  79 ++++++++++
 6 files changed, 365 insertions(+)
 create mode 100644 docs/source/user_guide/benchmarks/conformers.rst
 create mode 100644 ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
 create mode 100644 ml_peg/analysis/conformers/ACONFL/metrics.yml
 create mode 100644 ml_peg/app/conformers/ACONFL/app_ACONFL.py
 create mode 100644 ml_peg/calcs/conformers/ACONFL/calc_ACONFL.py

diff --git a/docs/source/user_guide/benchmarks/conformers.rst b/docs/source/user_guide/benchmarks/conformers.rst
new file mode 100644
index 000000000..5e9ed6d30
--- /dev/null
+++ b/docs/source/user_guide/benchmarks/conformers.rst
@@ -0,0 +1,42 @@
+==========
+Conformers
+==========
+
+ACONFL
+======
+
+Summary
+-------
+
+Performance in predicting relative conformer energies of 12 C12H26,
+16 C16H34 and 20 C20H42 conformers. Reference data from PNO-LCCSD(T)-F12/ AVQZ calculations.
+
+Metrics
+-------
+
+1. Conformer energy error
+
+For each complex, the the relative energy is calculated by taking the difference in energy
+between the given conformer and the reference (zero-energy) conformer. This is
+compared to the reference conformer energy, calculated in the same way.
+
+Computational cost
+------------------
+
+Low: tests are likely to take minutes to run on CPU.
+
+Data availability
+-----------------
+
+Input structures:
+
+* Conformational Energy Benchmark for Longer n-Alkane Chains
+  Sebastian Ehlert, Stefan Grimme, and Andreas Hansen
+  The Journal of Physical Chemistry A 2022 126 (22), 3521-3535
+  DOI: 10.1021/acs.jpca.2c02439
+
+Reference data:
+
+* Same as input data
+* :math:`PNO-LCCSD(T)-F12/ AVQZ` level of theory: a local, explicitly
+  correlated coupled cluster method.
diff --git a/docs/source/user_guide/benchmarks/index.rst b/docs/source/user_guide/benchmarks/index.rst
index 63333e784..ad3c82f96 100644
--- a/docs/source/user_guide/benchmarks/index.rst
+++ b/docs/source/user_guide/benchmarks/index.rst
@@ -15,3 +15,4 @@ Benchmarks
     lanthanides
     non_covalent_interactions
     tm_complexes
+    conformers
diff --git a/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py b/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
new file mode 100644
index 000000000..c3d450c40
--- /dev/null
+++ b/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
@@ -0,0 +1,149 @@
+"""
+Analyse the ACONFL dataset for molecular conformer relative energies.
+
+Conformational Energy Benchmark for Longer n-Alkane Chains
+Sebastian Ehlert, Stefan Grimme, and Andreas Hansen
+The Journal of Physical Chemistry A 2022 126 (22), 3521-3535
+DOI: 10.1021/acs.jpca.2c02439
+"""
+
+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)
+
+EV_TO_KCAL = units.mol / units.kcal
+CALC_PATH = CALCS_ROOT / "conformers" / "ACONFL" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "conformers" / "ACONFL"
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+
+def labels() -> list:
+    """
+    Get list of system names.
+
+    Returns
+    -------
+    list
+        List of all system names.
+    """
+    for model_name in MODELS:
+        labels_list = [path.stem for path in sorted((CALC_PATH / model_name).glob("*"))]
+        break
+    return labels_list
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_aconfl.json",
+    title="Energies",
+    x_label="Predicted energy / kcal/mol",
+    y_label="Reference energy / kcal/mol",
+    hoverdata={
+        "Labels": labels(),
+    },
+)
+def conformer_energies() -> dict[str, list]:
+    """
+    Get conformer energies for all systems.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted conformer energies.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+    ref_stored = False
+
+    for model_name in MODELS:
+        for label in labels():
+            atoms = read(CALC_PATH / model_name / f"{label}.xyz")
+
+            results[model_name].append(atoms.info["model_rel_energy"] * EV_TO_KCAL)
+            if not ref_stored:
+                results["ref"].append(atoms.info["ref_rel_energy"] * EV_TO_KCAL)
+
+            # Write structures for app
+            structs_dir = OUT_PATH / model_name
+            structs_dir.mkdir(parents=True, exist_ok=True)
+            write(structs_dir / f"{label}.xyz", atoms)
+        ref_stored = True
+    return results
+
+
+@pytest.fixture
+def get_mae(conformer_energies) -> dict[str, float]:
+    """
+    Get mean absolute error for conformer energies.
+
+    Parameters
+    ----------
+    conformer_energies
+        Dictionary of reference and predicted conformer energies.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted conformer energies errors for all models.
+    """
+    results = {}
+    for model_name in MODELS:
+        results[model_name] = mae(
+            conformer_energies["ref"], conformer_energies[model_name]
+        )
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "aconfl_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_aconfl(metrics: dict[str, dict]) -> None:
+    """
+    Run ACONFL test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return
diff --git a/ml_peg/analysis/conformers/ACONFL/metrics.yml b/ml_peg/analysis/conformers/ACONFL/metrics.yml
new file mode 100644
index 000000000..40d89a17d
--- /dev/null
+++ b/ml_peg/analysis/conformers/ACONFL/metrics.yml
@@ -0,0 +1,7 @@
+metrics:
+  MAE:
+    good: 0.0
+    bad: 2.0
+    unit: kcal/mol
+    tooltip: Mean Absolute Error for all systems
+    level_of_theory: PNO-LCCSD(T)-F12/ AVQZ
diff --git a/ml_peg/app/conformers/ACONFL/app_ACONFL.py b/ml_peg/app/conformers/ACONFL/app_ACONFL.py
new file mode 100644
index 000000000..d8d85b91a
--- /dev/null
+++ b/ml_peg/app/conformers/ACONFL/app_ACONFL.py
@@ -0,0 +1,87 @@
+"""Run ACONFL 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 = "ACONFL"
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/conformers.html#aconfl"
+DATA_PATH = APP_ROOT / "data" / "conformers" / "ACONFL"
+
+
+class ACONFLApp(BaseApp):
+    """ACONFL benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_aconfl.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        model_dir = DATA_PATH / MODELS[0]
+        if model_dir.exists():
+            labels = sorted([f.stem for f in model_dir.glob("*.xyz")])
+            structs = [
+                f"assets/conformers/ACONFL/{MODELS[0]}/{label}.xyz" for label in labels
+            ]
+        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() -> ACONFLApp:
+    """
+    Get ACONFL benchmark app layout and callback registration.
+
+    Returns
+    -------
+    ACONFLApp
+        Benchmark layout and callback registration.
+    """
+    return ACONFLApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting relative conformer energies "
+            "of 12 C12H26, 16 C16H34 and 20 C20H42 conformers. "
+            "Reference data from PNO-LCCSD(T)-F12/ AVQZ calculations."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "aconfl_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=8062, debug=True)
diff --git a/ml_peg/calcs/conformers/ACONFL/calc_ACONFL.py b/ml_peg/calcs/conformers/ACONFL/calc_ACONFL.py
new file mode 100644
index 000000000..a2e4cabf4
--- /dev/null
+++ b/ml_peg/calcs/conformers/ACONFL/calc_ACONFL.py
@@ -0,0 +1,79 @@
+"""
+Compute the ACONFL dataset for molecular conformer relative energies.
+
+Conformational Energy Benchmark for Longer n-Alkane Chains
+Sebastian Ehlert, Stefan Grimme, and Andreas Hansen
+The Journal of Physical Chemistry A 2022 126 (22), 3521-3535
+DOI: 10.1021/acs.jpca.2c02439
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+from typing import Any
+
+from ase import units
+from ase.io import read, write
+import pytest
+from tqdm import tqdm
+
+from ml_peg.calcs.utils.utils import download_s3_data
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+KCAL_TO_EV = units.kcal / units.mol
+
+OUT_PATH = Path(__file__).parent / "outputs"
+
+
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_aconfl_conformer_energies(mlip: tuple[str, Any]) -> None:
+    """
+    Benchmark the ACONFL dataset.
+
+    Parameters
+    ----------
+    mlip
+        Name of model use and model to get calculator.
+    """
+    model_name, model = mlip
+    # Use double precision
+    model.default_dtype = "float64"
+    calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
+
+    data_path = (
+        download_s3_data(
+            filename="ACONFL.zip",
+            key="inputs/conformers/ACONFL/ACONFL.zip",
+        )
+        / "ACONFL"
+    )
+
+    progress = tqdm(total=50)
+    with open(data_path / ".res") as lines:
+        for line in lines:
+            if "$tmer" in line:
+                items = line.strip().split()
+                zero_atoms_label = items[1].replace("/$f", "")
+                atoms_label = items[2].replace("/$f", "")
+                ref_rel_energy = float(items[7]) * KCAL_TO_EV
+                atoms = read(data_path / atoms_label / "struc.xyz")
+                atoms.calc = calc
+                atoms.info.update({"charge": 0, "spin": 1})
+                zero_atoms = read(data_path / zero_atoms_label / "struc.xyz")
+                zero_atoms.calc = calc
+                zero_atoms.info.update({"charge": 0, "spin": 1})
+                atoms.info["model_rel_energy"] = (
+                    atoms.get_potential_energy() - zero_atoms.get_potential_energy()
+                )
+                atoms.info["ref_rel_energy"] = ref_rel_energy
+
+                write_dir = OUT_PATH / model_name
+                write_dir.mkdir(parents=True, exist_ok=True)
+
+                write(write_dir / f"{atoms_label}.xyz", atoms)
+                progress.update()

From 954b429f18da79b58ab86f3e4f1125e0b9fb84ca Mon Sep 17 00:00:00 2001
From: Joseph Hart <92541539+joehart2001@users.noreply.github.com>
Date: Mon, 9 Mar 2026 10:59:25 +0000
Subject: [PATCH 16/27] Add loading wheels to site load and tab switching
 (#414)

---
 ml_peg/app/build_app.py | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/ml_peg/app/build_app.py b/ml_peg/app/build_app.py
index ff7b61ef3..6867dc10f 100644
--- a/ml_peg/app/build_app.py
+++ b/ml_peg/app/build_app.py
@@ -7,7 +7,7 @@
 
 from dash import Dash, Input, Output, callback
 from dash.dash_table import DataTable
-from dash.dcc import Store, Tab, Tabs
+from dash.dcc import Loading, Store, Tab, Tabs
 from dash.html import H1, H3, Div
 from yaml import safe_load
 
@@ -382,7 +382,25 @@ def build_tabs(
             [
                 H1("ML-PEG"),
                 Tabs(id="all-tabs", value="summary-tab", children=all_tabs),
-                Div(id="tabs-content"),
+                Loading(
+                    Div(id="tabs-content"),
+                    type="circle",
+                    color="#119DFF",
+                    fullscreen=False,
+                    # dont trigger both start up load wheel + tab change load wheel
+                    # (when switching to summary tab)
+                    target_components={"tabs-content": "children"},
+                    style={
+                        # Pin near the top so the spinner is visible on long pages
+                        # (default is centre of page)
+                        "position": "fixed",
+                        "top": "300px",
+                        "left": "50%",
+                        "transform": "translateX(-50%)",
+                        "zIndex": "1100",
+                    },
+                    parent_style={"position": "relative"},
+                ),
             ],
             style={"flex": "1", "marginBottom": "40px"},
         ),

From b6f2af1530a2cdddb37def6d035eeef520d78ced Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Mon, 9 Mar 2026 16:21:25 +0000
Subject: [PATCH 17/27] Update pre-commit (#418)

---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7066c22a4..6febbc5b2 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # pre-commit install
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
     - id: end-of-file-fixer
     - id: mixed-line-ending
@@ -11,7 +11,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.11.13
+  rev: v0.15.5
   hooks:
     # Run the linter.
     - id: ruff-check
@@ -20,7 +20,7 @@ repos:
     - id: ruff-format
 
 - repo: https://github.com/numpy/numpydoc
-  rev: v1.8.0
+  rev: v1.10.0
   hooks:
     - id: numpydoc-validation
       files: ^ml_peg/

From ff648f5babf5c9ef9c40f359a1d6ae6133f9636a Mon Sep 17 00:00:00 2001
From: Joseph Hart <92541539+joehart2001@users.noreply.github.com>
Date: Mon, 9 Mar 2026 18:25:45 +0000
Subject: [PATCH 18/27] Show structure file path in WEAS app (#417)

---
 ml_peg/app/utils/weas.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/ml_peg/app/utils/weas.py b/ml_peg/app/utils/weas.py
index 1a178f7bf..d790ccd59 100644
--- a/ml_peg/app/utils/weas.py
+++ b/ml_peg/app/utils/weas.py
@@ -42,6 +42,14 @@ def generate_weas_html(
     <!doctype html>
     <html lang="en">
     <body>
+        <div id="weas-title"
+             style="font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, 'Liberation Mono', 'Courier New', monospace;
+                    font-size: 12px;
+                    color: #444;
+                    margin: 0 0 8px 0;
+                    white-space: nowrap;
+                    overflow: hidden;
+                    text-overflow: ellipsis;"></div>
         <div id="viewer" style="position: relative; width: 100%; height: 500px"></div>
 
