From ca271d324b679755cbeebddb2df9812ad3dec9df Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Wed, 28 Jan 2026 15:11:55 +0000 Subject: [PATCH 01/19] Added calc_water_slab_dipoles.py --- .../user_guide/benchmarks/physicality.rst | 33 + .../calc_water_slab_dipoles.py | 127 ++ ml_peg/models/models.yml | 10 + pyproject.toml | 1 + uv.lock | 1061 ++++++++++++++++- 5 files changed, 1172 insertions(+), 60 deletions(-) create mode 100644 ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py diff --git a/docs/source/user_guide/benchmarks/physicality.rst b/docs/source/user_guide/benchmarks/physicality.rst index 0d5b55d25..7a3771795 100644 --- a/docs/source/user_guide/benchmarks/physicality.rst +++ b/docs/source/user_guide/benchmarks/physicality.rst @@ -135,3 +135,36 @@ Data availability ----------------- None required; diatomics are generated in ASE. + + +Water Slab Dipoles +================== + +Summary +------- + +Distribution of dipole of water slab, checking for width of distribution and structures with dielectric breakdown. + + +Metrics +------- + +1. Standard Deviation of Dipole Distribution + +For a number of samples from an MD simulation, the total dipole is calculated. Compare to a reference of a LR model trained on revPBE-D3. + +2. Number of structures with dielectric breakdown + +Estimate band gap based on dipole, count structures where band gap disappears. + + +Computational Cost +------------------ + +High: Requires around 500 ps of MD of 40 A slab to get converged distribution. + + +Data availability +----------------- + +Paper in preparation, contact Isaac Parker (ijp30@cam.ac.uk). diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py new file mode 100644 index 000000000..f6bf50b70 --- /dev/null +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -0,0 +1,127 @@ +"""Run calculations for water slab dipole tests.""" + +from __future__ import annotations + +from datetime import date +from pathlib import Path +from typing import Any + +from ase import units +from ase.io import read, write +from ase.md.npt import NPT +from ase.md.velocitydistribution import MaxwellBoltzmannDistribution +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" + +# Unit conversion +EV_TO_KJ_PER_MOL = units.mol / units.kJ + + +@pytest.mark.parametrize("mlip", MODELS.items()) +def test_water_dipole(mlip: tuple[str, Any]) -> None: + """ + Run water dipole test. + + Parameters + ---------- + mlip + Name of model use and model to get calculator. + """ + model_name, model = mlip + calc = model.get_calculator() + + # Add D3 calculator for this test (for models where applicable) + calc = model.add_d3_calculator(calc) + + out_name = "slab" + + md_t = 200 # 200000 # number of timesteps, here dt = 1fs + md_dt = 10 # 500 # intervals for printing energy, T, etc + th_dt = 10 # 500 # intervals for printing structures + temp = 300 # Kelvin + pres = 1.013 # bar + + ttime = 100 * units.fs # timescale themostat + + print("Reading start_config from " + DATA_PATH + "/init_38A_slab.xyz") + start_config = read(DATA_PATH + "/init_38A_slab.xyz", "-1") + start_config.set_cell(np.triu(start_config.get_cell())) # why? + start_config.info["charge"] = 0.0 + start_config.info["spin"] = 1 + + start_config.calc = calc + + velocities = start_config.get_velocities() + start_config.set_velocities(velocities) + MaxwellBoltzmannDistribution(start_config, temperature_K=300) + + md = NPT( + atoms=start_config, + timestep=1 * units.fs, + temperature_K=temp, + externalstress=pres * units.bar, + ttime=ttime, + pfactor=None, + ) + + # start_config_positions = start_config.positions.copy() + # start_config_com = start_config.get_center_of_mass().copy() + + # Write output structures + write_dir = OUT_PATH / model_name + write_dir.mkdir(parents=True, exist_ok=True) + + thermo_traj = open(write_dir + "/" + out_name + ".thermo", "w") # file for output + coord_traj_name = write_dir + "/" + out_name + ".xyz" # file for coordinate output + + def print_traj(a=start_config): + """ + Output trajectory (xyz in coord_traj_name, steps, T, and E in thermo_traj). + + Parameters + ---------- + a + Structure to evaluate. Defaults to start_config. + """ + calc_time = md.get_time() / units.fs + calc_temp = a.get_temperature() + # calc_dens = np.sum(a.get_masses())/a.get_volume()*densfact + # calc_pres = - \ + # np.trace(a.get_stress( + # include_ideal_gas=True, voigt=False))/3/units.bar + calc_epot = a.get_potential_energy() + # calc_msd = (((a.positions-a.get_center_of_mass()) - + # (start_config_positions-start_config_com))**2).mean(0).sum(0) + # calc_drft = ((a.get_center_of_mass()-start_config_com)**2).sum(0) + # calc_tens = -a.get_stress(include_ideal_gas=True, voigt=True)/units.bar + if md.nsteps % th_dt == 0: + thermo_traj.write( + ("%12d" + " %17.6f" * 2 + "\n") % (calc_time, calc_temp, calc_epot) + ) + thermo_traj.flush() + if md.nsteps % md_dt == 0: + print(f"Step {md.nsteps}") + write(coord_traj_name, a, append=True) + + # print_traj could also be done using MDLogger and write_traj + + thermo_traj.write( + "# ASE Dynamics. Date: " + date.today().strftime("%d %b %Y") + "\n" + ) + thermo_traj.write("# Time(fs) Temperature(K) Energy(eV) \n") + open(coord_traj_name, "w").close() + print_traj(start_config) + + print("Starting MD") + md.attach(print_traj) + md.run(md_t) + + thermo_traj.close() diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml index 77e54a16b..180925785 100644 --- a/ml_peg/models/models.yml +++ b/ml_peg/models/models.yml @@ -8,6 +8,16 @@ mace-mp-0a: kwargs: model: "medium" +mace-mp-0a-small: + module: mace.calculators + class_name: mace_mp + device: "auto" + default_dtype: float32 + trained_on_d3: false + level_of_theory: PBE + kwargs: + model: "small" + mace-mp-0b3: module: mace.calculators class_name: mace_mp diff --git a/pyproject.toml b/pyproject.toml index 64a36ff30..e455354da 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -53,6 +53,7 @@ grace = [ ] mace = [ "mace-torch==0.3.14", + "torch==2.6.0" ] mattersim = [ diff --git a/uv.lock b/uv.lock index f828ab629..af16e9f07 100644 --- a/uv.lock +++ b/uv.lock @@ -1275,7 +1275,8 @@ dependencies = [ { 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 = "nvidia-ml-py3" }, { name = "pymatgen" }, - { name = "torch" }, + { name = "torch", version = "2.6.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-6-ml-peg-mace' 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 = "torch", version = "2.8.0", source = { registry = "https://pypi.org/simple" }, marker = "extra == 'extra-6-ml-peg-mattersim' or extra == 'extra-6-ml-peg-uma' or extra != 'extra-6-ml-peg-mace'" }, { name = "typing-extensions" }, ] sdist = { url = "https://files.pythonhosted.org/packages/f6/05/1aaaecfaf9567dc93f33cd94a6deda0cc8ca0e665484636d8522978658d6/chgnet-0.4.0.tar.gz", hash = "sha256:1683fd61dbbf2ccb6540b6967589f25b239951b94c4b616f1dbbc3bce8313785", size = 8756128, upload-time = "2024-09-16T22:19:48.12Z" } @@ -2386,8 +2387,8 @@ dependencies = [ { name = "opt-einsum-fx" }, { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.11' and extra == 'extra-6-ml-peg-mace') or (python_full_version >= '3.11' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-mattersim') or (python_full_version >= '3.11' and extra == 'extra-6-ml-peg-grace' and extra == 'extra-6-ml-peg-uma') or (extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-mattersim') or (extra == 'extra-6-ml-peg-grace' and extra != 'extra-6-ml-peg-mace' and extra == 'extra-6-ml-peg-uma') or (extra != 'extra-6-ml-peg-grace' and extra == 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name = "sympy" }, - { name = "torch" }, + { name = "sympy", version = "1.13.1", source = { registry = "https://pypi.org/simple" } }, + { name = "torch", version = "2.6.0", source = { registry = "https://pypi.org/simple" } }, ] sdist = { url = "https://files.pythonhosted.org/packages/aa/98/8e7102dea93106603383fda23bf96649c397a37b910e7c76086e584cd92d/e3nn-0.4.4.tar.gz", hash = "sha256:51c91a84c1fb72e7e3600000958fa8caad48f8270937090fb8d0f8bfffbb3525", size = 361661, upload-time = "2021-12-16T08:49:23.382Z" } wheels = [ @@ -2424,8 +2425,8 @@ dependencies = [ { name = "opt-einsum-fx" }, { name = "scipy", version = "1.15.3", source = { registry = "https://pypi.org/simple" }, marker = "(python_full_version < '3.11' and extra == 'extra-6-ml-peg-mattersim') or (python_full_version < '3.11' and extra == 'extra-6-ml-peg-uma') 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 == 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"(python_full_version == '3.13.*' 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 == '3.13.*' 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 == '3.12.*' 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 == '3.12.