From 2d262e0045b32d1b0ca668fcdb75d653d55052f3 Mon Sep 17 00:00:00 2001 From: BowenD-UCB <84425382+BowenD-UCB@users.noreply.github.com> Date: Thu, 6 Apr 2023 17:15:47 -0700 Subject: [PATCH] 1. Fixed README.md 2. Modified Example --- README.md | 3 +- examples/CHGNet_examples.ipynb | 76 +++++++++++++++++++--------------- 2 files changed, 45 insertions(+), 34 deletions(-) diff --git a/README.md b/README.md index 9034848c..b7f4cf2f 100755 --- a/README.md +++ b/README.md @@ -47,7 +47,8 @@ pip install -e ./chgnet ### Direct Inference (Static Calculation) -Pretrained `CHGNet` can predict the energy (eV/atom), force (eV/$\dot{\text A}$), stress (GPa) and magmom ($\mu_B$) of a given structure. +Pretrained `CHGNet` can predict the energy (eV/atom), force (eV/$\AA$), stress (GPa) and +magmom ($\mu_B$) of a given structure. ```python from chgnet.model.model import CHGNet diff --git a/examples/CHGNet_examples.ipynb b/examples/CHGNet_examples.ipynb index 5c036336..ab18c8bf 100644 --- a/examples/CHGNet_examples.ipynb +++ b/examples/CHGNet_examples.ipynb @@ -1,7 +1,6 @@ { "cells": [ { - "attachments": {}, "cell_type": "markdown", "id": "f8c75a16", "metadata": {}, @@ -36,7 +35,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "id": "16eeae1e", "metadata": {}, @@ -89,7 +87,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "id": "abcc09b4", "metadata": {}, @@ -114,12 +111,11 @@ "source": [ "chgnet = CHGNet.load()\n", "\n", - "# Or you can read your own model\n", - "# model = CHGNet.from_file(model_path)" + "# Alternatively you can read your own model\n", + "# chgnet = CHGNet.from_file(model_path)" ] }, { - "attachments": {}, "cell_type": "markdown", "id": "961d51fc", "metadata": {}, @@ -143,18 +139,18 @@ "text": [ "CHGNet-predicted energy=-7.371591567993164\n", "\n", - "CHGNet-predicted forces=[[ 4.4703484e-08 -2.7939677e-08 2.4071123e-02]\n", - " [ 1.4901161e-08 -2.9918738e-08 -2.4071217e-02]\n", - " [-1.1920929e-07 1.0244548e-08 2.5402993e-02]\n", - " [-0.0000000e+00 -2.3283064e-08 -2.5402665e-02]\n", - " [-1.7881393e-07 6.6356733e-08 -2.1660209e-02]\n", - " [ 2.4139881e-06 -7.9928432e-06 9.5508099e-03]\n", - " [-2.2053719e-06 7.9749152e-06 -9.5512867e-03]\n", - " [-5.9604645e-08 -0.0000000e+00 2.1660507e-02]]\n", + "CHGNet-predicted forces=[[ 4.4703484e-08 -4.2840838e-08 2.4071064e-02]\n", + " [-4.4703484e-08 -1.4551915e-08 -2.4071217e-02]\n", + " [-1.7881393e-07 1.0244548e-08 2.5402933e-02]\n", + " [ 5.9604645e-08 -2.3283064e-08 -2.5402665e-02]\n", + " [-1.1920929e-07 6.6356733e-08 -2.1660209e-02]\n", + " [ 2.3543835e-06 -8.0077443e-06 9.5508099e-03]\n", + " [-2.2947788e-06 7.9898164e-06 -9.5513463e-03]\n", + " [-5.9604645e-08 -0.0000000e+00 2.1660626e-02]]\n", "\n", - "CHGNet-predicted stress=[[ 3.3677614e-01 -1.9665707e-07 -5.6416429e-06]\n", - " [ 4.9939729e-07 2.4675032e-01 1.8549043e-05]\n", - " [-4.0414070e-06 1.9096897e-05 4.0323928e-02]]\n", + "CHGNet-predicted stress=[[ 3.3677638e-01 -3.7330341e-07 -5.1117036e-06]\n", + " [ 1.0701370e-06 2.4674933e-01 1.8477700e-05]\n", + " [-4.4460303e-06 1.9265182e-05 4.0324528e-02]]\n", "\n", "CHGNet-predicted magmom=[0.00521556 0.0052153 3.8572898 3.8572903 0.02538028 0.03706942\n", " 0.03706949 0.02538028]\n", @@ -164,12 +160,13 @@ ], "source": [ "prediction = chgnet.predict_structure(structure)\n", - "for key in (\"energy\", \"forces\", \"stress\", \"magmom\"):\n", + "for key, _unit in zip(\n", + " (\"energy\", \"forces\", \"stress\", \"magmom\"), (\"eV/atom\", \"eV/A\", \"GPa\", \"mu_B\")\n", + "):\n", " print(f\"CHGNet-predicted {key}={prediction[key[0]]}\\n\")" ] }, { - "attachments": {}, "cell_type": "markdown", "id": "2258f2f5", "metadata": {}, @@ -205,24 +202,38 @@ "metadata": {}, "outputs": [ { - "data": { - "text/plain": [ - "4" - ] - }, - "execution_count": null, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "CHGNet took 29 steps. Relaxed structure:\n", + "Full Formula (Li2 Mn2 O4)\n", + "Reduced Formula: LiMnO2\n", + "abc : 2.865864 4.648716 5.827764\n", + "angles: 89.917211 90.239405 89.975425\n", + "pbc : True True True\n", + "Sites (8)\n", + " # SP a b c magmom\n", + "--- ---- --------- --------- -------- ----------\n", + " 0 Li+ 0.494018 0.479737 0.387171 0.00498427\n", + " 1 Li+ 0.008464 0.006131 0.625817 0.00512926\n", + " 2 Mn3+ 0.50073 0.502478 0.869608 3.85374\n", + " 3 Mn3+ 0.997815 -0.000319 0.139344 3.859\n", + " 4 O2- 0.502142 0.009453 0.363411 0.0253105\n", + " 5 O2- 1.00293 0.502592 0.104559 0.0366638\n", + " 6 O2- 0.493749 0.998092 0.903592 0.0365367\n", + " 7 O2- -0.002278 0.495108 0.645655 0.0248522\n" + ] } ], "source": [ - "result = relaxer.relax(structure)\n", + "structure.perturb(0.1)\n", + "result = relaxer.relax(structure, verbose=False)\n", "print(f\"\\nCHGNet took {len(result['trajectory'])} steps. Relaxed structure:\")\n", "print(result[\"final_structure\"])" ] }, { - "attachments": {}, "cell_type": "markdown", "id": "06f7e84c", "metadata": {}, @@ -271,7 +282,6 @@ ] }, { - "attachments": {}, "cell_type": "markdown", "id": "c6a10ec8", "metadata": {}, @@ -1806,9 +1816,9 @@ ], "metadata": { "kernelspec": { - "display_name": "py310", + "display_name": "Python (tf)", "language": "python", - "name": "python3" + "name": "myenv" }, "language_info": { "codemirror_mode": { @@ -1820,7 +1830,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.0" + "version": "3.9.10" } }, "nbformat": 4,