Finger_Pool2-checkpoint


Finger_Pool Notebooks are the ones used to create the fingerprints (without oxidation states for structures with <50 atoms in the unit cell. This could have been done in one cell using the Multiprocess.Pool.map function however I wanted to track progress using tqdm which is harder to do with Multiprocess module


In [1]:
import fingerprint as fp
struct_all=s_all=fp.read_pickle("struct_all.pickle")


/usr/local/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')

In [2]:
structs_lim_50=[x for x in struct_all if len(x.species)<50]

In [3]:
import tqdm
import numpy as np
import itertools
def phi_getter(i):
    phi_ones=fp.get_phi_scaled(i,obser='ones')
    phi_Z=fp.get_phi_scaled(i,obser='Z')
    phi_Chi=fp.get_phi_scaled(i,obser='Chi')
    return list(itertools.chain(phi_ones,phi_Z,phi_Chi))




lim1=7400
lim2=11100
finger_part=np.array([phi_getter(structs_lim_50[lim1+i]) for i in tqdm.tqdm_notebook(range(lim2-lim1))])

finger_part.shape



Out[3]:
(3700, 300)

In [4]:
np.savetxt("finger_part3.npz",finger_part)

In [ ]: