{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Al2O3/ZnO"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## import & prepare"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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-h_udnrlj\n",
      "  Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-h_udnrlj\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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      "\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  2202  100  2202    0     0   7080      0 --:--:-- --:--:-- --:--:--  7080\n",
      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
      "100   854  100   854    0     0   3105      0 --:--:-- --:--:-- --:--:--  3116\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/Al2O3_mp-1143_conventional_standard.cif -o 'cif_files/Al2O3_mp-1143_conventional_standard.cif'\n",
    "!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/ZnO_mp-2133_conventional_standard.cif -o 'cif_files/ZnO_mp-2133_conventional_standard.cif'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from interfacemaster.cellcalc import get_primitive_hkl\n",
    "from interfacemaster.interface_generator import core, convert_vector_index, get_disorientation\n",
    "from numpy import array, dot, round, cross, eye\n",
    "from numpy.linalg import inv, det, norm"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Define an interface core class"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://aip.scitation.org/doi/full/10.1063/1.3489687"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Warning!, this programme will rewrite the POSCAR file in this dir!\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/jasonxie/.local/lib/python3.8/site-packages/pymatgen/io/cif.py:1121: UserWarning: Issues encountered while parsing CIF: Some fractional co-ordinates rounded to ideal values to avoid issues with finite precision.\n",
      "  warnings.warn(\"Issues encountered while parsing CIF: %s\" % \"\\n\".join(self.warnings))\n"
     ]
    }
   ],
   "source": [
    "my_interface = core('cif_files/Al2O3_mp-1143_conventional_standard.cif',\\\n",
    "                    'cif_files/ZnO_mp-2133_conventional_standard.cif')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[-0.0673919 ,  0.8832738 , -0.46398893],\n",
       "       [-0.96109127,  0.0673919 ,  0.26788413],\n",
       "       [ 0.26788413,  0.46398893,  0.84436507]])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "R = get_disorientation(L1 = my_interface.conv_lattice_1, L2 = my_interface.conv_lattice_2, \\\n",
    "                       v1 = [-1,1,1], hkl1 = [1, -1, 2], \\\n",
    "                       v2 = [0,0,1], hkl2 = [1, 1, 0])\n",
    "R"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get combining two specified surfaces"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here, we want the (1,-1,0,2) plane of the Al2O3 coincident whith (1,1,-2,0) plane of ZnO.  \n",
    "Get the miller indices of these two planes expressed in the primitive lattices."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "hkl_1 = get_primitive_hkl([1, -1, 2], my_interface.conv_lattice_1, my_interface.lattice_1)\n",
    "hkl_2 = get_primitive_hkl([1, 1, 0], my_interface.conv_lattice_2, my_interface.lattice_2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Searching two_dimensional CSL\n",
    "To searching for 2D CSL, we use search_one_position_2D() function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Congrates, we found an appx CSL!\n",
      "\n",
      "U1 = \n",
      "[[ 0 -5]\n",
      " [-1  0]\n",
      " [ 1  0]]; sigma_1 = 7\n",
      "\n",
      "U2 = \n",
      "[[0 4]\n",
      " [0 8]\n",
      " [1 0]]; sigma_2 = 9\n",
      "\n",
      "D = \n",
      "[[ 1.00834944  0.02653473  0.00951351]\n",
      " [ 0.02653473  1.03898911 -0.00549263]\n",
      " [ 0.00951351 -0.00549263  0.98268735]]\n",
      "\n",
      "axis = [-18.19345118  10.50399394 -13.33003186] ; theta = 0.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "my_interface.parse_limit(du = 1e-1, S  = 1e-1, sgm1=100, sgm2=100, dd = 1e-1)\n",
    "\n",
    "#Do searching!\n",
    "my_interface.search_one_position_2D(hkl_1, hkl_2, theta_range = 2, \\\n",
    "                                    dtheta = 0.01, pre_R = R, match_tol = 0.01, pre_dt= True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get bicrystal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cell 1:\n",
      "[[ 0  0 -5]\n",
      " [-1 -1  0]\n",
      " [ 0  1  0]]\n",
      "cell 2:\n",
      "[[-1  0  4]\n",
      " [ 0  0  8]\n",
      " [ 0  1  0]]\n"
     ]
    }
   ],
   "source": [
    "my_interface.compute_bicrystal_two_D(hkl_1 = hkl_1, hkl_2=hkl_2, normal_ortho = False, lim = 50, tol_ortho = 1e-2, tol_integer=1e-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "my_interface.get_bicrystal(two_D = True, xyz_1 = [1,1,1], xyz_2 = [1,1,1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Please check the POSCAR file"
   ]
  }
 ],
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