         <script type="module">
@@ -67,6 +75,12 @@ def generate_weas_html(
 
         let structureData;
         const filename = "{str(filename)}";
+        const title = document.getElementById("weas-title");
+        if (title) {{
+            const basename = filename.split(/[/\\\\]/).pop() || filename;
+            title.textContent = `Viewing: ${{basename}}`;
+            title.title = basename;
+        }}
         console.log("filename: ", filename);
         structureData = await fetchFile(filename);
         console.log("structureData: ", structureData);

From 8d0badaa756620bb0afc500c6dd5a727e59dee48 Mon Sep 17 00:00:00 2001
From: Joseph Hart <92541539+joehart2001@users.noreply.github.com>
Date: Mon, 9 Mar 2026 19:04:01 +0000
Subject: [PATCH 19/27] Add structure visualisation for density scatter plots
 (#416)

Co-authored-by: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
---
 .../molecular_reactions/RDB7/analyse_RDB7.py  |  10 ++
 .../NCIA_D1200/analyse_NCIA_D1200.py          |  10 ++
 .../NCIA_D442x10/analyse_NCIA_D442x10.py      |  10 ++
 .../analyse_NCIA_HB300SPXx10.py               |  16 ++-
 .../NCIA_HB375x10/analyse_NCIA_HB375x10.py    |  16 ++-
 .../NCIA_IHB100x10/analyse_NCIA_IHB100x10.py  |  16 ++-
 .../NCIA_R739x5/analyse_NCIA_R739x5.py        |  16 ++-
 .../NCIA_SH250x10/analyse_NCIA_SH250x10.py    |  16 ++-
 ml_peg/analysis/utils/decorators.py           |  90 +++---------
 ml_peg/analysis/utils/utils.py                | 134 ++++++++++++++++++
 .../app/molecular_reactions/RDB7/app_RDB7.py  |  18 ++-
 .../NCIA_D1200/app_NCIA_D1200.py              |  20 ++-
 .../NCIA_D442x10/app_NCIA_D442x10.py          |  20 ++-
 .../NCIA_HB300SPXx10/app_NCIA_HB300SPXx10.py  |  20 ++-
 .../NCIA_HB375x10/app_NCIA_HB375x10.py        |  20 ++-
 .../NCIA_IHB100x10/app_NCIA_IHB100x10.py      |  20 ++-
 .../NCIA_R739x5/app_NCIA_R739x5.py            |  20 ++-
 .../NCIA_SH250x10/app_NCIA_SH250x10.py        |  20 ++-
 ml_peg/app/utils/load.py                      |  46 ++++++
 19 files changed, 448 insertions(+), 90 deletions(-)

diff --git a/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py b/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
index 234396d76..05dfa1e93 100644
--- a/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
+++ b/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
@@ -22,6 +22,7 @@
     build_d3_name_map,
     load_metrics_config,
     mae,
+    write_density_trajectories,
 )
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
@@ -110,6 +111,7 @@ def barrier_density(barrier_heights: dict[str, list]) -> dict[str, dict]:
         Mapping of model name to density-scatter data.
     """
     ref_vals = barrier_heights["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = barrier_heights.get(model_name, [])
@@ -118,6 +120,14 @@ def barrier_density(barrier_heights: dict[str, list]) -> dict[str, dict]:
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}_ts.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py b/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
index 7e33b47e6..98d832faa 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
@@ -16,6 +16,7 @@
     build_d3_name_map,
     load_metrics_config,
     mae,
+    write_density_trajectories,
 )
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
@@ -104,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -112,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
index feacb87b6..a447c3c7b 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
@@ -16,6 +16,7 @@
     build_d3_name_map,
     load_metrics_config,
     mae,
+    write_density_trajectories,
 )
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
@@ -104,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot inputs.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -112,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
index fc62b9669..1353392c5 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
@@ -12,7 +12,12 @@
     build_table,
     plot_density_scatter,
 )
-from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.analysis.utils.utils import (
+    build_d3_name_map,
+    load_metrics_config,
+    mae,
+    write_density_trajectories,
+)
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import load_models
@@ -100,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -108,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
index c709ea493..d20258b7c 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
@@ -12,7 +12,12 @@
     build_table,
     plot_density_scatter,
 )
-from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.analysis.utils.utils import (
+    build_d3_name_map,
+    load_metrics_config,
+    mae,
+    write_density_trajectories,
+)
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import load_models
@@ -100,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -108,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
index 778c50042..08b00c8fd 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
@@ -12,7 +12,12 @@
     build_table,
     plot_density_scatter,
 )
-from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.analysis.utils.utils import (
+    build_d3_name_map,
+    load_metrics_config,
+    mae,
+    write_density_trajectories,
+)
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import load_models
@@ -100,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -108,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py b/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
index 333e01f2e..776b3d200 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
@@ -12,7 +12,12 @@
     build_table,
     plot_density_scatter,
 )
-from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.analysis.utils.utils import (
+    build_d3_name_map,
+    load_metrics_config,
+    mae,
+    write_density_trajectories,
+)
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import load_models
@@ -100,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -108,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
index f623ae9eb..40a145078 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
@@ -12,7 +12,12 @@
     build_table,
     plot_density_scatter,
 )
-from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config, mae
+from ml_peg.analysis.utils.utils import (
+    build_d3_name_map,
+    load_metrics_config,
+    mae,
+    write_density_trajectories,
+)
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import load_models
@@ -100,6 +105,7 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
         Mapping of model names to density-plot payloads.
     """
     ref_vals = interaction_energies["ref"]
+    label_list = labels()
     density_inputs: dict[str, dict] = {}
     for model_name in MODELS:
         preds = interaction_energies.get(model_name, [])
@@ -108,6 +114,14 @@ def interaction_density(interaction_energies: dict[str, list]) -> dict[str, dict
             "pred": preds,
             "meta": {"system_count": len([val for val in preds if val is not None])},
         }
+        write_density_trajectories(
+            labels_list=label_list,
+            ref_vals=ref_vals,
+            pred_vals=preds,
+            struct_dir=OUT_PATH / model_name,
+            traj_dir=OUT_PATH / model_name / "density_traj",
+            struct_filename_builder=lambda label: f"{label}.xyz",
+        )
     return density_inputs
 
 
diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py
index cdcc72ba8..05a098931 100644
--- a/ml_peg/analysis/utils/decorators.py
+++ b/ml_peg/analysis/utils/decorators.py
@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-from collections import defaultdict
 from collections.abc import Callable
 import functools
 import json
@@ -15,7 +14,13 @@
 import pandas as pd
 import plotly.graph_objects as go
 
-from ml_peg.analysis.utils.utils import calc_table_scores
+from ml_peg.analysis.utils.utils import (
+    DENSITY_GRID_SIZE,
+    DENSITY_MAX_POINTS_PER_CELL,
+    DENSITY_SAMPLE_SEED,
+    calc_table_scores,
+    sample_density_grid,
+)
 from ml_peg.app.utils.utils import Thresholds
 from ml_peg.models.get_models import get_model_names, load_model_configs
 
@@ -541,9 +546,9 @@ def plot_density_scatter(
     y_label: str | None = None,
     filename: str = "density_scatter.json",
     colorbar_title: str = "Density",
-    grid_size: int = 80,
-    max_points_per_cell: int = 5,
-    seed: int = 0,
+    grid_size: int = DENSITY_GRID_SIZE,
+    max_points_per_cell: int = DENSITY_MAX_POINTS_PER_CELL,
+    seed: int = DENSITY_SAMPLE_SEED,
     hover_metadata: dict[str, str] | None = None,
     annotation_metadata: dict[str, str] | None = None,
 ) -> Callable:
@@ -621,70 +626,6 @@ def plot_density_wrapper(*args, **kwargs) -> dict[str, Any]:
             dict
                 Results dictionary.
             """
-
-            def _downsample(
-                ref_vals: np.ndarray, pred_vals: np.ndarray
-            ) -> tuple[list[float], list[float], list[int]]:
-                """
-                Downsample data points while keeping dense regions representative.
-
-                Parameters
-                ----------
-                ref_vals
-                    Reference (x-axis) values for all systems.
-                pred_vals
-                    Predicted (y-axis) values for all systems.
-
-                Returns
-                -------
-                tuple[list[float], list[float], list[int]]
-                    Downsampled reference values, predicted values, and density counts
-                    corresponding to each retained point.
-                """
-                if ref_vals.size == 0:
-                    return [], [], []
-
-                delta_x = ref_vals.max() - ref_vals.min()
-                delta_y = pred_vals.max() - pred_vals.min()
-                eps = 1e-9
-
-                norm_x = np.clip(
-                    # Normalise to [0, 1). Clamp to avoid hitting the upper bound so
-                    # bin indices always live in [0, grid_size - 1].
-                    (ref_vals - ref_vals.min()) / max(delta_x, eps),
-                    0.0,
-                    0.999999,
-                )
-                norm_y = np.clip(
-                    (pred_vals - pred_vals.min()) / max(delta_y, eps),
-                    0.0,
-                    0.999999,
-                )
-                bins_x = (norm_x * grid_size).astype(int)
-                bins_y = (norm_y * grid_size).astype(int)
-                cell_points: dict[tuple[int, int], list[int]] = defaultdict(list)
-                for idx, (cx, cy) in enumerate(zip(bins_x, bins_y, strict=True)):
-                    cell_points[(int(cx), int(cy))].append(idx)
-
-                rng = np.random.default_rng(seed)
-                sampled_x: list[float] = []
-                sampled_y: list[float] = []
-                sampled_density: list[int] = []
-                for indices in cell_points.values():
-                    if len(indices) > max_points_per_cell:
-                        chosen = rng.choice(
-                            indices, size=max_points_per_cell, replace=False
-                        )
-                    else:
-                        chosen = indices
-                    density = len(indices)
-                    for idx in chosen:
-                        sampled_x.append(float(ref_vals[idx]))
-                        sampled_y.append(float(pred_vals[idx]))
-                        sampled_density.append(density)
-
-                return sampled_x, sampled_y, sampled_density
-
             results = func(*args, **kwargs)
             if not isinstance(results, dict):
                 raise TypeError(
@@ -724,7 +665,16 @@ def _downsample(
                 if ref_vals.size == 0 or pred_vals.size == 0:
                     sampled = ([], [], [])
                 else:
-                    sampled = _downsample(ref_vals, pred_vals)
+                    sampled_indices, sampled_density, _ = sample_density_grid(
+                        ref_vals,
+                        pred_vals,
+                        grid_size=grid_size,
+                        max_points_per_cell=max_points_per_cell,
+                        seed=seed,
+                    )
+                    sampled_x = [float(ref_vals[idx]) for idx in sampled_indices]
+                    sampled_y = [float(pred_vals[idx]) for idx in sampled_indices]
+                    sampled = (sampled_x, sampled_y, sampled_density)
                     global_min = min(global_min, ref_vals.min(), pred_vals.min())
                     global_max = max(global_max, ref_vals.max(), pred_vals.max())
 
diff --git a/ml_peg/analysis/utils/utils.py b/ml_peg/analysis/utils/utils.py
index d317b00f6..e26137a5f 100644
--- a/ml_peg/analysis/utils/utils.py
+++ b/ml_peg/analysis/utils/utils.py
@@ -2,10 +2,12 @@
 
 from __future__ import annotations
 
+from collections import defaultdict
 from collections.abc import Callable, Iterable
 from pathlib import Path
 from typing import Any
 
+from ase.io import read, write
 from matplotlib import cm
 from matplotlib.colors import Colormap
 import numpy as np
@@ -165,6 +167,83 @@ def rmse(ref: list, prediction: list) -> float:
     return mean_squared_error(ref, prediction)
 
 
+DENSITY_GRID_SIZE = 80
+DENSITY_MAX_POINTS_PER_CELL = 5
+DENSITY_SAMPLE_SEED = 0
+
+
+def sample_density_grid(
+    ref_vals: list[float] | np.ndarray,
+    pred_vals: list[float] | np.ndarray,
+    *,
+    grid_size: int = DENSITY_GRID_SIZE,
+    max_points_per_cell: int = DENSITY_MAX_POINTS_PER_CELL,
+    seed: int = DENSITY_SAMPLE_SEED,
+) -> tuple[list[int], list[int], list[list[int]]]:
+    """
+    Sample indices from a density grid, returning density and cell memberships.
+
+    This is the shared implementation used by ``plot_density_scatter`` so the
+    sampling order stays consistent across density-driven artifacts.
+
+    Parameters
+    ----------
+    ref_vals
+        Reference (x-axis) values for all systems, in the same order as the
+        data passed to the density scatter fixture.
+    pred_vals
+        Predicted (y-axis) values, same order as ``ref_vals``.
+    grid_size
+        Number of bins per axis. Must match ``@plot_density_scatter`` default.
+    max_points_per_cell
+        Maximum sampled points per cell. Must match decorator default.
+    seed
+        RNG seed for deterministic sampling. Must match decorator default.
+
+    Returns
+    -------
+    tuple[list[int], list[int], list[list[int]]]
+        ``sampled_indices``: original indices kept in plotting order.
+        ``sampled_density``: density value per sampled index.
+        ``sampled_mapping``: list of source indices for each sampled point.
+    """
+    ref_arr = np.asarray(ref_vals, dtype=float)
+    pred_arr = np.asarray(pred_vals, dtype=float)
+
+    if ref_arr.size == 0 or pred_arr.size == 0:
+        return [], [], []
+
+    delta_x = ref_arr.max() - ref_arr.min()
+    delta_y = pred_arr.max() - pred_arr.min()
+    eps = 1e-9
+
+    norm_x = np.clip((ref_arr - ref_arr.min()) / max(delta_x, eps), 0.0, 0.999999)
+    norm_y = np.clip((pred_arr - pred_arr.min()) / max(delta_y, eps), 0.0, 0.999999)
+    bins_x = (norm_x * grid_size).astype(int)
+    bins_y = (norm_y * grid_size).astype(int)
+
+    cell_points: dict[tuple[int, int], list[int]] = defaultdict(list)
+    for idx, (cx, cy) in enumerate(zip(bins_x, bins_y, strict=True)):
+        cell_points[(int(cx), int(cy))].append(idx)
+
+    rng = np.random.default_rng(seed)
+    sampled_indices: list[int] = []
+    sampled_density: list[int] = []
+    sampled_mapping: list[list[int]] = []
+    for indices in cell_points.values():
+        if len(indices) > max_points_per_cell:
+            chosen = rng.choice(indices, size=max_points_per_cell, replace=False)
+        else:
+            chosen = indices
+        density = len(indices)
+        for idx in chosen:
+            sampled_indices.append(int(idx))
+            sampled_density.append(density)
+            sampled_mapping.append(indices)
+
+    return sampled_indices, sampled_density, sampled_mapping
+
+
 def build_density_inputs(
     models: list[str],
     model_results: dict[str, dict[str, Any]],
@@ -214,6 +293,61 @@ def build_density_inputs(
     return inputs
 
