{ "cells": [ { "cell_type": "code", "execution_count": 9, "id": "3200850a-b8fb-4f50-9815-16ae8da0f942", "metadata": { "tags": [] }, "outputs": [], "source": [ "import os\n", "from pathlib import Path\n", "\n", "import numpy as np\n", "import pandas as pd\n", "from ase import Atom, Atoms\n", "from ase.data import chemical_symbols, covalent_radii, vdw_alvarez\n", "from ase.io import read, write\n", "from pymatgen.core import Element\n", "from scipy import stats\n", "from scipy.interpolate import splrep, BSpline, CubicSpline, UnivariateSpline\n", "from tqdm.auto import tqdm\n", "\n", "from mlip_arena.models import MLIPEnum, REGISTRY\n", "\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "id": "02ff9cf9-49a2-4cec-80d3-56c6661a513b", "metadata": { "tags": [] }, "source": [ "# Compute MLIP homonuclear diatomics" ] }, { "cell_type": "code", "execution_count": 2, "id": "90887faa-1601-4c4c-9c44-d16731471d7f", "metadata": { "scrolled": true, "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "========== ORBv2 ==========\n", "Selected GPU cuda:0 with 40339.31 MB free memory from 1 GPUs\n", "Downloading ORB model from https://storage.googleapis.com/orbitalmaterials-public-models/forcefields/orb-v2-20241011.ckpt to /global/homes/c/cyrusyc/.cache/orb/orb-v2-20241011.ckpt...\n", "Download completed.\n", "GPU tensorfloat matmuls precision set to 'high'. This can achieve up to 2x speedup on Nvidia A100 and H100 devices.\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "fde27645a0014db6a912f33d326114d4", "version_major": 2, "version_minor": 0 }, "text/plain": [ " 0%| | 0/118 [00:00" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from matplotlib import pyplot as plt\n", "\n", "fig, axes = plt.subplots(2)\n", "axes[0].plot(rs, fs)\n", "axes[0].plot(rs, cs(rs))\n", "\n", "axes[1].plot(rs, fs - cs(rs))\n", "\n", "axes[1].text(0.9, 0.9, f\"MAE: { np.abs(fs - cs(rs)).mean(): .3f}\")" ] }, { "cell_type": "code", "execution_count": 14, "id": "e0dd4367-3dca-440f-a7a9-7fdd84183f2c", "metadata": { "tags": [] }, "outputs": [ { "data": { "text/html": [ "
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namemethodREFS^2force-flip-timesforce-total-variationenergy-diff-flip-timesenergy-grad-norm-max...energy-total-variationconservation-deviationspearman-descending-forcespearman-ascending-forcespearman-repulsion-energyspearman-attraction-energytortuosityforce-jumppbe-energy-maepbe-force-mae
117HHORB[3.7199999999999998, 3.70996794, 3.69993586, 3...[-2.253027916, -2.2530450821, -2.2531223297, -...[0.00029414, 0.00030291, 0.00033964, 0.0003847...[]4133.5637463102.248369...13.3615513.256510-0.9956130.578188-0.9746460.5031101.29445833.5989231.3806632.621806
118HeHeORB[4.433, 4.42297362, 4.41294724, 4.40292086, 4....[-0.0489044189, -0.0488109589, -0.0487890244, ...[0.00020237, 0.00022884, 0.00022473, 0.0002023...[]2125.7754583133.955726...13.1154192.880469-0.995071-0.047308-0.9713600.3394131.46219131.778227NaNNaN
119LiLiORB[6.572, 6.56198152, 6.55196304, 6.54194454, 6....[-0.6005258560000001, -0.600976944, -0.6010656...[-5.638e-05, -9.191e-05, -0.000119780000000000...[]121.673787411.264810...6.4845330.676364-0.9935050.999677-0.9997190.9489151.0486590.0691080.3040630.650049
120BeBeORB[6.138, 6.12797338, 6.11794676, 6.10792016, 6....[0.1439437866, 0.1446228027, 0.1446933746, 0.1...[0.00024622, 0.00020539, 0.00021473, 0.0002307...[]174.423075517.538560...11.7560503.683254-1.0000000.970939-0.9803680.6959561.0582020.021102NaNNaN
121BBORB[5.921, 5.91097088, 5.90094174, 5.89091262, 5....[-1.7345266341999999, -1.7349262238, -1.735033...[-5.236e-05, -9.37e-06, 1.198e-05, 1.637e-05, ...[]1149.497415833.563880...16.1967045.626231-1.0000000.923103-0.9875390.8153141.1908100.6720051.0812291.333676
..................................................................
