From f4b13f3236cf41e04c6fdb5e330464ac0fde9651 Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Wed, 28 Jan 2026 18:58:15 +0000 Subject: [PATCH 01/16] Initial ox_state calc directory --- .../oxidation_states/calc_oxidation_states.py | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py new file mode 100644 index 000000000..734473483 --- /dev/null +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -0,0 +1,87 @@ +"""Run calculation for aqueous FeCl oxidation states.""" + +from __future__ import annotations + +from pathlib import Path +from typing import Any + +from ase import Atoms, units +from ase.io import read +from janus_core.calculations.geom_opt import GeomOpt +from janus_core.calculations.md import NPT +from janus_core.calculations.single_point import SinglePoint +import numpy as np +import pytest + +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" + +IRON_SALTS = ["Fe2Cl, Fe3Cl"] + +@pytest.mark.slow +@pytest.mark.parametrize("mlip", MODELS.items()) +def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: + """ + Run MLMD for aqueous FeCl oxidation states tests. + + Parameters + ---------- + mlip + Name of model use and model to get calculator. + """ + + + for salt in IRON_SALTS: + struct_path = DATA_PATH / f"{salt}_start.xyz" + struct = read(struct_path, "0") + + npt = NPT( + struct=struct, + steps=40000, + timestep=0.5, + stats_every=50, + traj_every=50, + traj_append=True, + thermostat_time=50, + bulk_modulus=10, + barostat_time=1500, + pressure=pressure, + file_prefix=OUT_PATH / f"{salt}_{mlip}", + restart=True, + restart_auto=False, + ) + npt.run() + + +@pytest.mark.parametrize("mlip", MODELS.items()) +def test_static_md(mlip: tuple[str, Any]) -> None: + """ + Evaluate an existing AIMD trajectory for the static high-pressure hydrogen tests. + + Parameters + ---------- + mlip + Name of model use and model to get calculator. + """ + struct_path = DATA_PATH / "Hpres.xyz" + + model_name, model = mlip + calc = model.get_calculator() + + structs = read(struct_path, index="::50") + structs.calc = calc + for struct in structs: + struct.info["density"] = ( + np.sum(struct.get_masses()) / struct.get_volume() * DENS_FACT + ) + + SinglePoint( + struct=structs, + write_results=True, + file_prefix=OUT_PATH / f"H-static-{mlip}", + ).run() From e362d653819a75cf86a3b8b5b11095b1870db2ab Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Thu, 5 Feb 2026 22:09:25 +0000 Subject: [PATCH 02/16] Test calc script for aqueous iron chloride MD --- .../oxidation_states/calc_oxidation_states.py | 58 +++++-------------- 1 file changed, 16 insertions(+), 42 deletions(-) diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index 734473483..4ac182a89 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -5,12 +5,8 @@ from pathlib import Path from typing import Any -from ase import Atoms, units from ase.io import read -from janus_core.calculations.geom_opt import GeomOpt from janus_core.calculations.md import NPT -from janus_core.calculations.single_point import SinglePoint -import numpy as np import pytest from ml_peg.models.get_models import load_models @@ -21,7 +17,8 @@ DATA_PATH = Path(__file__).parent / "data" OUT_PATH = Path(__file__).parent / "outputs" -IRON_SALTS = ["Fe2Cl, Fe3Cl"] +IRON_SALTS = ["Fe2Cl", "Fe3Cl"] + @pytest.mark.slow @pytest.mark.parametrize("mlip", MODELS.items()) @@ -34,54 +31,31 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: mlip 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) for salt in IRON_SALTS: struct_path = DATA_PATH / f"{salt}_start.xyz" struct = read(struct_path, "0") + struct.calc = calc npt = NPT( struct=struct, - steps=40000, + steps=200, timestep=0.5, - stats_every=50, - traj_every=50, + stats_every=100, + traj_every=200, traj_append=True, thermostat_time=50, bulk_modulus=10, - barostat_time=1500, - pressure=pressure, - file_prefix=OUT_PATH / f"{salt}_{mlip}", - restart=True, - restart_auto=False, + barostat_time=None, + # pressure=pressure, + file_prefix=OUT_PATH / f"{salt}_{model_name}", + # restart=True, + # restart_auto=True, + # post_process_kwargs={"rdf_compute": True, "rdf_rmax": 6, "rdf_bins": 120}, ) npt.run() - - -@pytest.mark.parametrize("mlip", MODELS.items()) -def test_static_md(mlip: tuple[str, Any]) -> None: - """ - Evaluate an existing AIMD trajectory for the static high-pressure hydrogen tests. - - Parameters - ---------- - mlip - Name of model use and model to get calculator. - """ - struct_path = DATA_PATH / "Hpres.xyz" - - model_name, model = mlip - calc = model.get_calculator() - - structs = read(struct_path, index="::50") - structs.calc = calc - for struct in structs: - struct.info["density"] = ( - np.sum(struct.get_masses()) / struct.get_volume() * DENS_FACT - ) - - SinglePoint( - struct=structs, - write_results=True, - file_prefix=OUT_PATH / f"H-static-{mlip}", - ).run() From 543c3e4d4ded1d2bbfe12cb69f41c0a0221b4ad1 Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Fri, 6 Feb 2026 19:38:56 +0000 Subject: [PATCH 03/16] Core setup of Fe_oxidation_states benchmarks - fix to remove unecessary data files --- .../analyse_oxidation_states.py | 182 ++++++++++++++++++ .../physicality/oxidation_states/metrics.yml | 11 ++ ml_peg/analysis/utils/decorators.py | 32 ++- .../oxidation_states/app_oxidation_states.py | 88 +++++++++ .../oxidation_states/calc_oxidation_states.py | 51 ++++- pyproject.toml | 7 +- uv.lock | 112 ++++++++++- 7 files changed, 464 insertions(+), 19 deletions(-) create mode 100644 ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py create mode 100644 ml_peg/analysis/physicality/oxidation_states/metrics.yml create mode 100644 ml_peg/app/physicality/oxidation_states/app_oxidation_states.py diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py new file mode 100644 index 000000000..a5f218951 --- /dev/null +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -0,0 +1,182 @@ +"""Analyse aqueous Iron Chloride oxidation states.""" + +from __future__ import annotations + +from pathlib import Path + +import numpy as np +import pytest + +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 + +# MODELS = get_model_names(current_models) + +MODELS = ["mace-mp-0b3", "0totchrg_2L_fl32_new"] + +CALC_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "outputs" +OUT_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" + +METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml") +DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, _ = load_metrics_config(METRICS_CONFIG_PATH) + +IRON_SALTS = ["Fe2Cl", "Fe3Cl"] +TESTS = ["Fe-O RDF Peak Split", "Peak Within DFT Ref"] +REF_PEAK_RANGE = { + "Fe+2