 
+def write_density_trajectories(
+    *,
+    labels_list: list[str],
+    ref_vals: list[float],
+    pred_vals: list[float],
+    struct_dir: Path,
+    traj_dir: Path,
+    struct_filename_builder: Callable[[str], str],
+    grid_size: int = DENSITY_GRID_SIZE,
+    max_points_per_cell: int = DENSITY_MAX_POINTS_PER_CELL,
+    seed: int = DENSITY_SAMPLE_SEED,
+) -> None:
+    """
+    Write one extxyz trajectory per sampled density point for WEAS display.
+
+    Parameters
+    ----------
+    labels_list
+        Ordered system labels matching ``ref_vals``/``pred_vals``.
+    ref_vals
+        Reference values passed to the density scatter.
+    pred_vals
+        Predicted values passed to the density scatter.
+    struct_dir
+        Directory containing per-system structure files.
+    traj_dir
+        Output directory for sampled density trajectories.
+    struct_filename_builder
+        Function to convert each label into the source structure filename.
+    grid_size
+        Number of bins per axis. Must match ``@plot_density_scatter``.
+    max_points_per_cell
+        Maximum sampled points per occupied density cell.
+    seed
+        RNG seed for deterministic sampling.
+    """
+    _, _, sampled_mapping = sample_density_grid(
+        ref_vals,
+        pred_vals,
+        grid_size=grid_size,
+        max_points_per_cell=max_points_per_cell,
+        seed=seed,
+    )
+
+    traj_dir.mkdir(parents=True, exist_ok=True)
+
+    for point_idx, source_indices in enumerate(sampled_mapping):
+        frames = []
+        for source_idx in source_indices:
+            label = labels_list[source_idx]
+            struct_path = struct_dir / struct_filename_builder(label)
+            frames.append(read(struct_path))
+        write(traj_dir / f"{point_idx}.extxyz", frames)
+
+
 def calc_metric_scores(
     metrics_data: list[MetricRow],
     thresholds: Thresholds | None = None,
diff --git a/ml_peg/app/molecular_reactions/RDB7/app_RDB7.py b/ml_peg/app/molecular_reactions/RDB7/app_RDB7.py
index fd471061e..199452a12 100644
--- a/ml_peg/app/molecular_reactions/RDB7/app_RDB7.py
+++ b/ml_peg/app/molecular_reactions/RDB7/app_RDB7.py
@@ -9,8 +9,9 @@
 from ml_peg.app.base_app import BaseApp
 from ml_peg.app.utils.build_callbacks import (
     plot_from_table_cell,
+    struct_from_scatter,
 )
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -49,6 +50,20 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/molecular_reactions/RDB7",
+            models=MODELS,
+        )
+
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-barrier-figure",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> RDB7App:
     """
@@ -70,6 +85,7 @@ def get_app() -> RDB7App:
         table_path=DATA_PATH / "rdb7_barriers_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_D1200/app_NCIA_D1200.py b/ml_peg/app/non_covalent_interactions/NCIA_D1200/app_NCIA_D1200.py
index 9d4b4ea32..e249dac79 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_D1200/app_NCIA_D1200.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_D1200/app_NCIA_D1200.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -39,6 +39,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_D1200",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIAD1200App:
     """
@@ -60,6 +75,7 @@ def get_app() -> NCIAD1200App:
         table_path=DATA_PATH / "ncia_d1200_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_D442x10/app_NCIA_D442x10.py b/ml_peg/app/non_covalent_interactions/NCIA_D442x10/app_NCIA_D442x10.py
index af22dd273..5202f89fc 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_D442x10/app_NCIA_D442x10.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_D442x10/app_NCIA_D442x10.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -39,6 +39,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_D442x10",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIAD442x10App:
     """
@@ -60,6 +75,7 @@ def get_app() -> NCIAD442x10App:
         table_path=DATA_PATH / "ncia_d442x10_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_HB300SPXx10/app_NCIA_HB300SPXx10.py b/ml_peg/app/non_covalent_interactions/NCIA_HB300SPXx10/app_NCIA_HB300SPXx10.py
index 2b3288dec..16ae5db9f 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_HB300SPXx10/app_NCIA_HB300SPXx10.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_HB300SPXx10/app_NCIA_HB300SPXx10.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -42,6 +42,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_HB300SPXx10",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIANHB300SPXx10App:
     """
@@ -63,6 +78,7 @@ def get_app() -> NCIANHB300SPXx10App:
         table_path=DATA_PATH / "ncia_hb300spxx10_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_HB375x10/app_NCIA_HB375x10.py b/ml_peg/app/non_covalent_interactions/NCIA_HB375x10/app_NCIA_HB375x10.py
index 578a55e6c..6b1f9d39e 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_HB375x10/app_NCIA_HB375x10.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_HB375x10/app_NCIA_HB375x10.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -42,6 +42,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_HB375x10",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIANHB375x10App:
     """
@@ -63,6 +78,7 @@ def get_app() -> NCIANHB375x10App:
         table_path=DATA_PATH / "ncia_hb375x10_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_IHB100x10/app_NCIA_IHB100x10.py b/ml_peg/app/non_covalent_interactions/NCIA_IHB100x10/app_NCIA_IHB100x10.py
index f21bb8be6..5ef64908f 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_IHB100x10/app_NCIA_IHB100x10.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_IHB100x10/app_NCIA_IHB100x10.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -42,6 +42,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_IHB100x10",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIANIHB100x10App:
     """
@@ -63,6 +78,7 @@ def get_app() -> NCIANIHB100x10App:
         table_path=DATA_PATH / "ncia_ihb100x10_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_R739x5/app_NCIA_R739x5.py b/ml_peg/app/non_covalent_interactions/NCIA_R739x5/app_NCIA_R739x5.py
index f9ea4f6c6..d508d184f 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_R739x5/app_NCIA_R739x5.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_R739x5/app_NCIA_R739x5.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -42,6 +42,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_R739x5",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIAR739x5App:
     """
@@ -63,6 +78,7 @@ def get_app() -> NCIAR739x5App:
         table_path=DATA_PATH / "ncia_r739x5_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/non_covalent_interactions/NCIA_SH250x10/app_NCIA_SH250x10.py b/ml_peg/app/non_covalent_interactions/NCIA_SH250x10/app_NCIA_SH250x10.py
index d6a7c0391..c213b6053 100644
--- a/ml_peg/app/non_covalent_interactions/NCIA_SH250x10/app_NCIA_SH250x10.py
+++ b/ml_peg/app/non_covalent_interactions/NCIA_SH250x10/app_NCIA_SH250x10.py
@@ -7,8 +7,8 @@
 
 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_cell
-from ml_peg.app.utils.load import read_density_plot_for_model
+from ml_peg.app.utils.build_callbacks import plot_from_table_cell, struct_from_scatter
+from ml_peg.app.utils.load import collect_traj_assets, read_density_plot_for_model
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
@@ -42,6 +42,21 @@ def register_callbacks(self) -> None:
             cell_to_plot=density_plots,
         )
 
+        struct_trajs = collect_traj_assets(
+            data_path=DATA_PATH,
+            assets_prefix="assets/non_covalent_interactions/NCIA_SH250x10",
+            models=MODELS,
+            traj_dirname="density_traj",
+            suffix=".extxyz",
+        )
+        for model in struct_trajs:
+            struct_from_scatter(
+                scatter_id=f"{BENCHMARK_NAME}-{model}-density",
+                struct_id=f"{BENCHMARK_NAME}-struct-placeholder",
+                structs=struct_trajs[model],
+                mode="traj",
+            )
+
 
 def get_app() -> NCIASH250x10App:
     """
@@ -63,6 +78,7 @@ def get_app() -> NCIASH250x10App:
         table_path=DATA_PATH / "ncia_sh250x10_metrics_table.json",
         extra_components=[
             Div(id=f"{BENCHMARK_NAME}-figure-placeholder"),
+            Div(id=f"{BENCHMARK_NAME}-struct-placeholder"),
         ],
     )
 
diff --git a/ml_peg/app/utils/load.py b/ml_peg/app/utils/load.py
index 861c395c4..78abc20be 100644
--- a/ml_peg/app/utils/load.py
+++ b/ml_peg/app/utils/load.py
@@ -334,3 +334,49 @@ def read_density_plot_for_model(
         return None
 
     return Graph(id=id, figure=filtered_fig)
+
+
+def collect_traj_assets(
+    *,
+    data_path: Path,
+    assets_prefix: str,
+    models: list[str],
+    traj_dirname: str = "density_traj",
+    suffix: str = ".extxyz",
+) -> dict[str, list[str]]:
+    """
+    Collect trajectory asset paths for each model.
+
+    Parameters
+    ----------
+    data_path
+        Base data directory containing per-model folders.
+    assets_prefix
+        Assets URL prefix (e.g., ``"assets/molecular_reactions/RDB7"``).
+    models
+        Ordered list of model names to include.
+    traj_dirname
+        Subdirectory name containing trajectories (default: ``"density_traj"``).
+    suffix
+        File suffix to match (default: ``".extxyz"``).
+
+    Returns
+    -------
+    dict[str, list[str]]
+        Mapping of model name to list of asset paths.
+    """
+    assets_base = assets_prefix.rstrip("/")
+    struct_trajs: dict[str, list[str]] = {}
+
+    for model in models:
+        traj_dir = data_path / model / traj_dirname
+        traj_files = sorted(
+            traj_dir.glob(f"*{suffix}"), key=lambda path: int(path.stem)
+        )
+        if traj_files:
+            struct_trajs[model] = [
+                f"{assets_base}/{model}/{traj_dirname}/{traj_file.name}"
+                for traj_file in traj_files
+            ]
+
+    return struct_trajs

From e0a20cd4880ae5577ecf33ba07ac7f9b7aca74d0 Mon Sep 17 00:00:00 2001
From: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
Date: Mon, 9 Mar 2026 19:30:24 +0000
Subject: [PATCH 20/27] Update and add bounds for dependencies (#419)

---
 pyproject.toml |  21 +++---
 uv.lock        | 201 +++++++------------------------------------------
 2 files changed, 37 insertions(+), 185 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e631180c0..00cb1d2ce 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,19 +25,18 @@ readme = "README.md"
 
 dependencies = [
     "boto3<2,>=1.40.49",
-    "dash>=3.1.1",
-    "janus-core<1.0.0,>=0.8.2",
-    "kaleido>=1.0.0",
-    "mdanalysis>=2.9.0",
+    "dash<5,>=4.0.0",
+    "janus-core<1.0.0,>=0.8.6",
+    "kaleido<2,>=1.0.0",
+    "matcalc<0.5,>=0.4.5",
+    "matminer<0.10,>=0.9.3",
+    "mdanalysis<3,>=2.9.0",
     "mlipx<0.2,>=0.1.5",
-    "scikit-learn>=1.7.1",
+    "molify<0.3,>=0.2.2",
+    "openpyxl<4,>=3.1.5",
+    "scikit-learn<2,>=1.7.2",
+    "tqdm<5,>=4.67.3",
     "typer<1.0.0,>=0.19.1",
-    "matcalc",
-    "matminer",
-    "MDAnalysis",
-    "openpyxl",
-    "tqdm",
-    "molify>=0.2.2",
 ]
 
 [project.optional-dependencies]
diff --git a/uv.lock b/uv.lock
index 4324ccaac..fe728e80e 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1966,7 +1966,7 @@ wheels = [
 
