feature/SOF-7958 Feat: add NEB calculation notebook for QE neb.x #349
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There was a problem hiding this comment. Let's use HfO2, ferroelectric switch - and use transformation matrix for the final structure generation Reply via ReviewNB |
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| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "0", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Create Initial/Final Materials\n", | ||
| "\n", | ||
| "Build an ordered initial → (optional intermediates) → final set of materials from one starting structure, and write them to a subfolder under `uploads/` in path order for [`utils_create_material_set.ipynb`](utils_create_material_set.ipynb).\n", | ||
| "\n", | ||
| "Any calculation that takes an ordered start/end pair can use the output; a Nudged Elastic Band path ([`neb.ipynb`](workflows/neb.ipynb)) is one consumer.\n", | ||
| "\n", | ||
| "Order is preserved by **numbering material names** (`00_...`, `01_...`, …): `utils_create_material_set.ipynb` (and `load_materials_from_folder`) sort by filename, and filenames come from material names.\n", | ||
| "\n", | ||
| "## Usage\n", | ||
| "\n", | ||
| "1. Set the material and the names in cell 1.2.\n", | ||
| "1. Run 2.1, copy the coordinates of the atom you want to move, and paste them into 2.2.\n", | ||
| "1. Run the rest to build and write the path materials.\n", | ||
| "1. Open [`utils_create_material_set.ipynb`](utils_create_material_set.ipynb), set the same `SUBFOLDER_NAME` and `IS_ORDERED = True`, and run it to save the materials and create the platform set.\n", | ||
| "1. Use the printed set name as `MATERIAL_SET` in [`neb.ipynb`](workflows/neb.ipynb).\n", | ||
| "\n", | ||
| "## Summary\n", | ||
| "\n", | ||
| "1. Install packages and set parameters.\n", | ||
| "1. Load the starting material.\n", | ||
| "1. Clone it as the initial image; move one atom to make the final image.\n", | ||
| "1. Name members in path order and write them to `uploads/<SUBFOLDER_NAME>/`." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 1. Set up the environment and parameters\n", | ||
| "### 1.1. Install packages (JupyterLite)\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "2", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.notebooks_utils.packages import install_packages\n", | ||
| "\n", | ||
| "await install_packages(\"made|api_examples\")\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "3", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 1.2. Set parameters\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "4", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Starting material (uploads folder or Standata name match)\n", | ||
| "FOLDER = \"uploads\"\n", | ||
| "MATERIAL_NAME = \"Silicon (100) surface\"\n", | ||
| "\n", | ||
| "# Short base name for the written images: 00_<PATH_NAME>.json, 01_<PATH_NAME>.json.\n", | ||
| "PATH_NAME = \"initial-final-materials\"\n", | ||
| "\n", | ||
| "# Subfolder under uploads/ to write path materials into — use the same value as\n", | ||
| "SUBFOLDER_NAME = \"initial_final_materials\"" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "5", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## 2. Build path materials\n", | ||
| "### 2.1. Load the starting material\n", | ||
| "\n", | ||
| "To read an atom's coordinates from the viewer below: open **Measurements** (the ruler icon), turn on\n", | ||
| "**Copy Coordinates [C]** — or press `C` — then click the atom. Its coordinates go to the clipboard,\n", | ||
| "ready to paste into 2.2." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "6", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.material import Material\n", | ||
| "from mat3ra.standata.materials import Materials\n", | ||
| "from mat3ra.notebooks_utils.ipython.entity.material.visualize import visualize_materials as visualize\n", | ||
| "from mat3ra.notebooks_utils.material import load_material_from_folder\n", | ||
| "\n", | ||
| "source_material = load_material_from_folder(FOLDER, MATERIAL_NAME) or Material.create(\n", | ||
| " Materials.get_by_name_first_match(MATERIAL_NAME)\n", | ||
| ")\n", | ||
| "visualize(source_material, viewer=\"wave\")\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "7", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 2.2. Choose the atom to move\n", | ||
| "\n", | ||
| "`ATOM_COORDINATE` is the atom you copied above, in crystal coordinates; the nearest atom to it is the\n", | ||
| "one that moves.\n", | ||
| "\n", | ||
| "`TRANSLATION` is vector to move it, in Ångström." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "8", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Coordinates of the atom to move, copied from the viewer above.\n", | ||
