{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Compute Bicrystallographic properties\n",
    "\n",
    "In this code, we compute and save the bicrystallography properties for each $\\Sigma$-miorientation. These properties include:\n",
    "1. `sig_mats`: The $\\Sigma$-miorientation in the primitive $p$ reference frame. For example, we use the variable `T_p1top2_p1`\n",
    "2. `csl_mats`: The CSL lattice basis vectors in the primitive $p$ reference frame. For example, we use the variable `l_csl_p` denoting $\\Lambda_{csl}^p$\n",
    "3. `dsc_mats`: The DSC lattice basis vectors in the primitive $p$ reference frame. For example, we use the variable `l_dsc_p` denoting $\\Lambda_{dsc}^p$\n",
    "4. `bxt_symm_props`: The symmetry aspects of the $\\Sigma$-miorientation\n",
    "    + `bxt_symm_grp`: The point-group symmetry of the bicrystal. This is the symmetry for the Boundary-plane orientations.\n",
    "    + `symm_grp_ax`: The axes of the symmetry point-group."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import byxtal.lattice as gbl\n",
    "import byxtal.csl_utility_functions as cuf\n",
    "import byxtal.find_csl_dsc as fcd\n",
    "import numpy as np\n",
    "import byxtal.tools as gbt\n",
    "import byxtal.misorient_fz as mfz\n",
    "import byxtal.disorient_symm_props as dsp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "1. `l1`: The lattice object.\n",
    "2. `l_p_po`: $\\Lambda_p^{po}$"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3_1\n"
     ]
    },
    {
     "ename": "IndexError",
     "evalue": "list index out of range",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-2-0ea1f0f89914>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     25\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     26\u001b[0m \u001b[0;31m#         l_csl_p, l_dsc_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 27\u001b[0;31m         \u001b[0ml_csl_p\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfcd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfind_csl_dsc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ml_p_po\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mT_p1top2_p1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1e-6\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     28\u001b[0m         \u001b[0mcsl_mats\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0msig_id\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0ml_csl_p\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     29\u001b[0m \u001b[0;31m#         dsc_mats[sig_id] = l_dsc_p;\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/Leila_sndhard/codes/byxtal/byxtal/byxtal/find_csl_dsc.py\u001b[0m in \u001b[0;36mfind_csl_dsc\u001b[0;34m(l_p_po, T_p1top2_p1, tol1, print_check)\u001b[0m\n\u001b[1;32m    102\u001b[0m     \u001b[0;31m########################################################################\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    103\u001b[0m     \u001b[0;31m# l_csl_p = csl_finder(T_p1top2_p1, Sigma, l_p_po, tol1)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 104\u001b[0;31m     \u001b[0ml_csl_p\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcsl_finder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mT_p1top2_p1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ml_p_po\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtol1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    105\u001b[0m     \u001b[0mcheck_val1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcheck_csl\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ml_csl_p\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ml_p_po\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mT_p1top2_p1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mSigma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprint_check\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    106\u001b[0m     \u001b[0;31m########################################################################\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/Leila_sndhard/codes/byxtal/byxtal/byxtal/find_csl_dsc.py\u001b[0m in \u001b[0;36mcsl_finder\u001b[0;34m(T_p1top2_p1, l_p_po, tol1)\u001b[0m\n\u001b[1;32m    165\u001b[0m     \u001b[0minp_args\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'mat'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mTI_p1top2_p1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    166\u001b[0m     \u001b[0minp_args\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'sig_num'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSigma\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 