 [[package]]
 name = "dash"
-version = "3.4.0"
+version = "4.0.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "flask" },
@@ -1979,9 +1979,9 @@ dependencies = [
     { name = "typing-extensions" },
     { name = "werkzeug" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/7a/3a/322a583ca3479ad2dc6a8bfbaf7f8e4d01e16cc5030d8e7b45445bc22502/dash-3.4.0.tar.gz", hash = "sha256:3944beb32000ee8b22cd7fbb33545a0a43e25916c63aa41ba59ee5611997815e", size = 7581177, upload-time = "2026-01-20T20:46:47.43Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/20/dd/3aed9bfd81dfd8f44b3a5db0583080ac9470d5e92ee134982bd5c69e286e/dash-4.0.0.tar.gz", hash = "sha256:c5f2bca497af288f552aea3ae208f6a0cca472559003dac84ac21187a1c3a142", size = 6943263, upload-time = "2026-02-03T19:42:27.92Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/87/2e/8fa7d095f7ab28649ece149118ccbde8286be52037b02ab02fbe52c34601/dash-3.4.0-py3-none-any.whl", hash = "sha256:62b1c2eca3cfbe05f5e6ed8666e2c9a204aa08e2ceef89f01ce9bcccb3c18e95", size = 7921864, upload-time = "2026-01-20T20:46:36.088Z" },
+    { url = "https://files.pythonhosted.org/packages/0b/8c/dd63d210b28a7589f4bc1e84880525368147425c717d12834ab562f52d14/dash-4.0.0-py3-none-any.whl", hash = "sha256:e36b4b4eae9e1fa4136bf4f1450ed14ef76063bc5da0b10f8ab07bd57a7cb1ab", size = 7247521, upload-time = "2026-02-03T19:42:25.01Z" },
 ]
 
 [[package]]
@@ -4917,169 +4917,24 @@ sdist = { url = "https://files.pythonhosted.org/packages/6d/7b/89f7fe890fc17dd47
 name = "matminer"
 version = "0.9.3"
 source = { registry = "https://pypi.org/simple" }
-resolution-markers = [
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra == 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "(python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma') or (python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma')",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "(python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma') or (python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra != 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma')",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "(python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma') or (python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma')",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and platform_machine == 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "python_full_version < '3.11' and sys_platform == 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma'",
-    "(python_full_version < '3.11' and platform_machine != 'aarch64' and sys_platform == 'linux' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma') or (python_full_version < '3.11' and sys_platform != 'linux' and sys_platform != 'win32' and extra != 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra != 'extra-6-ml-peg-mattersim' and extra != 'extra-6-ml-peg-uma')",
-]
 dependencies = [
-    { name = "monty", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.11' and extra == 'extra-6-ml-peg-grace') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.11' and extra != 'extra-6-ml-peg-grace') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "pandas", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "pymatgen", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "pymongo", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "requests", marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
+    { name = "monty" },
+    { name = "numpy", version = "1.26.4", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.13' and extra == 'extra-6-ml-peg-grace') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
+    { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.13' or extra != 'extra-6-ml-peg-grace' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma')" },
+    { name = "pandas" },
+    { name = "pymatgen" },
+    { name = "pymongo" },
+    { name = "requests" },
     { name = "scikit-learn", version = "1.7.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
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-wheels = [
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-
 [[package]]
 name = "matplotlib"
 version = "3.10.8"
@@ -6002,8 +5857,7 @@ dependencies = [
     { name = "janus-core" },
     { name = "kaleido" },
     { name = "matcalc" },
-    { name = "matminer", version = "0.9.3", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
-    { name = "matminer", version = "0.10.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
+    { name = "matminer" },
     { name = "mdanalysis", version = "2.9.0", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11' or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma')" },
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     { name = "mlipx" },
@@ -6078,26 +5932,25 @@ prod = [
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     { name = "chgnet", marker = "extra == 'chgnet'", specifier = "==0.4.0" },
-    { name = "dash", specifier = ">=3.1.1" },
+    { name = "dash", specifier = ">=4.0.0,<5" },
     { name = "deepmd-kit", marker = "extra == 'dpa3'", specifier = "==3.1.0" },
     { name = "fairchem-core", marker = "extra == 'uma'", specifier = "==2.10.0" },
-    { name = "janus-core", specifier = ">=0.8.2,<1.0.0" },
-    { name = "kaleido", specifier = ">=1.0.0" },
+    { name = "janus-core", specifier = ">=0.8.6,<1.0.0" },
+    { name = "kaleido", specifier = ">=1.0.0,<2" },
     { name = "mace-torch", marker = "extra == 'mace'", specifier = "==0.3.15" },
-    { name = "matcalc" },
-    { name = "matminer" },
+    { name = "matcalc", specifier = ">=0.4.5,<0.5" },
+    { name = "matminer", specifier = ">=0.9.3,<0.10" },
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-    { name = "mdanalysis" },
-    { name = "mdanalysis", specifier = ">=2.9.0" },
+    { name = "mdanalysis", specifier = ">=2.9.0,<3" },
     { name = "mlipx", specifier = ">=0.1.5,<0.2" },
-    { name = "molify", specifier = ">=0.2.2" },
-    { name = "openpyxl" },
+    { name = "molify", specifier = ">=0.2.2,<0.3" },
+    { name = "openpyxl", specifier = ">=3.1.5,<4" },
     { name = "orb-models", marker = "python_full_version < '3.13' and sys_platform != 'win32' and extra == 'orb'", specifier = "==0.5.5" },
     { name = "pet-mad", marker = "sys_platform != 'win32' and extra == 'pet-mad'", specifier = "==1.4.4" },
-    { name = "scikit-learn", specifier = ">=1.7.1" },
+    { name = "scikit-learn", specifier = ">=1.7.2,<2" },
     { name = "tensorpotential", marker = "python_full_version < '3.13' and extra == 'grace'", specifier = "==0.5.1" },
     { name = "torch-dftd", marker = "extra == 'd3'", specifier = "==0.5.1" },
-    { name = "tqdm" },
+    { name = "tqdm", specifier = ">=4.67.3,<5" },
     { name = "typer", specifier = ">=0.19.1,<1.0.0" },
 ]
 provides-extras = ["chgnet", "d3", "dpa3", "grace", "mace", "mattersim", "orb", "pet-mad", "uma"]
@@ -11749,14 +11602,14 @@ wheels = [
 
 [[package]]
 name = "tqdm"
-version = "4.67.1"
+version = "4.67.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
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 ]
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+sdist = { url = "https://files.pythonhosted.org/packages/09/a9/6ba95a270c6f1fbcd8dac228323f2777d886cb206987444e4bce66338dd4/tqdm-4.67.3.tar.gz", hash = "sha256:7d825f03f89244ef73f1d4ce193cb1774a8179fd96f31d7e1dcde62092b960bb", size = 169598, upload-time = "2026-02-03T17:35:53.048Z" }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/16/e1/3079a9ff9b8e11b846c6ac5c8b5bfb7ff225eee721825310c91b3b50304f/tqdm-4.67.3-py3-none-any.whl", hash = "sha256:ee1e4c0e59148062281c49d80b25b67771a127c85fc9676d3be5f243206826bf", size = 78374, upload-time = "2026-02-03T17:35:50.982Z" },
 ]
 
 [[package]]

From ec090d49a429445e8fced7bf2d22dacdbc8d9792 Mon Sep 17 00:00:00 2001
From: Joseph Hart <92541539+joehart2001@users.noreply.github.com>
Date: Mon, 9 Mar 2026 21:44:01 +0000
Subject: [PATCH 21/27] Replace trained_on_d3 with trained_on_dispersion (#413)

---
 .../conformers/37Conf8/analyse_37Conf8.py     | 10 ++--
 .../conformers/ACONFL/analyse_ACONFL.py       | 10 ++--
 .../conformers/DipCONFS/analyse_DipCONFS.py   | 10 ++--
 .../Glucose205/analyse_Glucose205.py          | 10 ++--
 .../conformers/MPCONF196/analyse_MPCONF196.py | 10 ++--
 .../Maltose222/analyse_Maltose222.py          | 10 ++--
 .../OpenFF_Tors/analyse_OpenFF_Tors.py        | 10 ++--
 .../conformers/UpU46/analyse_UpU46.py         | 10 ++--
 .../solvMPCONF196/analyse_solvMPCONF196.py    | 10 ++--
 .../molecular/GMTKN55/analyse_GMTKN55.py      |  6 +--
 .../molecular/Wiggle150/analyse_Wiggle150.py  | 10 ++--
 .../CPOSS209/analyse_CPOSS209.py              | 10 ++--
 .../DMC_ICE13/analyse_DMC_ICE13.py            | 10 ++--
 .../molecular_crystal/X23/analyse_X23.py      | 10 ++--
 .../BH2O_36/analyse_BH2O_36.py                | 10 ++--
 .../molecular_reactions/BH9/analyse_BH9.py    | 10 ++--
 .../CYCLO70/analyse_CYCLO70.py                | 10 ++--
 .../Criegee22/analyse_Criegee22.py            | 10 ++--
 .../molecular_reactions/RDB7/analyse_RDB7.py  |  6 +--
 .../IONPI19/analyse_IONPI19.py                |  6 +--
 .../NCIA_D1200/analyse_NCIA_D1200.py          |  6 +--
 .../NCIA_D442x10/analyse_NCIA_D442x10.py      |  6 +--
 .../analyse_NCIA_HB300SPXx10.py               |  6 +--
 .../NCIA_HB375x10/analyse_NCIA_HB375x10.py    |  6 +--
 .../NCIA_IHB100x10/analyse_NCIA_IHB100x10.py  |  6 +--
 .../NCIA_R739x5/analyse_NCIA_R739x5.py        |  6 +--
 .../NCIA_SH250x10/analyse_NCIA_SH250x10.py    |  6 +--
 .../QUID/analyse_QUID.py                      | 10 ++--
 .../supramolecular/PLA15/analyse_PLA15.py     | 10 ++--
 .../supramolecular/PLF547/analyse_PLF547.py   | 10 ++--
 .../supramolecular/S30L/analyse_S30L.py       | 10 ++--
 .../analysis/surfaces/OC157/analyse_OC157.py  | 10 ++--
 ml_peg/analysis/surfaces/S24/analyse_S24.py   | 10 ++--
 .../tm_complexes/3dTMV/analyse_3dTMV.py       |  6 +--
 ml_peg/analysis/utils/analyse_gscdb138.py     |  6 +--
 ml_peg/analysis/utils/utils.py                | 29 ++++++++----
 ml_peg/models/get_models.py                   | 20 ++++----
 ml_peg/models/models.py                       | 28 +++++------
 ml_peg/models/models.yml                      | 47 ++++++++++---------
 39 files changed, 265 insertions(+), 161 deletions(-)

diff --git a/ml_peg/analysis/conformers/37Conf8/analyse_37Conf8.py b/ml_peg/analysis/conformers/37Conf8/analyse_37Conf8.py
index 226ad111c..cbc7ca78c 100644
--- a/ml_peg/analysis/conformers/37Conf8/analyse_37Conf8.py
+++ b/ml_peg/analysis/conformers/37Conf8/analyse_37Conf8.py
@@ -13,14 +13,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "37Conf8" / "outputs"
@@ -113,7 +117,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "37conf8_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py b/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
index c3d450c40..f15d642e1 100644
--- a/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
+++ b/ml_peg/analysis/conformers/ACONFL/analyse_ACONFL.py
@@ -16,14 +16,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "ACONFL" / "outputs"
@@ -116,7 +120,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "aconfl_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/DipCONFS/analyse_DipCONFS.py b/ml_peg/analysis/conformers/DipCONFS/analyse_DipCONFS.py
index b5b9e7d4d..e959f3005 100644
--- a/ml_peg/analysis/conformers/DipCONFS/analyse_DipCONFS.py
+++ b/ml_peg/analysis/conformers/DipCONFS/analyse_DipCONFS.py
@@ -13,14 +13,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "DipCONFS" / "outputs"
@@ -113,7 +117,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "dipconfs_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/Glucose205/analyse_Glucose205.py b/ml_peg/analysis/conformers/Glucose205/analyse_Glucose205.py
index bab17a63e..6a1b8b611 100644
--- a/ml_peg/analysis/conformers/Glucose205/analyse_Glucose205.py
+++ b/ml_peg/analysis/conformers/Glucose205/analyse_Glucose205.py
@@ -15,14 +15,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "Glucose205" / "outputs"
@@ -115,7 +119,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "glucose205_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/MPCONF196/analyse_MPCONF196.py b/ml_peg/analysis/conformers/MPCONF196/analyse_MPCONF196.py
index 000b9d9ef..efc62faab 100644
--- a/ml_peg/analysis/conformers/MPCONF196/analyse_MPCONF196.py
+++ b/ml_peg/analysis/conformers/MPCONF196/analyse_MPCONF196.py
@@ -14,14 +14,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "MPCONF196" / "outputs"
@@ -115,7 +119,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "mpconf196_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/Maltose222/analyse_Maltose222.py b/ml_peg/analysis/conformers/Maltose222/analyse_Maltose222.py
index 7ee1f4483..a05e64aa3 100644
--- a/ml_peg/analysis/conformers/Maltose222/analyse_Maltose222.py
+++ b/ml_peg/analysis/conformers/Maltose222/analyse_Maltose222.py
@@ -15,14 +15,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "conformers" / "Maltose222" / "outputs"
@@ -115,7 +119,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "maltose222_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/OpenFF_Tors/analyse_OpenFF_Tors.py b/ml_peg/analysis/conformers/OpenFF_Tors/analyse_OpenFF_Tors.py
index f5df1a643..3f7378a94 100644
--- a/ml_peg/analysis/conformers/OpenFF_Tors/analyse_OpenFF_Tors.py
+++ b/ml_peg/analysis/conformers/OpenFF_Tors/analyse_OpenFF_Tors.py
@@ -14,14 +14,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "conformers" / "OpenFF_Tors" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "conformers" / "OpenFF_Tors"
@@ -117,7 +121,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "openff_tors_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/UpU46/analyse_UpU46.py b/ml_peg/analysis/conformers/UpU46/analyse_UpU46.py
index d93bb89b9..8f35e4268 100644
--- a/ml_peg/analysis/conformers/UpU46/analyse_UpU46.py
+++ b/ml_peg/analysis/conformers/UpU46/analyse_UpU46.py
@@ -15,14 +15,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 
 EV_TO_KCAL = units.mol / units.kcal
@@ -118,7 +122,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "upu46_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/conformers/solvMPCONF196/analyse_solvMPCONF196.py b/ml_peg/analysis/conformers/solvMPCONF196/analyse_solvMPCONF196.py
index e28fa5abf..550931053 100644
--- a/ml_peg/analysis/conformers/solvMPCONF196/analyse_solvMPCONF196.py
+++ b/ml_peg/analysis/conformers/solvMPCONF196/analyse_solvMPCONF196.py
@@ -13,14 +13,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "conformers" / "solvMPCONF196" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "conformers" / "solvMPCONF196"
@@ -128,7 +132,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "solv_mpconf196_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular/GMTKN55/analyse_GMTKN55.py b/ml_peg/analysis/molecular/GMTKN55/analyse_GMTKN55.py
index 149e87e19..20272be20 100644
--- a/ml_peg/analysis/molecular/GMTKN55/analyse_GMTKN55.py
+++ b/ml_peg/analysis/molecular/GMTKN55/analyse_GMTKN55.py
@@ -11,14 +11,14 @@
 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
+from ml_peg.analysis.utils.utils import build_dispersion_name_map, load_metrics_config
 from ml_peg.app import APP_ROOT
 from ml_peg.calcs import CALCS_ROOT
 from ml_peg.models.get_models import get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "molecular" / "GMTKN55" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular" / "GMTKN55"
 
