Nearest Neighbour


I am not able to fetch the structure of all “Mn” based elements via their mp-id’s
#Code- Python3.6 script
import pandas as pd
import matplotlib.pyplot as plt
import csv
import matplotlib.ticker as ticker
import numpy as np
from pymatgen.analysis.local_env import CrystalNN
from pymatgen import MPRester
m = MPRester(api-key)
df = pd.read_csv(‘f.csv’)
data_id = m.query( criteria={“elements”: {"$all": [“Mn”]}}, properties=[“task_ids”])
c = 0
for i in range(len(data_id)):
id = data_id[i][“task_ids”][0]

struct = m.get_structure_by_material_id(id)
c = c+1
for k, v in nn.get_cn_dict(struct,i).items():
	if k == 'Mn':
		with open('last.csv',a) as f:

Code is able to run a few of the mp-id’s and for others I am getting the following error:
Traceback (most recent call last):
File “”, line 24, in
struct = m.get_structure_by_material_id(id)
File “/home/username/.local/lib/python3.7/site-packages/pymatgen/ext/”, line 542, in get_structure_by_material_id
return data[0][prop]
IndexError: list index out of range
Anyone having any idea about the error or have any alternate to fetch structure (or first nearest neighbor) of elements, Plz help me !!!


You’re using the wrong field to search for materials. You want to reference task_id not task_ids. Also please don’t hammer the REST API this way. Use the query to grab all the structures you want and then process them.

data = m.query( criteria={“elements”: {"$all": [“Mn”]}}, properties=[“task_id”,"structure"])
for d in data:
	struct = d["structure"]
1 Like

Thanks for the help and suggestions.