{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Si symmetric tilt -exact"
   ]
  },
  {
   "attachments": {},
   "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-_tof5zgf\n",
      "  Running command git clone --filter=blob:none --quiet https://github.com/nmdl-mizo/interface_master.git /tmp/pip-req-build-_tof5zgf\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  1059  100  1059    0     0  22531      0 --:--:-- --:--:-- --:--:-- 22531\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/Si_mp-149_conventional_standard.cif -o 'cif_files/Si_mp-149_conventional_standard.cif'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from interfacemaster.cellcalc import get_primitive_hkl, rot\n",
    "from interfacemaster.interface_generator import core, convert_vector_index\n",
    "from numpy import array, dot, round, var, average, pi\n",
    "from numpy.linalg import inv\n",
    "from gb_code.csl_generator import print_list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Define an interface core class"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Input two cif files.For GBs, input the same file; for interfaces, input two different files.\n",
    "\n",
    "\n",
    "The first structure is non-changed while the second one can be deformed to form an approximate CSL\n",
    "\n",
    "Please input files of CONVENTIONAL cells if you are not familiar with the indices in the primitive cell."
   ]
  },
  {
   "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"
     ]
    }
   ],
   "source": [
    "my_interface = core('cif_files/Si_mp-149_conventional_standard.cif','cif_files/Si_mp-149_conventional_standard.cif')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Specify the rotation axis and searching parameters to find an approximate CSL"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Since this is for a cubic lattice, we have determined rotation axis/angle to give a specific CSL"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Sigma:     1  Theta:   0.00 \n",
      "Sigma:     3  Theta:  70.53 \n",
      "Sigma:     9  Theta:  38.94 \n",
      "Sigma:    11  Theta:  50.48 \n",
      "Sigma:    17  Theta:  86.63 \n",
      "Sigma:    19  Theta:  26.53 \n",
      "Sigma:    27  Theta:  31.59 \n",
      "Sigma:    33  Theta:  20.05 \n",
      "Sigma:    41  Theta:  55.88 \n",
      "Sigma:    43  Theta:  80.63 \n",
      "Sigma:    51  Theta:  16.10 \n",
      "Sigma:    57  Theta:  44.00 \n",
      "Sigma:    59  Theta:  45.98 \n",
      "Sigma:    67  Theta:  62.44 \n",
      "Sigma:    73  Theta:  13.44 \n",
      "Sigma:    81  Theta:  77.88 \n",
      "Sigma:    83  Theta:  17.86 \n",
      "Sigma:    89  Theta:  34.89 \n",
      "Sigma:    97  Theta:  61.02 \n",
      "Sigma:    99  Theta:  11.54 \n"
     ]
    }
   ],
   "source": [
    "print_list([1,1,0],100)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "#rotation matrix\n",
    "R = rot([1,1,0],38.94/180*pi)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "To calculate an exact CSL, we use the search_fixed function by setting exact=True"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Congrates, we found an appx CSL!\n",
      "\n",
      "U1 = \n",
      "[[ 1 -1 -1]\n",
      " [ 0  3  0]\n",
      " [ 0 -2  3]]; sigma_1 = 9\n",
      "\n",
      "U2 = \n",
      "[[ 1 -2  0]\n",
      " [ 0  3 -2]\n",
      " [ 0  0  3]]; sigma_2 = 9\n",
      "\n",
      "D = \n",
      "[[1. 0. 0.]\n",
      " [0. 1. 0.]\n",
      " [0. 0. 1.]]\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "my_interface.parse_limit(du = 1e-2, S  = 1e-2, sgm1=100, sgm2=100, dd = 1e-2)\n",
    "my_interface.search_fixed(R, exact=True, tol = 1e-3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "'U1', 'U2' are two sets of indices of the CSL in the two crystals' frames,\n",
    "'D' is the deformation applied to the crystal 2 to form an approximate CSL\n",
    "\n",
    "As you can see, to form a twinning structure we need to deform the structure provided!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Convert the miller indices to be expressed in the primitive cell"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now we need to specify the orientation of our interface, which is by giving a miller indices in expressed in the primitive cell."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 0,  1, -3])"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\"\"\"\n",
