{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# TiO2 surface slab"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## import & prepare"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Defaulting to user installation because normal site-packages is not writeable\n",
      "Collecting git+https://github.com/nmdl-mizo/interface_master.git@develop\n",
      "  Cloning https://github.com/nmdl-mizo/interface_master.git (to revision develop) to /tmp/pip-req-build-uugit09c\n",
      "  Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-uugit09c\n",
      "  Resolved https://github.com/nmdl-mizo/interface_master.git to commit 2bdf96ed4835b036557ac18de82b4fa2afdabf24\n",
      "  Preparing metadata (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25hRequirement already satisfied: pymatgen in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (2023.1.30)\n",
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      "Requirement already satisfied: setuptools in /usr/local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (65.5.1)\n",
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      "Requirement already satisfied: future in /home/vscode/.local/lib/python3.10/site-packages (from uncertainties>=3.1.4->pymatgen->interfacemaster==1.1.1) (0.18.3)\n",
      "Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/site-packages (from pandas->pymatgen->interfacemaster==1.1.1) (2022.7.1)\n",
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      "Requirement already satisfied: mpmath>=0.19 in /home/vscode/.local/lib/python3.10/site-packages (from sympy->pymatgen->interfacemaster==1.1.1) (1.2.1)\n",
      "Requirement already satisfied: pydantic>=1.10.2 in /home/vscode/.local/lib/python3.10/site-packages (from emmet-core>=0.39.8->mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (1.10.5)\n",
      "\n",
      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip available: \u001b[0m\u001b[31;49m22.3.1\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m23.0.1\u001b[0m\n",
      "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n",
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100   955  100   955    0     0      0      0 --:--:-- --:--:-- --:--:--     0     0   2713      0 --:--:-- --:--:-- --:--:--  2705\n"
     ]
    }
   ],
   "source": [
    "!pip install git+https://github.com/nmdl-mizo/interface_master.git@develop\n",
    "!mkdir -p cif_files\n",
    "!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/TiO2_mp-2657_conventional_standard.cif -o 'cif_files/TiO2_mp-2657_conventional_standard.cif'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from interfacemaster.interface_generator import get_surface_slab, terminates_scanner_slab_structure\n",
    "from interfacemaster.cellcalc import get_primitive_hkl\n",
    "from pymatgen.core.structure import Structure\n",
    "from numpy import ceil"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Load structures"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "primitive_unit_structure =  Structure.from_file('cif_files/TiO2_mp-2657_conventional_standard.cif', \\\n",
    "                                     primitive=True, sort=False, merge_tol=0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "conv_unit_structure = Structure.from_file('cif_files/TiO2_mp-2657_conventional_standard.cif', \\\n",
    "                                     primitive=False, sort=False, merge_tol=0.0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cross vector: \n",
      "[[1]\n",
      " [0]\n",
      " [0]]\n",
      "length: 2.969203\n",
      "plane basis: \n",
      "[[ 0  1]\n",
      " [ 0 -1]\n",
      " [ 1  0]]\n",
      "length: 4.653272 5.519882857560747\n"
     ]
    }
   ],
   "source": [
    "#get all the non-identical terminations\n",
    "hkl_in_pri = get_primitive_hkl(hkl=[1,0,1], C_lattice=conv_unit_structure.lattice.matrix.T, \\\n",
    "                              P_lattice=primitive_unit_structure.lattice.matrix.T)\n",
    "plane_list, element_list, dp_list = terminates_scanner_slab_structure(primitive_unit_structure, hkl_in_pri)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[0.7623739121169246, 1.7406639121169247, 2.5030439121169246]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#height\n",
    "dp_list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The function below generates a slab with its bc-plane is a specified (hkl) lattice plane\n",
    "### Customerization options:  \n",
    "**replica** --- expand from primitive slab cell, **default: [1,1,1]**  \n",
    "**inclination_tol** --- required minimum cos value of the angle between the basic crossing vector and the surface, **default: gamma angle > 45 degrees**  \n",
    "**termi_shift** --- shift the termination of the surface, **default: 0**  \n",
    "**vacuum_height** --- height of vaccum, **default:  0**  \n",
    "**plane_normal** --- whether requiring the two vectors in the surface plane to be perpendicular, **default: False**  \n",
    "**normal_perp** --- whether requiring the crossing vector to be perpendicular to the plane, **default:  False**  \n",
    "**normal_tol** --- tolerance to judge whether normal/perpendicular, **default: 1e-3**  \n",
    "**lim** --- control the number of generated vectors to search for the crossing vectors and perpendicular vectors, **default: 20**    \n",
    "**filename** --- name of the generated atom files, **default:  'POSCAR'**  \n",
    "**filetype** --- type of the generated atom files (for VASP or LAMMPS), **default: 'VASP'**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cross vector: \n",
      "[[2]\n",
      " [0]\n",
      " [5]]\n",
      "length: 17.521869837553325\n",
      "plane basis: \n",
      "[[ 0  1]\n",
      " [-1  0]\n",
      " [ 0 -1]]\n",
      "length: 4.653272 5.519882857560747\n"
     ]
    }
   ],
   "source": [
    "#get orthogonal cell\n",
    "slab_structure = get_surface_slab(conv_unit_structure, hkl = [1,0,1], vacuum_height = 15, \\\n",
    "                                  plane_normal = True, normal_perp = True, termi_shift = 1.75)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cross vector: \n",
      "[[-1]\n",
      " [-1]\n",
      " [ 0]]\n",
      "length: 6.580720371810977\n",
      "plane basis: \n",
      "[[ 0 -1]\n",
      " [ 0  1]\n",
      " [ 1  0]]\n",
      "length: 2.969203 6.580720371810977\n"
     ]
    }
   ],
   "source": [
    "#expansion to reach a required slab size with length_a > 5, length_b > 10, length_c > 10\n",
    "da, db, dc = ceil(5/6.580720371810977), ceil(10/2.969203), ceil(10/6.580720371810977)\n",
    "slab_structure = get_surface_slab(unit_structure, hkl = [1,1,0], replica = [da, db, dc], vacuum_height = 20)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Try other customerization options :D**"
   ]
  }
 ],
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