@@ -291,7 +291,7 @@ def weighted_error(subset_errors: dict[str, dict[str, float]]) -> dict[str, floa
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     weights=DEFAULT_WEIGHTS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     category_errors: dict[str, dict[str, float]], weighted_error: dict[str, float]
diff --git a/ml_peg/analysis/molecular/Wiggle150/analyse_Wiggle150.py b/ml_peg/analysis/molecular/Wiggle150/analyse_Wiggle150.py
index bfbf10479..d94545c15 100644
--- a/ml_peg/analysis/molecular/Wiggle150/analyse_Wiggle150.py
+++ b/ml_peg/analysis/molecular/Wiggle150/analyse_Wiggle150.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "molecular" / "Wiggle150" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular" / "Wiggle150"
 
@@ -161,7 +165,7 @@ def wiggle150_mae(relative_energies) -> dict[str, float]:
     filename=OUT_PATH / "wiggle150_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(wiggle150_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_crystal/CPOSS209/analyse_CPOSS209.py b/ml_peg/analysis/molecular_crystal/CPOSS209/analyse_CPOSS209.py
index 93bb44594..81d0229c9 100644
--- a/ml_peg/analysis/molecular_crystal/CPOSS209/analyse_CPOSS209.py
+++ b/ml_peg/analysis/molecular_crystal/CPOSS209/analyse_CPOSS209.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "molecular_crystal" / "CPOSS209" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_crystal" / "CPOSS209"
 
@@ -971,7 +975,7 @@ def cposs209_errors(
     filename=OUT_PATH / "cposs209_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
     weights=DEFAULT_WEIGHTS,
 )
 def metrics(
diff --git a/ml_peg/analysis/molecular_crystal/DMC_ICE13/analyse_DMC_ICE13.py b/ml_peg/analysis/molecular_crystal/DMC_ICE13/analyse_DMC_ICE13.py
index a3f1e0a9b..3c5f0b080 100644
--- a/ml_peg/analysis/molecular_crystal/DMC_ICE13/analyse_DMC_ICE13.py
+++ b/ml_peg/analysis/molecular_crystal/DMC_ICE13/analyse_DMC_ICE13.py
@@ -8,14 +8,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "molecular_crystal" / "DMC_ICE13" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_crystal" / "DMC_ICE13"
 
@@ -136,7 +140,7 @@ def dmc_ice13_errors(lattice_energies) -> dict[str, float]:
     filename=OUT_PATH / "dmc_ice13_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(dmc_ice13_errors: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_crystal/X23/analyse_X23.py b/ml_peg/analysis/molecular_crystal/X23/analyse_X23.py
index fc180e3e5..d7110c24f 100644
--- a/ml_peg/analysis/molecular_crystal/X23/analyse_X23.py
+++ b/ml_peg/analysis/molecular_crystal/X23/analyse_X23.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "molecular_crystal" / "X23" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_crystal" / "X23"
 
@@ -139,7 +143,7 @@ def x23_errors(lattice_energies) -> dict[str, float]:
     filename=OUT_PATH / "x23_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(x23_errors: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_reactions/BH2O_36/analyse_BH2O_36.py b/ml_peg/analysis/molecular_reactions/BH2O_36/analyse_BH2O_36.py
index 9519ef837..ccaef305d 100644
--- a/ml_peg/analysis/molecular_reactions/BH2O_36/analyse_BH2O_36.py
+++ b/ml_peg/analysis/molecular_reactions/BH2O_36/analyse_BH2O_36.py
@@ -13,14 +13,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "molecular_reactions" / "BH2O_36" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_reactions" / "BH2O_36"
@@ -174,7 +178,7 @@ def get_mae(barrier_heights) -> dict[str, float]:
     filename=OUT_PATH / "bh2o_36_barriers_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_reactions/BH9/analyse_BH9.py b/ml_peg/analysis/molecular_reactions/BH9/analyse_BH9.py
index 6828aef19..757763f8f 100644
--- a/ml_peg/analysis/molecular_reactions/BH9/analyse_BH9.py
+++ b/ml_peg/analysis/molecular_reactions/BH9/analyse_BH9.py
@@ -14,14 +14,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "molecular_reactions" / "BH9" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_reactions" / "BH9"
@@ -174,7 +178,7 @@ def get_mae(barrier_heights: dict[str, list]) -> dict[str, float]:
     filename=OUT_PATH / "bh9_barriers_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_reactions/CYCLO70/analyse_CYCLO70.py b/ml_peg/analysis/molecular_reactions/CYCLO70/analyse_CYCLO70.py
index ce113d3f1..52f9dc7c4 100644
--- a/ml_peg/analysis/molecular_reactions/CYCLO70/analyse_CYCLO70.py
+++ b/ml_peg/analysis/molecular_reactions/CYCLO70/analyse_CYCLO70.py
@@ -17,14 +17,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "molecular_reactions" / "CYCLO70" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_reactions" / "CYCLO70"
@@ -130,7 +134,7 @@ def get_mae(barrier_heights) -> dict[str, float]:
     filename=OUT_PATH / "cyclo70_barriers_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_reactions/Criegee22/analyse_Criegee22.py b/ml_peg/analysis/molecular_reactions/Criegee22/analyse_Criegee22.py
index 867335abb..7f2917b95 100644
--- a/ml_peg/analysis/molecular_reactions/Criegee22/analyse_Criegee22.py
+++ b/ml_peg/analysis/molecular_reactions/Criegee22/analyse_Criegee22.py
@@ -13,14 +13,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "molecular_reactions" / "Criegee22" / "outputs"
@@ -119,7 +123,7 @@ def get_mae(barrier_heights) -> dict[str, float]:
     filename=OUT_PATH / "criegee22_barriers_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py b/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
index 05dfa1e93..a1d31efe6 100644
--- a/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
+++ b/ml_peg/analysis/molecular_reactions/RDB7/analyse_RDB7.py
@@ -19,7 +19,7 @@
 
 from ml_peg.analysis.utils.decorators import build_table, plot_density_scatter
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -30,7 +30,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "molecular_reactions" / "RDB7" / "outputs"
@@ -157,7 +157,7 @@ def get_mae(barrier_heights) -> dict[str, float]:
     filename=OUT_PATH / "rdb7_barriers_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/IONPI19/analyse_IONPI19.py b/ml_peg/analysis/non_covalent_interactions/IONPI19/analyse_IONPI19.py
index 92c6d6491..bdb21d5b0 100644
--- a/ml_peg/analysis/non_covalent_interactions/IONPI19/analyse_IONPI19.py
+++ b/ml_peg/analysis/non_covalent_interactions/IONPI19/analyse_IONPI19.py
@@ -10,7 +10,7 @@
 
 from ml_peg.analysis.utils.decorators import build_table, plot_parity
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
 )
@@ -20,7 +20,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 
@@ -166,7 +166,7 @@ def get_mae(conformer_energies) -> dict[str, float]:
     filename=OUT_PATH / "ionpi19_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py b/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
index 98d832faa..b30930574 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_D1200/analyse_NCIA_D1200.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_D1200" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_d1200_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
index a447c3c7b..fa9f38bbf 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_D442x10/analyse_NCIA_D442x10.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_D442x10" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_d442x10_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
index 1353392c5..8a4cf3670 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_HB300SPXx10/analyse_NCIA_HB300SPXx10.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_HB300SPXx10" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_hb300spxx10_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
index d20258b7c..a9282f12e 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_HB375x10/analyse_NCIA_HB375x10.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_HB375x10" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_hb375x10_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
index 08b00c8fd..6ae6c6d88 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_IHB100x10/analyse_NCIA_IHB100x10.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_IHB100x10" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_ihb100x10_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py b/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
index 776b3d200..c7b7336c1 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_R739x5/analyse_NCIA_R739x5.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_R739x5" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_r739x5_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py b/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
index 40a145078..d51aabe84 100644
--- a/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
+++ b/ml_peg/analysis/non_covalent_interactions/NCIA_SH250x10/analyse_NCIA_SH250x10.py
@@ -13,7 +13,7 @@
     plot_density_scatter,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
     write_density_trajectories,
@@ -24,7 +24,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "NCIA_SH250x10" / "outputs"
@@ -153,7 +153,7 @@ def get_mae(interaction_energies) -> dict[str, float]:
     filename=OUT_PATH / "ncia_sh250x10_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(get_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py b/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
index 4c3b7c460..687b68f38 100644
--- a/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
+++ b/ml_peg/analysis/non_covalent_interactions/QUID/analyse_QUID.py
@@ -16,14 +16,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "non_covalent_interactions" / "QUID" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "non_covalent_interactions" / "QUID"
@@ -198,7 +202,7 @@ def dissociation_mae(interaction_energies) -> dict[str, float]:
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     weights=DEFAULT_WEIGHTS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     total_mae: dict[str, float],
diff --git a/ml_peg/analysis/supramolecular/PLA15/analyse_PLA15.py b/ml_peg/analysis/supramolecular/PLA15/analyse_PLA15.py
index f8da46021..1fb5c79d0 100644
--- a/ml_peg/analysis/supramolecular/PLA15/analyse_PLA15.py
+++ b/ml_peg/analysis/supramolecular/PLA15/analyse_PLA15.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "supramolecular" / "PLA15" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "supramolecular" / "PLA15"
@@ -258,7 +262,7 @@ def pla15_ion_neutral_mae(interaction_energies) -> dict[str, float]:
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     weights=DEFAULT_WEIGHTS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     pla15_mae: dict[str, float],
diff --git a/ml_peg/analysis/supramolecular/PLF547/analyse_PLF547.py b/ml_peg/analysis/supramolecular/PLF547/analyse_PLF547.py
index d7ca36b5d..d5b716f8e 100755
--- a/ml_peg/analysis/supramolecular/PLF547/analyse_PLF547.py
+++ b/ml_peg/analysis/supramolecular/PLF547/analyse_PLF547.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "supramolecular" / "PLF547" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "supramolecular" / "PLF547"
@@ -193,7 +197,7 @@ def neutral_mae(interaction_energies) -> dict[str, float]:
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     weights=DEFAULT_WEIGHTS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     total_mae: dict[str, float],
diff --git a/ml_peg/analysis/supramolecular/S30L/analyse_S30L.py b/ml_peg/analysis/supramolecular/S30L/analyse_S30L.py
index a2b66e92f..82b53053f 100644
--- a/ml_peg/analysis/supramolecular/S30L/analyse_S30L.py
+++ b/ml_peg/analysis/supramolecular/S30L/analyse_S30L.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 CALC_PATH = CALCS_ROOT / "supramolecular" / "S30L" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "supramolecular" / "S30L"
@@ -221,7 +225,7 @@ def s30l_neutral_mae(interaction_energies) -> dict[str, float]:
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
     weights=DEFAULT_WEIGHTS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     s30l_mae: dict[str, float],
diff --git a/ml_peg/analysis/surfaces/OC157/analyse_OC157.py b/ml_peg/analysis/surfaces/OC157/analyse_OC157.py
index 96a932930..a0b447560 100644
--- a/ml_peg/analysis/surfaces/OC157/analyse_OC157.py
+++ b/ml_peg/analysis/surfaces/OC157/analyse_OC157.py
@@ -9,14 +9,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "surfaces" / "OC157" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "surfaces" / "OC157"
 
