examples/calculate.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "68158073",
   "metadata": {},
   "source": [
    "# Example notebook for the functions contained in cry_calculate.py"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "56179e55",
   "metadata": {},
   "source": [
    "### Calculate the BSSE"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "032121ab",
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "ename": "ImportError",
     "evalue": "cannot import name 'cry_bsse' from 'CRYSTALpytools.calculate' (/Users/brunocamino/miniconda3/envs/test_env/lib/python3.9/site-packages/CRYSTALpytools/calculate.py)",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m/var/folders/f2/8kc7y9697m59bwltxjd42y300000gn/T/ipykernel_6345/1711536738.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mCRYSTALpytools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcalculate\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mcry_bsse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mImportError\u001b[0m: cannot import name 'cry_bsse' from 'CRYSTALpytools.calculate' (/Users/brunocamino/miniconda3/envs/test_env/lib/python3.9/site-packages/CRYSTALpytools/calculate.py)"
     ]
    }
   ],
   "source": [
    "from CRYSTALpytools.calculate import cry_bsse"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8db78784",
   "metadata": {},
   "source": [
    "### Generate a pymatgen structure (substrate+adsorbate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "633aad3d",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "<frozen importlib._bootstrap>:228: RuntimeWarning: scipy._lib.messagestream.MessageStream size changed, may indicate binary incompatibility. Expected 56 from C header, got 64 from PyObject\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "(29, 29, 29, 29)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import sys\n",
    "sys.path.insert(1, '../')\n",
    "\n",
    "from pymatgen.core import Structure, Lattice\n",
    "from pymatgen.symmetry.analyzer import SpacegroupAnalyzer\n",
    "from pymatgen.core.surface import SlabGenerator\n",
    "\n",
    "#from cry_crystal_io import write_gui \n",
    "import numpy as np\n",
    "\n",
    "substrate = Structure.from_spacegroup(\"Fm-3m\", Lattice.cubic(3.597), [\"Cu\"], [[0, 0, 0]])\n",
    "substrate = SpacegroupAnalyzer(substrate).get_conventional_standard_structure()\n",
    "substrate = SpacegroupAnalyzer(substrate).get_symmetrized_structure()\n",
    "\n",
    "\n",
    "slab = SlabGenerator(substrate, (1,0,0), 5., 10., center_slab=True).get_slab()\n",
    "substrate.atomic_numbers"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "d62a4450",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48.0\n",
      "Rot:\n",
      "[[ 6.1232340e-17  1.0000000e+00  0.0000000e+00]\n",
      " [-1.0000000e+00 -6.1232340e-17  0.0000000e+00]\n",
      " [-2.1890417e-33  1.2246468e-16 -1.0000000e+00]]\n",
      "tau\n",
      "[0. 0. 0.]\n",
      "[[ 6.1232340e-17  1.0000000e+00  0.0000000e+00  0.0000000e+00]\n",
      " [-1.0000000e+00 -6.1232340e-17  0.0000000e+00  0.0000000e+00]\n",
      " [-2.1890417e-33  1.2246468e-16 -1.0000000e+00  0.0000000e+00]\n",
      " [ 0.0000000e+00  0.0000000e+00  0.0000000e+00  1.0000000e+00]]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "array([[ 6.1232340e-17,  1.0000000e+00,  0.0000000e+00],\n",
       "       [-1.0000000e+00, -6.1232340e-17,  0.0000000e+00],\n",
       "       [-2.1890417e-33,  1.2246468e-16, -1.0000000e+00],\n",
       "       [ 0.0000000e+00,  0.0000000e+00,  0.0000000e+00]])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "n_symmops = len(SpacegroupAnalyzer(substrate).get_space_group_operations())\n",
    "print(n_symmops/4)\n",
    "print(SpacegroupAnalyzer(substrate).get_point_group_operations(cartesian=True)[3])\n",
    "print(np.array(SpacegroupAnalyzer(substrate).get_point_group_operations(cartesian=True)[3].as_dict()['matrix']))\n",
    "np.array(SpacegroupAnalyzer(substrate).get_point_group_operations(cartesian=True)[3].as_dict()['matrix'])[0:4,0:3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "a312ce53",
   "metadata": {
    "collapsed": true
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   "outputs": [
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      "\n",
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      "\n",
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      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
      "0.0 1.0 0.0\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
      "0.0 1.0 0.0\n",
      "\n",
      "1.0 0.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
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      "\n",
      "-1.0 -0.0 0.0\n",
      "\n",
      "-0.0 1.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
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      "\n",
      "0.0 -1.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
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      "\n",
      "0.0 1.0 0.0\n",
      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
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      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
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      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-0.0 -1.0 0.0\n",
      "\n",
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      "\n",
      "-1.0 -0.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "1.0 0.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "0.0 -1.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-1.0 -0.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "-0.0 1.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "0.0 -1.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "-1.0 -0.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-0.0 1.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "1.0 0.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-1.0 -0.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "-0.0 1.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "1.0 0.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "0.0 -1.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-0.0 -1.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "1.0 0.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "0.0 1.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "-1.0 0.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-1.0 -0.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "-0.0 -1.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "1.0 0.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "0.0 1.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-0.0 1.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "-1.0 0.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "0.0 -1.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "1.0 0.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "1.0 0.0 0.0\n",
      "\n",
      "0.0 0.0 -1.0\n",
      "\n",
      "0.0 1.0 -0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n",
      "-1.0 -0.0 -0.0\n",
      "\n",
      "-0.0 -0.0 1.0\n",
      "\n",
      "-0.0 -1.0 0.0\n",
      "\n",
      "0.0 0.0 0.0\n",
      "\n"
     ]
    }
   ],
   "source": [
    "for i in range(len(SpacegroupAnalyzer(substrate).get_space_group_operations())):\n",
    "    for symmops in np.array(SpacegroupAnalyzer(substrate).get_point_group_operations(cartesian=True)[i].as_dict()['matrix'])[0:4,0:3]:    \n",
    "        print('{}\\n'.format(' '.join(str(np.around(n,8)) for n in symmops)))"
   ]
  }
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