From b0df23253f331d2f174d04e5748c69e8775050cd Mon Sep 17 00:00:00 2001 From: doublylinkedlist Date: Fri, 8 Sep 2023 02:34:13 -0500 Subject: [PATCH] Update pacmof.py --- mofa/simulation/pacmof.py | 51 +++++++++++++++++++-------------------- 1 file changed, 25 insertions(+), 26 deletions(-) diff --git a/mofa/simulation/pacmof.py b/mofa/simulation/pacmof.py index f1156655..1e6a87f6 100644 --- a/mofa/simulation/pacmof.py +++ b/mofa/simulation/pacmof.py @@ -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 @@ -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) @@ -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.