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Add NEB CLI tutorial (#482)
* add neb cli tutorial
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‎docs/source/tutorials/cli/neb.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {
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"colab_type": "text",
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"id": "view-in-github"
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},
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"source": [
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"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/cli/neb.ipynb)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Command-line interface (CLI) with nudge elastic bands"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"id": "4vcbRxmIhHLL"
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},
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"source": [
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"`janus-core` contains various machine learnt interatomic potentials (MLIPs), including MACE based models (MACE-MP, MACE-OFF), CHGNet, SevenNet and more, full list on https://github.com/stfc/janus-core.\n",
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"\n",
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"Other will be added as their utility is proven beyond a specific material."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Aim\n",
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"\n",
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"We showcase the use of NEB with janus and MLIPs by stuing Ethanol oxidation reactions catalyzed by water molecules, the full study was carried out in this paper Chemical Physics Letters 363 (2002) 80–86\n",
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"\n",
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"https://doi.org/10.1016/S0009-2614(02)01142-9"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Set up environment (optional)\n",
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"\n",
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"These steps are required for Google Colab, but may work on other systems too:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"id": "TF-EiWxyuMc7"
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},
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"outputs": [],
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"source": [
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"# import locale\n",
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"# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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"# !python3 -m pip install janus-core[all] data-tutorials"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Use `data_tutorials` to get the data required for this tutorial:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from data_tutorials.data import get_data\n",
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"\n",
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"get_data(\n",
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" url=\"https://raw.githubusercontent.com/stfc/janus-tutorials/main/data/\",\n",
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" filename=[\"ethanol_reactants.extxyz\", \"ethanol_products.extxyz\",\"ethanol_reactants_1water.extxyz\",\"ethanol_products_1water.extxyz\",\"ethanol_reactants_2water.extxyz\",\"ethanol_products_2water.extxyz\"],\n",
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" folder=\"data\",\n",
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")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Command-line help and options"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Once `janus-core` is installed, the `janus` CLI command should be available:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"! janus neb --help"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## run a simple Nudge Elastic Bands\n",
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"\n",
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"### 0 water molecules case"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"%%writefile neb.yml\n",
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"\n",
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"init_struct: data/ethanol_reactants.extxyz\n",
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"final_struct: data/ethanol_products.extxyz\n",
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"n_images: 11\n",
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"device: cpu\n",
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"arch: mace_mp\n",
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"minimize: True\n",
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"plot_band: True\n",
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"write_band: True\n",
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"calc-kwargs:\n",
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" dispersion: True\n",
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" model: medium-omat-0"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"visualise the inputs"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from ase.io import read\n",
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"from weas_widget import WeasWidget\n",
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"\n",
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"r = read(\"data/ethanol_reactants.extxyz\")\n",
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"p = read(\"data/ethanol_products.extxyz\")\n",
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"\n",
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"v=WeasWidget()\n",
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"v.from_ase([r,p])\n",
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"v.avr.model_style = 1\n",
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"v.avr.show_hydrogen_bonds = True\n",
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"v\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!janus neb --config neb.yml"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!ls janus_results/"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.display import SVG, display\n",
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"display(SVG(\"janus_results/ethanol_reactants-neb-plot.svg\"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"nebp = read(\"janus_results/ethanol_reactants-neb-band.extxyz\", index=\":\")\n",
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"\n",
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"w=WeasWidget()\n",
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"w.from_ase(nebp)\n",
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"w.avr.model_style = 1\n",
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"w.avr.show_hydrogen_bonds = True\n",
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"w"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"is the barrier realistic? compare with the numbers from the paper.\n",
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"\n",
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"### 1 water molecule\n",
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"\n",
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"we can use the previous config and just overwrite the init and final structures"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"! janus neb --config neb.yml --init-struct data/ethanol_reactants_1water.extxyz --final-struct data/ethanol_products_1water.extxyz"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!ls janus_results/"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"display(SVG(\"janus_results/ethanol_reactants_1water-neb-plot.svg\"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from ase.io import read\n",
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"from weas_widget import WeasWidget\n",
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"nebp = read(\"janus_results/ethanol_reactants_1water-neb-band.extxyz\", index=\":\")\n",
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"\n",
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"w1=WeasWidget()\n",
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"w1.from_ase(nebp)\n",
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"w1.avr.model_style = 1\n",
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"w1.avr.show_hydrogen_bonds = True\n",
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"w1"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### 2 water molecules"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"! janus neb --config neb.yml --init-struct data/ethanol_reactants_2water.extxyz --final-struct data/ethanol_products_2water.extxyz"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"display(SVG(\"janus_results/ethanol_reactants_2water-neb-plot.svg\"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from ase.io import read\n",
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"from weas_widget import WeasWidget\n",
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"nebp = read(\"janus_results/ethanol_reactants_2water-neb-band.extxyz\", index=\":\")\n",
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"\n",
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"w2=WeasWidget()\n",
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"w2.from_ase(nebp)\n",
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"w2.avr.model_style = 1\n",
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"w2.avr.show_hydrogen_bonds = True\n",
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"w2"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### extra bits\n",
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"\n",
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"\n",
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"- analyse the barrier height trend.\n",
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"- consider redoing the same exercise with a different potential... remember if you use mace-off dispersion needs to be off.\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": []
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": []
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}
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],
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"metadata": {
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"accelerator": "GPU",
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"colab": {
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"authorship_tag": "ABX9TyNvtIsPHVgkt0NvUv51T6ZG",
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"gpuType": "T4",
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"include_colab_link": true,
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"private_outputs": true,
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"provenance": []
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},
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.0"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎docs/source/tutorials/data/ethanol_products.extxyz‎