@@ -186,7 +190,7 @@ def ranking_error(relative_energies: dict[str, list]) -> dict[str, float]:
     filename=OUT_PATH / "oc157_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(
     oc157_mae: dict[str, float], ranking_error: dict[str, float]
diff --git a/ml_peg/analysis/surfaces/S24/analyse_S24.py b/ml_peg/analysis/surfaces/S24/analyse_S24.py
index 9d8f0aef7..e3966f852 100644
--- a/ml_peg/analysis/surfaces/S24/analyse_S24.py
+++ b/ml_peg/analysis/surfaces/S24/analyse_S24.py
@@ -8,14 +8,18 @@
 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.analysis.utils.utils import (
+    build_dispersion_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 get_model_names
 from ml_peg.models.models import current_models
 
 MODELS = get_model_names(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 CALC_PATH = CALCS_ROOT / "surfaces" / "S24" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "surfaces" / "S24"
 
@@ -165,7 +169,7 @@ def s24_mae(adsorption_energies) -> dict[str, float]:
     filename=OUT_PATH / "s24_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
 )
 def metrics(s24_mae: dict[str, float]) -> dict[str, dict]:
     """
diff --git a/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
index 304d488f8..0391cfa50 100644
--- a/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
+++ b/ml_peg/analysis/tm_complexes/3dTMV/analyse_3dTMV.py
@@ -13,7 +13,7 @@
     plot_parity,
 )
 from ml_peg.analysis.utils.utils import (
-    build_d3_name_map,
+    build_dispersion_name_map,
     load_metrics_config,
     mae,
 )
@@ -23,7 +23,7 @@
 from ml_peg.models.models import current_models
 
 MODELS = load_models(current_models)
-D3_MODEL_NAMES = build_d3_name_map(MODELS)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 CALC_PATH = CALCS_ROOT / "tm_complexes" / "3dTMV" / "outputs"
@@ -235,7 +235,7 @@ def total_mae(ionization_energies) -> dict[str, float]:
     filename=OUT_PATH / "3dtmv_metrics_table.json",
     metric_tooltips=DEFAULT_TOOLTIPS,
     thresholds=DEFAULT_THRESHOLDS,
-    mlip_name_map=D3_MODEL_NAMES,
+    mlip_name_map=DISPERSION_NAME_MAP,
     weights=DEFAULT_WEIGHTS,
 )
 def metrics(
diff --git a/ml_peg/analysis/utils/analyse_gscdb138.py b/ml_peg/analysis/utils/analyse_gscdb138.py
index cdffc72da..6c943c519 100644
--- a/ml_peg/analysis/utils/analyse_gscdb138.py
+++ b/ml_peg/analysis/utils/analyse_gscdb138.py
@@ -8,13 +8,13 @@
 from ase.io import read, write
 
 from ml_peg.analysis.utils.decorators import build_table, plot_parity
-from ml_peg.analysis.utils.utils import build_d3_name_map, mae
+from ml_peg.analysis.utils.utils import build_dispersion_name_map, mae
 from ml_peg.app.utils.utils import Thresholds
 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)
+DISPERSION_NAME_MAP = build_dispersion_name_map(MODELS)
 
 EV_TO_KCAL = units.mol / units.kcal
 
@@ -176,7 +176,7 @@ def get_gscdb138_metrics(
         metric_tooltips=metric_tooltips,
         thresholds=thresholds,
         weights=weights,
-        mlip_name_map=D3_MODEL_NAMES,
+        mlip_name_map=DISPERSION_NAME_MAP,
     )
     def metrics() -> dict[str, dict]:
         """
diff --git a/ml_peg/analysis/utils/utils.py b/ml_peg/analysis/utils/utils.py
index e26137a5f..ff6c92e73 100644
--- a/ml_peg/analysis/utils/utils.py
+++ b/ml_peg/analysis/utils/utils.py
@@ -26,31 +26,42 @@
 TableRow = dict[str, object]
 
 
-def build_d3_name_map(
+def build_dispersion_name_map(
     models: Iterable[str],
     suffix: str = "-D3",
 ) -> dict[str, str]:
     """
-    Return a suffix map for models requiring runtime D3 corrections.
+    Return a suffix map for models requiring runtime dispersion corrections.
 
     Parameters
     ----------
     models
         Iterable of model identifiers to inspect.
     suffix
-        String appended to model names that need the D3 indicator.
+        String appended to model names that need the dispersion correction indicator.
+        Defaults to "-D3" for D3 dispersion corrections.
 
     Returns
     -------
     dict[str, str]
-        Mapping of model -> display name for models not trained with D3 dispersion.
+        Mapping of model -> display name for models not trained with dispersion.
     """
     configs, _ = load_model_configs(tuple(models))
-    return {
-        model: f"{model}{suffix}"
-        for model in models
-        if not configs[model]["trained_on_d3"]
-    }
+    name_map: dict[str, str] = {}
+
+    for model in models:
+        if configs[model]["trained_on_dispersion"]:
+            continue
+        dispersion_kwargs = configs[model].get("dispersion_kwargs") or {}
+        label = dispersion_kwargs.get("label")
+        suffix_to_use = (
+            label.strip() if isinstance(label, str) and label.strip() else suffix
+        )
+        if not suffix_to_use.startswith("-"):
+            suffix_to_use = f"-{suffix_to_use}"
+        name_map[model] = f"{model}{suffix_to_use}"
+
+    return name_map
 
 
 def load_metrics_config(config_path: Path) -> tuple[Thresholds, dict[str, str]]:
diff --git a/ml_peg/models/get_models.py b/ml_peg/models/get_models.py
index a2c441eac..bb5c3a652 100644
--- a/ml_peg/models/get_models.py
+++ b/ml_peg/models/get_models.py
@@ -116,8 +116,8 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
                     task_name=kwargs.get("task_name", "omat"),
                     device=cfg.get("device", "cpu"),
                     overrides=kwargs.get("overrides", {}),
-                    trained_on_d3=cfg.get("trained_on_d3", False),
-                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                    trained_on_dispersion=cfg.get("trained_on_dispersion", False),
+                    dispersion_kwargs=cfg.get("dispersion_kwargs", {}),
                 )
             case "OrbCalc":
                 kwargs = cfg.get("kwargs", {})
@@ -125,8 +125,8 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
                     name=kwargs["name"],
                     device=cfg.get("device", "cpu"),
                     default_dtype=cfg.get("default_dtype", "float32"),
-                    trained_on_d3=cfg.get("trained_on_d3", False),
-                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                    trained_on_dispersion=cfg.get("trained_on_dispersion", False),
+                    dispersion_kwargs=cfg.get("dispersion_kwargs", {}),
                 )
             case "mace" | "mace_mp" | "mace_off" | "mace_omol" | "mace_polar":
                 loaded_models[name] = GenericASECalc(
@@ -135,8 +135,8 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
                     device=cfg.get("device", "auto"),
                     default_dtype=cfg.get("default_dtype", "float32"),
                     kwargs=cfg.get("kwargs", {}),
-                    trained_on_d3=cfg.get("trained_on_d3", False),
-                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                    trained_on_dispersion=cfg.get("trained_on_dispersion", False),
+                    dispersion_kwargs=cfg.get("dispersion_kwargs", {}),
                 )
             case "PETMADCalculator":
                 loaded_models[name] = PetMadCalc(
@@ -145,8 +145,8 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
                     device=cfg.get("device", "cpu"),
                     default_dtype=cfg.get("default_dtype", "float32"),
                     kwargs=cfg.get("kwargs", {}),
-                    trained_on_d3=cfg.get("trained_on_d3", False),
-                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                    trained_on_dispersion=cfg.get("trained_on_dispersion", False),
+                    dispersion_kwargs=cfg.get("dispersion_kwargs", {}),
                 )
             case _:
                 loaded_models[name] = GenericASECalc(
@@ -154,8 +154,8 @@ def load_models(models: None | str | Iterable = None) -> dict[str, Any]:
                     class_name=cfg["class_name"],
                     device=cfg.get("device", "auto"),
                     kwargs=cfg.get("kwargs", {}),
-                    trained_on_d3=cfg.get("trained_on_d3", False),
-                    d3_kwargs=cfg.get("d3_kwargs", {}),
+                    trained_on_dispersion=cfg.get("trained_on_dispersion", False),
+                    dispersion_kwargs=cfg.get("dispersion_kwargs", {}),
                 )
 
     return loaded_models
diff --git a/ml_peg/models/models.py b/ml_peg/models/models.py
index 002f0959d..e8b868cef 100644
--- a/ml_peg/models/models.py
+++ b/ml_peg/models/models.py
@@ -20,33 +20,33 @@
 @dataclasses.dataclass(kw_only=True)
 class SumCalc:
     """
-    Base class that tracks whether a model already includes D3 dispersion.
+    Base class that tracks whether a model already includes dispersion corrections.
 
     ``add_d3_calculator`` only wraps calculators with an explicit TorchDFTD3
-    correction when ``trained_on_d3`` is ``False``; otherwise the original
+    correction when ``trained_on_dispersion`` is ``False``; otherwise the original
     calculator is returned untouched.
     """
 
-    trained_on_d3: bool = False
-    d3_kwargs: dict = dataclasses.field(default_factory=dict)
+    trained_on_dispersion: bool = False
+    dispersion_kwargs: dict = dataclasses.field(default_factory=dict)
 
     def add_d3_calculator(self, calcs) -> Calculator | SumCalculator:
         """
-        Add D3 dispersion to calculator(s).
+        Add dispersion corrections to calculator(s).
 
         Parameters
         ----------
         calcs
-            Calculator, or list of calculators, to add D3 dispersion to via a
+            Calculator, or list of calculators, to add dispersion corrections to via a
             SumCalculator.
 
         Returns
         -------
         SumCalculator | Calculator
-            Calculator(s) with D3 dispersion added, or the original calculator when
-            the model is already trained with D3 corrections.
+            Calculator(s) with dispersion corrections added, or the original calculator
+            when the model is already trained with dispersion corrections.
         """
-        if self.trained_on_d3:
+        if self.trained_on_dispersion:
             return calcs
         from ase import units
         from ase.calculators.mixing import SumCalculator
@@ -57,11 +57,11 @@ def add_d3_calculator(self, calcs) -> Calculator | SumCalculator:
             calcs = [calcs]
 
         d3_calc = TorchDFTD3Calculator(
-            device=self.d3_kwargs.get("device", "cpu"),
-            damping=self.d3_kwargs.get("damping", "bj"),
-            xc=self.d3_kwargs.get("xc", "pbe"),
-            dtype=getattr(torch, self.d3_kwargs.get("dtype", "float32")),
-            cutoff=self.d3_kwargs.get("cutoff", 40.0 * units.Bohr),
+            device=self.dispersion_kwargs.get("device", "cpu"),
+            damping=self.dispersion_kwargs.get("damping", "bj"),
+            xc=self.dispersion_kwargs.get("xc", "pbe"),
+            dtype=getattr(torch, self.dispersion_kwargs.get("dtype", "float32")),
+            cutoff=self.dispersion_kwargs.get("cutoff", 40.0 * units.Bohr),
         )
         calcs.append(d3_calc)
 
diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml
index ce83dd31f..1d69c64be 100644
--- a/ml_peg/models/models.yml
+++ b/ml_peg/models/models.yml
@@ -3,7 +3,7 @@ mace-mp-0a:
   class_name: mace_mp
   device: "auto"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBE
   kwargs:
     model: "medium"
@@ -13,7 +13,7 @@ mace-mp-0b3:
   class_name: mace_mp
   device: "auto"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBE
   kwargs:
     model: "medium-0b3"
@@ -23,7 +23,7 @@ mace-mpa-0:
   class_name: mace_mp
   device: "auto"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBE
   kwargs:
     model: "medium-mpa-0"
@@ -33,7 +33,7 @@ mace-omat-0:
   class_name: mace_mp
   device: "auto"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBE
   kwargs:
     model: "medium-omat-0"
@@ -43,20 +43,21 @@ mace-matpes-r2scan:
   class_name: mace_mp
   device: "auto"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: r2SCAN
   kwargs:
     model: "mace-matpes-r2scan-0"
     head: "matpes_pbe"
-  d3_kwargs:
+  dispersion_kwargs:
     xc: r2scan
+    label: D4
 
 # mace-mh-1-omat:
 #   module: mace.calculators
 #   class_name: mace_mp
 #   device: "auto"
 #   default_dtype: float32
-#   trained_on_d3: false
+#   trained_on_dispersion: false
 #   level_of_theory: PBE
 #   kwargs:
 #     model: "mh-1"
@@ -67,7 +68,7 @@ orb-v3-consv-inf-omat:
   class_name: OrbCalc
   device: "cpu"
   default_dtype: float32-high
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBE
   kwargs:
     name: "orb_v3_conservative_inf_omat"
@@ -77,7 +78,7 @@ orb-v3-consv-inf-omat:
 #   class_name: OrbCalc
 #   device: "cpu"
 #   default_dtype: float32-high
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: PBE
 #   kwargs:
 #     name: "orb_v3_conservative_omol"
@@ -87,7 +88,7 @@ orb-v3-consv-inf-omat:
 #   class_name: MatterSimCalculator
 #   device: "cpu"
 #   load_path: "mattersim-v1.0.0-5m"
-#   trained_on_d3: false
+#   trained_on_dispersion: false
 #   level_of_theory: PBE
 
