data_process.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"name":"data_process.ipynb","provenance":[],"collapsed_sections":[],"authorship_tag":"ABX9TyOjUwR7sCQ4l2zdu6KnPNSs"},"kernelspec":{"name":"python3","display_name":"Python 3"}},"cells":[{"cell_type":"code","metadata":{"id":"rFhTJtliftzk"},"source":["from google.colab import drive\r\n","drive.mount('/content/drive')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"4Wwb9c4wf2R3"},"source":["cd drive/"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"zejDIS8Wf49h"},"source":["cd MyDrive/"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"psGtkU98f7p_"},"source":["cd cgcnn_hoip/"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"0DySFceBf9nh"},"source":["!pip3 install pymatgen"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"a7WB-vSLgEU6"},"source":["sample_dataset = CIFData('sample-regression')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"C6xNpz_JgFt0"},"source":["from pymatgen.ext.matproj import MPRester\r\n","from pymatgen.ext.matproj import MPRestError\r\n","# input API key from Materials Project\r\n","mp_query_obj = MPRester('')"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"45mLmdYvgNbA"},"source":["csv_read_obj = open('material-data/mp-ids-27430.csv')\r\n","for id in csv_read_obj:\r\n","    print(id)\r\n","    break"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"dcdKcsf9gOAD"},"source":["id = 'mp-754118'\r\n","temp_dict = {\r\n","    'material_id':str(id)\r\n","}\r\n","# results=mp_query_obj.query({\"material_id\":'mp-754118'}, properties=[\"cif\"])\r\n","results = mp_query_obj.query(temp_dict, properties=['cif', 'band_gap', 'diel'])\r\n","# print(results[0]['cif'])\r\n","print(results[0]['diel'])"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"xcN7W4nCgPaw"},"source":["csv_read_obj = open('ABX3.csv')\r\n","for m, material in enumerate(csv_read_obj):\r\n","    if m > 0:\r\n","        print(material.strip().split(',')[0].strip(\"\\\"\"))\r\n","        break"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"gaNo7YCcgR5W"},"source":["id = 'mp-1025377'\r\n","temp_dict = {\r\n","    'material_id':str(id)\r\n","}\r\n","# results=mp_query_obj.query({\"material_id\":'mp-754118'}, properties=[\"cif\"])\r\n","results = mp_query_obj.query(temp_dict, properties=['cif', 'band_gap', 'diel'])\r\n","print(results[0]['diel']['n'])\r\n","# print(results)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"bQJvCg91gSjI"},"source":["import os\r\n","from os.path import join\r\n","from pymatgen.io.cif import CifParser\r\n","from pymatgen import Structure\r\n","\r\n","def find_band_gap(cif_text):\r\n","    for line in cif_text:\r\n","        try:\r\n","            if line[0] == '#':\r\n","                # print(line.split(' '))\r\n","                temp = line.split(' ')\r\n","                if temp[1] == 'Bandgap,' and temp[2] == 'GGA':\r\n","                    return temp[-1]\r\n","        except IndexError:\r\n","            pass\r\n","\r\n","def find_refractive_index(cif_text):\r\n","    for line in cif_text:\r\n","        try:\r\n","            if line[0] == '#':\r\n","                temp = line.split(' ')\r\n","                if temp[1] == 'Refractive':\r\n","                    return temp[-1]\r\n","        except IndexError:\r\n","            pass\r\n","\r\n","all_cifs = os.listdir('cif_merge')\r\n","hoip_band_gap = open('hoip_band_gap.csv', 'w+')\r\n","hoip_band_gap.write('id,BandGap\\n')\r\n","for fptr in all_cifs:\r\n","    # stuct = Structure.from_file(join('cif_merge', fptr))\r\n","    # temp_parser = CifParser(join('cif_merge', fptr))\r\n","    # struct = temp_parser.get_structures()[0]\r\n","    # print(struct.)\r\n","    # break\r\n","    with open(join('cif_merge', fptr)) as fobj:\r\n","        temp = fobj.read().split('\\n')\r\n","        prop = find_band_gap(temp)\r\n","        # print(fptr.split('.')[0])\r\n","        line = str(fptr.split('.')[0]) + ',' + prop + '\\n'\r\n","        # print(line)\r\n","        hoip_band_gap.write(line)\r\n","        fobj.close()\r\n","    # break\r\n","hoip_band_gap.close()"],"execution_count":null,"outputs":[]}]}