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Update pacmof.py
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@williamyxl
williamyxl authored Sep 8, 2023
1 parent 5058f3a commit b0df232
Showing 1 changed file with 25 additions and 26 deletions.
51 changes: 25 additions & 26 deletions mofa/simulation/pacmof.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
# forked from pacmof: https://github.com/arung-northwestern/pacmof
import io
import os
import re
import pickle
import warnings
import pandas as pd
Expand Down Expand Up @@ -68,30 +67,30 @@ def find_neighbors_oxynitro(i, atoms):
indices = indices[indices != i] # * Remove self
return indices.tolist(), np.mean(distances[indices])

radius = {'H': 0.31, 'He': 0.28, 'Li': 1.28, 'Be': 0.96,
'B': 0.84, 'C': 0.73, 'N': 0.71, 'O': 0.66,
'F': 0.57, 'Ne': 0.58, 'Na': 1.66, 'Mg': 1.41,
'Al': 1.21, 'Si': 1.11, 'P': 1.07, 'S': 1.05,
'Cl': 1.02, 'Ar': 1.06, 'K': 2.03, 'Ca': 1.76,
'Sc': 1.70, 'Ti': 1.60, 'V': 1.53, 'Cr': 1.39,
'Mn': 1.50, 'Fe': 1.42, 'Co': 1.38, 'Ni': 1.24,
'Cu': 1.32, 'Zn': 1.22, 'Ga': 1.22, 'Ge': 1.20,
'As': 1.19, 'Se': 1.20, 'Br': 1.20, 'Kr': 1.16,
'Rb': 2.20, 'Sr': 1.95, 'Y': 1.90, 'Zr': 1.75,
'Nb': 1.64, 'Mo': 1.54, 'Tc': 1.47, 'Ru': 1.46,
'Rh': 1.42, 'Pd': 1.39, 'Ag': 1.45, 'Cd': 1.44,
'In': 1.42, 'Sn': 1.39, 'Sb': 1.39, 'Te': 1.38,
'I': 1.39, 'Xe': 1.40, 'Cs': 2.44, 'Ba': 2.15,
'La': 2.07, 'Ce': 2.04, 'Pr': 2.03, 'Nd': 2.01,
'Pm': 1.99, 'Sm': 1.98, 'Eu': 1.98, 'Gd': 1.96,
'Tb': 1.94, 'Dy': 1.92, 'Ho': 1.92, 'Er': 1.89,
'Tm': 1.90, 'Yb': 1.87, 'Lu': 1.87, 'Hf': 1.75,
'Ta': 1.70, 'W': 1.62, 'Re': 1.51, 'Os': 1.44,
'Ir': 1.41, 'Pt': 1.36, 'Au': 1.36, 'Hg': 1.32,
'Tl': 1.45, 'Pb': 1.46, 'Bi': 1.48, 'Po': 1.40,
'At': 1.50, 'Rn': 1.50, 'Fr': 2.60, 'Ra': 2.21,
'Ac': 2.15, 'Th': 2.06, 'Pa': 2.00, 'U': 1.96,
'Np': 1.90, 'Pu': 1.87, 'Am': 1.80, 'Cm': 1.69}
# radius = {'H': 0.31, 'He': 0.28, 'Li': 1.28, 'Be': 0.96,
# 'B': 0.84, 'C': 0.73, 'N': 0.71, 'O': 0.66,
# 'F': 0.57, 'Ne': 0.58, 'Na': 1.66, 'Mg': 1.41,
# 'Al': 1.21, 'Si': 1.11, 'P': 1.07, 'S': 1.05,
# 'Cl': 1.02, 'Ar': 1.06, 'K': 2.03, 'Ca': 1.76,
# 'Sc': 1.70, 'Ti': 1.60, 'V': 1.53, 'Cr': 1.39,
# 'Mn': 1.50, 'Fe': 1.42, 'Co': 1.38, 'Ni': 1.24,
# 'Cu': 1.32, 'Zn': 1.22, 'Ga': 1.22, 'Ge': 1.20,
# 'As': 1.19, 'Se': 1.20, 'Br': 1.20, 'Kr': 1.16,
# 'Rb': 2.20, 'Sr': 1.95, 'Y': 1.90, 'Zr': 1.75,
# 'Nb': 1.64, 'Mo': 1.54, 'Tc': 1.47, 'Ru': 1.46,
# 'Rh': 1.42, 'Pd': 1.39, 'Ag': 1.45, 'Cd': 1.44,
# 'In': 1.42, 'Sn': 1.39, 'Sb': 1.39, 'Te': 1.38,
# 'I': 1.39, 'Xe': 1.40, 'Cs': 2.44, 'Ba': 2.15,
# 'La': 2.07, 'Ce': 2.04, 'Pr': 2.03, 'Nd': 2.01,
# 'Pm': 1.99, 'Sm': 1.98, 'Eu': 1.98, 'Gd': 1.96,
# 'Tb': 1.94, 'Dy': 1.92, 'Ho': 1.92, 'Er': 1.89,
# 'Tm': 1.90, 'Yb': 1.87, 'Lu': 1.87, 'Hf': 1.75,
# 'Ta': 1.70, 'W': 1.62, 'Re': 1.51, 'Os': 1.44,
# 'Ir': 1.41, 'Pt': 1.36, 'Au': 1.36, 'Hg': 1.32,
# 'Tl': 1.45, 'Pb': 1.46, 'Bi': 1.48, 'Po': 1.40,
# 'At': 1.50, 'Rn': 1.50, 'Fr': 2.60, 'Ra': 2.21,
# 'Ac': 2.15, 'Th': 2.06, 'Pa': 2.00, 'U': 1.96,
# 'Np': 1.90, 'Pu': 1.87, 'Am': 1.80, 'Cm': 1.69}
# electronegativity in pauling scale from CRC Handbook of Chemistry and
# Physics (For elements not having pauling electronegativity, Allred
# Rochow electronegativity is taken)
Expand Down Expand Up @@ -175,7 +174,7 @@ def find_neighbors_oxynitro(i, atoms):
# neighbor_list.append(neigh)
# avg_neighbor_dist.append(ave_neigh)
neighbor_list, avg_neighbor_dist = zip(
*Parallel(n_jobs=1)(delayed(func_dict[flags[i]])(i, data) for i in range(number_of_atoms)))
*[func_dict[flags[i]](i, data) for i in range(number_of_atoms)])
neighbor_list, avg_neighbor_dist = list(
neighbor_list), list(avg_neighbor_dist)
# * Find all the atoms with no neighbors, hopefully there aren't any such atoms.
Expand Down

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