*' 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 == 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-0.08588018 -0.30236904 566 2 189 0.42380000 _ _ -0.85427900 -0.96314299 -0.57510486 +H 63.42067099 14.20135075 30.30389431 0.42380000 1.00800000 0.13763148 0.09665023 -0.09814504 567 2 189 0.42380000 _ _ -0.09947263 1.60249729 0.98616161 +O 2.98549836 44.41280120 31.87996888 -0.84760000 15.99940000 0.60693754 0.60544334 -0.89316712 568 1 190 -0.84760000 568(1),569(1) 568-569(1) 1.61996350 -0.94367260 2.08317582 +H 3.41943563 43.47203809 31.82721057 0.42380000 1.00800000 0.06963409 0.02052149 -0.06917593 569 2 190 0.42380000 _ _ -0.47602154 1.76448135 0.26436442 +H 3.27574553 44.75358772 32.80443265 0.42380000 1.00800000 -0.12273330 0.12337048 0.06538906 570 2 190 0.42380000 _ _ -0.53990982 -0.69273160 -2.03975998 +O 35.83867954 -71.95020803 33.50168774 -0.84760000 15.99940000 -0.29459695 -0.58543005 -0.61601323 571 1 191 -0.84760000 571(1),572(1) 571-572(1) -1.11404874 -0.98624106 -0.34845328 +H 35.84871604 -72.67884773 32.79404976 0.42380000 1.00800000 0.22046117 -0.20936553 0.12627692 572 2 191 0.42380000 _ _ -0.33724234 0.65787974 0.76925700 +H 35.03264758 -72.16255039 34.10515333 0.42380000 1.00800000 -0.02466385 -0.10470070 -0.02966081 573 2 191 0.42380000 _ _ 1.31663489 0.10773729 -0.79176029 +O 7.90688282 12.68653673 19.20194547 -0.84760000 15.99940000 -0.13428332 0.11091393 0.27592626 574 1 192 -0.84760000 574(1),575(1) 574-575(1) 0.16032922 0.92779918 -0.83824224 +H 6.98724327 12.94600884 19.51723548 0.42380000 1.00800000 0.07512030 0.41485681 -0.13917734 575 2 192 0.42380000 _ _ 0.95504212 0.20268504 -0.82919626 +H 8.34242503 13.38349992 18.60543325 0.42380000 1.00800000 -0.06275126 -0.11056073 -0.02226819 576 2 192 0.42380000 _ _ -1.34408115 -0.46958712 1.54095680 From 219b7826d97918ad55f1c0be3b8a0b483a4ddcb2 Mon Sep 17 00:00:00 2001 From: Mandy Julie Hoffmann Date: Wed, 28 Jan 2026 17:45:48 +0100 Subject: [PATCH 03/19] Small fixes and added FF model for testing. --- .../water_slab_dipoles/calc_water_slab_dipoles.py | 8 ++++---- ml_peg/models/models.yml | 10 ++++++++++ 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py index f6bf50b70..2a78c7c94 100644 --- a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -51,8 +51,8 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: ttime = 100 * units.fs # timescale themostat - print("Reading start_config from " + DATA_PATH + "/init_38A_slab.xyz") - start_config = read(DATA_PATH + "/init_38A_slab.xyz", "-1") + print("Reading start_config from ", DATA_PATH / "init_38A_slab.xyz") + start_config = read(DATA_PATH / "init_38A_slab.xyz", "-1") start_config.set_cell(np.triu(start_config.get_cell())) # why? start_config.info["charge"] = 0.0 start_config.info["spin"] = 1 @@ -79,8 +79,8 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: write_dir = OUT_PATH / model_name write_dir.mkdir(parents=True, exist_ok=True) - thermo_traj = open(write_dir + "/" + out_name + ".thermo", "w") # file for output - coord_traj_name = write_dir + "/" + out_name + ".xyz" # file for coordinate output + thermo_traj = open(write_dir / (out_name + ".thermo"), "w") # file for output + coord_traj_name = write_dir / (out_name + ".xyz") # file for coordinate output def print_traj(a=start_config): """ diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml index 180925785..f8e5b68f0 100644 --- a/ml_peg/models/models.yml +++ b/ml_peg/models/models.yml @@ -119,6 +119,16 @@ orb-v3-consv-inf-omat: # kwargs: # model: "/Users/joehart/Desktop/0_Cambridge/0_MPhil_Scientific_Computing/MPhil_project/mlipx_testing/models/GRACE-2L-OAM_28Jan25" +small_FF_SR_water_model: + module: mace.calculators + class_name: mace_mp + device: "auto" + default_dtype: float32 + trained_on_d3: true + level_of_theory: revPBE-D3 + kwargs: + model: "/leonardo_work/EUHPC_R04_130/mjh300/projects/ml-peg/models/FF_SR_small.model" + # MACE-OFF23(L): # module: mace.calculators # class_name: mace_off From 33db2520d0aa3585933f84085dffc56019ee2953 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 29 Jan 2026 11:46:22 +0000 Subject: [PATCH 04/19] Merged changes --- .../analyse_water_slab_dipoles.py | 152 ++++++++++++++++++ .../water_slab_dipoles/metrics.yml | 13 ++ 2 files changed, 165 insertions(+) create mode 100644 ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py create mode 100644 ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py new file mode 100644 index 000000000..4f61e065e --- /dev/null +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -0,0 +1,152 @@ +"""Analyse water slab dipole benchmark.""" + +from __future__ import annotations + +from pathlib import Path + +from ase import units +from ase.io import read +import numpy as np +import pytest +from scipy.constants import e, epsilon_0 + +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.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) +CALC_PATH = CALCS_ROOT / "physicality" / "water_slab_dipoles" / "outputs" +OUT_PATH = APP_ROOT / "data" / "physicality" / "water_slab_dipoles" + +METRICS_CONFIG_PATH = Path(__file__).with_name("metrics.yml") +DEFAULT_THRESHOLDS, DEFAULT_TOOLTIPS, DEFAULT_WEIGHTS = load_metrics_config( + METRICS_CONFIG_PATH +) + +# Unit conversion +EV_TO_KJ_PER_MOL = units.mol / units.kJ + + +def get_dipoles() -> dict[str, np.ndarray]: + """ + Get total dipole per unit area in z direction. + + Returns + ------- + dict[str, np.ndarray] + Dictionary with array of dipoles for each model. + """ + results = {} + for model_name in MODELS: + model_dir = CALC_PATH / model_name + if model_dir.exists(): + if model_dir.glob("dipoles.npy"): + results[model_name] = np.load(model_dir / "dipoles.npy") + else: + atoms = read(model_dir / "slab.xyz") + dipoles = np.zeros(len(atoms)) + for i, struc in enumerate(atoms): + o_index = [atom.index for atom in struc if atom.number == 8] + h_index = [atom.index for atom in struc if atom.number == 1] + dipoles[i] = ( + np.sum(struc.positions[o_index, 2]) * (-0.8476) + + np.sum(struc.positions[h_index, 2]) * 0.4238 + ) + dipoles_unit_area = dipoles / atoms[0].cell[0, 0] / atoms[0].cell[1, 1] + results[model_name] = dipoles_unit_area + np.save(model_dir / "dipoles.npy", dipoles_unit_area) + return results + + +@pytest.fixture +def dipole_std() -> dict[str, float]: + """ + Get standard deviation of total z dipole per unit area (in e/A). + + Returns + ------- + dict[str, float] + Dictionary of standard deviation of dipole distribution for all models. + """ + dipoles = get_dipoles() + results = {} + for model_name in MODELS: + if dipoles[model_name]: + results[model_name] = np.std(dipoles[model_name]) + else: + results[model_name] = None + return results + + +@pytest.fixture +def n_bad() -> dict[str, float]: + """ + Get fraction of dipoles that are bad. + + Returns + ------- + dict[str, float] + Dictionary of percentage of breakdown candidates for all models. + """ + dipoles = get_dipoles() + + # We consider a dipole as bad if the expected band gap is <= 0 + # The expected band gap is 4.50 V - |P_z_per_unit_area| / epsilon_0 + # Hence "bad" is |P_z_per_unit_area| > 4.50 V * epsilon_0 / e * 10^(-10) + # epsilon_0 is in F/m = C/(V*m), so this gives it in e/(V*A) + dipole_bad_threshold = 4.50 * epsilon_0 / e * 10 ** (-10) + + results = {} + for model_name in MODELS: + if dipoles[model_name]: + results[model_name] = ( + np.abs(dipoles[model_name]) > dipole_bad_threshold + ).sum() / len(dipoles[model_name]) + else: + results[model_name] = None + return results + + +@pytest.fixture +@build_table( + filename=OUT_PATH / "water_slab_dipoles_metrics_table.json", + metric_tooltips=DEFAULT_TOOLTIPS, + thresholds=DEFAULT_THRESHOLDS, + mlip_name_map=D3_MODEL_NAMES, +) +def metrics(dipole_std: dict[str, float], n_bad: dict[str, float]) -> dict[str, dict]: + """ + Get all water slab dipoles metrics. + + Parameters + ---------- + dipole_std + Standard deviation of dipole distribution. + n_bad + Percentage of tested structures with dipole larger than water band gap. + + Returns + ------- + dict[str, dict] + Metric names and values for all models. + """ + return { + "sigma": dipole_std, + "Fraction Breakdown Candidates": n_bad, + } + + +def test_water_slab_dipoles(metrics: dict[str, dict]) -> None: + """ + Run water slab dipoles test. + + Parameters + ---------- + metrics + All water slab dipole metrics. + """ + return diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml b/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml new file mode 100644 index 000000000..d7d705eef --- /dev/null +++ b/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml @@ -0,0 +1,13 @@ +metrics: + sigma: + good: + bad: + unit: e/A + tooltip: Standard deviation of total dipole in z direction + level of theory: null + Fraction Breakdown Candidates: + good: 0 + bad: 1 + unit: null + tooltip: Fraction of structures with dipole larger than band gap + level of theory: revPBE-D3 From 8e0f1e37ce9a854761dd2c4139cfcf72b778f426 Mon Sep 17 00:00:00 2001 From: Mandy Julie Hoffmann Date: Thu, 29 Jan 2026 13:18:23 +0100 Subject: [PATCH 05/19] Added