{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# GaN/Fe"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## import & prepare"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "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-pi2px8wp\n",
      "  Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-pi2px8wp\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: mp-api>=0.27.3 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.30.10)\n",
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      "Requirement already satisfied: emmet-core>=0.39.8 in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (0.44.0)\n",
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      "Requirement already satisfied: PyYAML>=3.01 in /usr/local/lib/python3.10/site-packages (from pybtex->pymatgen->interfacemaster==1.1.1) (6.0)\n",
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      "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   951  100   951    0     0   2926      0 --:--:-- --:--:-- --:--:--  2935\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/GaN_mp-804_conventional_standard.cif -o 'cif_files/GaN_mp-804_conventional_standard.cif'\n",
    "!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/Fe_mp-13_conventional_standard.cif -o 'cif_files/Fe_mp-13_conventional_standard.cif'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from interfacemaster.cellcalc import get_primitive_hkl, get_pri_vec_inplane, get_normal_index, get_normal_from_MI, rot\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": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Warning!, this programme will rewrite the POSCAR file in this dir!\n"
     ]
    }
   ],
   "source": [
    "my_interface = core('cif_files/GaN_mp-804_conventional_standard.cif',\\\n",
    "                    'cif_files/Fe_mp-13_conventional_standard.cif')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[ 3.21633760e-01,  5.00000000e-01,  8.04084401e-01],\n",
       "       [-1.85695338e-01,  8.66025404e-01, -4.64238345e-01],\n",
       "       [-9.28476691e-01,  4.28707594e-17,  3.71390676e-01]])"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#target disorientation\n",
    "R = get_disorientation(L1 = my_interface.conv_lattice_1, L2 = my_interface.conv_lattice_2, \\\n",
    "                       v1 = [-1,-1,0], hkl1 = [1, -1, 0], \\\n",
    "                       v2 = [0,-1,0], hkl2 = [2, 0, 5])\n",
    "R"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "#combining two specified surfaces\n",
    "hkl_1 = get_primitive_hkl([1, -1, 0], my_interface.conv_lattice_1, my_interface.lattice_1)\n",
    "hkl_2 = get_primitive_hkl([2, 0, 5], my_interface.conv_lattice_2, my_interface.lattice_2)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Searching two_dimensional CSL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Congrates, we found an appx CSL!\n",
      "\n",
      "U1 = \n",
      "[[4 0]\n",
      " [0 0]\n",
      " [0 3]]; sigma_1 = 12\n",
      "\n",
      "U2 = \n",
      "[[-5  5]\n",
      " [ 0  7]\n",
      " [-5  2]]; sigma_2 = 52\n",
      "\n",
      "D = \n",
      "[[ 0.97649518 -0.04071154  0.        ]\n",
      " [-0.04071154  0.92948554  0.        ]\n",
      " [-0.         -0.          1.02783677]]\n",
      "\n",
      "axis = [14.59533203 -8.42661887  0.        ] ; theta = 0.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "my_interface.parse_limit(du = 1e-1, S  = 1e-1, sgm1=200, sgm2=200, dd = 1e-1)\n",
    "\n",
    "#Do searching!\n",
    "my_interface.search_one_position_2D(hkl_1, hkl_2, theta_range = 1, \\\n",
    "                                    dtheta = 0.01, pre_R=R, pre_dt= True, integer_tol = 1e-4)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get bicrystal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cell 1:\n",
      "[[-1  4  0]\n",
      " [-2  0  0]\n",
      " [ 0  0  3]]\n",
      "cell 2:\n",
      "[[ 1 -5  5]\n",
      " [-1  0  7]\n",
      " [-2 -5  2]]\n"
     ]
    }
   ],
   "source": [
    "my_interface.compute_bicrystal_two_D(hkl_1 = hkl_1, hkl_2=hkl_2, normal_ortho = True, lim = 50, tol_ortho = 1e-2, tol_integer=1e-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "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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