{ "nbformat": 4, "nbformat_minor": 0, "metadata": { "colab": { "provenance": [], "include_colab_link": true }, "kernelspec": { "name": "python3", "display_name": "Python 3" }, "language_info": { "name": "python" }, "accelerator": "GPU" }, "cells": [ { "cell_type": "markdown", "metadata": { "id": "view-in-github", "colab_type": "text" }, "source": [ "\"Open" ] }, { "cell_type": "markdown", "source": [ "# Lesson 6: DeepPot-Smooth Edition Fitting Neural Network with Machine Learning Potentials (DeepPot-SE-FNN MLP)\n", "\n", "$\\Delta$ MLP with PyTorch for the Claisen Rearrangement reaction\n", "\n", "For this tutorial, we will be combining the Fitting Neural Network (FNN) from Lesson 1 and the DeepPot-Smooth Edition (DeepPot-SE) from Lesson 4 to train a $\\Delta$ Machine Learning Potential ($\\Delta$MLP) model to reproduce the energy and forces for the Claisen Rearrangement reaction. With a DeepPot-SE-FNN, we can utilize the properties from the local environment defined in the DeepPot-SE model for feature extraction and use the FNN for training. The goal of this model is to train with data calculated using semiempirical (PM3) and DFT (B3LYP) levels of theory. The DeepPot-SE-FNN will be used to correct the semiempirical values to obtain DFT level accuracy, that makes it a $\\Delta$MLP model.\n", "The reaction coordinate is constructed by stretching the $d_2$ bond distance, while shrinking the $d_1$ bond distance. The reaction is sampled with 21 windows along the $d_1-d_2$ reaction coordinate\n", "\n", "Total of 2100 frames (1 ps/window) are saved every 1 fs.\n", "\n", "\n" ], "metadata": { "id": "d5swkZB6PnNA" } }, { "cell_type": "code", "source": [ "from IPython.display import HTML\n", "\n", "HTML(f\"\"\"