 # uma-s-1p1-omat:
@@ -95,7 +96,7 @@ orb-v3-consv-inf-omat:
 #   class_name: FAIRChemCalculator
 #   device: "cpu"
 #   level_of_theory: PBE
-#   trained_on_d3: false
+#   trained_on_dispersion: false
 #   kwargs:
 #     model_name: "uma-s-1p1"
 #     task_name: "omat"
@@ -105,7 +106,7 @@ orb-v3-consv-inf-omat:
 #   class_name: FAIRChemCalculator
 #   device: "cpu"
 #   level_of_theory: PBE
-#   trained_on_d3: false
+#   trained_on_dispersion: false
 #   kwargs:
 #     model_name: "uma-m-1p1"
 #     task_name: "omat"
@@ -115,7 +116,7 @@ orb-v3-consv-inf-omat:
 #   class_name: TPCalculator
 #   device: "cpu"
 #   default_dtype: float32
-#   trained_on_d3: false
+#   trained_on_dispersion: false
 #   kwargs:
 #     model: "/Users/joehart/Desktop/0_Cambridge/0_MPhil_Scientific_Computing/MPhil_project/mlipx_testing/models/GRACE-2L-OAM_28Jan25"
 
@@ -124,7 +125,7 @@ orb-v3-consv-inf-omat:
 #   class_name: mace_off
 #   device: "auto"
 #   default_dtype: float32
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   kwargs:
 #     name: large
 
@@ -132,7 +133,7 @@ orb-v3-consv-inf-omat:
 #   module: mace.calculators
 #   class_name: mace_omol
 #   device: "auto"
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V/def2-TZVPD
 #   default_dtype: float32
 #   kwargs:
@@ -143,7 +144,7 @@ orb-v3-consv-inf-omat:
 #   class_name: mace_mp
 #   device: "auto"
 #   default_dtype: float32
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V/def2-TZVPD
 #   kwargs:
 #     model: "mh-1"
@@ -153,7 +154,7 @@ orb-v3-consv-inf-omat:
 #   module: fairchem.core
 #   class_name: FAIRChemCalculator
 #   device: "cpu"
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V/def2-TZVPD
 #   kwargs:
 #     model_name: "uma-s-1p1"
@@ -163,7 +164,7 @@ orb-v3-consv-inf-omat:
 #   module: fairchem.core
 #   class_name: FAIRChemCalculator
 #   device: "cpu"
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V/def2-TZVPD
 #   kwargs:
 #     model_name: "uma-m-1p1"
@@ -174,11 +175,11 @@ pet-mad:
   class_name: PETMADCalculator
   device: "cpu"
   default_dtype: float32
-  trained_on_d3: false
+  trained_on_dispersion: false
   level_of_theory: PBEsol
   kwargs:
     version: "v1.0.2"
-  d3_kwargs:
+  dispersion_kwargs:
     xc: pbesol
 
 # mace-polar-1-s:
@@ -186,7 +187,7 @@ pet-mad:
 #   class_name: mace_polar
 #   device: "cpu"
 #   default_dtype: float32
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V
 #   kwargs:
 #     model: "polar-1-s"
@@ -196,7 +197,7 @@ pet-mad:
 #   class_name: mace_polar
 #   device: "cpu"
 #   default_dtype: float32
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V
 #   kwargs:
 #     model: "polar-1-m"
@@ -206,7 +207,7 @@ pet-mad:
 #   class_name: mace_polar
 #   device: "cpu"
 #   default_dtype: float32
-#   trained_on_d3: true
+#   trained_on_dispersion: true
 #   level_of_theory: ωB97M-V
 #   kwargs:
 #     model: "polar-1-l"

From 77d0008d5775a8d3bc597224f5f6fe4fbb320f92 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 00:52:08 +0000
Subject: [PATCH 22/27] Allow custom options to be passed to calculations

---
 ml_peg/cli/cli.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/ml_peg/cli/cli.py b/ml_peg/cli/cli.py
index 36471650a..82a8876af 100644
--- a/ml_peg/cli/cli.py
+++ b/ml_peg/cli/cli.py
@@ -4,7 +4,7 @@
 
 from typing import Annotated
 
-from typer import Exit, Option, Typer
+from typer import Context, Exit, Option, Typer
 
 from ml_peg import __version__
 
@@ -57,8 +57,13 @@ def run_dash_app(
     run_app(category=category, port=port, debug=debug)
 
 
-@app.command(name="calc", help="Run calculations")
+@app.command(
+    name="calc",
+    help="Run calculations",
+    context_settings={"allow_extra_args": True, "ignore_unknown_options": True},
+)
 def run_calcs(
+    ctx: Context,
     models: Annotated[
         str | None,
         Option(
@@ -86,6 +91,8 @@ def run_calcs(
 
     Parameters
     ----------
+    ctx
+        Typer Context. Automatically set.
     models
         Models to run calculations for, in comma-separated list. Default is `None`,
         corresponding to all available models.
@@ -124,6 +131,9 @@ def run_calcs(
     if models:
         options.extend(["--models", models])
 
+    # Parse any custom options to pytest
+    options.extend(ctx.args)
+
     pytest.main(options)
 
 

From 291fa134f5fc088a5e5839758b701cb74cd56597 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 00:56:33 +0000
Subject: [PATCH 23/27] Water density calc

---
 .../water_density/calc_water_density.py       | 167 ++++++++++++++++++
 .../water_density/conftest.py                 |  35 ++++
 2 files changed, 202 insertions(+)
 create mode 100644 ml_peg/calcs/molecular_dynamics/water_density/calc_water_density.py
 create mode 100644 ml_peg/calcs/molecular_dynamics/water_density/conftest.py

diff --git a/ml_peg/calcs/molecular_dynamics/water_density/calc_water_density.py b/ml_peg/calcs/molecular_dynamics/water_density/calc_water_density.py
new file mode 100644
index 000000000..c0a0a3003
--- /dev/null
+++ b/ml_peg/calcs/molecular_dynamics/water_density/calc_water_density.py
@@ -0,0 +1,167 @@
+"""Calculate density of water at different temperatures."""
+
+from __future__ import annotations
+
+import logging
+import os
+from pathlib import Path
+import time
+from typing import Any
+
+from ase import Atoms, units
+from ase.io import Trajectory, read
+from ase.md.nose_hoover_chain import IsotropicMTKNPT
+import pytest
+
+from ml_peg.calcs.utils.utils import download_s3_data
+from ml_peg.models.get_models import load_models
+from ml_peg.models.models import current_models
+
+MODELS = load_models(current_models)
+
+KCAL_TO_EV = units.kcal / units.mol
+TEMPERATURES = [270.0, 290.0, 300.0, 330.0]
+
+OUT_PATH = Path(__file__).parent / "outputs"
+
+AU_TO_G_CM3 = 1e24 / units.mol
+NUM_MD_STEPS = 1000_000
+TIMESTEP = 1 * units.fs
+LOG_INTERVAL = 100
+ATM = 1.01325 * units.bar
+
+
+def get_density_g_cm3(atoms: Atoms):
+    """
+    Get the density of the system in g/cm^3.
+
+    Parameters
+    ----------
+    atoms
+        ASE.Atoms object of the periodic system.
+
+    Returns
+    -------
+    float
+        Density in g/cm^3.
+    """
+    mass = atoms.get_masses().sum()
+    volume = atoms.get_volume()
+    return AU_TO_G_CM3 * mass / volume
+
+
+def log_md(dyn, start_time):
+    """
+    Log molecular dynamics simulation.
+
+    Parameters
+    ----------
+    dyn
+        ASE molecular dynamics object.
+    start_time
+        Real time of the simulation start, in seconds.
+    """
+    current_time = time.time() - start_time
+    energy = dyn.atoms.get_potential_energy()
+    density = get_density_g_cm3(dyn.atoms)
+    temperature = dyn.atoms.get_temperature()
+    t = dyn.get_time() / (1000 * units.fs)
+    logging.info(
+        f"""t: {t:>8.3f} ps\
+            Walltime: {current_time:>10.3f} s\
+            T: {temperature:.1f} K\
+            Epot: {energy:.2f} eV\
+            density: {density:.3f} g/cm^3\
+        """
+    )
+
+
+def run_npt(atoms, calc, output_fname, temperature):
+    """
+    Run NPT molecular dynamics using the isotropic MTK barostat.
+
+    Parameters
+    ----------
+    atoms
+        ASE Atoms of the system.
+    calc
+        ASE Calculator.
+    output_fname
+        File name to save the trajectory to.
+    temperature
+        Temperature to perform MD at.
+    """
+    if os.path.exists(output_fname):
+        try:
+            traj = Trajectory(output_fname)
+            atoms = traj[-1]
+            nsteps = (len(traj) - 1) * LOG_INTERVAL
+        except Exception as e:
+            print(e)
+            nsteps = 0
+    else:
+        nsteps = 0
+
+    atoms.calc = calc
+
+    dyn = IsotropicMTKNPT(
+        atoms=atoms,
+        timestep=TIMESTEP,
+        temperature_K=temperature,
+        pressure_au=ATM,
+        tdamp=50 * units.fs,
+        pdamp=500 * units.fs,
+        trajectory=output_fname,
+        loginterval=LOG_INTERVAL,
+        append_trajectory=True,
+    )
+    dyn.nsteps = nsteps
+    dyn.attach(log_md, interval=LOG_INTERVAL, dyn=dyn, start_time=time.time())
+    dyn.run(steps=NUM_MD_STEPS - nsteps)
+
+
+@pytest.mark.parametrize("mlip", MODELS.items())
+def test_liquid_densities(mlip: tuple[str, Any], system_id) -> None:
+    """
+    Run Liquid Densities benchmark.
+
+    Parameters
+    ----------
+    mlip
+        Name of model use and model to get calculator.
+    system_id
+        Identifier of the system to run MD on.
+    """
+    # Download data
+    data_path = (
+        download_s3_data(
+            filename="water_density.zip",
+            key="inputs/molecular_dynamics/water_density/water_density.zip",
+        )
+        / "water_density"
+    )
+    temperature = TEMPERATURES[system_id]
+    # Get system name
+    input_xyz_path = data_path / f"water_T_{temperature:.1f}/water_equilib.xyz"
+    system_name = f"water_{temperature:.1f}_K"
+
+    model_name, model = mlip
+    model.default_dtype = "float32"
+    calc = model.get_calculator()
+    # Add D3 calculator for this test
+    calc = model.add_d3_calculator(calc)
+
+    out_dir = OUT_PATH / model_name
+    out_dir.mkdir(exist_ok=True, parents=True)
+
+    logging.basicConfig(
+        format="%(message)s",
+        level=logging.INFO,
+        filename=out_dir / f"{system_name}.log",
+        filemode="a",
+        force=True,
+    )
+
+    atoms = read(input_xyz_path)
+    output_fname = out_dir / f"{system_name}.traj"
+    run_npt(atoms, calc, output_fname, temperature)
diff --git a/ml_peg/calcs/molecular_dynamics/water_density/conftest.py b/ml_peg/calcs/molecular_dynamics/water_density/conftest.py
new file mode 100644
index 000000000..32750d7ae
--- /dev/null
+++ b/ml_peg/calcs/molecular_dynamics/water_density/conftest.py
@@ -0,0 +1,35 @@
+"""Obtain the system_id input argument."""
+
+from __future__ import annotations
+
+import pytest
+
+
+def pytest_addoption(parser):
+    """
+    Add pytest option.
+
+    Parameters
+    ----------
+    parser
+        Parser to use.
+    """
+    parser.addoption("--system_id", action="store", default=0, type=int)
+
+
+@pytest.fixture
+def system_id(request):
+    """
+    Get system_id argument.
+
+    Parameters
+    ----------
+    request
+        Request.
+
+    Returns
+    -------
+    option
+        Requested command line argument.
+    """
+    return request.config.getoption("--system_id")

From 9ce882cf9ea679a6e8190098aef2aa685428b714 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 01:00:27 +0000
Subject: [PATCH 24/27] Rename test and compute mean density from log