Ref": [2.0, 2.2], + "Fe+3
Ref": [1.9, 2.0], +} + + +def get_rdf_results( + model: str, +) -> dict[str, tuple[list[float], list[float]]]: + """ + Get a model's Fe-O RDFs for the aqueous Fe2Cl and Fe3Cl MD. + + Parameters + ---------- + model + Name of MLIP. + + Returns + ------- + results + RDF Radii and intensities for the aqueous Fe2Cl and Fe3Cl systems. + """ + results = {salt: [] for salt in IRON_SALTS} + + for salt in IRON_SALTS: + rdf_file = CALC_PATH / f"OFe_inter_{salt}_{model}.rdf" + + fe_o_rdf = np.loadtxt(rdf_file) + r = list(fe_o_rdf[:, 0]) + g_r = list(fe_o_rdf[:, 1]) + + results[salt].append(r) + results[salt].append(g_r) + + return results + + +def plot_rdfs(model: str, results: dict[str, tuple[list[float], list[float]]]) -> None: + """ + Plot Fe-O RDFs. + + Parameters + ---------- + model + Name of MLIP. + results + RDF Radii and intensities for the aqueous Fe2Cl and Fe3Cl systems. + """ + + @plot_scatter( + filename=OUT_PATH / f"Fe-O_{model}_RDF_scatter.json", + title="Fe-O RDF", + x_label="R / Å", + y_label="Fe-O G(r)", + show_line=True, + show_markers=False, + highlight_area=True, + highlight_range=REF_PEAK_RANGE, + ) + def plot_result() -> dict[str, tuple[list[float], list[float]]]: + """ + Plot the RDFs. + + Returns + ------- + model_results + Dictionary of model Fe-O RDFs for the aqueous Fe2Cl and Fe3Cl systems. + """ + return results + + plot_result() + + +@pytest.fixture +def get_oxidation_states_passfail() -> dict[str, dict]: + """ + Test whether model RDF peaks are split and they fall within the reference range. + + Returns + ------- + oxidation_states_passfail + Dictionary of pass fail per model. + """ + oxidation_state_passfail = {test: {} for test in TESTS} + + fe_2_ref = [2.0, 2.2] + fe_3_ref = [1.9, 2.0] + + for model in MODELS: + peak_positions = {} + results = get_rdf_results(model) + plot_rdfs(model, results) + + for salt in IRON_SALTS: + r = results[salt][0] + g_r = results[salt][1] + peak_positions[salt] = r[g_r.index(max(g_r))] + + peak_difference = abs(peak_positions["Fe2Cl"] - peak_positions["Fe3Cl"]) + + if peak_difference > 0.05: + oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 1.0 + + if ( + fe_2_ref[0] <= peak_positions["Fe2Cl"] <= fe_2_ref[1] + and fe_3_ref[0] <= peak_positions["Fe3Cl"] <= fe_3_ref[1] + ): + oxidation_state_passfail["Peak Within DFT Ref"][model] = 1.0 + + else: + oxidation_state_passfail["Peak Within DFT Ref"][model] = 1.0 + + else: + oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 0.0 + oxidation_state_passfail["Peak Within DFT Ref"][model] = 0.0 + + return oxidation_state_passfail + + +@pytest.fixture +@build_table( + filename=OUT_PATH / "oxidation_states_table.json", + metric_tooltips=DEFAULT_TOOLTIPS, + thresholds=DEFAULT_THRESHOLDS, +) +def oxidation_states_passfail_metrics( + get_oxidation_states_passfail: dict[str, dict], +) -> dict[str, dict]: + """ + Get all oxidation states pass fail metrics. + + Parameters + ---------- + get_oxidation_states_passfail + Dictionary of pass fail per model. + + Returns + ------- + dict[str, dict] + Dictionary of pass fail per model. + """ + return get_oxidation_states_passfail + + +def test_oxidation_states_passfail_metrics( + oxidation_states_passfail_metrics: dict[str, dict], +) -> None: + """ + Run oxidation states test. + + Parameters + ---------- + oxidation_states_passfail_metrics + All oxidation states pass fail. + """ + return diff --git a/ml_peg/analysis/physicality/oxidation_states/metrics.yml b/ml_peg/analysis/physicality/oxidation_states/metrics.yml new file mode 100644 index 000000000..449e0b810 --- /dev/null +++ b/ml_peg/analysis/physicality/oxidation_states/metrics.yml @@ -0,0 +1,11 @@ +metrics: + Fe-O RDF Peak Split: + good: 0.5 + bad: 0.0 + unit: null + tooltip: Whether there is a split between Fe-O RDF peaks for different iron oxidation states + Peak Within DFT Ref: + good: 0.5 + bad: 0.0 + unit: null + tooltip: Whether the RDF peak positions match PBE peaks diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index cdcc72ba8..6ff98f8a5 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -13,6 +13,7 @@ from dash import dash_table import numpy as np import pandas as pd +import plotly.colors as pc import plotly.graph_objects as go from ml_peg.analysis.utils.utils import calc_table_scores @@ -431,8 +432,11 @@ def plot_scatter( x_label: str | None = None, y_label: str | None = None, show_line: bool = False, + show_markers: bool = True, hoverdata: dict | None = None, filename: str = "scatter.json", + highlight_area: bool = False, + highlight_range: dict = None, ) -> Callable: """ Plot scatter plot of MLIP results. @@ -447,10 +451,16 @@ def plot_scatter( Label for y-axis. Default is `None`. show_line Whether to show line between points. Default is False. + show_markers + Whether to show markers on the plot. Default is True. hoverdata Hover data dictionary. Default is `{}`. filename Filename to save plot as JSON. Default is "scatter.json". + highlight_area + Whether to add a highlighted rectangle to the plot. + highlight_range + Dictionary of rectangle title and x-axis endpoints. Returns ------- @@ -499,7 +509,13 @@ def plot_scatter_wrapper(*args, **kwargs) -> dict[str, Any]: hovertemplate += f"{key}: %{{customdata[{i}]}}