    "The interface plane is the [0,-1,-2] plane in the conventional cell and now we \\\n",
    "transform it into primitive cell\n",
    "\"\"\"\n",
    "hkl = get_primitive_hkl(array([-2,2,1]), my_interface.conv_lattice_1, my_interface.lattice_1, tol = 1e-3)\n",
    "hkl"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Compute the indices of the two slabs to make bicrystal"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Now let's compute the indices of the two slabs forming the interface\n",
    "If you want a near orthogonal bicrystal, please set 'orthogonal to yes, \n",
    "and adjust the lim & tol."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "cell 1:\n",
      "[[ 1  1  2]\n",
      " [ 3  0 -3]\n",
      " [-5  0 -1]]\n",
      "cell 2:\n",
      "[[-1  1  2]\n",
      " [ 5  0 -1]\n",
      " [-3  0 -3]]\n"
     ]
    }
   ],
   "source": [
    "my_interface.compute_bicrystal(hkl, normal_ortho = True, plane_ortho = True, \\\n",
    "                               lim = 50, tol_ortho = 1e-2, tol_integer = 1e-3)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Lattice\n",
       "    abc : 3.8669746532647453 3.8669746532647453 3.8669746532647453\n",
       " angles : 59.99999999999999 59.99999999999999 59.99999999999999\n",
       " volume : 40.88829284866483\n",
       "      A : -2.734364 -2.734364 0.0\n",
       "      B : -2.734364 0.0 -2.734364\n",
       "      C : 1.6743150601518765e-16 -2.734364 -2.734364"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_interface.bicrystal_structure.lattice"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Here we obtained the two sets of indices to build a bicrystal"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Make a bicrystal!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "You can adjust the bicrystal by\n",
    "1. do expansion by set 'xyz' = [dimX, dimY, dimZ]\n",
    "2. do RBT by 'dzdy' = a translation vector \n",
    "(please confine dzdy in the interface plane, \n",
    "for RBT in the normal, please use 'dp1' and 'dp2', to make vacuum in the interface use 'dx');\n",
    "3. introduce vacuum in the interface by 'dx' = the distance spacing the two crystals\n",
    "4. adjust the termination by 'dp1', 'dp2' = length of shift of the position of \n",
    "the termination from the interface into the bulk\n",
    "5. introduce vacuum to make a surface in the end of the bicrystal by\n",
    "'vx' = length of the vaccumn\n",
    "\n",
    "default: xyz = [1,1,1] and others = 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "my_interface.get_bicrystal(xyz_1 = [1,1,1], xyz_2 = [1,1,1], filetype='LAMMPS',dydz=  1 * my_interface.CNID[:,1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "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": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "terminating_sampling...\n",
      "completed\n"
     ]
    }
   ],
   "source": [
    "my_interface.sample_lattice_planes(filetype='VASP')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Good! You have made a 'POSCAR' file of this bicrystal, we also generated two files named 'cell_1.cif' and 'cell_2.cif' providing the structure of the two slabs."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import shutil\n",
    "try:\n",
    "    shutil.rmtree('CNID_inputs')\n",
    "except:\n",
    "    print('No existing files')\n",
    "#To sample the CNID, try\n",
    "my_interface.sample_CNID(grid = [4,4], xyz_1 = [1,1,1], xyz_2 = [1,1,1])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Please check the generated 'POSCAR.x.y' files. \n",
    "The CNID here is expressed in the primitive cell's frame.\n",
    "You can refer to the cartesian coordinates or in the conventional cell's frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "CNID_cartesian = round(my_interface.CNID,8)\n",
    "CNID_cartesian"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "CNID_conv = round(dot(inv(my_interface.conv_lattice_1)\\\n",
    "                              , my_interface.CNID),8)\n",
    "CNID_conv"
   ]
  }
 ],
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