| "ATOM_COORDINATE = [0.0, 0.5, 0.5633]\n", | ||
| "\n", | ||
| "# Displacement in Angstrom.\n", | ||
| "TRANSLATION = [0.0, 0.0, -2.0]" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "9", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 2.3. Clone as the initial image\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "10", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "initial_material = source_material.clone()\n", | ||
| "visualize(initial_material, rotation=\"-90x\")\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "11", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 2.4. Transform into the final image (example)\n", | ||
| "\n", | ||
| "Default: move the atom at `ATOM_COORDINATE` by `TRANSLATION`. Replace with any other transformation (defects, swaps, custom coordinates, …).\n", | ||
| "\n", | ||
| "2.5 below shows the same move done as a displacement *field* instead, which is what you want when the neighbours should relax along with the atom.\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "12", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.made.tools.analyze.other import get_closest_site_id_from_coordinate\n", | ||
| "from mat3ra.made.tools.operations.core.unary import translate_atoms\n", | ||
| "\n", | ||
| "atom_id = get_closest_site_id_from_coordinate(initial_material, ATOM_COORDINATE)\n", | ||
| "final_material = translate_atoms(initial_material, [atom_id], TRANSLATION)\n", | ||
| "\n", | ||
| "visualize([initial_material, final_material], viewer=\"wave\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "13", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 2.5. Alternative: move the atom with a perturbation function (example)\n", | ||
| "\n", | ||
| "`translate_atoms` above applies a fixed vector. A perturbation function instead returns `∆z` for\n", | ||
| "*every* atom from `f(x, y, z)`, so a Gaussian centred on one atom keeps the displacement local to\n", | ||
| "it — and lets the path be shaped (neighbours relaxing along with it, a wave, a decaying tail)\n", | ||
| "rather than a rigid shift.\n", | ||
| "\n", | ||
| "Left commented out so \"Run All\" uses the simple translation. Uncomment it to overwrite\n", | ||
| "`final_material`, run, and compare the two structures in the viewer." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "14", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# import numpy as np\n", | ||
| "# import sympy as sp\n", | ||
| "# from mat3ra.made.tools.build_components.operations.core.modifications.perturb import FunctionHolder\n", | ||
| "# from mat3ra.made.tools.operations.core.unary import perturb\n", | ||
| "#\n", | ||
| "# SIGMA = 0.5 # Angstrom — how tightly the displacement is localised around the atom\n", | ||
| "#\n", | ||
| "# center_x, center_y, center_z = np.array(ATOM_COORDINATE) @ np.array(\n", | ||
| "# initial_material.lattice.vector_arrays\n", | ||
| "# )\n", | ||
| "#\n", | ||
| "# x, y, z = sp.symbols(\"x y z\")\n", | ||
| "# displacement_function = TRANSLATION[2] * sp.exp(\n", | ||
| "# -(((x - center_x) ** 2 + (y - center_y) ** 2 + (z - center_z) ** 2) / (2 * SIGMA**2))\n", | ||
| "# )\n", | ||
| "#\n", | ||
| "# final_material = perturb(\n", | ||
| "# initial_material,\n", | ||
| "# FunctionHolder(function=displacement_function),\n", | ||
| "# use_cartesian_coordinates=True,\n", | ||
| "# )\n", | ||
| "# visualize([initial_material, final_material], viewer=\"wave\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "15", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### 2.6. Name members in path order and write to the subfolder\n", | ||
| "\n", | ||
| "Numeric prefixes control load order in `utils_create_material_set.ipynb` (filenames are sorted; filenames come from material names).\n" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "16", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from mat3ra.notebooks_utils.material import set_materials\n", | ||
| "from mat3ra.notebooks_utils.settings import UPLOADS_FOLDER\n", | ||
| "\n", | ||
| "path_materials = [initial_material, final_material]\n", | ||
| "for index, material in enumerate(path_materials):\n", | ||
| " material.name = f\"{index:02d}_{PATH_NAME}\"\n", | ||
| "\n", | ||
| "subfolder_path = f\"{UPLOADS_FOLDER}/{SUBFOLDER_NAME}\"\n", | ||
| "set_materials(path_materials, folder_path=subfolder_path)\n" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "name": "python", | ||
| "pygments_lexer": "ipython3" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } | ||
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"Create initial/final materials" and move to "Perturbation 3D"
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