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Properties=species:S:1:pos:R:3:mace_mp_forces:R:3:forces:R:3 Ethanol=T initial_spacegroup units="_JSON {\"energy\": \"eV\", \"forces\": \"ev/Ang\", \"stress\": \"ev/Ang^3\"}" final_spacegroup model_path=../ml/models/mace-omat-0-medium.model arch=mace_mp mace_mp_energy=-44.96710136891945 system_name=ethanol_reactants energy=-44.96710136891945 pbc="F F F"
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H 2.21252233 -0.24833443 0.74736958 0.00006429 0.00001342 -0.00010172 0.00006429 0.00001342 -0.00010172
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C 1.60736052 0.14373518 -0.08545979 -0.00010665 -0.00020321 0.00002484 -0.00010665 -0.00020321 0.00002484
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H 1.78463902 1.23000029 -0.13164203 0.00007171 0.00009147 -0.00003627 0.00007171 0.00009147 -0.00003627
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H 1.86174463 -0.34391689 -1.02943516 0.00012753 0.00007105 0.00010169 0.00012753 0.00007105 0.00010169
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C 0.14958063 -0.07874383 0.25000376 -0.00013935 0.00016028 0.00006731 -0.00013935 0.00016028 0.00006731
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H -2.57133357 0.04440644 1.78179096 -0.00009307 0.00022931 0.00037864 -0.00009307 0.00022931 0.00037864
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H -0.14604684 0.40316655 1.20433475 0.00000365 -0.00010029 -0.00008260 0.00000365 -0.00010029 -0.00008260
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H -2.33056910 -0.26604350 1.14200600 0.00008485 -0.00023228 -0.00036041 0.00008485 -0.00023228 -0.00036041

‎docs/source/tutorials/data/ethanol_products_1water.extxyz‎

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XYZ file generated by Avogadro.
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C -2.38024 0.55852 0.26888
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C -1.68958 -0.72815 0.66580
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H -1.34230 0.84971 0.22717
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O -3.07569 1.00826 -0.57726
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H -3.57080 0.31220 2.17960
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H -0.92672 -1.15690 0.02361
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H -1.13392 -0.42099 1.54581
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H -2.45593 -1.05063 1.34149
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H -4.45258 1.07363 -0.01683
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O -4.93716 0.96200 0.82966
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H -5.11712 1.81389 1.18201
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H -4.01580 0.66329 1.68800

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