good and bad for sigma metric --- ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml | 4 ++-- .../physicality/water_slab_dipoles/calc_water_slab_dipoles.py | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml b/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml index d7d705eef..299ea291d 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml +++ b/ml_peg/analysis/physicality/water_slab_dipoles/metrics.yml @@ -1,7 +1,7 @@ metrics: sigma: - good: - bad: + good: 0.007 + bad: 0.015 unit: e/A tooltip: Standard deviation of total dipole in z direction level of theory: null diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py index 2a78c7c94..9ac70886f 100644 --- a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -78,6 +78,7 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: # Write output structures write_dir = OUT_PATH / model_name write_dir.mkdir(parents=True, exist_ok=True) + print("Writing to ", write_dir) thermo_traj = open(write_dir / (out_name + ".thermo"), "w") # file for output coord_traj_name = write_dir / (out_name + ".xyz") # file for coordinate output From 52367404f776af57405286b25618c0d111d4681b Mon Sep 17 00:00:00 2001 From: Mandy Julie Hoffmann Date: Thu, 29 Jan 2026 13:49:12 +0100 Subject: [PATCH 06/19] Got analysis working --- .../water_slab_dipoles/analyse_water_slab_dipoles.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 4f61e065e..2c78031bb 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -44,10 +44,10 @@ def get_dipoles() -> dict[str, np.ndarray]: for model_name in MODELS: model_dir = CALC_PATH / model_name if model_dir.exists(): - if model_dir.glob("dipoles.npy"): + if (model_dir / "dipoles.npy").is_file(): results[model_name] = np.load(model_dir / "dipoles.npy") else: - atoms = read(model_dir / "slab.xyz") + atoms = read(model_dir / "slab.xyz", ":") dipoles = np.zeros(len(atoms)) for i, struc in enumerate(atoms): o_index = [atom.index for atom in struc if atom.number == 8] @@ -75,7 +75,7 @@ def dipole_std() -> dict[str, float]: dipoles = get_dipoles() results = {} for model_name in MODELS: - if dipoles[model_name]: + if model_name in dipoles.keys(): results[model_name] = np.std(dipoles[model_name]) else: results[model_name] = None @@ -102,7 +102,7 @@ def n_bad() -> dict[str, float]: results = {} for model_name in MODELS: - if dipoles[model_name]: + if model_name in dipoles.keys(): results[model_name] = ( np.abs(dipoles[model_name]) > dipole_bad_threshold ).sum() / len(dipoles[model_name]) From 56260945debc35ec843414f6d45461ad77f57b9f Mon Sep 17 00:00:00 2001 From: Mandy Julie Hoffmann Date: Thu, 29 Jan 2026 14:41:37 +0100 Subject: [PATCH 07/19] Added timestamps to thermo file --- .../water_slab_dipoles/calc_water_slab_dipoles.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py index 9ac70886f..33e775da1 100644 --- a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -2,7 +2,7 @@ from __future__ import annotations -from datetime import date +from datetime import date, datetime from pathlib import Path from typing import Any @@ -115,7 +115,7 @@ def print_traj(a=start_config): # print_traj could also be done using MDLogger and write_traj thermo_traj.write( - "# ASE Dynamics. Date: " + date.today().strftime("%d %b %Y") + "\n" + "# ASE Dynamics. Date: " + date.today().strftime("%d %b %Y") + ", started: " + datetime.now().strftime("%H:%M:%S") + "\n" ) thermo_traj.write("# Time(fs) Temperature(K) Energy(eV) \n") open(coord_traj_name, "w").close() @@ -125,4 +125,7 @@ def print_traj(a=start_config): md.attach(print_traj) md.run(md_t) + thermo_traj.write( + "# Date: " + date.today().strftime("%d %b %Y") + ", finished: " + datetime.now().strftime("%H:%M:%S") + "\n" + ) thermo_traj.close() From fc15626939f8cb950d5a980740594fcd862a7ba0 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 29 Jan 2026 13:58:53 +0000 Subject: [PATCH 08/19] Added app file --- .../app_water_slab_dipoles.py | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py new file mode 100644 index 000000000..b3ce7146f --- /dev/null +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -0,0 +1,48 @@ +"""Run water slab dipoles 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 + +# Get all models +MODELS = get_model_names(current_models) +BENCHMARK_NAME = "Dipoles of Water Slabs" +DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/physicality.html#water_slab_dipoles" +DATA_PATH = APP_ROOT / "data" / "molecular_crystal" / "water_slab_dipoles" + + +class WaterSlabDipolesApp(BaseApp): + """Water slab dipole benchmark app layout and callbacks.""" + + def register_callbacks(self) -> None: + """Register callbacks to app.""" + return + + +def get_app() -> WaterSlabDipolesApp: + """ + Get water slab dipoles benchmark app layout and callback registration. + + Returns + ------- + WaterSlabDipolesApp + Benchmark layout and callback registration. + """ + return WaterSlabDipolesApp( + name=BENCHMARK_NAME, + description="Dipole distribution of a 38 A water slab", + docs_url=DOCS_URL, + table_path=DATA_PATH / "water_slab_dipoles_metrics_table.json", + extra_components=[], + ) From 5d750403fe582eed131048725b0f78cd2d533967 Mon Sep 17 00:00:00 2001 From: Mandy Julie Hoffmann Date: Thu, 29 Jan 2026 15:33:25 +0100 Subject: [PATCH 09/19] App can run now --- .../app_water_slab_dipoles.py | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index b3ce7146f..82e97799c 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -2,8 +2,8 @@ from __future__ import annotations -# from dash import Dash -# from dash.html import Div +from dash import Dash +from dash.html import Div from ml_peg.app import APP_ROOT from ml_peg.app.base_app import BaseApp @@ -19,7 +19,7 @@ MODELS = get_model_names(current_models) BENCHMARK_NAME = "Dipoles of Water Slabs" DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/physicality.html#water_slab_dipoles" -DATA_PATH = APP_ROOT / "data" / "molecular_crystal" / "water_slab_dipoles" +DATA_PATH = APP_ROOT / "data" / "physicality" / "water_slab_dipoles" class WaterSlabDipolesApp(BaseApp): @@ -46,3 +46,15 @@ def get_app() -> WaterSlabDipolesApp: table_path=DATA_PATH / "water_slab_dipoles_metrics_table.json", extra_components=[], ) + +if __name__ == "__main__": + # Create Dash app + full_app = Dash(__name__, assets_folder=DATA_PATH.parent.parent) + + # Construct layout and register callbacks + dipole_app = get_app() + full_app.layout = dipole_app.layout + dipole_app.register_callbacks() + + # Run app + full_app.run(port=8055, debug=True) From 09e77585f5fce5f219b70f3df64db459f9233463 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 29 Jan 2026 15:34:09 +0000 Subject: [PATCH 10/19] Changed length of MD in calc --- .../app_water_slab_dipoles.py | 19 ++++++++++++++++--- .../calc_water_slab_dipoles.py | 18 +++++++++++++----- 2 files changed, 29 insertions(+), 8 deletions(-) diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index b3ce7146f..3c4aff348 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -2,8 +2,8 @@ from __future__ import annotations -# from dash import Dash -# from dash.html import Div +from dash import Dash + from ml_peg.app import APP_ROOT from ml_peg.app.base_app import BaseApp @@ -19,7 +19,7 @@ MODELS = get_model_names(current_models) BENCHMARK_NAME = "Dipoles of Water Slabs" DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/physicality.html#water_slab_dipoles" -DATA_PATH = APP_ROOT / "data" / "molecular_crystal" / "water_slab_dipoles" +DATA_PATH = APP_ROOT / "data" / "physicality" / "water_slab_dipoles" class WaterSlabDipolesApp(BaseApp): @@ -46,3 +46,16 @@ def get_app() -> WaterSlabDipolesApp: table_path=DATA_PATH / "water_slab_dipoles_metrics_table.json", extra_components=[], ) + + +if __name__ == "__main__": + # Create Dash app + full_app = Dash(__name__, assets_folder=DATA_PATH.parent.parent) + + # Construct layout and register callbacks + dipole_app = get_app() + full_app.layout = dipole_app.layout + dipole_app.register_callbacks() + + # Run app + full_app.run(port=8055, debug=True) diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py index 33e775da1..3be31b9e8 100644 --- a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -43,9 +43,9 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: out_name = "slab" - md_t = 200 # 200000 # number of timesteps, here dt = 1fs - md_dt = 10 # 500 # intervals for printing energy, T, etc - th_dt = 10 # 500 # intervals for printing structures + md_t = 200000 # number of timesteps, here dt = 1fs + md_dt = 500 # intervals for printing energy, T, etc + th_dt = 500 # intervals for printing structures temp = 300 # Kelvin pres = 1.013 # bar @@ -115,7 +115,11 @@ def print_traj(a=start_config): # print_traj could also be done using MDLogger and write_traj thermo_traj.write( - "# ASE Dynamics. Date: " + date.today().strftime("%d %b %Y") + ", started: " + datetime.now().strftime("%H:%M:%S") + "\n" + "# ASE Dynamics. Date: " + + date.today().strftime("%d %b %Y") + + ", started: " + + datetime.now().strftime("%H:%M:%S") + + "\n" ) thermo_traj.write("# Time(fs) Temperature(K) Energy(eV) \n") open(coord_traj_name, "w").close() @@ -126,6 +130,10 @@ def print_traj(a=start_config): md.run(md_t) thermo_traj.write( - "# Date: " + date.today().strftime("%d %b %Y") + ", finished: " + datetime.now().strftime("%H:%M:%S") + "\n" + "# Date: " + + date.today().strftime("%d %b %Y") + + ", finished: " + + datetime.now().strftime("%H:%M:%S") + + "\n" ) thermo_traj.close() From 53966208b733c6b4c8474cbef50f8a652b487737 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Fri, 30 Jan 2026 11:05:42 +0000 Subject: [PATCH 11/19] Drafted histogram function (one hist for each model). --- ml_peg/analysis/utils/decorators.py | 174 ++++++++++++++++++++++++++++ 1 file changed, 174 insertions(+) diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 3641aab51..35167bbd0 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.express as px import plotly.graph_objects as go from ml_peg.analysis.utils.utils import calc_table_scores @@ -426,6 +427,179 @@ def wrapper(*args, **kwargs): return decorator +def model_to_hist( + *, + filename: str | Path, + datadir: Path, + dataname: str, + bins: Any | None = None, + good: float | None = None, + bad: float | None = None, + x_label: str | None = None, + title: str | None = None, + title_template: str = "{model} - {title}", +) -> Callable: + """ + Pre-generate histogram plots for each table row (model). + + Use this for benchmarks where each table CELL generates its own scatter plot + (e.g., clicking MACE's ω_max shows a scatter for that specific model-metric + pair). For benchmarks where clicking a COLUMN shows all models on one scatter + (like S24 or OC157), use @plot_parity instead. + + This decorator generates complete Plotly figures during analysis instead of + saving raw points for the app to process on-the-fly. + + Parameters + ---------- + filename + Path where JSON data with pre-made figures will be saved. + datadir + Directory in which modeldir with data for plotting are. + dataname + Name of data file for each model. + bins + Bins for the histogram. Default is None. + good + Line to be plotted for marking outliers. Default is None. + bad + Line to be plotted for marking outliers. Default is None. + x_label + Label for x-axis. Default is None. + title + Title for the plot to be used in template. Default is None. + title_template + Template for plot titles with {model} and {title} placeholders. + Default is "{model} - {title}". + + Returns + ------- + Callable + Decorator that wraps analysis functions to pre-generate scatter figures. + """ + + def decorator(func: Callable) -> Callable: + """ + Wrap the decorated callable to pre-generate scatter figures. + + Parameters + ---------- + func + Analysis function returning the dataset consumed by the Dash app. + + Returns + ------- + Callable + Wrapped function that runs ``func`` and emits Plotly figures. + """ + + @functools.wraps(func) + def wrapper(*args, **kwargs): + """ + Execute func and generate scatter plots for each model-metric pair. + + Parameters + ---------- + *args + Positional arguments forwarded to ``func``. + **kwargs + Keyword arguments forwarded to ``func``. + + Returns + ------- + dict + The dataset produced by ``func`` (with ``figures`` entries). + """ + data_bundle = func(*args, **kwargs) + + # Extract metadata + # metric_labels = data_bundle.get("metrics", {}) + models_data = data_bundle.get("models", {}) + hist_data = {} + + # Create figures for each model-metric pair + for model_name, model_data in models_data.items(): + model_data["figures"] = {} + # metrics_data = model_data.get("metrics", {}) + hist_data[model_name] = np.load(datadir / model_name / dataname) + + # for metric_key, metric_info in metrics_data.items(): + # points = metric_info.get("points", []) + # if not points: + # continue + + # Extract ref and pred values + # refs = [p["ref"] for p in points] + # preds = [p["pred"] for p in points] + # ids = [p.get("id", "") for p in points] + + # Build hovertemplate + # hovertemplate = ( + # "Pred: %{x}
Ref: %{y}
" + # "ID: %{customdata[0]}
" + # ) + # customdata = [[id_val] for id_val in ids] + + # Create figure + # counts, np_bins = np.histogram(hist_data[model_name], bins = bins) + fig = px.histogram( + hist_data[model_name], histnorm="probability density", x=bins + ) + + # Add good & bad threshold line + full_fig = fig.full_figure_for_development() + y_range = full_fig.layout.yaxis.range + if good is not None: + lims = [ + np.min([good, y_range]), + np.max([good, y_range]), + ] + fig.add_trace( + go.Scatter( + x=lims, + y=lims, + mode="lines", + showlegend=False, + ) + ) + if bad is not None: + lims = [ + np.min([bad, y_range]), + np.max([bad, y_range]), + ] + fig.add_trace( + go.Scatter( + x=lims, + y=lims, + mode="lines", + showlegend=False, + ) + ) + + # Update layout + fig_title = title_template.format(model=model_name, title=title) + fig.update_layout( + title={"text": fig_title}, + xaxis={"title": {"text": x_label}}, + # yaxis={"title": {"text": y_label}}, + # no label, y axis is probability density + ) + + # Store figure as JSON-serializable dict + model_data["figures"] = json.loads(fig.to_json()) + + # Save to file + Path(filename).parent.mkdir(parents=True, exist_ok=True) + with open(filename, "w", encoding="utf8") as f: + dump(data_bundle, f) + + return data_bundle + + return wrapper + + return decorator + + def plot_scatter( title: str | None = None, x_label: str | None = None, From f57c08809f593f6a3abd0e0f346b0f3734376fa0 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Fri, 30 Jan 2026 12:16:16 +0000 Subject: [PATCH 12/19] Changed plot-hist to be more like plot_hist --- .../analyse_water_slab_dipoles.py | 47 ++++- ml_peg/analysis/utils/decorators.py | 194 ++++++++---------- .../app_water_slab_dipoles.py | 31 ++- 3 files changed, 143 insertions(+), 129 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 2c78031bb..218ebddb0 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -10,7 +10,7 @@ import pytest from scipy.constants import e, epsilon_0 -from ml_peg.analysis.utils.decorators import build_table # , plot_parity +from ml_peg.analysis.utils.decorators import build_table, plot_hist from ml_peg.analysis.utils.utils import build_d3_name_map, load_metrics_config from ml_peg.app import APP_ROOT from ml_peg.calcs import CALCS_ROOT @@ -30,6 +30,12 @@ # Unit conversion EV_TO_KJ_PER_MOL = units.mol / units.kJ +# We consider a dipole as bad if the expected band gap is <= 0 +# The expected band gap is 4.50 V - |P_z_per_unit_area| / epsilon_0 +# Hence "bad" is |P_z_per_unit_area| > 4.50 V * epsilon_0 / e * 10^(-10) +# epsilon_0 is in F/m = C/(V*m), so this gives it in e/(V*A) +DIPOLE_BAD_THRESHOLD = 4.50 * epsilon_0 / e * 10 ** (-10) + def get_dipoles() -> dict[str, np.ndarray]: """ @@ -94,23 +100,48 @@ def n_bad() -> dict[str, float]: """ dipoles = get_dipoles() - # We consider a dipole as bad if the expected band gap is <= 0 - # The expected band gap is 4.50 V - |P_z_per_unit_area| / epsilon_0 - # Hence "bad" is |P_z_per_unit_area| > 4.50 V * epsilon_0 / e * 10^(-10) - # epsilon_0 is in F/m = C/(V*m), so this gives it in e/(V*A) - dipole_bad_threshold = 4.50 * epsilon_0 / e * 10 ** (-10) - results = {} for model_name in MODELS: if model_name in dipoles.keys(): results[model_name] = ( - np.abs(dipoles[model_name]) > dipole_bad_threshold + np.abs(dipoles[model_name]) > DIPOLE_BAD_THRESHOLD ).sum() / len(dipoles[model_name]) else: results[model_name] = None return results +def plot_distribution(model: str) -> None: + """ + Plot NEB paths and save all structure files. + + Parameters + ---------- + model + Name of MLIP. + """ + + @plot_hist( + filename=OUT_PATH / f"figure_{model}_dipoledistr.json", + title=f"Dipole Distribution {model}", + x_label="Total z-Dipole per unit area [e/A]", + good=-DIPOLE_BAD_THRESHOLD, + bad=DIPOLE_BAD_THRESHOLD, + ) + def plot_distr() -> dict[str, np.ndarray]: + """ + Plot a NEB and save the structure file. + + Returns + ------- + dict[str, np.ndarray] + Dictionary of array with all dipoles for each model. + """ + return get_dipoles() + + plot_distr() + + @pytest.fixture @build_table( filename=OUT_PATH / "water_slab_dipoles_metrics_table.json", diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 35167bbd0..b88fdcd53 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -427,177 +427,145 @@ def wrapper(*args, **kwargs): return decorator -def model_to_hist( +def plot_hist( *, - filename: str | Path, - datadir: Path, - dataname: str, bins: Any | None = None, good: float | None = None, bad: float | None = None, - x_label: str | None = None, title: str | None = None, - title_template: str = "{model} - {title}", + x_label: str | None = None, + filename: str | Path, ) -> Callable: """ - Pre-generate histogram plots for each table row (model). - - Use this for benchmarks