---
 .../WaterDensity/analyse_WaterDensity.py      | 197 ------------------
 .../WaterDensity/metrics.yml                  |   8 -
 .../WaterDensity/app_WaterDensity.py          |  69 ------
 3 files changed, 274 deletions(-)
 delete mode 100644 ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
 delete mode 100644 ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
 delete mode 100644 ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py

diff --git a/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py b/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
deleted file mode 100644
index 511598e90..000000000
--- a/ml_peg/analysis/molecular_dynamics/WaterDensity/analyse_WaterDensity.py
+++ /dev/null
@@ -1,197 +0,0 @@
-"""Analyse water densities."""
-
-from __future__ import annotations
-
-from pathlib import Path
-
-from ase import units
-import numpy as np
-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.calcs.utils.utils import download_s3_data
-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)
-
-CALC_PATH = CALCS_ROOT / "molecular_dynamics" / "WaterDensity" / "outputs"
-OUT_PATH = APP_ROOT / "data" / "molecular_dynamics" / "WaterDensity"
-
-METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
-DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
-    METRICS_CONFIG_PATH
-)
-
-EV_TO_KCAL = units.mol / units.kcal
-INFO = [270, 290, 300, 330]
-
-experimental_data = {
-    "temperature": np.array(
-        [
-            270,
-            273.15,
-            277,
-            280,
-            283,
-            286,
-            290,
-            293,
-            296,
-            300,
-            303,
-            306,
-            310,
-            313,
-            316,
-            320,
-            323,
-            326,
-            330,
-            333,
-            336,
-            340,
-        ]
-    ),
-    "density": np.array(
-        [
-            0.9998,
-            0.9999,
-            1.0000,
-            0.9999,
-            0.9998,
-            0.9997,
-            0.9991,
-            0.9985,
-            0.9978,
-            0.9970,
-            0.9957,
-            0.9944,
-            0.9927,
-            0.9910,
-            0.9893,
-            0.9871,
-            0.9849,
-            0.9827,
-            0.9802,
-            0.9777,
-            0.9752,
-            0.9723,
-        ]
-    ),  # g/cm³
-}
-
-DATA_PATH = (
-    download_s3_data(
-        filename="WaterDensities.zip",
-        key="inputs/molecular_dynamics/WaterDensities/WaterDensities.zip",
-    )
-    / "WaterDensities"
-)
-
-
-@pytest.fixture
-@plot_parity(
-    filename=OUT_PATH / "figure_WaterDensity.json",
-    title="Water density",
-    x_label="Predicted density / g/cm^3",
-    y_label="Reference density / g/cm^3",
-    hoverdata={"Labels": INFO},
-)
-def densities() -> dict[str, list]:
-    """
-    Get water density for all the teperatures.
-
-    Returns
-    -------
-    dict[str, list]
-        Dictionary of all reference and predicted densities.
-    """
-    results = {"ref": []} | {mlip: [] for mlip in MODELS}
-
-    results["ref"] = [
-        density
-        for density, temp in zip(
-            experimental_data["density"], experimental_data["temperature"], strict=False
-        )
-        if temp in INFO
-    ]
-
-    for model_name in MODELS:
-        for temperature in INFO:
-            instantaneous_densities = []
-            with open(
-                DATA_PATH / model_name / f"water_T_{temperature:.1f}" / "water.log"
-            ) as lines:
-                skip_time_ps = 500
-                for line in lines:
-                    items = line.strip().split()
-                    time = float(items[1])
-                    if time < skip_time_ps:
-                        continue
-                    instantaneous_densities.append(float(items[13]))
-
-            results[model_name].append(np.mean(instantaneous_densities))
-    return results
-
-
-@pytest.fixture
-def get_mae(densities) -> dict[str, float]:
-    """
-    Get mean absolute error for densities for all temperatures.
-
-    Parameters
-    ----------
-    densities
-        Dictionary of reference and predicted densities.
-
-    Returns
-    -------
-    dict[str, float]
-        Dictionary of predicted densities errors for all models.
-    """
-    results = {}
-    for model_name in MODELS:
-        results[model_name] = mae(densities["ref"], densities[model_name])
-    return results
-
-
-@pytest.fixture
-@build_table(
-    filename=OUT_PATH / "WaterDensity_metrics_table.json",
-    metric_tooltips=DEFAULT_TOOLTIPS,
-    thresholds=DEFAULT_THRESHOLDS,
-    weights=DEFAULT_WEIGHTS,
-    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_water_density(metrics: dict[str, dict]) -> None:
-    """
-    Run water density test.
-
-    Parameters
-    ----------
-    metrics
-        All new benchmark metric names and dictionary of values for each model.
-    """
-    return
diff --git a/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml b/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
deleted file mode 100644
index 0754e9a91..000000000
--- a/ml_peg/analysis/molecular_dynamics/WaterDensity/metrics.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-metrics:
-   MAE:
-    good: 0.0
-    bad: 0.2
-    unit: g/cm^3
-    tooltip: Mean Absolute Error in density for all systems
-    level_of_theory: Experimental density
-    weight: 1
diff --git a/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py b/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py
deleted file mode 100644
index 74fee5f61..000000000
--- a/ml_peg/app/molecular_dynamics/WaterDensity/app_WaterDensity.py
+++ /dev/null
@@ -1,69 +0,0 @@
-"""Run water density 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,
-)
-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 = "WaterDensity"
-DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/molecular_dynamics.html#Water_Density"
-DATA_PATH = APP_ROOT / "data" / "molecular_dynamics" / "WaterDensity"
-
-
-class WaterDensityApp(BaseApp):
-    """Water density benchmark app layout and callbacks."""
-
-    def register_callbacks(self) -> None:
-        """Register callbacks to app."""
-        scatter = read_plot(
-            DATA_PATH / "figure_water_density.json",
-            id=f"{BENCHMARK_NAME}-figure",
-        )
-
-        plot_from_table_column(
-            table_id=self.table_id,
-            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
-            column_to_plot={"MAE": scatter},
-        )
-
-
-def get_app() -> WaterDensityApp:
-    """
-    Get water density benchmark app layout and callback registration.
-
-    Returns
-    -------
-    WaterDensityApp
-        Benchmark layout and callback registration.
-    """
-    return WaterDensityApp(
-        name=BENCHMARK_NAME,
-        description=(
-            "Performance in predicting water density at different temperatures."
-            "Reference data is experimental densities."
-        ),
-        docs_url=DOCS_URL,
-        table_path=DATA_PATH / "water_density_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=8063, debug=True)

From 9adbfec7808c0d92c788ba8ffb675fc2b7e1b103 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 13:48:20 +0000
Subject: [PATCH 25/27] Water density app

---
 .../water_density/analyse_water_density.py    | 182 ++++++++++++++++++
 .../water_density/metrics.yml                 |   8 +
 2 files changed, 190 insertions(+)
 create mode 100644 ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
 create mode 100644 ml_peg/analysis/molecular_dynamics/water_density/metrics.yml

diff --git a/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py b/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
new file mode 100644
index 000000000..7dc8fc624
--- /dev/null
+++ b/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
@@ -0,0 +1,182 @@
+"""Analyse the water density benchmark."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+from ase.io import Trajectory, write
+import numpy as np
+import pytest
+
+from ml_peg.analysis.utils.decorators import build_table, plot_parity
+from ml_peg.analysis.utils.utils import (
+    build_dispersion_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_dispersion_name_map(MODELS)
+
+INTERVAL_PS = 1
+EQUILIB_TIME_PS = 2
+
+CALC_PATH = CALCS_ROOT / "molecular_dynamics" / "water_density" / "outputs"
+OUT_PATH = APP_ROOT / "data" / "molecular_dynamics" / "water_density"
+
+
+METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml")
+DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config(
+    METRICS_CONFIG_PATH
+)
+
+EXPERIMENTAL_DATA = {
+    "water_270.0_K": 0.9998,
+    "water_290.0_K": 0.9991,
+    "water_300.0_K": 0.9970,
+    "water_330.0_K": 0.9802,
+}
+
+
+def labels() -> list:
+    """
+    Get list of system names.
+
+    Returns
+    -------
+    list
+        List of all system names.
+    """
+    for model_name in MODELS:
+        return [path.stem for path in (CALC_PATH / model_name).glob("*.log")]
+    return []
+
+
+def compute_density(fname, density_col=13):
+    """
+    Compute average density from NPT log file.
+
+    Parameters
+    ----------
+    fname
+        Path to the log file.
+    density_col
+        Which column the density numbers are in.
+
+    Returns
+    -------
+    float
+        Average density in g/cm3.
+    """
+    density_series = []
+    with open(fname) as lines:
+        for line in lines:
+            items = line.strip().split()
+            if len(items) != 15:
+                continue
+            density_series.append(float(items[13]))
+    skip_frames = int(EQUILIB_TIME_PS / INTERVAL_PS)
+    return np.mean(density_series[skip_frames:])
+
+
+@pytest.fixture
+@plot_parity(
+    filename=OUT_PATH / "figure_water_density.json",
+    title="Densities",
+    x_label="Predicted density / kcal/mol",
+    y_label="Reference density / kcal/mol",
+    hoverdata={
+        "Labels": labels(),
+    },
+)
+def water_density() -> dict[str, list]:
+    """
+    Get water densities for all temperatures.
+
+    Returns
+    -------
+    dict[str, list]
+        Dictionary of all reference and predicted densities.
+    """
+    results = {"ref": []} | {mlip: [] for mlip in MODELS}
+    ref_stored = False
+
+    for model_name in MODELS:
+        for label in labels():
+            atoms = Trajectory(CALC_PATH / model_name / f"{label}.traj")[-1]
+
+            results[model_name].append(
+                compute_density(CALC_PATH / model_name / f"{label}.log")
+            )
+            if not ref_stored:
+                results["ref"].append(EXPERIMENTAL_DATA[label])
+
+            # Write structures for app
+            structs_dir = OUT_PATH / model_name
+            structs_dir.mkdir(parents=True, exist_ok=True)
+            write(structs_dir / f"{label}.xyz", atoms)
+        ref_stored = True
+    return results
+
+
+@pytest.fixture
+def get_mae(water_density) -> dict[str, float]:
+    """
+    Get mean absolute error for water densities.
+
+    Parameters
+    ----------
+    water_density
+        Dictionary of reference and predicted water densities.
+
+    Returns
+    -------
+    dict[str, float]
+        Dictionary of predicted water density errors for all models.
+    """
+    results = {}
+    for model_name in MODELS:
+        results[model_name] = mae(water_density["ref"], water_density[model_name])
+    return results
+
+
+@pytest.fixture
+@build_table(
+    filename=OUT_PATH / "water_density_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_water_density(metrics: dict[str, dict]) -> None:
+    """
+    Run water density test.
+
+    Parameters
+    ----------
+    metrics
+        All new benchmark metric names and dictionary of values for each model.
+    """
+    return
diff --git a/ml_peg/analysis/molecular_dynamics/water_density/metrics.yml b/ml_peg/analysis/molecular_dynamics/water_density/metrics.yml
new file mode 100644
index 000000000..0754e9a91
--- /dev/null
+++ b/ml_peg/analysis/molecular_dynamics/water_density/metrics.yml
@@ -0,0 +1,8 @@
+metrics:
+   MAE:
+    good: 0.0
+    bad: 0.2
+    unit: g/cm^3
+    tooltip: Mean Absolute Error in density for all systems
+    level_of_theory: Experimental density
+    weight: 1

From 2aede59da8190369f8a9e1267172f6e7fe4a32a9 Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 13:49:38 +0000
Subject: [PATCH 26/27] Water density app

---
 .../water_density/app_water_density.py        | 69 +++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 ml_peg/app/molecular_dynamics/water_density/app_water_density.py

diff --git a/ml_peg/app/molecular_dynamics/water_density/app_water_density.py b/ml_peg/app/molecular_dynamics/water_density/app_water_density.py
new file mode 100644
index 000000000..b5f7c5769
--- /dev/null
+++ b/ml_peg/app/molecular_dynamics/water_density/app_water_density.py
@@ -0,0 +1,69 @@
+"""Run water density 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,
+)
+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 = "WaterDensity"
+DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/molecular_dynamics.html#Water_Density"
+DATA_PATH = APP_ROOT / "data" / "molecular_dynamics" / "water_density"
+
+
+class WaterDensityApp(BaseApp):
+    """Water density benchmark app layout and callbacks."""
+
+    def register_callbacks(self) -> None:
+        """Register callbacks to app."""
+        scatter = read_plot(
+            DATA_PATH / "figure_water_density.json",
+            id=f"{BENCHMARK_NAME}-figure",
+        )
+
+        plot_from_table_column(
+            table_id=self.table_id,
+            plot_id=f"{BENCHMARK_NAME}-figure-placeholder",
+            column_to_plot={"MAE": scatter},
+        )
+
+
+def get_app() -> WaterDensityApp:
+    """
+    Get water density benchmark app layout and callback registration.
+
+    Returns
+    -------
+    WaterDensityApp
+        Benchmark layout and callback registration.
+    """
+    return WaterDensityApp(
+        name=BENCHMARK_NAME,
+        description=(
+            "Performance in predicting water density at different temperatures."
+            "Reference data is experimental densities."
+        ),
+        docs_url=DOCS_URL,
+        table_path=DATA_PATH / "water_density_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=8063, debug=True)

From a3148504f4de5ffa14f544262f8b1443db83667f Mon Sep 17 00:00:00 2001
From: Domantas Kuryla <dk584@icepc16>
Date: Thu, 12 Mar 2026 13:50:37 +0000
Subject: [PATCH 27/27] Reset default equilib time and log interval in analysis

---
 .../molecular_dynamics/water_density/analyse_water_density.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py b/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
index 7dc8fc624..b8516743c 100644
--- a/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
+++ b/ml_peg/analysis/molecular_dynamics/water_density/analyse_water_density.py
@@ -22,8 +22,8 @@
 MODELS = load_models(current_models)
 D3_MODEL_NAMES = build_dispersion_name_map(MODELS)
 
-INTERVAL_PS = 1
-EQUILIB_TIME_PS = 2
+INTERVAL_PS = 0.1
+EQUILIB_TIME_PS = 500
 
 CALC_PATH = CALCS_ROOT / "molecular_dynamics" / "water_density" / "outputs"
 OUT_PATH = APP_ROOT / "data" / "molecular_dynamics" / "water_density"