346NhNhORBv2[6.0, 5.989982779999999, 5.979965579999999, 5....[-1.2127504348754883, -1.2130546569824219, -1....[0.0, 7.4e-07, 0.0, 7e-08, 9.54e-06, 4.87e-06,...[]1418.1774641066.461493...23.66890438.121299-0.9395790.981659-0.3461160.9923991.721098344.819311NaNNaN
347FlFlORBv2[6.0, 5.989982779999999, 5.979965579999999, 5....[-1.6584091186523438, -1.6582937240600586, -1....[0.0, 2.79e-06, 0.0, 4.8e-07, -1.968e-05, 7.6e...[]1414.5900971137.387570...18.53737346.828852-0.9797670.996953-0.3474580.9974011.522742353.778117NaNNaN
348McMcORBv2[6.0, 5.989982779999999, 5.979965579999999, 5....[0.09161853790283203, 0.09169960021972656, 0.0...[0.0, -9.4e-07, 0.0, -2.38e-06, 0.0, 0.0, 0.0,...[]1429.250003474.488620...28.76540829.080300-0.8258200.849567-0.2623980.9789961.466244332.199750NaNNaN
349LvLvORBv2[6.0, 5.989982779999999, 5.979965579999999, 5....[0.1532306671142578, 0.15334033966064453, 0.15...[0.0, -3.56e-06, 0.0, 6.36e-06, -4.78e-06, 8.1...[]1412.500944432.615990...21.35258935.098622-0.9820430.959481-0.6443780.9999911.982194344.140646NaNNaN
350TsTsORBv2[6.0, 5.989982779999999, 5.979965579999999, 5....[0.2908821105957031, 0.2906169891357422, 0.290...[0.0, 4.57e-06, 0.0, -3.1e-07, -1.051e-05, -2....[]1393.376749690.260724...21.17041630.675171-0.9917440.996975-0.8681410.7969692.002857334.536066NaNNaN
\n", "

234 rows × 21 columns

\n", "
" ], "text/plain": [ " name method R \\\n", "117 HH ORB [3.7199999999999998, 3.70996794, 3.69993586, 3... \n", "118 HeHe ORB [4.433, 4.42297362, 4.41294724, 4.40292086, 4.... \n", "119 LiLi ORB [6.572, 6.56198152, 6.55196304, 6.54194454, 6.... \n", "120 BeBe ORB [6.138, 6.12797338, 6.11794676, 6.10792016, 6.... \n", "121 BB ORB [5.921, 5.91097088, 5.90094174, 5.89091262, 5.... \n", ".. ... ... ... \n", "346 NhNh ORBv2 [6.0, 5.989982779999999, 5.979965579999999, 5.... \n", "347 FlFl ORBv2 [6.0, 5.989982779999999, 5.979965579999999, 5.... \n", "348 McMc ORBv2 [6.0, 5.989982779999999, 5.979965579999999, 5.... \n", "349 LvLv ORBv2 [6.0, 5.989982779999999, 5.979965579999999, 5.... \n", "350 TsTs ORBv2 [6.0, 5.989982779999999, 5.979965579999999, 5.... \n", "\n", " E \\\n", "117 [-2.253027916, -2.2530450821, -2.2531223297, -... \n", "118 [-0.0489044189, -0.0488109589, -0.0487890244, ... \n", "119 [-0.6005258560000001, -0.600976944, -0.6010656... \n", "120 [0.1439437866, 0.1446228027, 0.1446933746, 0.1... \n", "121 [-1.7345266341999999, -1.7349262238, -1.735033... \n", ".. ... \n", "346 [-1.2127504348754883, -1.2130546569824219, -1.... \n", "347 [-1.6584091186523438, -1.6582937240600586, -1.... \n", "348 [0.09161853790283203, 0.09169960021972656, 0.0... \n", "349 [0.1532306671142578, 0.15334033966064453, 0.15... \n", "350 [0.2908821105957031, 0.2906169891357422, 0.290... \n", "\n", " F S^2 force-flip-times \\\n", "117 [0.00029414, 0.00030291, 0.00033964, 0.0003847... [] 4 \n", "118 [0.00020237, 0.00022884, 0.00022473, 0.0002023... [] 2 \n", "119 [-5.638e-05, -9.191e-05, -0.000119780000000000... [] 1 \n", "120 [0.00024622, 0.00020539, 0.00021473, 0.0002307... [] 1 \n", "121 [-5.236e-05, -9.37e-06, 1.198e-05, 1.637e-05, ... [] 1 \n", ".. ... .. ... \n", "346 [0.0, 7.4e-07, 0.0, 7e-08, 9.54e-06, 4.87e-06,... [] 1 \n", "347 [0.0, 2.79e-06, 0.0, 4.8e-07, -1.968e-05, 7.6e... [] 1 \n", "348 [0.0, -9.4e-07, 0.0, -2.38e-06, 0.0, 0.0, 0.0,... [] 1 \n", "349 [0.0, -3.56e-06, 0.0, 6.36e-06, -4.78e-06, 8.1... [] 1 \n", "350 [0.0, 4.57e-06, 0.0, -3.1e-07, -1.051e-05, -2.... [] 1 \n", "\n", " force-total-variation energy-diff-flip-times energy-grad-norm-max ... \\\n", "117 133.563746 3 102.248369 ... \n", "118 125.775458 3 133.955726 ... \n", "119 21.673787 4 11.264810 ... \n", "120 74.423075 5 17.538560 ... \n", "121 149.497415 8 33.563880 ... \n", ".. ... ... ... ... \n", "346 418.177464 10 66.461493 ... \n", "347 414.590097 11 37.387570 ... \n", "348 429.250003 4 74.488620 ... \n", "349 412.500944 4 32.615990 ... \n", "350 393.376749 6 90.260724 ... \n", "\n", " energy-total-variation conservation-deviation \\\n", "117 13.361551 3.256510 \n", "118 13.115419 2.880469 \n", "119 6.484533 0.676364 \n", "120 11.756050 3.683254 \n", "121 16.196704 5.626231 \n", ".. ... ... \n", "346 23.668904 38.121299 \n", "347 18.537373 46.828852 \n", "348 28.765408 29.080300 \n", "349 21.352589 35.098622 \n", "350 21.170416 30.675171 \n", "\n", " spearman-descending-force spearman-ascending-force \\\n", "117 -0.995613 0.578188 \n", "118 -0.995071 -0.047308 \n", "119 -0.993505 0.999677 \n", "120 -1.000000 0.970939 \n", "121 -1.000000 0.923103 \n", ".. ... ... \n", "346 -0.939579 0.981659 \n", "347 -0.979767 0.996953 \n", "348 -0.825820 0.849567 \n", "349 -0.982043 0.959481 \n", "350 -0.991744 0.996975 \n", "\n", " spearman-repulsion-energy spearman-attraction-energy tortuosity \\\n", "117 -0.974646 0.503110 1.294458 \n", "118 -0.971360 0.339413 1.462191 \n", "119 -0.999719 0.948915 1.048659 \n", "120 -0.980368 0.695956 1.058202 \n", "121 -0.987539 0.815314 1.190810 \n", ".. ... ... ... \n", "346 -0.346116 0.992399 1.721098 \n", "347 -0.347458 0.997401 1.522742 \n", "348 -0.262398 0.978996 1.466244 \n", "349 -0.644378 0.999991 1.982194 \n", "350 -0.868141 0.796969 2.002857 \n", "\n", " force-jump pbe-energy-mae pbe-force-mae \n", "117 33.598923 1.380663 2.621806 \n", "118 31.778227 NaN NaN \n", "119 0.069108 0.304063 0.650049 \n", "120 0.021102 NaN NaN \n", "121 0.672005 1.081229 1.333676 \n", ".. ... ... ... \n", "346 344.819311 NaN NaN \n", "347 353.778117 NaN NaN \n", "348 332.199750 NaN NaN \n", "349 344.140646 NaN NaN \n", "350 334.536066 NaN NaN \n", "\n", "[234 rows x 21 columns]" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "df" ] }, { "cell_type": "code", "execution_count": null, "id": "4e6ae884-89f3-43f2-8fd9-19bf00c91566", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "mlip-arena", "language": "python", "name": "mlip-arena" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.11.8" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": { "002c7d9693744207aec1bbd45f460c65": { "model_module": "@jupyter-widgets/controls", "model_module_version": "2.0.0", "model_name": "ProgressStyleModel", "state": { "description_width": "" } }, 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