where each table CELL generates its own scatter plot - (e.g., clicking MACE's ω_max shows a scatter for that specific model-metric - pair). For benchmarks where clicking a COLUMN shows all models on one scatter - (like S24 or OC157), use @plot_parity instead. - - This decorator generates complete Plotly figures during analysis instead of - saving raw points for the app to process on-the-fly. + Plot scatter plot of MLIP results. Parameters ---------- - filename - Path where JSON data with pre-made figures will be saved. - datadir - Directory in which modeldir with data for plotting are. - dataname - Name of data file for each model. bins - Bins for the histogram. Default is None. + Bins for histogram. Default is None. good - Line to be plotted for marking outliers. Default is None. + Minimum threshold for good values to draw line at. + Default is None. bad - Line to be plotted for marking outliers. Default is None. - x_label - Label for x-axis. Default is None. + Maximum threshold for good values to draw line at. + Default is None. title - Title for the plot to be used in template. Default is None. - title_template - Template for plot titles with {model} and {title} placeholders. - Default is "{model} - {title}". + Graph title. + x_label + Label for x-axis. Default is `None`. + + filename + Filename to save plot as JSON. Default is "scatter.json". Returns ------- Callable - Decorator that wraps analysis functions to pre-generate scatter figures. + Decorator to wrap function. """ - def decorator(func: Callable) -> Callable: + def plot_hist_decorator(func: Callable) -> Callable: """ - Wrap the decorated callable to pre-generate scatter figures. + Decorate function to plot scatter. Parameters ---------- func - Analysis function returning the dataset consumed by the Dash app. + Function being wrapped. Returns ------- Callable - Wrapped function that runs ``func`` and emits Plotly figures. + Wrapped function. """ @functools.wraps(func) - def wrapper(*args, **kwargs): + def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: """ - Execute func and generate scatter plots for each model-metric pair. + Wrap function to plot scatter. Parameters ---------- *args - Positional arguments forwarded to ``func``. + Arguments to pass to the function being wrapped. **kwargs - Keyword arguments forwarded to ``func``. + Key word arguments to pass to the function being wrapped. Returns ------- dict - The dataset produced by ``func`` (with ``figures`` entries). + Results dictionary. """ - data_bundle = func(*args, **kwargs) + results = func(*args, **kwargs) - # Extract metadata - # metric_labels = data_bundle.get("metrics", {}) - models_data = data_bundle.get("models", {}) - hist_data = {} - - # Create figures for each model-metric pair - for model_name, model_data in models_data.items(): - model_data["figures"] = {} - # metrics_data = model_data.get("metrics", {}) - hist_data[model_name] = np.load(datadir / model_name / dataname) - - # for metric_key, metric_info in metrics_data.items(): - # points = metric_info.get("points", []) - # if not points: - # continue - - # Extract ref and pred values - # refs = [p["ref"] for p in points] - # preds = [p["pred"] for p in points] - # ids = [p.get("id", "") for p in points] - - # Build hovertemplate - # hovertemplate = ( - # "Pred: %{x}
Ref: %{y}
" - # "ID: %{customdata[0]}
" - # ) - # customdata = [[id_val] for id_val in ids] + # hovertemplate = "Pred: %{x}
" + "Ref: %{y}
" + # customdata = [] + # if hoverdata: + # for i, key in enumerate(hoverdata): + # hovertemplate += f"{key}: %{{customdata[{i}]}}
" + # customdata = list(zip(*hoverdata.values(), strict=True)) + fig = go.Figure() + for model_name, hist_data in results.items(): # Create figure # counts, np_bins = np.histogram(hist_data[model_name], bins = bins) - fig = px.histogram( - hist_data[model_name], histnorm="probability density", x=bins + fig.add_trace( + px.histogram( + hist_data, + histnorm="probability density", + x=bins, + title=model_name, + ) ) - # Add good & bad threshold line - full_fig = fig.full_figure_for_development() - y_range = full_fig.layout.yaxis.range - if good is not None: - lims = [ - np.min([good, y_range]), - np.max([good, y_range]), - ] - fig.add_trace( - go.Scatter( - x=lims, - y=lims, - mode="lines", - showlegend=False, - ) + # Add good & bad threshold line + full_fig = fig.full_figure_for_development() + y_range = full_fig.layout.yaxis.range + if good is not None: + lims = [ + np.min([good, y_range]), + np.max([good, y_range]), + ] + fig.add_trace( + go.Scatter( + x=lims, + y=lims, + mode="lines", + showlegend=False, ) - if bad is not None: - lims = [ - np.min([bad, y_range]), - np.max([bad, y_range]), - ] - fig.add_trace( - go.Scatter( - x=lims, - y=lims, - mode="lines", - showlegend=False, - ) + ) + if bad is not None: + lims = [ + np.min([bad, y_range]), + np.max([bad, y_range]), + ] + fig.add_trace( + go.Scatter( + x=lims, + y=lims, + mode="lines", + showlegend=False, ) + ) - # Update layout - fig_title = title_template.format(model=model_name, title=title) - fig.update_layout( - title={"text": fig_title}, - xaxis={"title": {"text": x_label}}, - # yaxis={"title": {"text": y_label}}, - # no label, y axis is probability density - ) + # Update layout + fig.update_layout( + title={"text": title}, + xaxis={"title": {"text": x_label}}, + # yaxis={"title": {"text": y_label}}, + # no label, y axis is probability density + ) - # Store figure as JSON-serializable dict - model_data["figures"] = json.loads(fig.to_json()) + fig.update_traces() - # Save to file + # Write to file Path(filename).parent.mkdir(parents=True, exist_ok=True) - with open(filename, "w", encoding="utf8") as f: - dump(data_bundle, f) + fig.write_json(filename) - return data_bundle + return results - return wrapper + return plot_hist_wrapper - return decorator + return plot_hist_decorator def plot_scatter( diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index 3c4aff348..6f600cb9c 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -3,15 +3,15 @@ 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.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 @@ -27,7 +27,20 @@ class WaterSlabDipolesApp(BaseApp): def register_callbacks(self) -> None: """Register callbacks to app.""" - return + hists = { + model: { + "Dipole Distribution": read_plot( + DATA_PATH / f"figure_{model}_dipoledistr.json", + id=f"{BENCHMARK_NAME}-{model}-figure", + ), + } + for model in MODELS + } + plot_from_table_cell( + table_id=self.table_id, + plot_id=f"{BENCHMARK_NAME}-figure-placeholder", + cell_to_plot=hists, + ) def get_app() -> WaterSlabDipolesApp: @@ -44,7 +57,9 @@ def get_app() -> WaterSlabDipolesApp: description="Dipole distribution of a 38 A water slab", docs_url=DOCS_URL, table_path=DATA_PATH / "water_slab_dipoles_metrics_table.json", - extra_components=[], + extra_components=[ + Div(id=f"{BENCHMARK_NAME}-figure-placeholder"), + ], ) From 21717059f4ad58c0a13dc9111e945823bf53ee88 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Fri, 30 Jan 2026 12:56:55 +0000 Subject: [PATCH 13/19] It's actually calling the hist decorator now --- .../analyse_water_slab_dipoles.py | 1 + ml_peg/analysis/utils/decorators.py | 29 ++++++++----------- 2 files changed, 13 insertions(+), 17 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 218ebddb0..c6e32cfce 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -103,6 +103,7 @@ def n_bad() -> dict[str, float]: results = {} for model_name in MODELS: if model_name in dipoles.keys(): + plot_distribution(model_name) results[model_name] = ( np.abs(dipoles[model_name]) > DIPOLE_BAD_THRESHOLD ).sum() / len(dipoles[model_name]) diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index b88fdcd53..fb4014458 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -13,7 +13,6 @@ from dash import dash_table import numpy as np import pandas as pd -import plotly.express as px import plotly.graph_objects as go from ml_peg.analysis.utils.utils import calc_table_scores @@ -509,11 +508,11 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: # Create figure # counts, np_bins = np.histogram(hist_data[model_name], bins = bins) fig.add_trace( - px.histogram( - hist_data, + go.Histogram( + x=hist_data, histnorm="probability density", - x=bins, - title=model_name, + nbinsx=bins, + name=model_name, ) ) @@ -521,27 +520,23 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: full_fig = fig.full_figure_for_development() y_range = full_fig.layout.yaxis.range if good is not None: - lims = [ - np.min([good, y_range]), - np.max([good, y_range]), - ] + x = [0, y_range] + y = [good, good] fig.add_trace( go.Scatter( - x=lims, - y=lims, + x=x, + y=y, mode="lines", showlegend=False, ) ) if bad is not None: - lims = [ - np.min([bad, y_range]), - np.max([bad, y_range]), - ] + x = [0, y_range] + y = [bad, bad] fig.add_trace( go.Scatter( - x=lims, - y=lims, + x=x, + y=y, mode="lines", showlegend=False, ) From