" customdata = list(zip(*hoverdata.values(), strict=True)) - mode = "lines+markers" if show_line else "markers" + modes = [] + if show_line: + modes.append("lines") + if show_markers: + modes.append("markers") + + mode = "+".join(modes) fig = go.Figure() for mlip, value in results.items(): @@ -515,6 +531,20 @@ def plot_scatter_wrapper(*args, **kwargs) -> dict[str, Any]: ) ) + colors = pc.qualitative.Plotly + + if highlight_area: + for i, (title, range) in enumerate(highlight_range.items()): + fig.add_vrect( + x0=range[0], + x1=range[1], + annotation_text=title, + annotation_position="top", + fillcolor=colors[i], + opacity=0.25, + line_width=0, + ) + fig.update_layout( title={"text": title}, xaxis={"title": {"text": x_label}}, diff --git a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py new file mode 100644 index 000000000..259fa3744 --- /dev/null +++ b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py @@ -0,0 +1,88 @@ +"""Run oxidation states 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_cell, +) +from ml_peg.app.utils.load import read_plot +from ml_peg.calcs import CALCS_ROOT + +# MODELS = get_model_names(current_models) +MODELS = ["mace-mp-0b3", "omol", "0totchrg_2L_fl32_new"] + +BENCHMARK_NAME = "Iron Oxidation States" +DATA_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" +REF_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "data" + + +class FeOxidationStatesApp(BaseApp): + """Fe Oxidation States benchmark app layout and callbacks.""" + + def register_callbacks(self) -> None: + """Register callbacks to app.""" + scatter_plots = { + model: { + "Fe-O RDF Peak Split": read_plot( + DATA_PATH / f"Fe-O_{model}_RDF_scatter.json", + id=f"{BENCHMARK_NAME}-{model}-figure-Fe-O-RDF", + ), + "Peak Within DFT Ref": read_plot( + DATA_PATH / f"Fe-O_{model}_RDF_scatter.json", + id=f"{BENCHMARK_NAME}-{model}-figure-Fe-O-RDF", + ), + } + for model in MODELS + } + + plot_from_table_cell( + table_id=self.table_id, + plot_id=f"{BENCHMARK_NAME}-figure-placeholder", + cell_to_plot=scatter_plots, + ) + + +def get_app() -> FeOxidationStatesApp: + """ + Get Fe Oxidation States benchmark app layout and callback registration. + + Returns + ------- + FeOxidationStatesApp + Benchmark layout and callback registration. + """ + return FeOxidationStatesApp( + name=BENCHMARK_NAME, + description=( + "Evaluate model ability to capture different oxidation states of Fe" + "from aqueous Fe 2Cl and Fe 3Cl MD RDFs" + ), + # docs_url=DOCS_URL, + table_path=DATA_PATH / "oxidation_states_table.json", + extra_components=[ + Div(id=f"{BENCHMARK_NAME}-figure-placeholder"), + Div(id=f"{BENCHMARK_NAME}-struct-placeholder"), + ], + ) + + +if __name__ == "__main__": + # Create Dash app + full_app = Dash( + __name__, + assets_folder=DATA_PATH.parent.parent, + suppress_callback_exceptions=True, + ) + + # Construct layout and register callbacks + FeOxidationStatesApp = get_app() + full_app.layout = FeOxidationStatesApp.layout + FeOxidationStatesApp.register_callbacks() + + # Run app + full_app.run(port=8054, debug=True) diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index 4ac182a89..41c831b2c 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -6,7 +6,9 @@ from typing import Any from ase.io import read +from aseMolec import anaAtoms from janus_core.calculations.md import NPT +import numpy as np import pytest from ml_peg.models.get_models import load_models @@ -20,7 +22,7 @@ IRON_SALTS = ["Fe2Cl", "Fe3Cl"] -@pytest.mark.slow +@pytest.mark.very_slow @pytest.mark.parametrize("mlip", MODELS.items()) def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: """ @@ -29,9 +31,13 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: Parameters ---------- mlip - Name of model use and model to get calculator. + Name of model use and model. """ model_name, model = mlip + model.device = "cuda" + model.default_dtype = "float32" + model.kwargs["enable_cueq"] = True + calc = model.get_calculator() # Add D3 calculator for this test @@ -44,18 +50,43 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: npt = NPT( struct=struct, - steps=200, + steps=40000, timestep=0.5, - stats_every=100, - traj_every=200, + stats_every=50, + traj_every=100, traj_append=True, thermostat_time=50, - bulk_modulus=10, barostat_time=None, - # pressure=pressure, file_prefix=OUT_PATH / f"{salt}_{model_name}", - # restart=True, - # restart_auto=True, - # post_process_kwargs={"rdf_compute": True, "rdf_rmax": 6, "rdf_bins": 120}, ) npt.run() + + +@pytest.mark.parametrize("mlip", MODELS.items()) +def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: + """ + Calculate Fe-O RDFs from MLMD for oxidation states tests. + + Parameters + ---------- + mlip + Name of model used and model. + """ + model_name, model = mlip + fct = {"Fe": 0.1, "O": 0.7, "H": 0.7, "Cl": 0.1} + + for salt in IRON_SALTS: + md_path = OUT_PATH / f"{salt}_{model_name}-traj.extxyz" + traj = read(md_path, ":") + rdfs, radii = anaAtoms.compute_rdfs_traj_avg( + traj, rmax=6.0, nbins=100, fct=fct + ) # need to skip initial equilibration frames + + rdf_data = np.column_stack((radii, rdfs["OFe_inter"])) + + rdf_path = OUT_PATH / f"OFe_inter_{salt}_{model_name}.rdf" + np.savetxt( + rdf_path, + rdf_data, + header="r g(r)", + ) diff --git a/pyproject.toml b/pyproject.toml index ad9493ff6..b0e7a7183 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -37,6 +37,7 @@ dependencies = [ "MDAnalysis", "openpyxl", "tqdm", + "aseMolec @ https://github.com/imagdau/aseMolec.git" ] [project.optional-dependencies] @@ -53,7 +54,11 @@ grace = [ "tensorpotential == 0.5.1; python_version < '3.13'", ] mace = [ - "mace-torch==0.3.14", + "mace-torch @ https://github.com/ACEsuit/mace.git", + "cuequivariance==0.8.1", + "cuequivariance-ops-cu12==0.8.1", + "cuequivariance-ops-torch-cu12==0.8.1", + "cuequivariance-torch==0.8.1", ] mattersim = [ diff --git a/uv.lock b/uv.lock index 9a9810a70..e3730a954 100644 --- a/uv.lock +++ b/uv.lock @@ -502,6 +502,32 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/90/24/35e57bdbd6d1c37ae889b669c4bf06b159fa275afe189a81460d392d187e/ase_db_backends-0.11.0-py3-none-any.whl", hash = "sha256:dd5959b9a3cbe3deb5726724afa0045d7d009e04e08be5f4b7ffae703a563a99", size = 44738, upload-time = "2025-11-12T08:02:49.215Z" }, ] +[[package]] +name = "ase-ga" +version = "1.0.3" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "ase" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/62/3f/0cb20510b115ac2eef57cca0551e8e59c439c1617daaeba352b161faa28b/ase_ga-1.0.3.tar.gz", hash = "sha256:48997ca75ac0db5aeb9cdee4c7c0f406dbb0921e173272360bdbb73cdab3c767", size = 237296, upload-time = "2025-11-06T14:47:53.317Z" } +wheels = [ + { url = 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">=1.40.49,<2" }, { name = "chgnet", marker = "extra == 'chgnet'", specifier = "==0.4.0" }, + { name = "cuequivariance", marker = "extra == 'mace'", specifier = "==0.8.1" }, + { name = "cuequivariance-ops-cu12", marker = "extra == 'mace'", specifier = "==0.8.1" }, + { name = "cuequivariance-ops-torch-cu12", marker = "extra == 'mace'", specifier = "==0.8.1" }, + { name = "cuequivariance-torch", marker = "extra == 'mace'", specifier = "==0.8.1" }, { name = "dash", specifier = ">=3.1.1" }, { 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 = "mace-torch", marker = "extra == 'mace'", specifier = "==0.3.14" }, + { name = "mace-torch", marker = "extra == 'mace'", git = "https://github.com/ACEsuit/mace.git" }, { name = "matcalc" }, { name = "matminer" }, { name = "mattersim", marker = "extra == 'mattersim'", specifier = "==1.2.0" }, From ba819fc473c0f5a68117fe90a2a8cca807788947 Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Fri, 13 Feb 2026 12:51:02 +0000 Subject: [PATCH 04/16] Fix metrics, highlight ref on the plots, fix analysis, add rdf calculation function - edited to remove unecessary data files --- .../analyse_oxidation_states.py | 32 +- .../physicality/oxidation_states/metrics.yml | 9 +- .../oxidation_states/app_oxidation_states.py | 4 +- .../oxidation_states/calc_oxidation_states.py | 29 +- .../oxidation_states/data/Fe2Cl_start.xyz | 341 +++++++++++++++++ .../oxidation_states/data/Fe3Cl_start.xyz | 342 ++++++++++++++++++ .../outputs/Fe2Cl_mace-mp-0b3-final.extxyz | 341 +++++++++++++++++ .../outputs/Fe2Cl_omol-final.extxyz | 341 +++++++++++++++++ .../outputs/Fe3Cl_mace-mp-0b3-final.extxyz | 342 ++++++++++++++++++ .../outputs/Fe3Cl_omol-final.extxyz | 342 ++++++++++++++++++ .../outputs/O-Fe_Fe2Cl_mace-mp-0b3.rdf | 201 ++++++++++ .../outputs/O-Fe_Fe2Cl_omol.rdf | 151 ++++++++ .../outputs/O-Fe_Fe3Cl_mace-mp-0b3.rdf | 201 ++++++++++ .../outputs/O-Fe_Fe3Cl_omol.rdf | 151 ++++++++ 14 files changed, 2791 insertions(+), 36 deletions(-) create mode 100644 ml_peg/calcs/physicality/oxidation_states/data/Fe2Cl_start.xyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/data/Fe3Cl_start.xyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/Fe2Cl_mace-mp-0b3-final.extxyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/Fe2Cl_omol-final.extxyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/Fe3Cl_mace-mp-0b3-final.extxyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/Fe3Cl_omol-final.extxyz create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_mace-mp-0b3.rdf create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_omol.rdf create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_mace-mp-0b3.rdf create mode 100644 ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_omol.rdf diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py index a5f218951..3c37a200e 100644 --- a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -14,7 +14,7 @@ # MODELS = get_model_names(current_models) -MODELS = ["mace-mp-0b3", "0totchrg_2L_fl32_new"] +MODELS = ["mace-mp-0b3", "omol"] CALC_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "outputs" OUT_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" @@ -23,7 +23,7 @@ DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, _ = load_metrics_config(METRICS_CONFIG_PATH) IRON_SALTS = ["Fe2Cl", "Fe3Cl"] -TESTS = ["Fe-O RDF Peak Split", "Peak Within DFT Ref"] +TESTS = ["Fe-O RDF Peak Split", "Peak Within Experimental Ref"] REF_PEAK_RANGE = { "Fe+2
Ref": [2.0, 2.2], "Fe+3
Ref": [1.9, 2.0], @@ -49,7 +49,7 @@ def get_rdf_results( results = {salt: [] for salt in IRON_SALTS} for salt in IRON_SALTS: - rdf_file = CALC_PATH / f"OFe_inter_{salt}_{model}.rdf" + rdf_file = CALC_PATH / f"O-Fe_{salt}_{model}.rdf" fe_o_rdf = np.loadtxt(rdf_file) r = list(fe_o_rdf[:, 0]) @@ -113,32 +113,28 @@ def get_oxidation_states_passfail() -> dict[str, dict]: fe_3_ref = [1.9, 2.0] for model in MODELS: - peak_positions = {} + peak_position = {} results = get_rdf_results(model) plot_rdfs(model, results) for salt in IRON_SALTS: r = results[salt][0] g_r = results[salt][1] - peak_positions[salt] = r[g_r.index(max(g_r))] + peak_position[salt] = r[g_r.index(max(g_r))] - peak_difference = abs(peak_positions["Fe2Cl"] - peak_positions["Fe3Cl"]) + peak_difference = abs(peak_position["Fe2Cl"] - peak_position["Fe3Cl"]) - if peak_difference > 0.05: - oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 1.0 + oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 0.0 + oxidation_state_passfail["Peak Within Experimental Ref"][model] = 0.0 - if ( - fe_2_ref[0] <= peak_positions["Fe2Cl"] <= fe_2_ref[1] - and fe_3_ref[0] <= peak_positions["Fe3Cl"] <= fe_3_ref[1] - ): - oxidation_state_passfail["Peak Within DFT Ref"][model] = 1.0 + if peak_difference > 0.1: + oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 1.0 - else: - oxidation_state_passfail["Peak Within DFT Ref"][model] = 1.0 + if fe_2_ref[0] <= peak_position["Fe2Cl"] <= fe_2_ref[1]: + oxidation_state_passfail["Peak Within Experimental Ref"][model] += 0.5 - else: - oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 0.0 - oxidation_state_passfail["Peak Within DFT Ref"][model] = 0.0 + if fe_3_ref[0] <= peak_position["Fe3Cl"] <= fe_3_ref[1]: + oxidation_state_passfail["Peak Within Experimental Ref"][model] += 0.5 return oxidation_state_passfail diff --git a/ml_peg/analysis/physicality/oxidation_states/metrics.yml b/ml_peg/analysis/physicality/oxidation_states/metrics.yml index 449e0b810..3b679212c 100644 --- a/ml_peg/analysis/physicality/oxidation_states/metrics.yml +++ b/ml_peg/analysis/physicality/oxidation_states/metrics.yml @@ -1,11 +1,12 @@ metrics: Fe-O RDF Peak Split: - good: 0.5 + good: 1.0 bad: 0.0 - unit: null + unit: Yes(1)/No(0) tooltip: Whether there is a split between Fe-O RDF peaks for different iron oxidation states - Peak Within DFT Ref: - good: 0.5 + Peak Within Experimental Ref: + good: 1.0 bad: 0.0 unit: null tooltip: Whether the RDF peak positions match PBE peaks + level_of_theory: Experiment diff --git a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py index 259fa3744..1aaabc794 100644 --- a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py +++ b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py @@ -14,7 +14,7 @@ from ml_peg.calcs import CALCS_ROOT # MODELS = get_model_names(current_models) -MODELS = ["mace-mp-0b3", "omol", "0totchrg_2L_fl32_new"] +MODELS = ["mace-mp-0b3", "omol"] BENCHMARK_NAME = "Iron Oxidation States" DATA_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" @@ -32,7 +32,7 @@ def register_callbacks(self) -> None: DATA_PATH / f"Fe-O_{model}_RDF_scatter.json", id=f"{BENCHMARK_NAME}-{model}-figure-Fe-O-RDF", ), - "Peak Within DFT Ref": read_plot( + "Peak Within Experimental Ref": read_plot( DATA_PATH / f"Fe-O_{model}_RDF_scatter.json", id=f"{BENCHMARK_NAME}-{model}-figure-Fe-O-RDF", ), diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index 41c831b2c..210a1053e 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -5,8 +5,8 @@ from pathlib import Path from typing import Any +from ase.geometry.rdf import get_rdf from ase.io import read -from aseMolec import anaAtoms from janus_core.calculations.md import NPT import numpy as np import pytest @@ -34,9 +34,7 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: Name of model use and model. """ model_name, model = mlip - model.device = "cuda" model.default_dtype = "float32" - model.kwargs["enable_cueq"] = True calc = model.get_calculator() @@ -65,7 +63,7 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: @pytest.mark.parametrize("mlip", MODELS.items()) def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: """ - Calculate Fe-O RDFs from MLMD for oxidation states tests. + Calculate Fe-O RDFs from NVT MLMD for oxidation states tests. Parameters ---------- @@ -73,18 +71,25 @@ def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: Name of model used and model. """ model_name, model = mlip - fct = {"Fe": 0.1, "O": 0.7, "H": 0.7, "Cl": 0.1} + rmax = 6.0 + nbins = 200 for salt in IRON_SALTS: + rdf_list = [] md_path = OUT_PATH / f"{salt}_{model_name}-traj.extxyz" traj = read(md_path, ":") - rdfs, radii = anaAtoms.compute_rdfs_traj_avg( - traj, rmax=6.0, nbins=100, fct=fct - ) # need to skip initial equilibration frames - - rdf_data = np.column_stack((radii, rdfs["OFe_inter"])) - - rdf_path = OUT_PATH / f"OFe_inter_{salt}_{model_name}.rdf" + for atoms in traj: + rdf, r = get_rdf( + atoms, + rmax=rmax, + nbins=nbins, + elements=(26, 8), # Fe (26), O (8) + ) + rdf_list.append(rdf) + g_mean = np.mean(rdf_list, axis=0) # NVT so this is ok + + rdf_data = np.column_stack((r, g_mean)) + rdf_path = OUT_PATH / f"O-Fe_{salt}_{model_name}.rdf" np.savetxt( rdf_path, rdf_data, diff --git a/ml_peg/calcs/physicality/oxidation_states/data/Fe2Cl_start.xyz b/ml_peg/calcs/physicality/oxidation_states/data/Fe2Cl_start.xyz new file mode 100644 index 000000000..5bed05d32 --- /dev/null +++ b/ml_peg/calcs/physicality/oxidation_states/data/Fe2Cl_start.xyz @@ -0,0 +1,341 @@ +339 +Lattice="14.653976132640961 0.0 0.0 0.0 14.653976132640961 0.0 0.0 0.0 14.653976132640961" Properties=species:S:1:pos:R:3:momenta:R:3:molID:I:1 total_charge=0 exec_time=1758997627.7455804 step=159600 time_fs=79799.999999925 time_ps=79.799999999925 charge=0 spin=5 Nmols=115 Comp=---UNK_Cl(2):UNK_Fe(1):UNK_H2O(112) pbc="T T T" +Fe 7.31388897 12.83019064 10.66706879 -0.46735654 -1.21436723 -1.55823168 0 +Cl 7.14485757 10.94077497 6.25292789 0.24997392 0.57498803 1.16801883 1 +Cl 1.05171484 2.81912733 7.50684378 -1.79568861 1.29361266 1.52889486 2 +O 4.02738321 10.47528816 8.31140856 1.21687918 -0.46681284 -0.08727318 3 +H 4.47846131 11.28098056 7.99334890 -0.01329951 -0.33815540 -0.16911986 3 +H 4.46701224 9.70065142 7.89887267 -0.04855593 0.03804000 0.01049591 3 +O 5.48356052 8.98506079 13.17975531 0.97243121 0.10612434 -0.11093342 4 +H 5.11006044 8.07192557 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b/ml_peg/calcs/physicality/oxidation_states/data/Fe3Cl_start.xyz new file mode 100644 index 000000000..6c89e5a54 --- /dev/null +++ b/ml_peg/calcs/physicality/oxidation_states/data/Fe3Cl_start.xyz @@ -0,0 +1,342 @@ +340 +Lattice="14.560660492283056 0.0 0.0 0.0 14.560660492283056 0.0 0.0 0.0 14.560660492283056" Properties=species:S:1:pos:R:3:momenta:R:3:molID:I:1 total_charge=0 exec_time=1758997221.2454898 step=156400 time_fs=78199.99999992663 time_ps=78.19999999992663 charge=0 spin=6 Nmols=116 Comp=---UNK_Cl(3):UNK_Fe(1):UNK_H2O(112) pbc="T T T" +Fe 7.76173318 10.38217203 7.89765110 0.97442658 -1.60700182 0.04167982 0 +Cl 13.45808177 4.97999239 9.35203431 0.02804458 -0.25546975 -1.26136108 1 +Cl 4.05846134 14.44491557 7.68964140 0.57534441 -2.04015542 0.89683076 2 +Cl 11.40618101 7.53704877 12.31723337 -1.92982412 -1.01575202 -0.45560013 3 +O 6.31467407 9.75622884 6.73835185 -0.83742687 -1.56654527 -0.21566894 4 +H 5.60494396 10.42428953 6.47634562 0.03678271 -0.12040612 0.02167857 4 +H 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a/ml_peg/calcs/physicality/oxidation_states/outputs/Fe2Cl_mace-mp-0b3-final.extxyz b/ml_peg/calcs/physicality/oxidation_states/outputs/Fe2Cl_mace-mp-0b3-final.extxyz new file mode 100644 index 000000000..b8ddffa04 --- /dev/null +++ b/ml_peg/calcs/physicality/oxidation_states/outputs/Fe2Cl_mace-mp-0b3-final.extxyz @@ -0,0 +1,341 @@ +339 +Lattice="14.653976132640961 0.0 0.0 0.0 14.653976132640961 0.0 0.0 0.0 14.653976132640961" Properties=species:S:1:pos:R:3:momenta:R:3:masses:R:1:forces:R:3 total_charge=0 exec_time=1758997627.7455804 step=40000 time_fs=79799.999999925 time_ps=79.799999999925 charge=0 spin=5 Nmols=115 Comp=---UNK_Cl(2):UNK_Fe(1):UNK_H2O(112) units="_JSON {\"energy\": \"eV\", \"forces\": \"ev/Ang\", \"stress\": \"ev/Ang^3\", \"time\": \"fs\", \"real_time\": \"s\", \"temperature\": \"K\", \"pressure\": \"GPa\", \"density\": \"g/cm^3\", \"momenta\": \"(eV*u)^0.5\", \"target_temperature\": \"K\"}" time=19999.999999985655 density=1.1316014953983986 temperature=311.2362304925718 target_temperature=300 config_type=md energy=-1669.3258681112495 stress="-0.0024759978987276554 0.0013459925539791584 -0.0005026559811085463 0.0013459925539791584 -0.0002117040567100048 -0.0036345808766782284 -0.0005026559811085463 -0.0036345808766782284 -0.0015533273108303547" pbc="T T T" +Fe 7.03594970 12.77546447 10.48987774 0.40635039 2.83616545 -1.94849549 55.84500000 -0.53455859 -0.15604883 -0.10380957 +Cl 10.34581929 11.21221613 2.43601140 1.72837566 -0.81950394 -1.06409014 35.45000000 -0.13846107 0.09757968 0.05453793 +Cl 2.98495164 2.18861699 8.85193424 0.13509128 0.04038346 1.13125619 35.45000000 0.20903677 0.06147720 0.24753672 +O 3.49269215 9.75903335 