{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Graphene/BN"
   ]
  },
  {
   "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/C_mp-990448_conventional_standard.cif -o 'cif_files/C_mp-990448_conventional_standard.cif'\n",
    "!curl https://raw.githubusercontent.com/nmdl-mizo/interface_master/develop/test_files/cif_files/BN_mp-984_conventional_standard.cif -o 'cif_files/BN_mp-984_conventional_standard.cif'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "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\n",
    "from interfacemaster.symmetric_tilt import get_csl_twisted_graphenes\n",
    "from numpy import array, dot, round, cross, eye, pi, ceil, column_stack, arange\n",
    "from numpy.linalg import inv, det, norm\n",
    "from gb_code.csl_generator import print_list\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Define an interface core class"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "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/C_mp-990448_conventional_standard.cif',\\\n",
    "                    'cif_files/BN_mp-984_conventional_standard.cif')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Searching two_dimensional CSL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "#combining two specified surfaces\n",
    "hkl_1 = get_primitive_hkl([0, 0, 1], my_interface.conv_lattice_1, my_interface.lattice_1)\n",
    "hkl_2 = get_primitive_hkl([0, 0, 1], my_interface.conv_lattice_2, my_interface.lattice_2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 146,
   "metadata": {},
   "outputs": [],
   "source": [
    "#thetas with small sigmas: 10.89, 25.3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 143,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Congrates, we found an appx CSL!\n",
      "\n",
      "U1 = \n",
      "[[-4 -6]\n",
      " [ 2 -4]\n",
      " [ 0  0]]; sigma_1 = 28\n",
      "\n",
      "U2 = \n",
      "[[-3 -6]\n",
      " [ 3 -3]\n",
      " [ 0  0]]; sigma_2 = 27\n",
      "\n",
      "D = \n",
      "[[ 1.0005109e+00  5.9280000e-05  0.0000000e+00]\n",
      " [-5.9280000e-05  1.0005109e+00  0.0000000e+00]\n",
      " [ 0.0000000e+00  0.0000000e+00  1.0000000e+00]]\n",
      "\n",
      "axis = [ 3.23108364e-16  5.59640103e-16 -5.27676003e+00] ; theta = 10.89\n",
      "\n"
     ]
    }
   ],
   "source": [
    "my_interface.parse_limit(du = 1e-2, S = 1e-2, sgm1=50, sgm2=50, dd = 1e-2)\n",
    "#Do searching!\n",
    "my_interface.search_one_position_2D(hkl_1, hkl_2, theta_range = 10, dtheta = 0.01, exact=False, start = 10.89)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get bicrystal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 144,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cell 1:\n",
      "[[ 0 -4 -6]\n",
      " [ 0  2 -4]\n",
      " [ 1  0  0]]\n",
      "cell 2:\n",
      "[[ 0 -3 -6]\n",
      " [ 0  3 -3]\n",
      " [ 1  0  0]]\n"
     ]
    }
   ],
   "source": [
    "hkl = get_primitive_hkl([0, 0, 1], my_interface.conv_lattice_1, my_interface.lattice_1)\n",
    "my_interface.compute_bicrystal_two_D(hkl_1, hkl_2, normal_ortho = False, lim = 50, tol_ortho = 1e-2, tol_integer=1e-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 145,
   "metadata": {},
   "outputs": [],
   "source": [
    "layer_displacement = 3.4\n",
    "my_interface.get_bicrystal(two_D=True,xyz_1 = [1,1,1], xyz_2 = [1,1,1], \\\n",
    "                           dp1 = 9.99905800e+00 - layer_displacement, filetype= 'VASP')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Sample CNID "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "gridsize = 0.3\n",
    "n1 = int(ceil(norm(my_interface.CNID[:,0])/gridsize))\n",
    "n2 = int(ceil(norm(my_interface.CNID[:,1])/gridsize))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "CNID\n",
      "[[ 0.42857143 -0.28571429]\n",
      " [ 0.14285714 -0.42857143]\n",
      " [ 0.          0.        ]]\n",
      "making 16 files...\n",
      "completed\n"
     ]
    }
   ],
   "source": [
    "import shutil\n",
    "try:\n",
    "    shutil.rmtree('CNID_inputs')\n",
    "except:\n",
    "    print('No existing files')\n",
    "my_interface.sample_CNID([n1,n2], dp1 = 9.99905800e+00 - layer_displacement)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Please check the POSCAR file"
   ]
  }
 ],
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