fb1e5fe54dceb6ffb9261128d472f40ae4ae3a86 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Wed, 4 Feb 2026 10:44:36 +0000 Subject: [PATCH 14/19] Plots are actually visible now --- .../analyse_water_slab_dipoles.py | 64 +++---- .../app_water_slab_dipoles.py | 12 +- ml_peg/app/utils/build_callbacks.py | 9 + ml_peg/app/utils/load.py | 4 + ml_peg/models/models.yml | 164 +++++++++--------- 5 files changed, 138 insertions(+), 115 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index c6e32cfce..2b647b7b8 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -68,6 +68,38 @@ def get_dipoles() -> dict[str, np.ndarray]: return results +def plot_distribution(model: str) -> None: + """ + Plot Dipole Distribution. + + Parameters + ---------- + model + Name of MLIP. + """ + + @plot_hist( + filename=OUT_PATH / f"figure_{model}_dipoledistr.json", + title=f"Dipole Distribution {model}", + x_label="Total z-Dipole per unit area [e/A]", + good=-DIPOLE_BAD_THRESHOLD, + bad=DIPOLE_BAD_THRESHOLD, + bins=20, + ) + def plot_distr() -> dict[str, np.ndarray]: + """ + Plot a NEB and save the structure file. + + Returns + ------- + dict[str, np.ndarray] + Dictionary of array with all dipoles for each model. + """ + return get_dipoles() # {'sigma': get_dipoles(), 'n_bad': get_dipoles()} + + plot_distr() + + @pytest.fixture def dipole_std() -> dict[str, float]: """ @@ -82,6 +114,7 @@ def dipole_std() -> dict[str, float]: results = {} for model_name in MODELS: if model_name in dipoles.keys(): + plot_distribution(model_name) results[model_name] = np.std(dipoles[model_name]) else: results[model_name] = None @@ -112,37 +145,6 @@ def n_bad() -> dict[str, float]: return results -def plot_distribution(model: str) -> None: - """ - Plot NEB paths and save all structure files. - - Parameters - ---------- - model - Name of MLIP. - """ - - @plot_hist( - filename=OUT_PATH / f"figure_{model}_dipoledistr.json", - title=f"Dipole Distribution {model}", - x_label="Total z-Dipole per unit area [e/A]", - good=-DIPOLE_BAD_THRESHOLD, - bad=DIPOLE_BAD_THRESHOLD, - ) - def plot_distr() -> dict[str, np.ndarray]: - """ - Plot a NEB and save the structure file. - - Returns - ------- - dict[str, np.ndarray] - Dictionary of array with all dipoles for each model. - """ - return get_dipoles() - - plot_distr() - - @pytest.fixture @build_table( filename=OUT_PATH / "water_slab_dipoles_metrics_table.json", diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index 6f600cb9c..6cb296aa6 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -27,15 +27,22 @@ class WaterSlabDipolesApp(BaseApp): def register_callbacks(self) -> None: """Register callbacks to app.""" + print(" Registering callbacks to app") hists = { model: { - "Dipole Distribution": read_plot( + "sigma": read_plot( + DATA_PATH / f"figure_{model}_dipoledistr.json", + id=f"{BENCHMARK_NAME}-{model}-figure", + ), + "Fraction Breakdown Candidates": read_plot( DATA_PATH / f"figure_{model}_dipoledistr.json", id=f"{BENCHMARK_NAME}-{model}-figure", ), } for model in MODELS } + for model in MODELS: + print("Read plot from ", DATA_PATH / f"figure_{model}_dipoledistr.json") plot_from_table_cell( table_id=self.table_id, plot_id=f"{BENCHMARK_NAME}-figure-placeholder", @@ -52,6 +59,7 @@ def get_app() -> WaterSlabDipolesApp: WaterSlabDipolesApp Benchmark layout and callback registration. """ + print("Id of extra components: ", f"{BENCHMARK_NAME}-figure-placeholder") return WaterSlabDipolesApp( name=BENCHMARK_NAME, description="Dipole distribution of a 38 A water slab", @@ -65,7 +73,7 @@ def get_app() -> WaterSlabDipolesApp: if __name__ == "__main__": # Create Dash app - full_app = Dash(__name__, assets_folder=DATA_PATH.parent.parent) + full_app = Dash(__name__, assets_folder=DATA_PATH.parent) # Construct layout and register callbacks dipole_app = get_app() diff --git a/ml_peg/app/utils/build_callbacks.py b/ml_peg/app/utils/build_callbacks.py index f3aab2ee2..66c09035d 100644 --- a/ml_peg/app/utils/build_callbacks.py +++ b/ml_peg/app/utils/build_callbacks.py @@ -111,21 +111,30 @@ def show_plot(active_cell, current_table_data) -> Div: Message explaining interactivity, or plot on cell click. """ if not active_cell: + print("Not active cell; active_cell = ", active_cell) return Div("Click on a metric to view plot.") column_id = active_cell.get("column_id", None) row_id = active_cell.get("row_id", None) row_index = active_cell.get("row", None) + print("Active cell: ", column_id, row_id, row_index) + print("Current table data: ", current_table_data) # Check if cell value is None (no data for this model) if current_table_data and row_index is not None: + print("Trying to get cell_value") try: cell_value = current_table_data[row_index].get(column_id) + print("cell_value = ", cell_value) if cell_value is None: return Div("No data available for this model.") except (IndexError, KeyError, TypeError): pass # Fall through to normal handling + print("Cell to plot: ", cell_to_plot) + print(f"Want to plot: cell_to_plot[{row_id}][{column_id}] = ") + print(f"{cell_to_plot[row_id][column_id]}") if row_id in cell_to_plot and column_id in cell_to_plot[row_id]: + print(f"Plotting {cell_to_plot[row_id][column_id]}") return Div(cell_to_plot[row_id][column_id]) return Div("Click on a metric to view plot.") diff --git a/ml_peg/app/utils/load.py b/ml_peg/app/utils/load.py index b4f10d7cd..cb4ef61d0 100644 --- a/ml_peg/app/utils/load.py +++ b/ml_peg/app/utils/load.py @@ -226,6 +226,10 @@ def read_plot(filename: str | Path, id: str = "figure-1") -> Graph: Loaded plotly Graph. """ figure = read_json(filename) if Path(filename).exists() else None + print(f"Opening plot from {filename}") + print(f"exists: {Path(filename).exists()}") + print("Figure: ", figure) + print("id: ", id) return Graph(id=id, figure=figure) diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml index f8e5b68f0..0dc156c34 100644 --- a/ml_peg/models/models.yml +++ b/ml_peg/models/models.yml @@ -1,65 +1,65 @@ -mace-mp-0a: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBE - kwargs: - model: "medium" - -mace-mp-0a-small: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBE - kwargs: - model: "small" - -mace-mp-0b3: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBE - kwargs: - model: "medium-0b3" - -mace-mpa-0: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBE - kwargs: - model: "medium-mpa-0" - -mace-omat-0: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBE - kwargs: - model: "medium-omat-0" - -mace-matpes-r2scan: - module: mace.calculators - class_name: mace_mp - device: "auto" - default_dtype: float32 - trained_on_d3: false - level_of_theory: r2SCAN - kwargs: - model: "mace-matpes-r2scan-0" - head: "matpes_pbe" - d3_kwargs: - xc: r2scan +#mace-mp-0a: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# model: "medium" +# +#mace-mp-0a-small: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# model: "small" +# +#mace-mp-0b3: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# model: "medium-0b3" +# +#mace-mpa-0: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# model: "medium-mpa-0" +# +#mace-omat-0: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# model: "medium-omat-0" +# +#mace-matpes-r2scan: +# module: mace.calculators +# class_name: mace_mp +# device: "auto" +# default_dtype: float32 +## trained_on_d3: false +# level_of_theory: r2SCAN +# kwargs: +# model: "mace-matpes-r2scan-0" +# head: "matpes_pbe" +# d3_kwargs: +# xc: r2scan # mace-mh-1-omat: # module: mace.calculators @@ -72,15 +72,15 @@ mace-matpes-r2scan: # model: "mh-1" # head: omat_pbe -orb-v3-consv-inf-omat: - module: orb_models.forcefield - class_name: OrbCalc - device: "cpu" - default_dtype: float32-high - trained_on_d3: false - level_of_theory: PBE - kwargs: - name: "orb_v3_conservative_inf_omat" +#orb-v3-consv-inf-omat: +# module: orb_models.forcefield +# class_name: OrbCalc +# device: "cpu" +# default_dtype: float32-high +# trained_on_d3: false +# level_of_theory: PBE +# kwargs: +# name: "orb_v3_conservative_inf_omat" # mattersim-5M: # module: mattersim.forcefield @@ -179,14 +179,14 @@ small_FF_SR_water_model: # model_name: "uma-s-1p1" # task_name: "omol" -pet-mad: - module: pet_mad.calculator - class_name: PETMADCalculator - device: "cpu" - default_dtype: float32 - trained_on_d3: false - level_of_theory: PBEsol - kwargs: - version: "v1.0.2" - d3_kwargs: - xc: pbesol +#pet-mad: +# module: pet_mad.calculator +# class_name: PETMADCalculator +# device: "cpu" +# default_dtype: float32 +# trained_on_d3: false +# level_of_theory: PBEsol +# kwargs: +# version: "v1.0.2" +# d3_kwargs: +# xc: pbesol From 8ec510328d35ccbc30f2756abf61bac11d7e6378 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Wed, 4 Feb 2026 18:05:53 +0000 Subject: [PATCH 15/19] Plot exists for mp0a now, D3 names removed --- .../analyse_water_slab_dipoles.py | 6 +++++- .../app_water_slab_dipoles.py | 2 ++ ml_peg/models/models.yml | 20 +++++++++---------- 3 files changed, 17 insertions(+), 11 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 2b647b7b8..19878c9ae 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -49,6 +49,8 @@ def get_dipoles() -> dict[str, np.ndarray]: results = {} for model_name in MODELS: model_dir = CALC_PATH / model_name + print("Trying to open: ", model_dir) + print("Exists: ", model_dir.exists()) if model_dir.exists(): if (model_dir / "dipoles.npy").is_file(): results[model_name] = np.load(model_dir / "dipoles.npy") @@ -65,6 +67,7 @@ def get_dipoles() -> dict[str, np.ndarray]: dipoles_unit_area = dipoles / atoms[0].cell[0, 0] / atoms[0].cell[1, 1] results[model_name] = dipoles_unit_area np.save(model_dir / "dipoles.npy", dipoles_unit_area) + print("Results: ", results) return results @@ -113,7 +116,9 @@ def dipole_std() -> dict[str, float]: dipoles = get_dipoles() results = {} for model_name in MODELS: + print("Searching for dipole key: ", model_name) if model_name in dipoles.keys(): + print("Found it") plot_distribution(model_name) results[model_name] = np.std(dipoles[model_name]) else: @@ -150,7 +155,6 @@ def n_bad() -> dict[str, float]: filename=OUT_PATH / "water_slab_dipoles_metrics_table.json", metric_tooltips=DEFAULT_TOOLTIPS, thresholds=DEFAULT_THRESHOLDS, - mlip_name_map=D3_MODEL_NAMES, ) def metrics(dipole_std: dict[str, float], n_bad: dict[str, float]) -> dict[str, dict]: """ diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index 6cb296aa6..99506ea9d 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -5,6 +5,7 @@ from dash import Dash from dash.html import Div +from ml_peg.analysis.utils.utils import build_d3_name_map from ml_peg.app import APP_ROOT from ml_peg.app.base_app import BaseApp from ml_peg.app.utils.build_callbacks import ( @@ -17,6 +18,7 @@ # Get all models MODELS = get_model_names(current_models) +D3_MODEL_NAMES = build_d3_name_map(MODELS) BENCHMARK_NAME = "Dipoles of Water Slabs" DOCS_URL = "https://ddmms.github.io/ml-peg/user_guide/benchmarks/physicality.html#water_slab_dipoles" DATA_PATH = APP_ROOT / "data" / "physicality" / "water_slab_dipoles" diff --git a/ml_peg/models/models.yml b/ml_peg/models/models.yml index 0dc156c34..c7f1a7b70 100644 --- a/ml_peg/models/models.yml +++ b/ml_peg/models/models.yml @@ -8,16 +8,16 @@ # kwargs: # model: "medium" # -#mace-mp-0a-small: -# module: mace.calculators -# class_name: mace_mp -# device: "auto" -# default_dtype: float32 -# trained_on_d3: false -# level_of_theory: PBE -# kwargs: -# model: "small" -# +mace-mp-0a-small: + module: mace.calculators + class_name: mace_mp + device: "auto" + default_dtype: float32 + trained_on_d3: false + level_of_theory: PBE + kwargs: + model: "small" + #mace-mp-0b3: # module: mace.calculators # class_name: mace_mp From 74b4616f43f0b2d3edff7b8f83cb544ca133ec27 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Wed, 4 Feb 2026 18:18:13 +0000 Subject: [PATCH 16/19] Hist has labels now. --- .../water_slab_dipoles/analyse_water_slab_dipoles.py | 1 + ml_peg/analysis/utils/decorators.py | 6 ++++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 19878c9ae..b4692c614 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -85,6 +85,7 @@ def plot_distribution(model: str) -> None: filename=OUT_PATH / f"figure_{model}_dipoledistr.json", title=f"Dipole Distribution {model}", x_label="Total z-Dipole per unit area [e/A]", + y_label="Probability Density", good=-DIPOLE_BAD_THRESHOLD, bad=DIPOLE_BAD_THRESHOLD, bins=20, diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index fb4014458..d3fc6d5ca 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -433,6 +433,7 @@ def plot_hist( bad: float | None = None, title: str | None = None, x_label: str | None = None, + y_label: str | None = None, filename: str | Path, ) -> Callable: """ @@ -452,7 +453,8 @@ def plot_hist( Graph title. x_label Label for x-axis. Default is `None`. - + y_label + Label for y axis. Default is `None`. filename Filename to save plot as JSON. Default is "scatter.json". @@ -546,7 +548,7 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: fig.update_layout( title={"text": title}, xaxis={"title": {"text": x_label}}, - # yaxis={"title": {"text": y_label}}, + yaxis={"title": {"text": y_label}}, # no label, y axis is probability density ) From 6c7a5e45377a4e1c1b275b701a63f55f6f5932d5 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 5 Feb 2026 17:00:26 +0000 Subject: [PATCH 17/19] Coloring of histogram works now --- .../analyse_water_slab_dipoles.py | 9 +- ml_peg/analysis/utils/decorators.py | 93 ++++++++++--------- 2 files changed, 58 insertions(+), 44 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index b4692c614..352b936dc 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -80,6 +80,9 @@ def plot_distribution(model: str) -> None: model Name of MLIP. """ + bins_start = -1.5 * DIPOLE_BAD_THRESHOLD + bins_stop = 1.5 * DIPOLE_BAD_THRESHOLD + bins_size = 3 * DIPOLE_BAD_THRESHOLD / 40 @plot_hist( filename=OUT_PATH / f"figure_{model}_dipoledistr.json", @@ -88,7 +91,7 @@ def plot_distribution(model: str) -> None: y_label="Probability Density", good=-DIPOLE_BAD_THRESHOLD, bad=DIPOLE_BAD_THRESHOLD, - bins=20, + bins={"start": bins_start, "end": bins_stop, "size": bins_size}, ) def plot_distr() -> dict[str, np.ndarray]: """ @@ -99,7 +102,9 @@ def plot_distr() -> dict[str, np.ndarray]: dict[str, np.ndarray] Dictionary of array with all dipoles for each model. """ - return get_dipoles() # {'sigma': get_dipoles(), 'n_bad': get_dipoles()} + return { + model: get_dipoles()[model] + } # {'sigma': get_dipoles(), 'n_bad': get_dipoles()} plot_distr() diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index d3fc6d5ca..9541ac609 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -442,12 +442,13 @@ def plot_hist( Parameters ---------- bins - Bins for histogram. Default is None. + Bins for histogram. Either int or directory + with start, end, size. Default is None. good - Minimum threshold for good values to draw line at. + Minimum threshold for good values. Requires bins dict. Default is None. bad - Maximum threshold for good values to draw line at. + Maximum threshold for good values. Requires bins dict. Default is None. title Graph title. @@ -463,6 +464,7 @@ def plot_hist( Callable Decorator to wrap function. """ + print(f"bins = {bins}") def plot_hist_decorator(func: Callable) -> Callable: """ @@ -506,51 +508,58 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: # customdata = list(zip(*hoverdata.values(), strict=True)) fig = go.Figure() + data_all = [] for model_name, hist_data in results.items(): # Create figure # counts, np_bins = np.histogram(hist_data[model_name], bins = bins) - fig.add_trace( - go.Histogram( - x=hist_data, - histnorm="probability density", - nbinsx=bins, - name=model_name, - ) - ) - - # Add good & bad threshold line - full_fig = fig.full_figure_for_development() - y_range = full_fig.layout.yaxis.range - if good is not None: - x = [0, y_range] - y = [good, good] - fig.add_trace( - go.Scatter( - x=x, - y=y, - mode="lines", - showlegend=False, + for point in hist_data: + data_all.append(point) + if bins is None or isinstance(bins, int) or isinstance(bins, float): + fig.add_trace( + go.Histogram( + x=hist_data, + histnorm="probability density", + nbinsx=bins, + name=model_name, + ) ) - ) - if bad is not None: - x = [0, y_range] - y = [bad, bad] - fig.add_trace( - go.Scatter( - x=x, - y=y, - mode="lines", - showlegend=False, + else: + fig.add_trace( + go.Histogram( + x=hist_data, + histnorm="probability density", + xbins=bins, + autobinx=False, + name=model_name, + ) ) - ) - # Update layout - fig.update_layout( - title={"text": title}, - xaxis={"title": {"text": x_label}}, - yaxis={"title": {"text": y_label}}, - # no label, y axis is probability density - ) + if good is not None and bad is not None and isinstance(bins, dict): + print("Using coloring") + actual_bins = [min(data_all)] + point = actual_bins[0] + while point < max(data_all): + point += bins["size"] + actual_bins.append(point) + colors = np.zeros_like(actual_bins) + bad_exists = False + for i, point in enumerate(actual_bins): + if point < good or point > bad: + bad_exists = True + colors[i] = bins["start"] + else: + colors[i] = bins["end"] + if not bad_exists: + colors = "#276419" + print("colors = ", colors) + fig.update_traces(marke_color=colors) + # Update layout + fig.update_layout( + title={"text": title}, + xaxis={"title": {"text": x_label}}, + yaxis={"title": {"text": y_label}}, + # no label, y axis is probability density + ) fig.update_traces() From 1d28c19c88138d29b424e1d7220859d98925b960 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 5 Feb 2026 19:06:49 +0000 Subject: [PATCH 18/19] Removed bug-fixing prints --- .../analyse_water_slab_dipoles.py | 9 +-------- ml_peg/analysis/utils/decorators.py | 3 --- .../app_water_slab_dipoles.py | 2 -- ml_peg/app/utils/build_callbacks.py | 9 --------- .../calc_water_slab_dipoles.py | 18 +++++------------- 5 files changed, 6 insertions(+), 35 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 352b936dc..0a9107525 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -49,8 +49,6 @@ def get_dipoles() -> dict[str, np.ndarray]: results = {} for model_name in MODELS: model_dir = CALC_PATH / model_name - print("Trying to open: ", model_dir) - print("Exists: ", model_dir.exists()) if model_dir.exists(): if (model_dir / "dipoles.npy").is_file(): results[model_name] = np.load(model_dir / "dipoles.npy") @@ -67,7 +65,6 @@ def get_dipoles() -> dict[str, np.ndarray]: dipoles_unit_area = dipoles / atoms[0].cell[0, 0] / atoms[0].cell[1, 1] results[model_name] = dipoles_unit_area np.save(model_dir / "dipoles.npy", dipoles_unit_area) - print("Results: ", results) return results @@ -102,9 +99,7 @@ def plot_distr() -> dict[str, np.ndarray]: dict[str, np.ndarray] Dictionary of array with all dipoles for each model. """ - return { - model: get_dipoles()[model] - } # {'sigma': get_dipoles(), 'n_bad': get_dipoles()} + return {model: get_dipoles()[model]} plot_distr() @@ -122,9 +117,7 @@ def dipole_std() -> dict[str, float]: dipoles = get_dipoles() results = {} for model_name in MODELS: - print("Searching for dipole key: ", model_name) if model_name in dipoles.keys(): - print("Found it") plot_distribution(model_name) results[model_name] = np.std(dipoles[model_name]) else: diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 9541ac609..7262c3149 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -511,7 +511,6 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: data_all = [] for model_name, hist_data in results.items(): # Create figure - # counts, np_bins = np.histogram(hist_data[model_name], bins = bins) for point in hist_data: data_all.append(point) if bins is None or isinstance(bins, int) or isinstance(bins, float): @@ -551,14 +550,12 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: colors[i] = bins["end"] if not bad_exists: colors = "#276419" - print("colors = ", colors) fig.update_traces(marke_color=colors) # Update layout fig.update_layout( title={"text": title}, xaxis={"title": {"text": x_label}}, yaxis={"title": {"text": y_label}}, - # no label, y axis is probability density ) fig.update_traces() diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index 99506ea9d..ced1f3331 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -43,8 +43,6 @@ def register_callbacks(self) -> None: } for model in MODELS } - for model in MODELS: - print("Read plot from ", DATA_PATH / f"figure_{model}_dipoledistr.json") plot_from_table_cell( table_id=self.table_id, plot_id=f"{BENCHMARK_NAME}-figure-placeholder", diff --git a/ml_peg/app/utils/build_callbacks.py b/ml_peg/app/utils/build_callbacks.py index 66c09035d..f3aab2ee2 100644 --- a/ml_peg/app/utils/build_callbacks.py +++ b/ml_peg/app/utils/build_callbacks.py @@ -111,30 +111,21 @@ def show_plot(active_cell, current_table_data) -> Div: Message explaining interactivity, or plot on cell click. """ if not active_cell: - print("Not active cell; active_cell = ", active_cell) return Div("Click on a metric to view plot.") column_id = active_cell.get("column_id", None) row_id = active_cell.get("row_id", None) row_index = active_cell.get("row", None) - print("Active cell: ", column_id, row_id, row_index) - print("Current table data: ", current_table_data) # Check if cell value is None (no data for this model) if current_table_data and row_index is not None: - print("Trying to get cell_value") try: cell_value = current_table_data[row_index].get(column_id) - print("cell_value = ", cell_value) if cell_value is None: return Div("No data available for this model.") except (IndexError, KeyError, TypeError): pass # Fall through to normal handling - print("Cell to plot: ", cell_to_plot) - print(f"Want to plot: cell_to_plot[{row_id}][{column_id}] = ") - print(f"{cell_to_plot[row_id][column_id]}") if row_id in cell_to_plot and column_id in cell_to_plot[row_id]: - print(f"Plotting {cell_to_plot[row_id][column_id]}") return Div(cell_to_plot[row_id][column_id]) return Div("Click on a metric to view plot.") diff --git a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py index 3be31b9e8..3aa601c13 100644 --- a/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py +++ b/ml_peg/calcs/physicality/water_slab_dipoles/calc_water_slab_dipoles.py @@ -43,9 +43,12 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: out_name = "slab" + # One could consider increasing the length of simulation, + # so far I only reduced the printing intervals to get more + # samples. md_t = 200000 # number of timesteps, here dt = 1fs - md_dt = 500 # intervals for printing energy, T, etc - th_dt = 500 # intervals for printing structures + md_dt = 100 # intervals for printing energy, T, etc + th_dt = 100 # intervals for printing structures temp = 300 # Kelvin pres = 1.013 # bar @@ -72,9 +75,6 @@ def test_water_dipole(mlip: tuple[str, Any]) -> None: pfactor=None, ) - # start_config_positions = start_config.positions.copy() - # start_config_com = start_config.get_center_of_mass().copy() - # Write output structures write_dir = OUT_PATH / model_name write_dir.mkdir(parents=True, exist_ok=True) @@ -94,15 +94,7 @@ def print_traj(a=start_config): """ calc_time = md.get_time() / units.fs calc_temp = a.get_temperature() - # calc_dens = np.sum(a.get_masses())/a.get_volume()*densfact - # calc_pres = - \ - # np.trace(a.get_stress( - # include_ideal_gas=True, voigt=False))/3/units.bar calc_epot = a.get_potential_energy() - # calc_msd = (((a.positions-a.get_center_of_mass()) - - # (start_config_positions-start_config_com))**2).mean(0).sum(0) - # calc_drft = ((a.get_center_of_mass()-start_config_com)**2).sum(0) - # calc_tens = -a.get_stress(include_ideal_gas=True, voigt=True)/units.bar if md.nsteps % th_dt == 0: thermo_traj.write( ("%12d" + " %17.6f" * 2 + "\n") % (calc_time, calc_temp, calc_epot) From 73385eab18927b8925ce99b54ef8dc0f17906b32 Mon Sep 17 00:00:00 2001 From: Mandy Hoffmann Date: Thu, 5 Feb 2026 19:22:35 +0000 Subject: [PATCH 19/19] Bug fix for hist marker, remove more prints --- .../water_slab_dipoles/analyse_water_slab_dipoles.py | 1 + ml_peg/analysis/utils/decorators.py | 4 +--- .../physicality/water_slab_dipoles/app_water_slab_dipoles.py | 1 - ml_peg/app/utils/load.py | 4 ---- 4 files changed, 2 insertions(+), 8 deletions(-) diff --git a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py index 0a9107525..2370af68d 100644 --- a/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py +++ b/ml_peg/analysis/physicality/water_slab_dipoles/analyse_water_slab_dipoles.py @@ -80,6 +80,7 @@ def plot_distribution(model: str) -> None: bins_start = -1.5 * DIPOLE_BAD_THRESHOLD bins_stop = 1.5 * DIPOLE_BAD_THRESHOLD bins_size = 3 * DIPOLE_BAD_THRESHOLD / 40 + # one might want to consider reducing the bin size further... @plot_hist( filename=OUT_PATH / f"figure_{model}_dipoledistr.json", diff --git a/ml_peg/analysis/utils/decorators.py b/ml_peg/analysis/utils/decorators.py index 7262c3149..e77a9ae60 100644 --- a/ml_peg/analysis/utils/decorators.py +++ b/ml_peg/analysis/utils/decorators.py @@ -464,7 +464,6 @@ def plot_hist( Callable Decorator to wrap function. """ - print(f"bins = {bins}") def plot_hist_decorator(func: Callable) -> Callable: """ @@ -534,7 +533,6 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: ) if good is not None and bad is not None and isinstance(bins, dict): - print("Using coloring") actual_bins = [min(data_all)] point = actual_bins[0] while point < max(data_all): @@ -550,7 +548,7 @@ def plot_hist_wrapper(*args, **kwargs) -> dict[str, Any]: colors[i] = bins["end"] if not bad_exists: colors = "#276419" - fig.update_traces(marke_color=colors) + fig.update_traces(marker_color=colors) # Update layout fig.update_layout( title={"text": title}, diff --git a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py index ced1f3331..827b043ca 100644 --- a/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py +++ b/ml_peg/app/physicality/water_slab_dipoles/app_water_slab_dipoles.py @@ -59,7 +59,6 @@ def get_app() -> WaterSlabDipolesApp: WaterSlabDipolesApp Benchmark layout and callback registration. """ - print("Id of extra components: ", f"{BENCHMARK_NAME}-figure-placeholder") return WaterSlabDipolesApp( name=BENCHMARK_NAME, description="Dipole distribution of a 38 A water slab", diff --git a/ml_peg/app/utils/load.py b/ml_peg/app/utils/load.py index cb4ef61d0..b4f10d7cd 100644 --- a/ml_peg/app/utils/load.py +++ b/ml_peg/app/utils/load.py @@ -226,10 +226,6 @@ def read_plot(filename: str | Path, id: str = "figure-1") -> Graph: Loaded plotly Graph. """ figure = read_json(filename) if Path(filename).exists() else None - print(f"Opening plot from {filename}") - print(f"exists: {Path(filename).exists()}") - print("Figure: ", figure) - print("id: ", id) return Graph(id=id, figure=figure)