6.39915911 -0.78008373 0.83640620 1.27538047 15.99900000 -0.07493977 0.15984516 0.59301502 +H 2.74755021 10.15588272 5.87573205 -0.20849707 0.08913621 0.07636867 1.00800000 0.07505612 -0.25376368 -0.57296699 +H 3.69729494 8.86819231 6.00306122 0.02080326 -0.10853801 -0.32525208 1.00800000 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0.0 14.560660492283056 0.0 0.0 0.0 14.560660492283056" Properties=species:S:1:pos:R:3:momenta:R:3:masses:R:1:forces:R:3 total_charge=0 exec_time=1758997221.2454898 step=40000 time_fs=78199.99999992663 time_ps=78.19999999992663 charge=0 spin=6 Nmols=116 Comp=---UNK_Cl(3):UNK_Fe(1):UNK_H2O(112) units="_JSON {\"energy\": \"eV\", \"forces\": \"ev/Ang\", \"stress\": \"ev/Ang^3\", \"time\": \"fs\", \"real_time\": \"s\", \"temperature\": \"K\", \"pressure\": \"GPa\", \"density\": \"g/cm^3\", \"momenta\": \"(eV*u)^0.5\", \"target_temperature\": \"K\"}" time=19999.999999985655 density=1.1725664245876124 temperature=305.47535572106324 target_temperature=300 config_type=md energy=-1670.7497086961373 stress="0.0012572314590215683 9.1813944891328e-06 -0.0015597229357808828 9.1813944891328e-06 0.0014058391097933054 -0.0006914917612448335 -0.0015597229357808828 -0.0006914917612448335 -2.880208194255829e-05" pbc="T T T" +Fe 8.41266438 9.73076350 7.99864154 -0.10248248 0.49284604 -0.57567016 55.84500000 -0.11216053 0.23665205 0.09508379 +Cl 11.82870106 4.60423937 10.93939034 -0.85454484 -1.75318975 0.67051463 35.45000000 0.21274742 -0.37777770 -0.16215990 +Cl 3.68871634 13.71953266 7.37113119 0.84731200 -0.24238767 1.10367491 35.45000000 0.22869338 0.22582260 0.41646594 +Cl 7.91526982 8.01606696 13.03482097 0.48389707 -0.41085081 0.57810036 35.45000000 0.81438661 0.02704233 -0.25778922 +O 6.87591286 8.93706757 6.92776759 0.34612279 -0.22230067 -0.25764415 15.99900000 0.07593521 -0.22466460 0.72254622 +H 6.88997466 9.28554959 6.02023616 -0.06734496 0.08539588 -0.08844895 1.00800000 -0.36310449 0.42979872 -0.65905672 +H 5.99568804 8.55945427 7.24976108 -0.20068433 -0.18254565 -0.00858254 1.00800000 0.42419249 -0.02566014 0.01881730 +O 3.90293435 11.30216260 11.98924273 -0.74696550 0.29882899 -1.82950686 15.99900000 1.53722572 -0.33849284 0.96049225 +H 3.45224614 11.81949022 11.31973768 -0.12379650 0.21824462 -0.04416889 1.00800000 -0.86261529 0.64145559 -0.96051419 +H 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a/ml_peg/calcs/physicality/oxidation_states/outputs/Fe3Cl_omol-final.extxyz b/ml_peg/calcs/physicality/oxidation_states/outputs/Fe3Cl_omol-final.extxyz new file mode 100644 index 000000000..0d737c6e0 --- /dev/null +++ b/ml_peg/calcs/physicality/oxidation_states/outputs/Fe3Cl_omol-final.extxyz @@ -0,0 +1,342 @@ +340 +Lattice="14.560660492283056 0.0 0.0 0.0 14.560660492283056 0.0 0.0 0.0 14.560660492283056" Properties=species:S:1:pos:R:3:momenta:R:3:masses:R:1:forces:R:3 total_charge=0 exec_time=1758997221.2454898 step=40000 time_fs=78199.99999992663 time_ps=78.19999999992663 charge=0 spin=6 Nmols=116 Comp=---UNK_Cl(3):UNK_Fe(1):UNK_H2O(112) units="_JSON {\"energy\": \"eV\", \"forces\": \"ev/Ang\", \"stress\": \"ev/Ang^3\", \"time\": \"fs\", \"real_time\": \"s\", \"temperature\": \"K\", \"pressure\": \"GPa\", \"density\": \"g/cm^3\", \"momenta\": \"(eV*u)^0.5\", \"target_temperature\": \"K\"}" time=19999.999999985655 density=1.1725664245876124 temperature=301.68287781321146 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+5.459999999999999076e+00 1.027476190419443602e+00 +5.499999999999999112e+00 8.950532488753613070e-01 +5.539999999999999147e+00 1.131679051504515643e+00 +5.579999999999998295e+00 1.133079610576577245e+00 +5.619999999999998330e+00 1.129996293902110427e+00 +5.659999999999998366e+00 1.178108768570164111e+00 +5.699999999999998401e+00 1.161631993330552559e+00 +5.739999999999998437e+00 1.066641697606485417e+00 +5.779999999999998472e+00 1.117419415807511918e+00 +5.819999999999998508e+00 1.102112541537661139e+00 +5.859999999999998543e+00 1.023404167813937615e+00 +5.899999999999998579e+00 1.048857651770177091e+00 +5.939999999999998614e+00 9.223874858951869316e-01 +5.979999999999998650e+00 1.040101908003807862e+00 From 28fde443c87dad756e2dfc2bc7b298cdcc5ac80c Mon Sep 17 00:00:00 2001 From: PKourtis <92691577+PKourtis@users.noreply.github.com> Date: Mon, 16 Feb 2026 11:34:57 +0000 Subject: [PATCH 05/16] Apply suggestion from @ElliottKasoar Co-authored-by: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com> --- .../physicality/oxidation_states/analyse_oxidation_states.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py index 3c37a200e..e6803908a 100644 --- a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -12,9 +12,7 @@ from ml_peg.app import APP_ROOT from ml_peg.calcs import CALCS_ROOT -# MODELS = get_model_names(current_models) - -MODELS = ["mace-mp-0b3", "omol"] +MODELS = get_model_names(current_models) CALC_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "outputs" OUT_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" From 6ea9158590b20f8644cf20e052df82c7eff64e30 Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Mon, 16 Feb 2026 16:34:33 +0000 Subject: [PATCH 06/16] Applied PR suggestion on highighted_range for the plot scatter decorator and edited the analysis script accordingly --- .../physicality/oxidation_states/analyse_oxidation_states.py | 3 +-- ml_peg/analysis/utils/decorators.py | 5 +---- .../app/physicality/oxidation_states/app_oxidation_states.py | 5 ++++- .../{O-Fe_Fe2Cl_omol.rdf => O-Fe_Fe2Cl_mace-omol.rdf} | 0 .../{O-Fe_Fe3Cl_omol.rdf => O-Fe_Fe3Cl_mace-omol.rdf} | 0 5 files changed, 6 insertions(+), 7 deletions(-) rename ml_peg/calcs/physicality/oxidation_states/outputs/{O-Fe_Fe2Cl_omol.rdf => O-Fe_Fe2Cl_mace-omol.rdf} (100%) rename ml_peg/calcs/physicality/oxidation_states/outputs/{O-Fe_Fe3Cl_omol.rdf => O-Fe_Fe3Cl_mace-omol.rdf} (100%) diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py index e6803908a..17d247706 100644 --- a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -12,7 +12,7 @@ from ml_peg.app import APP_ROOT from ml_peg.calcs import CALCS_ROOT -MODELS = get_model_names(current_models) +MODELS = ["mace-mp-0b3", "mace-omol"] # get_model_names(current_models) CALC_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "outputs" OUT_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" @@ -78,7 +78,6 @@ def plot_rdfs(model: str, results: dict[str, tuple[list[float], list[float]]]) - y_label="Fe-O G(r)", show_line=True, show_markers=False, - highlight_area=True, highlight_range=REF_PEAK_RANGE, ) def plot_result() -> dict[str, tuple[list[float], list[float]]]: diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 6ff98f8a5..4e42af54b 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -435,7 +435,6 @@ def plot_scatter( show_markers: bool = True, hoverdata: dict | None = None, filename: str = "scatter.json", - highlight_area: bool = False, highlight_range: dict = None, ) -> Callable: """ @@ -457,8 +456,6 @@ def plot_scatter( Hover data dictionary. Default is `{}`. filename Filename to save plot as JSON. Default is "scatter.json". - highlight_area - Whether to add a highlighted rectangle to the plot. highlight_range Dictionary of rectangle title and x-axis endpoints. @@ -533,7 +530,7 @@ def plot_scatter_wrapper(*args, **kwargs) -> dict[str, Any]: colors = pc.qualitative.Plotly - if highlight_area: + if highlight_range: for i, (title, range) in enumerate(highlight_range.items()): fig.add_vrect( x0=range[0], diff --git a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py index 1aaabc794..8e40f9cdc 100644 --- a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py +++ b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py @@ -12,9 +12,12 @@ ) from ml_peg.app.utils.load import read_plot 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) -MODELS = ["mace-mp-0b3", "omol"] +# MODELS = ["mace-mp-0b3", "mace-omol"] +MODELS = get_model_names(current_models) BENCHMARK_NAME = "Iron Oxidation States" DATA_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" diff --git a/ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_omol.rdf b/ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_mace-omol.rdf similarity index 100% rename from ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_omol.rdf rename to ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe2Cl_mace-omol.rdf diff --git a/ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_omol.rdf b/ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_mace-omol.rdf similarity index 100% rename from ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_omol.rdf rename to ml_peg/calcs/physicality/oxidation_states/outputs/O-Fe_Fe3Cl_mace-omol.rdf From fb343dc494b8fd9aca9ebe75abe4990754b72aad Mon Sep 17 00:00:00 2001 From: "Panos Kourtis (PGR)" Date: Wed, 18 Feb 2026 17:44:04 +0000 Subject: [PATCH 07/16] Revert pyproject.toml to upstream version --- pyproject.toml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b0e7a7183..5677eea25 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,11 +54,7 @@ grace = [ "tensorpotential == 0.5.1; python_version < '3.13'", ] mace = [ - "mace-torch @ https://github.com/ACEsuit/mace.git", - "cuequivariance==0.8.1", - "cuequivariance-ops-cu12==0.8.1", - "cuequivariance-ops-torch-cu12==0.8.1", - "cuequivariance-torch==0.8.1", + "mace-torch==0.3.14", ] mattersim = [ From a91247ed528b07ea55e39f705b6474e9b0a32738 Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 19:24:26 +0000 Subject: [PATCH 08/16] Cleaned up model declaration in the app.py --- ml_peg/app/physicality/oxidation_states/app_oxidation_states.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py index 8e40f9cdc..a823107ec 100644 --- a/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py +++ b/ml_peg/app/physicality/oxidation_states/app_oxidation_states.py @@ -15,8 +15,6 @@ from ml_peg.models.get_models import get_model_names from ml_peg.models.models import current_models -# MODELS = get_model_names(current_models) -# MODELS = ["mace-mp-0b3", "mace-omol"] MODELS = get_model_names(current_models) BENCHMARK_NAME = "Iron Oxidation States" From d232e12011ca368923e6e1ebc4dabc3b1fb695a7 Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 19:26:34 +0000 Subject: [PATCH 09/16] Each model has its own directory within outputs and the rdf tests get skipped if the MD trajs are not present --- .../oxidation_states/calc_oxidation_states.py | 20 ++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index 210a1053e..b7e4814fc 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -35,12 +35,13 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: """ 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(parents=True, exist_ok=True) + for salt in IRON_SALTS: struct_path = DATA_PATH / f"{salt}_start.xyz" struct = read(struct_path, "0") @@ -55,7 +56,7 @@ def test_iron_oxidation_state_md(mlip: tuple[str, Any]) -> None: traj_append=True, thermostat_time=50, barostat_time=None, - file_prefix=OUT_PATH / f"{salt}_{model_name}", + file_prefix=out_dir / f"{salt}_{model_name}", ) npt.run() @@ -71,12 +72,21 @@ def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: Name of model used and model. """ model_name, model = mlip + out_dir = OUT_PATH / model_name rmax = 6.0 nbins = 200 for salt in IRON_SALTS: rdf_list = [] - md_path = OUT_PATH / f"{salt}_{model_name}-traj.extxyz" + md_path = out_dir / f"{salt}_{model_name}-traj.extxyz" + + if not md_path.exists(): + pytest.skip( + "MD trajectory data missing, please check for " + "already existing data on S3 or run" + "test_iron_oxidation_state_md with -m very_slow" + ) + traj = read(md_path, ":") for atoms in traj: rdf, r = get_rdf( @@ -89,7 +99,7 @@ def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: g_mean = np.mean(rdf_list, axis=0) # NVT so this is ok rdf_data = np.column_stack((r, g_mean)) - rdf_path = OUT_PATH / f"O-Fe_{salt}_{model_name}.rdf" + rdf_path = out_dir / f"O-Fe_{salt}_{model_name}.rdf" np.savetxt( rdf_path, rdf_data, From dc8867474c79fcfaa967e33672a6937b067077cf Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 19:32:02 +0000 Subject: [PATCH 10/16] Updated metrics level of theory to Experimental --- ml_peg/analysis/physicality/oxidation_states/metrics.