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materialsproject · Feb 9, 2024 · cdefd48 · cdefd48
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,4 +1,4 @@
-exclude: ^(docs|tests)
+exclude: ^(tests)
 
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
@@ -35,7 +35,7 @@ repos:
       --skip, "*.ipynb,./tests,*paper*",
       ]
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
+  rev: 0.7.1
   hooks:
     - id: nbstripout
       args: [

diff --git a/docs/source/content/defect-finder.ipynb b/docs/source/content/defect-finder.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "22bb4abc-3e14-40c0-92af-6269729a4d3a",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Defect Finder\n",
@@ -18,7 +18,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b6e1d6fa",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "873288d3",
+   "id": "2",
    "metadata": {},
    "source": [
     "The last structure (for `q=2`) demonstrates that doing this in a smaller simulation cell with large distortions can be problematic so always double-check your results.\n",
@@ -58,7 +58,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "01e7e997",
+   "id": "3",
    "metadata": {},
    "source": [
     "## How does it work?\n",

diff --git a/docs/source/content/defining-defects.ipynb b/docs/source/content/defining-defects.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -33,7 +32,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "from pathlib import Path\n",
@@ -44,7 +45,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "from pymatgen.analysis.defects.core import DefectComplex, Substitution, Vacancy\n",
@@ -58,7 +61,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -93,7 +95,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -134,7 +135,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -155,7 +155,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -184,7 +183,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -207,7 +205,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -228,6 +225,73 @@
     "#sc_struct_smaller = mg_ga_defect0.get_supercell_structure(max_atoms=100)\n",
     "#sc_struct_smaller.num_sites"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Generating Defects\n",
+    "\n",
+    "Intersitial defects are usually hard to define due to a lack of reference points for the site.\n",
+    "Extensive symmetry can be done to identifiy highly symmetric sites in the structure for interstitial insertion.\n",
+    "However, the recommended method to create interstitial defects is to use the `ChargeInterstitialGenerator` which analyzes the charge density to identify interstitial sites.  The code snippet to generate the interstitial sites are given below.\n",
+    "\n",
+    "For more details, check out this [paper].(https://www.nature.com/articles/s41524-020-00422-3)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "from pymatgen.io.vasp import Chgcar\n",
+    "from pymatgen.analysis.defects.generators import ChargeInterstitialGenerator, generate_all_native_defects\n",
+    "\n",
+    "chgcar = Chgcar.from_file(TEST_FILES / \"CHGCAR.Fe3O4.vasp\")\n",
+    "cig = ChargeInterstitialGenerator()\n",
+    "for defect in cig.generate(chgcar, insert_species=[\"H\"]):\n",
+    "    print(defect)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "You can geneate all native defects in an atomic structure using the `generate_all_native_defects` function."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "for defect in generate_all_native_defects(chgcar):\n",
+    "    print(defect)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you have access the to materials project charge density API,\n",
+    "you can obtain the data from the API directly:\n",
+    "\n",
+    "```python\n",
+    "\n",
+    "from pymatgen.ext.matproj import MPRester\n",
+    "with MPRester() as mpr:\n",
+    "    chgcar = mpr.get_charge_density_from_material_id(\"mp-804\")\n",
+    "    \n",
+    "for defect in generate_all_native_defects(chgcar):\n",
+    "    print(defect)\n",
+    "```"
+   ]
   }
  ],
  "metadata": {
@@ -241,7 +305,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/docs/source/content/nonradiative.ipynb b/docs/source/content/nonradiative.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "6930b94a-4443-45b0-94a5-452f6280fd5a",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Shockley-Read-Hall Recombination\n",
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "239c7281-3a24-49cb-a161-64124c59dbc4",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -31,7 +31,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2d5264bc-c907-4d74-bb70-bc79c9050e7a",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -40,7 +40,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e410b507-e465-438b-95e3-64dce28f6f00",
+   "id": "3",
    "metadata": {},
    "source": [
     "## Read a single Harmonic Defect\n",
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ceaa50d4-57d2-4438-80e7-7cb4491985c1",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -74,7 +74,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "8e0c86ec-8fa4-4399-9900-c161b8149fbe",
+   "id": "5",
    "metadata": {},
    "source": [
     "Note that `HarmonicDefect.defect_band` consists of multiple states presented as `(iband, ikpt, ispin)` index tuples, if `defect_band` was not provided to the constructor, the `relaxed_index` entry in the directory list will be checked for a Procar file, which will be parsed to give the \"best guess\" of the defect state in the band structure.\n",
@@ -88,7 +88,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "43e620e9-93be-4883-b3a0-ecf5218a6355",
+   "id": "6",
    "metadata": {},
    "source": [
     "### Potential energy surface\n",
@@ -103,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c4226814-ccfc-41f9-8eeb-5ad6a2d58eeb",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -122,7 +122,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d169180d",
+   "id": "8",
    "metadata": {},
    "source": [
     "The band structure of the relaxed structure has a state that can be identified as the defect state using the inverse participation ratio."
@@ -131,7 +131,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a8b9111d-40dd-4be5-ac24-2140c4ce7570",
+   "id": "9",
    "metadata": {
     "tags": []
    },
@@ -149,7 +149,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "104ac837",
+   "id": "10",
    "metadata": {},
    "source": [
     "## Evaluating the Electron-Phonon Matrix Element with PAWs\n",
@@ -179,7 +179,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7c149d93",
+   "id": "11",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -191,7 +191,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d7f9b645",
+   "id": "12",
    "metadata": {},
    "source": [
     "The epME is computed by the `HarmonicDefect.get_elph_me` method, which requires the defect band index.\n",
@@ -201,7 +201,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "433f5f29",
+   "id": "13",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -214,7 +214,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "66aafe95",
+   "id": "14",
    "metadata": {},
    "source": [
     "## Calculating the SRH Capture Coefficient\n",
@@ -225,7 +225,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "133e213c",
+   "id": "15",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -238,7 +238,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "a7d97c23",
+   "id": "16",
    "metadata": {},
    "source": [
     "With the initial and final potential energy surfaces, and the `WSWQ` data for the initial state, we can calculate the SRH capture coefficient using the `get_SRH_coefficient` function to compute the capture coefficient as a function of temperature."
@@ -247,7 +247,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2f08c3b9",
+   "id": "17",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -260,11 +260,6 @@
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "mp",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",