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Add NEB tutorial (#435)
* Add NEB tutorial * Update docs for NEB tutorial * Tidy notebook output
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‎README.md‎

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@@ -146,6 +146,7 @@ Jupyter Notebook tutorials illustrating the use of currently available calculati
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- [Molecular Dynamics](docs/source/tutorials/md.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/md.ipynb)
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- [Equation of State](docs/source/tutorials/eos.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/eos.ipynb)
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- [Phonons](docs/source/tutorials/phonons.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/phonons.ipynb)
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- [Nudged Elastic Band](docs/source/tutorials/neb.ipynb) [![badge](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/neb.ipynb)
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### Calculation outputs

‎docs/source/tutorials/index.rst‎

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md
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eos
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phonons
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neb

‎docs/source/tutorials/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/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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"# Nudged Elastic Band"
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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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"In this tutorial, we will determine the activation energies of Li diffusion along the [010] and [001] directions (referred to as paths b and c respectively) in lithium iron phosphate (LiFePO_4), a cathode material for lithium ion batteries.\n",
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"\n",
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"DFT references energies are:\n",
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"\n",
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"- Barrier heights:\n",
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" - path b = 0.27 eV\n",
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" - path c = 2.5 eV\n",
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" \n",
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"(see table 1 in https://doi.org/10.1039/C5TA05062F)"
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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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"You can toggle the following to investigate different models:"
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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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"model_params = {\"arch\": \"mace_mp\", \"model_path\": \"medium-0b3\"}\n",
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"# model_params = {\"arch\": \"mace_mp\", \"model_path\": \"medium-mpa-0\"}\n",
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"# model_params = {\"arch\": \"mace_mp\", \"model_path\": \"medium-omat-0\"}\n",
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"# model_params = {\"arch\": \"chgnet\"}\n",
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"# model_params = {\"arch\": \"sevennet\"}"
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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]"
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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.visualize import view\n",
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"from ase.io import read\n",
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"from data_tutorials.data import get_data\n",
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"\n",
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"from janus_core.calculations.geom_opt import GeomOpt\n",
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"from janus_core.calculations.neb import NEB"
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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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"get_data(\n",
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" # url=\"https://raw.githubusercontent.com/stfc/janus-core/main/tests/data/\",\n",
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" url=\"https://raw.githubusercontent.com/stfc/janus-tutorials/main/neb/data/\",\n",
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" filename=\"LiFePO4_supercell.cif\",\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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"id": "857K7R9Cenca"
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},
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"source": [
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"## Preparing end structures"
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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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"The initial structure can be downloaded from the Materials Project (mp-19017):"
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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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"LFPO = read(\"data/LiFePO4_supercell.cif\")\n",
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"view(LFPO,viewer=\"x3d\")"
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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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"First, we will relax the supercell:"
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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": "cgch8VQ--AES"
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},
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"outputs": [],
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"source": [
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"GeomOpt(struct=LFPO, **model_params).run()\n",
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"\n",
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"view(LFPO,viewer=\"x3d\")"
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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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"Next, we will create the start and end 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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"# NEB path along b and c directions have the same starting image.\n",
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"# For start bc remove site 5\n",
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"LFPO_start_bc = LFPO.copy()\n",
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"del LFPO_start_bc[5]\n",
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"\n",
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"# For end b remove site 11 \n",
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"LFPO_end_b = LFPO.copy()\n",
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"del LFPO_end_b[11]\n",
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"\n",
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"# For end c remove site 4\n",
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"LFPO_end_c = LFPO.copy()\n",
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"del LFPO_end_c[4]"
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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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"## Path b"
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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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"We can now calculate the barrier height along path b.\n",
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"\n",
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"This also includes running geometry optimization on the end points of this path."
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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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"n_images = 7\n",
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"interpolator=\"pymatgen\" # ASE interpolation performs poorly in this case\n",
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"\n",
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"neb_b = NEB(\n",
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" init_struct=LFPO_start_bc,\n",
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" final_struct=LFPO_end_b,\n",
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" n_images=n_images,\n",
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" interpolator=interpolator,\n",
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" minimize=True,\n",
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" fmax=0.1,\n",
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" **model_params,\n",
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")"
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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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"results = neb_b.run()"
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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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"The results include the barrier (without any interpolation between highest images) and maximum force at the point in the simulation "
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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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"print(results)"
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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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"We can also plot the band:"
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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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"fig = neb_b.nebtools.plot_band()"
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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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"## Path c"
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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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"We can calculate the barrier height along path c similarly"
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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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"n_images = 7\n",
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"interpolator=\"pymatgen\"\n",
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"\n",
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"neb_c = NEB(\n",
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" init_struct=LFPO_start_bc,\n",
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" final_struct=LFPO_end_c,\n",
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" n_images=n_images,\n",
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" interpolator=interpolator,\n",
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" minimize=True,\n",
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" fmax=0.1,\n",
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" **model_params,\n",
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")"
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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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"results = neb_c.run()"
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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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"print(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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"fig = neb_c.nebtools.plot_band()"
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]
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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": ".venv",
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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": "3.12.8"
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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/user_guide/python.rst‎

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:target: https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/phonons.ipynb
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:alt: Launch phonons Colab
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.. |neb| image:: https://colab.research.google.com/assets/colab-badge.svg
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:target: https://colab.research.google.com/github/stfc/janus-core/blob/main/docs/source/tutorials/neb.ipynb
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:alt: Launch NEB Colab
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- :doc:`Single Point </tutorials/single_point>` |single_point|
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- :doc:`Geometry Optimization </tutorials/geom_opt>` |geom_opt|
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- :doc:`Molecular Dynamics </tutorials/md>` |md|
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- :doc:`Equation of State </tutorials/eos>` |eos|
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- :doc:`Phonons </tutorials/phonons>` |phonons|
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- :doc:`Nudged Elastic Band </tutorials/neb>` |neb|
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Calculation outputs

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