{
 "cells": [
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Graphene/GaN"
   ]
  },
  {
   "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",
      "Requirement already satisfied: matplotlib in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (3.7.0)\n",
      "Requirement already satisfied: gb_code in /home/vscode/.local/lib/python3.10/site-packages (from interfacemaster==1.1.1) (1.0.0)\n",
      "Requirement already satisfied: numpy>=1.14.0 in /home/vscode/.local/lib/python3.10/site-packages (from gb_code->interfacemaster==1.1.1) (1.24.2)\n",
      "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (2.8.2)\n",
      "Requirement already satisfied: pillow>=6.2.0 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (9.4.0)\n",
      "Requirement already satisfied: cycler>=0.10 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (0.11.0)\n",
      "Requirement already satisfied: fonttools>=4.22.0 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (4.38.0)\n",
      "Requirement already satisfied: pyparsing>=2.3.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (3.0.9)\n",
      "Requirement already satisfied: contourpy>=1.0.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (1.0.7)\n",
      "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (23.0)\n",
      "Requirement already satisfied: kiwisolver>=1.0.1 in /home/vscode/.local/lib/python3.10/site-packages (from matplotlib->interfacemaster==1.1.1) (1.4.4)\n",
      "Requirement already satisfied: networkx>=2.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.0)\n",
      "Requirement already satisfied: tqdm in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (4.64.1)\n",
      "Requirement already satisfied: scipy>=1.5.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.10.1)\n",
      "Requirement already satisfied: requests in /usr/local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2.28.2)\n",
      "Requirement already satisfied: monty>=3.0.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2022.9.9)\n",
      "Requirement already satisfied: pandas in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.5.3)\n",
      "Requirement already satisfied: pybtex in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.24.0)\n",
      "Requirement already satisfied: uncertainties>=3.1.4 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.1.7)\n",
      "Requirement already satisfied: ruamel.yaml>=0.17.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.17.21)\n",
      "Requirement already satisfied: palettable>=3.1.1 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (3.3.0)\n",
      "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",
      "Requirement already satisfied: spglib>=2.0.2 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (2.0.2)\n",
      "Requirement already satisfied: tabulate in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (0.9.0)\n",
      "Requirement already satisfied: sympy in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (1.11.1)\n",
      "Requirement already satisfied: plotly>=4.5.0 in /home/vscode/.local/lib/python3.10/site-packages (from pymatgen->interfacemaster==1.1.1) (5.13.0)\n",
      "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",
      "Requirement already satisfied: msgpack in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (1.0.4)\n",
      "Requirement already satisfied: typing-extensions>=3.7.4.1 in /home/vscode/.local/lib/python3.10/site-packages (from mp-api>=0.27.3->pymatgen->interfacemaster==1.1.1) (4.5.0)\n",
      "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",
      "Requirement already satisfied: tenacity>=6.2.0 in /home/vscode/.local/lib/python3.10/site-packages (from plotly>=4.5.0->pymatgen->interfacemaster==1.1.1) (8.2.1)\n",
      "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/site-packages (from python-dateutil>=2.7->matplotlib->interfacemaster==1.1.1) (1.16.0)\n",
      "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (3.0.1)\n",
      "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (3.4)\n",
      "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (1.26.14)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/site-packages (from requests->pymatgen->interfacemaster==1.1.1) (2022.12.7)\n",
      "Requirement already satisfied: ruamel.yaml.clib>=0.2.6 in /home/vscode/.local/lib/python3.10/site-packages (from ruamel.yaml>=0.17.0->pymatgen->interfacemaster==1.1.1) (0.2.7)\n",
      "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",
      "Requirement already satisfied: latexcodec>=1.0.4 in /home/vscode/.local/lib/python3.10/site-packages (from pybtex->pymatgen->interfacemaster==1.1.1) (2.0.1)\n",
      "Requirement already satisfied: PyYAML>=3.01 in /usr/local/lib/python3.10/site-packages (from pybtex->pymatgen->interfacemaster==1.1.1) (6.0)\n",
      "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   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/GaN_mp-804_conventional_standard.cif -o 'cif_files/GaN_mp-804_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\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": 13,
   "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/C_mp-990448_conventional_standard.cif',\\\n",
    "                    'cif_files/GaN_mp-804_conventional_standard.cif')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Searching two_dimensional CSL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "#combining two specified surfaces\n",
    "hkl_1 = get_primitive_hkl([1, 0, 0], 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": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Congrates, we found an appx CSL!\n",
      "\n",
      "U1 = \n",
      "[[ 0  7]\n",
      " [ 0  0]\n",
      " [-1  0]]; sigma_1 = 7\n",
      "\n",
      "U2 = \n",
      "[[ 3  0]\n",
      " [-3  9]\n",
      " [-3 -9]]; sigma_2 = 66\n",
      "\n",
      "D = \n",
      "[[ 1.         -0.         -0.        ]\n",
      " [ 0.          0.99296184  0.        ]\n",
      " [ 0.          0.          1.04239279]]\n",
      "\n",
      "axis = [8.44281605e+01 5.16973382e-15 0.00000000e+00] ; theta = 0.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "my_interface.parse_limit(du = 1e-1, S  = 1e-1, sgm1=50, sgm2=50, dd = 1e-1)\n",
    "my_interface.search_one_position_2D(hkl_1, hkl_2, theta_range = 30, \\\n",
    "                                    dtheta = 0.01, integer_tol = 1e-4, start = 0)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get bicrystal"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cell 1:\n",
      "[[ 0  0  7]\n",
      " [-1  0  0]\n",
      " [ 0 -1  0]]\n",
      "cell 2:\n",
      "[[ 1  3  0]\n",
      " [ 0 -3  9]\n",
      " [ 0 -3 -9]]\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": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on method get_bicrystal in module interfacemaster.interface_generator:\n",
      "\n",
      "get_bicrystal(dydz=array([0., 0., 0.]), dx=0, dp1=0, dp2=0, xyz_1=[1, 1, 1], xyz_2=[1, 1, 1], vx=0, filename='POSCAR', two_D=False, filetype='VASP', mirror=False, KTI=False) method of interfacemaster.interface_generator.core instance\n",
      "    generate a cif file for the bicrystal structure\n",
      "    \n",
      "    Parameters\n",
      "    ----------\n",
      "    dydz : numpy array\n",
      "        translation vector in the interface\n",
      "    dx : float\n",
      "        translation normal to the interface\n",
      "    dp1, dp2 : float\n",
      "        termination of slab 1, 2\n",
      "    xyz1, xyz2 : list\n",
      "        expansion of slab 1, 2\n",
      "    vx : float\n",
      "        vacuum spacing, default 0\n",
      "    filename : str\n",
      "        filename, default 'POSCAR'\n",
      "    two_D : bool\n",
      "        whether a two CSL\n",
      "    filetype : str\n",
      "        filetype, 'VASP' or 'LAMMPS', default 'VASP'\n",
      "    mirror : bool\n",
      "        mirror, default False\n",
      "    KTI : bool\n",
      "        KTI, default False\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(my_interface.get_bicrystal)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "layer_displacement = 3.4\n",
    "my_interface.get_bicrystal(xyz_1 = [1,1,1], xyz_2 = [1,1,1], \\\n",
    "                           filetype= 'VASP', dydz = [0, 0, -2], dp1 = -0.5)"
   ]
  },
  {
   "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"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.9"
  },
  "vscode": {
   "interpreter": {
    "hash": "949777d72b0d2535278d3dc13498b2535136f6dfe0678499012e853ee9abcab1"
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}