getWyckoffFromStructure.ipynb

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   "source": [
    "## How to Obtain a Prototype Name for an Arbitrary Bulk Structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Some house-keeping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import ase.build\n",
    "import ase.io\n",
    "import requests\n",
    "import json\n",
    "import pprint\n",
    "try:\n",
    "    import io\n",
    "except ImportError:\n",
    "    import StringIO as io\n",
    "WYCKOFF_URL = 'https://api.catalysis-hub.org/apps/bulkEnumerator/get_wyckoff_from_structure'\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generate a Bulk Structure"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First we just create a simple bulk structure, in this case Pd face-centered cubic."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "bulk = ase.build.bulk('Pd', 'fcc')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next, we write the bulk structure into a temporary file in memory in CIF format which is understood by the API. We send the file to the backend. The filename `a.cif` is a dummy name, but necessary to signal that the provided input format is cif. If our file is in a different format, we could state this here as well."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "with io.StringIO() as cif_file:\n",
    "    ase.io.write(cif_file, bulk, format='cif')\n",
    "    response = requests.post(WYCKOFF_URL, files={'file': ('a.cif', cif_file.getvalue())})"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can now extract the requested information about spacegroup, wyckoff sites from the return JSON payload."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'cif': 'data_image0\\n'\n",
      "        '_cell_length_a       3.89001\\n'\n",
      "        '_cell_length_b       3.89001\\n'\n",
      "        '_cell_length_c       3.89001\\n'\n",
      "        '_cell_angle_alpha    90\\n'\n",
      "        '_cell_angle_beta     90\\n'\n",
      "        '_cell_angle_gamma    90\\n'\n",
      "        '\\n'\n",
      "        '_symmetry_space_group_name_H-M    \"P 1\"\\n'\n",
      "        '_symmetry_int_tables_number       1\\n'\n",
      "        '\\n'\n",
      "        'loop_\\n'\n",
      "        '  _symmetry_equiv_pos_as_xyz\\n'\n",
      "        \"  'x, y, z'\\n\"\n",
      "        '\\n'\n",
      "        'loop_\\n'\n",
      "        '  _atom_site_label\\n'\n",
      "        '  _atom_site_occupancy\\n'\n",
      "        '  _atom_site_fract_x\\n'\n",
      "        '  _atom_site_fract_y\\n'\n",
      "        '  _atom_site_fract_z\\n'\n",
      "        '  _atom_site_thermal_displace_type\\n'\n",
      "        '  _atom_site_B_iso_or_equiv\\n'\n",
      "        '  _atom_site_type_symbol\\n'\n",
      "        '  Pd1      1.0000 0.00000  0.00000  0.00000  Biso   1.000  Pd\\n'\n",
      "        '  Pd2      1.0000 0.00000  0.50000  0.50000  Biso   1.000  Pd\\n'\n",
      "        '  Pd3      1.0000 0.50000  0.00000  0.50000  Biso   1.000  Pd\\n'\n",
      "        '  Pd4      1.0000 0.50000  0.50000  0.00000  Biso   1.000  Pd\\n',\n",
      " 'name': \"b'A_a_225'\",\n",
      " 'parameter_values': [{'name': \"b'a'\", 'value': 3.8900065353415534}],\n",
      " 'poscar': 'Auto-generated \\n'\n",
      "           '1.0\\n'\n",
      "           '3.89001\\t0\\t0\\t\\n'\n",
      "           '0\\t3.89001\\t0\\t\\n'\n",
      "           '0\\t0\\t3.89001\\t\\n'\n",
      "           'Pd\\t\\n'\n",
      "           '4\\t\\n'\n",
      "           'Direct\\n'\n",
      "           '0 0 0 \\n'\n",
      "           '0 0.5 0.5 \\n'\n",
      "           '0.5 0 0.5 \\n'\n",
      "           '0.5 0.5 0 \\n',\n",
      " 'runtime': 0.035282135009765625,\n",
      " 'spacegroup': 225,\n",
      " 'species': [\"b'Pd'\"],\n",
      " 'species_permutations': [\"b'Pd'\"],\n",
      " 'wyckoff': [\"b'a'\"],\n",
      " 'wyckoff_list': [{'if_repeatable': 1, 'multiplicity': 192, 'symbol': \"b'l'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 96, 'symbol': \"b'k'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 96, 'symbol': \"b'j'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 48, 'symbol': \"b'i'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 48, 'symbol': \"b'h'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 48, 'symbol': \"b'g'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 32, 'symbol': \"b'f'\"},\n",
      "                  {'if_repeatable': 1, 'multiplicity': 24, 'symbol': \"b'e'\"},\n",
      "                  {'if_repeatable': -1, 'multiplicity': 24, 'symbol': \"b'd'\"},\n",
      "                  {'if_repeatable': -1, 'multiplicity': 8, 'symbol': \"b'c'\"},\n",
      "                  {'if_repeatable': -1, 'multiplicity': 4, 'symbol': \"b'b'\"},\n",
      "                  {'if_repeatable': -1, 'multiplicity': 4, 'symbol': \"b'a'\"}]}\n"
     ]
    }
   ],
   "source": [
    "pprint.pprint(response.json())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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