167\u001b[0;31m     \u001b[0ml_csl1_p\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrpl\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcall_sage_math\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mexec_str\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minp_args\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    168\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    169\u001b[0m     \u001b[0ml_csl_csl1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrpl\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreduce_po_lat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ml_csl1_p\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ml_p_po\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtol1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/Leila_sndhard/codes/byxtal/byxtal/byxtal/reduce_po_lat.py\u001b[0m in \u001b[0;36mcall_sage_math\u001b[0;34m(exec_str, inp_args)\u001b[0m\n\u001b[1;32m     36\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mi1\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSz\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     37\u001b[0m         \u001b[0;32mfor\u001b[0m \u001b[0mj1\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mSz\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 38\u001b[0;31m             \u001b[0mM_out\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mi1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mj1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr_out\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mct1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     39\u001b[0m             \u001b[0mct1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mct1\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     40\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mIndexError\u001b[0m: list index out of range"
     ]
    }
   ],
   "source": [
    "l1 = gbl.Lattice('Al')\n",
    "sig_type = 'common'\n",
    "l_p_po = l1.l_p_po\n",
    "\n",
    "### For cubic only odd Sigma numbers exist!\n",
    "n1 = 1\n",
    "n2 = 10\n",
    "sig_nums = 2*np.arange(n1,n2)+1\n",
    "\n",
    "num_sigs = 0\n",
    "sig_mats = {}\n",
    "csl_mats = {}\n",
    "dsc_mats = {}\n",
    "bxt_symm_props = {}\n",
    "\n",
    "for sig_num in sig_nums:\n",
    "    s1 = cuf.csl_rotations(sig_num, sig_type, l1)\n",
    "    for ct1 in range(np.shape(s1['N'])[0]):\n",
    "        symm_grp_props = {}\n",
    "        sig_id = str(sig_num)+'_'+str(ct1+1)\n",
    "        print(sig_id)\n",
    "        #### Store the sigma-misorientation (in 'p' reference frame)\n",
    "        T_p1top2_p1 = s1['N'][ct1]/s1['D'][ct1]\n",
    "        sig_mats[sig_id] = T_p1top2_p1\n",
    "\n",
    "#         l_csl_p, l_dsc_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)\n",
    "        l_csl_p = fcd.find_csl_dsc(l_p_po, T_p1top2_p1, 1e-6, False)\n",
    "        csl_mats[sig_id] = l_csl_p\n",
    "#         dsc_mats[sig_id] = l_dsc_p;\n",
    "\n",
    "        #### Generate boundary-planpe orientations\n",
    "        l_p_po = l1.l_p_po\n",
    "        l_po_p = np.linalg.inv(l_p_po)\n",
    "        T_p1top2_po1 = np.dot(l_p_po, np.dot(T_p1top2_p1, l_po_p))\n",
    "\n",
    "        ## Find the corresponding disorientation\n",
    "        quat1 = gbt.mat2quat(T_p1top2_po1)\n",
    "        # print(quat1)\n",
    "        dis_quat1 = mfz.misorient_fz(quat1, l1.cryst_ptgrp)\n",
    "        # print(dis_quat1)\n",
    "        x_g, y_g, z_g, bxt_symm_grp = dsp.disorient_symm_props(dis_quat1, l1.cryst_ptgrp)\n",
    "        symm_grp_ax = (np.vstack((x_g, y_g, z_g))).transpose()\n",
    "        symm_grp_props['symm_grp_ax'] = symm_grp_ax\n",
    "        symm_grp_props['bxt_symm_grp'] = bxt_symm_grp\n",
    "        bxt_symm_props[sig_id] = symm_grp_props\n",
    "        num_sigs = num_sigs + 1\n",
    "        print(num_sigs)\n",
    "\n",
    "import pickle as pkl;\n",
    "pkl_name = l1.elem_type+'_byxtal_props.pkl'\n",
    "csl_props = {}\n",
    "csl_props['sig_mats'] = sig_mats\n",
    "csl_props['csl_mats'] = csl_mats\n",
    "csl_props['dsc_mats'] = dsc_mats\n",
    "csl_props['csl_symm_props'] = bxt_symm_props\n",
    "\n",
    "jar = open(pkl_name, 'wb')\n",
    "pkl.dump(csl_props, jar)\n",
    "jar.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "csl_props"
   ]
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  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
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