Add more examples (#39)

* Add second example

* Add vacancy detection example

* Add example to set point defects

.gitignore

@@ -1 +1,2 @@
-*.pyc
+*.pyc
+.ipynb_checkpoints

examples/1_Getting_Started.ipynb

@@ -91,7 +91,7 @@
    "metadata": {},
    "source": [
     "## Annoate Crystal Structure \n",
-    "Is identified crystal structures is satisfactory add information to the knowledge graph"
+    "If identified crystal structures is satisfactory add information to the knowledge graph"
    ]
   },
   {

examples/2_Setting_Crystal_Structure.ipynb

@@ -0,0 +1,104 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from atomid.annotate import AnnotateCrystal"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Read crystal structure file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "file_path = \"../tests/data/fcc/Al/no_defect/Al.cif\"\n",
+    "\n",
+    "annotate_crystal = AnnotateCrystal()\n",
+    "\n",
+    "annotate_crystal.read_crystal_structure_file(file_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Set Crystal Structure Manually"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotate_crystal.set_crystal_structure(\"fcc\")\n",
+    "annotate_crystal.set_lattice_constant(4.5)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Annoate Crystal Structure \n",
+    "Add information to the knowledge graph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotate_crystal.annotate_crystal_structure()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Write ouput crystal structure file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotate_crystal.write_to_file(\"crystal_kg.ttl\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "atomid-venv",
+   "language": "python",
+   "name": "atomid-venv"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

examples/3_Identify_Point_Defects.ipynb

@@ -0,0 +1,153 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from atomid.annotate import AnnotateCrystal"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Read crystal structure file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "file_path = \"../tests/data/fcc/Al/defect/vacancy/Al_vacancy.cif\"\n",
+    "\n",
+    "annotate_crystal_vacancy = AnnotateCrystal()\n",
+    "\n",
+    "annotate_crystal_vacancy.read_crystal_structure_file(file_path)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Identify and Annotate Crystal Structure"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[92mCrystal structure: fcc\u001b[0m\n",
+      "\u001b[92mLattice constant: 4.05\u001b[0m\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Identify the crystal structure\n",
+    "annotate_crystal_vacancy.identify_crystal_structure()\n",
+    "\n",
+    "# Annotate the crystal structure\n",
+    "annotate_crystal_vacancy.annotate_crystal_structure()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Identify Point defects\n",
+    "Point defects are identified using the Wigner-Seitz algorithm, which requires a reference file structure for identification."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[92mIdentified defects:\u001b[0m\n",
+      "\u001b[92mvacancies:\u001b[0m Count: 40 Concentration: 0.01\n"
+     ]
+    }
+   ],
+   "source": [
+    "ref_file = \"../tests/data/fcc/Al/no_defect/Al.cif\"\n",
+    "\n",
+    "# Identify point defects using the reference file\n",
+    "annotate_crystal_vacancy.identify_point_defects(\n",
+    "    reference_data_file=ref_file, ref_format=\"cif\"\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add information to Knowledge graph"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotate_crystal_vacancy.annotate_point_defects()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Write ouput crystal structure file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "annotate_crystal_vacancy.write_to_file(\"crystal_kg.ttl\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "atomid-venv",
+   "language": "python",
+   "name": "atomid-venv"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}