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/ml_peg/analysis/physicality/oxidation_states/metrics.yml b/ml_peg/analysis/physicality/oxidation_states/metrics.yml index 3b679212c..77ac0b24f 100644 --- a/ml_peg/analysis/physicality/oxidation_states/metrics.yml +++ b/ml_peg/analysis/physicality/oxidation_states/metrics.yml @@ -4,9 +4,10 @@ metrics: bad: 0.0 unit: Yes(1)/No(0) tooltip: Whether there is a split between Fe-O RDF peaks for different iron oxidation states + level_of_theory: Experimental Peak Within Experimental Ref: good: 1.0 bad: 0.0 unit: null - tooltip: Whether the RDF peak positions match PBE peaks - level_of_theory: Experiment + tooltip: Whether the RDF peak positions match experimental peaks + level_of_theory: Experimental From 174b602197b6a6c08c062b09c32ac2e4dfcd29a3 Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 19:46:05 +0000 Subject: [PATCH 11/16] Updated analysis to match outputs/model_name data directory pattern --- .../oxidation_states/analyse_oxidation_states.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py index 17d247706..043b17ac6 100644 --- a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -11,8 +11,10 @@ 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 = ["mace-mp-0b3", "mace-omol"] # get_model_names(current_models) +MODELS = get_model_names(current_models) CALC_PATH = CALCS_ROOT / "physicality" / "oxidation_states" / "outputs" OUT_PATH = APP_ROOT / "data" / "physicality" / "oxidation_states" @@ -46,8 +48,10 @@ def get_rdf_results( """ results = {salt: [] for salt in IRON_SALTS} + model_calc_path = CALC_PATH / model + for salt in IRON_SALTS: - rdf_file = CALC_PATH / f"O-Fe_{salt}_{model}.rdf" + rdf_file = model_calc_path / f"O-Fe_{salt}_{model}.rdf" fe_o_rdf = np.loadtxt(rdf_file) r = list(fe_o_rdf[:, 0]) From 8b8b8077bc8917c618fec8048f40125fe364b519 Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 19:47:26 +0000 Subject: [PATCH 12/16] Added download from S3 bucket function for the input data --- .../physicality/oxidation_states/calc_oxidation_states.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index b7e4814fc..fd4cbd33b 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -11,12 +11,16 @@ import numpy as np 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) -DATA_PATH = Path(__file__).parent / "data" +DATA_PATH = download_s3_data( + filename="oxidation_states.zip", + key="inputs/physicality/oxidation_states/oxidation_states.zip", +) OUT_PATH = Path(__file__).parent / "outputs" IRON_SALTS = ["Fe2Cl", "Fe3Cl"] From 3f920039fdf0242a6f91d6365916c8cae9310bae Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 20:39:54 +0000 Subject: [PATCH 13/16] Added yes/no units --- ml_peg/analysis/physicality/oxidation_states/metrics.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ml_peg/analysis/physicality/oxidation_states/metrics.yml b/ml_peg/analysis/physicality/oxidation_states/metrics.yml index 77ac0b24f..c4adee145 100644 --- a/ml_peg/analysis/physicality/oxidation_states/metrics.yml +++ b/ml_peg/analysis/physicality/oxidation_states/metrics.yml @@ -8,6 +8,6 @@ metrics: Peak Within Experimental Ref: good: 1.0 bad: 0.0 - unit: null + unit: Yes(1)/No(0) tooltip: Whether the RDF peak positions match experimental peaks level_of_theory: Experimental From 0e1854c4f19e6b66818b19f033ee99610ce18e8f Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 20:49:12 +0000 Subject: [PATCH 14/16] Fixed plot_scatter highlighted range title and plot title mixup --- ml_peg/analysis/utils/decorators.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 4e42af54b..d4ba1e2ea 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -531,11 +531,11 @@ def plot_scatter_wrapper(*args, **kwargs) -> dict[str, Any]: colors = pc.qualitative.Plotly if highlight_range: - for i, (title, range) in enumerate(highlight_range.items()): + for i, (h_text, range) in enumerate(highlight_range.items()): fig.add_vrect( x0=range[0], x1=range[1], - annotation_text=title, + annotation_text=h_text, annotation_position="top", fillcolor=colors[i], opacity=0.25, From e32407551e618144af2e44590ec4f09a2634b0d2 Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 21:04:35 +0000 Subject: [PATCH 15/16] Download MD starting structures from S3 bucket and save outputs in the form of outputs / model / {salt}-traj.extxyz --- .../physicality/oxidation_states/calc_oxidation_states.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py index fd4cbd33b..7a637e655 100644 --- a/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py +++ b/ml_peg/calcs/physicality/oxidation_states/calc_oxidation_states.py @@ -17,10 +17,11 @@ MODELS = load_models(current_models) -DATA_PATH = download_s3_data( +DATA_PATH = download_s3_data( filename="oxidation_states.zip", key="inputs/physicality/oxidation_states/oxidation_states.zip", -) +) / Path("oxidation_states") +print(DATA_PATH) OUT_PATH = Path(__file__).parent / "outputs" IRON_SALTS = ["Fe2Cl", "Fe3Cl"] @@ -83,7 +84,7 @@ def test_iron_oxygen_rdfs(mlip: tuple[str, Any]) -> None: for salt in IRON_SALTS: rdf_list = [] md_path = out_dir / f"{salt}_{model_name}-traj.extxyz" - + if not md_path.exists(): pytest.skip( "MD trajectory data missing, please check for " From 642ad10e75b31ec1030361a710498f5a51e9148a Mon Sep 17 00:00:00 2001 From: Panos Kourtis Date: Thu, 19 Feb 2026 21:07:12 +0000 Subject: [PATCH 16/16] Added model name to the scatter title --- .../oxidation_states/analyse_oxidation_states.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py index 043b17ac6..0e7ae0781 100644 --- a/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py +++ b/ml_peg/analysis/physicality/oxidation_states/analyse_oxidation_states.py @@ -49,7 +49,7 @@ def get_rdf_results( results = {salt: [] for salt in IRON_SALTS} model_calc_path = CALC_PATH / model - + for salt in IRON_SALTS: rdf_file = model_calc_path / f"O-Fe_{salt}_{model}.rdf" @@ -77,8 +77,8 @@ def plot_rdfs(model: str, results: dict[str, tuple[list[float], list[float]]]) - @plot_scatter( filename=OUT_PATH / f"Fe-O_{model}_RDF_scatter.json", - title="Fe-O RDF", - x_label="R / Å", + title=f"{model} MD", + x_label="r [Å]", y_label="Fe-O G(r)", show_line=True, show_markers=False, @@ -128,7 +128,7 @@ def get_oxidation_states_passfail() -> dict[str, dict]: oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 0.0 oxidation_state_passfail["Peak Within Experimental Ref"][model] = 0.0 - if peak_difference > 0.1: + if peak_difference > 0.07: oxidation_state_passfail["Fe-O RDF Peak Split"][model] = 1.0 if fe_2_ref[0] <= peak_position["Fe2Cl"] <= fe_2_ref[1]: