generation_example.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Unit cell preparation and xyz generation from matid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "from tqdm import tqdm\n",
    "from scipy.io import savemat\n",
    "from manipulatt import *\n",
    "from manipulatt.util import trim_filename\n",
    "from manipulatt.write import write_xyz_prism"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "rotation_supercell = manipulate.supercell()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Generate supercells"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "protodf = pd.read_csv('../data/prototype_count.csv')\n",
    "#matdf = pd.read_csv('../data/training_dataset_allCrys.csv')\n",
    "count = protodf['Prototype'].count()\n",
    "max_dim = [50, 50 ,500]\n",
    "\n",
    "for i in tqdm(range(count)):\n",
    "    #try:\n",
    "        string = protodf['Prototype'].iloc[i+1]\n",
    "        unit_cell = rotation_supercell.find_unitcell_mat_proj(string.split('_')[0],int(string.split('_')[1]))\n",
    "        supercell = rotation_supercell.construct_supercell_from_unitcell(unit_cell, max_dim)\n",
    "        supercell_dict = {\"supercell_unrotated\": supercell, \"label\": \"unrotated\"}\n",
    "        \n",
    "        filename_mat = 'matlab_data/supercell_' + trim_filename(str(unit_cell.composition))+ '_unrotated' +'.mat'\n",
    "        filename_prism = 'prismatic_data/supercell_' + trim_filename(str(unit_cell.composition))+ '_unrotated' +'.xyz'\n",
    "        \n",
    "        print('writing file {} ... \\n'.format(filename_mat))\n",
    "        savemat(filename_mat, supercell_dict)\n",
    "        write_xyz_prism(supercell[:,3:], supercell[:,:3], max_dim, dw=None, fname=filename_prism)\n",
    "        print('success {} \\n'.format(filename_mat))\n",
    "        \n",
    "        #Rotation zxz high tilt\n",
    "        \n",
    "        theta1 = (180/np.pi)*np.random.uniform(-np.pi, np.pi, 10)\n",
    "        phi    = (180/np.pi)*np.arccos(np.random.uniform(-1,1,10))\n",
    "        theta2 = (180/np.pi)*np.random.uniform(-np.pi, np.pi, 10)\n",
    "\n",
    "        zxzrotation  = np.asarray([theta1, phi, theta2])\n",
    "    \n",
    "        for zxz in tqdm(range(zxzrotation.shape[1])):        \n",
    "            rotation = zxzrotation[:,zxz]\n",
    "            print('Constructing supercell ... \\n')\n",
    "            \n",
    "            unit_cell_rot=rotation_supercell.rotate_tilt_unitcell(unit_cell, rotation)\n",
    "            super_cell=rotation_supercell.construct_supercell_from_unitcell(unit_cell_rot, max_dim)\n",
    "            supercell_dict = {\"supercell_rotated\": super_cell, \"label\": \"rotated\"}\n",
    "            \n",
    "            filename_mat = 'matlab_data/supercell_' + trim_filename(str(unit_cell.composition)) + str('_') +str(rotation[0].astype(np.int32)) + str(rotation[1].astype(np.int32)) +str(rotation[2].astype(np.int32)) + '.mat'\n",
    "            filename_prism = 'prismatic_data/supercell_' + trim_filename(str(unit_cell.composition)) + str('_') +str(rotation[0].astype(np.int32)) + str(rotation[1].astype(np.int32)) +str(rotation[2].astype(np.int32)) + '.xyz'\n",
    "   \n",
    "            #comment = 'supercell_' + str(unit_cell.composition)\n",
    "            \n",
    "            print('writing file {} ... \\n'.format(filename_mat))\n",
    "            savemat(filename_mat, supercell_dict)\n",
    "            #write_xyz(supercell, filename)\n",
    "            write_xyz_prism(super_cell[:,3:], super_cell[:,:3], max_dim, dw=None, fname=filename_prism)\n",
    "            print('success {} \\n'.format(filename_mat))\n",
    "            \n",
    "            \n",
    "        #Zoneaxis rotation\n",
    "        zoneaxis = np.array([(1,1,1),(0,0,1),(0,1,1)])\n",
    "        zoneaxis = np.vstack((zoneaxis , np.random.randint(3, size=(7, 3)))) \n",
    "            \n",
    "        for zxz in tqdm(range(zoneaxis.shape[0])):  \n",
    "            zone = zoneaxis[zxz,:]\n",
    "            print('Constructing supercell ... \\n')\n",
    "            \n",
    "            unit_cell_zone=rotation_supercell.zoneaxis_rotate_tilt_unitcell(unit_cell,zone)\n",
    "            super_cell=rotation_supercell.construct_supercell_from_unitcell(unit_cell_zone, [50,50,500])\n",
    "            supercell_dict = {\"supercell_zoneaxis\": super_cell, \"label\": \"zoneaxis\"}\n",
    "            \n",
    "            filename_mat = 'matlab_data/supercell_' + trim_filename(str(unit_cell.composition)) + str('_') +str(zone[0])+str(zone[1])+str(zone[2]) + '.mat'\n",
    "            filename_prism = 'prismatic_data/supercell_' + trim_filename(str(unit_cell.composition)) + str('_') +str(zone[0])+str(zone[1])+str(zone[2]) + '.xyz'\n",
    "            #comment = 'supercell_' + str(unit_cell.composition)\n",
    "            \n",
    "            print('writing file {} ... \\n'.format(filename_mat))\n",
    "            savemat(filename_mat, supercell_dict)\n",
    "            #write_xyz(supercell, filename)\n",
    "            write_xyz_prism(super_cell[:,3:], super_cell[:,:3], max_dim, dw=None, fname=filename_prism)\n",
    "            print('success {} \\n'.format(filename_mat))\n",
    "            \n",
    "    #except:\n",
    "     #   print('{} is not valid prototype'.format(protodf['Prototype'].iloc[i])) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from scipy.io import savemat\n",
    "import pandas as pd\n",
    "#protodf = pd.read_csv('../data/prototype_count.csv')\n",
    "matdf = pd.read_csv('../data/training_dataset_allCrys.csv')\n",
    "count = matdf['composition'].count()\n",
    "\n",
    "for i in tqdm(range(count)):\n",
    "    try:\n",
    "        mpr = MPRester(\"RyfhcbEkpUtKPxC6\")\n",
    "        unit_cell = mpr.get_structure_by_material_id(matdf['mat_id'].iloc[i])\n",
    "        supercell = construct_supercell(unit_cell, [50,50,500])\n",
    "        supercell_dict = {\"supercell_unrotated\": supercell, \"label\": \"unrotated\"}\n",
    "        \n",
    "        filename_mat = 'matlab_data/supercell_' + remove(str(unit_cell.composition))+ '_unrotated' +'.mat'\n",
    "        filename_prism = 'prismatic_data/supercell_' + remove(str(unit_cell.composition))+ '_unrotated' +'.xyz'\n",
    "        \n",
    "        print('writing file {} ... \\n'.format(filename_mat))\n",
    "        savemat(filename_mat, supercell_dict)\n",
    "        write_xyz_prism(supercell[:,3:], supercell[:,:3], [50,50,500], dw=None, fname=filename_prism)\n",
    "        print('success {} \\n'.format(filename_mat))\n",
    "        \n",
    "        #Rotation zxz high tilt\n",
    "        \n",
    "        theta1 = (180/np.pi)*np.random.uniform(-np.pi, np.pi, 10)\n",
    "        phi    = (180/np.pi)*np.arccos(np.random.uniform(-1,1,10))\n",
    "        theta2 = (180/np.pi)*np.random.uniform(-np.pi, np.pi, 10)\n",
    "\n",
    "        zxzrotation  = np.asarray([theta1, phi, theta2])\n",
    "    \n",
    "        for zxz in tqdm(range(zxzrotation.shape[1])):        \n",
    "            rotation = zxzrotation[:,zxz]\n",
    "            print('Constructing supercell ... \\n')\n",
    "            \n",
    "            unit_cell_rot=rotate_tilt_unitcell(unit_cell, rotation)\n",
    "            super_cell=construct_supercell(unit_cell_rot, [50,50,500])\n",
    "            supercell_dict = {\"supercell_rotated\": super_cell, \"label\": \"rotated\"}\n",
    "            \n",
    "            filename_mat = 'matlab_data/supercell_' + remove(str(unit_cell.composition)) + str('_') +str(rotation[0].astype(np.int32)) + str(rotation[1].astype(np.int32)) +str(rotation[2].astype(np.int32)) + '.mat'\n",
    "            filename_prism = 'prismatic_data/supercell_' + remove(str(unit_cell.composition)) + str('_') +str(rotation[0].astype(np.int32)) + str(rotation[1].astype(np.int32)) +str(rotation[2].astype(np.int32)) + '.xyz'\n",
    "   \n",
    "            #comment = 'supercell_' + str(unit_cell.composition)\n",
    "            \n",
    "            print('writing file {} ... \\n'.format(filename_mat))\n",
    "            savemat(filename_mat, supercell_dict)\n",
    "            #write_xyz(supercell, filename)\n",
    "            write_xyz_prism(super_cell[:,3:], super_cell[:,:3], [50,50,500], dw=None, fname=filename_prism)\n",
    "            print('success {} \\n'.format(filename_mat))\n",
    "            \n",
    "            \n",
    "        #Zoneaxis rotation\n",
    "        zoneaxis = np.array([(1,1,1),(0,0,1),(0,1,1)])\n",
    "        zoneaxis = np.vstack((zoneaxis , np.random.randint(3, size=(7, 3)))) \n",
    "            \n",
    "        for zxz in tqdm(range(zoneaxis.shape[0])):  \n",
    "            zone = zoneaxis[zxz,:]\n",
    "            print('Constructing supercell ... \\n')\n",
    "            \n",
    "            unit_cell_zone=zoneaxis_rotate_tilt_unitcell(unit_cell,zone)\n",
    "            super_cell=construct_supercell(unit_cell_zone, [50,50,500])\n",
    "            supercell_dict = {\"supercell_zoneaxis\": super_cell, \"label\": \"zoneaxis\"}\n",
    "            \n",
    "            filename_mat = 'matlab_data/supercell_' + remove(str(unit_cell.composition)) + str('_') +str(zone[0])+str(zone[1])+str(zone[2]) + '.mat'\n",
    "            filename_prism = 'prismatic_data/supercell_' + remove(str(unit_cell.composition)) + str('_') +str(zone[0])+str(zone[1])+str(zone[2]) + '.xyz'\n",
    "            #comment = 'supercell_' + str(unit_cell.composition)\n",
    "            \n",
    "            print('writing file {} ... \\n'.format(filename_mat))\n",
    "            savemat(filename_mat, supercell_dict)\n",
    "            #write_xyz(supercell, filename)\n",
    "            write_xyz_prism(super_cell[:,3:], super_cell[:,:3], [50,50,500], dw=None, fname=filename_prism)\n",
    "            print('success {} \\n'.format(filename_mat))\n",
    "            \n",
    "    except:\n",
    "        print('{} is not valid prototype'.format(matdf['composition'].iloc[i])) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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