In [1]:
import sys, os, re, time
import numpy as np
import platform
import notebook
import ase
from ASE_db_tools import *
import matplotlib.pyplot as plt
from IPython.display import Markdown, display
from tabulate import tabulate
%matplotlib inline
print("Date : " + time.strftime("%d/%m/%Y %H:%M"))
print("Python : " + platform.python_version())
print("OS : " + str(platform.dist()))
print("Notebook : " + notebook.__version__)
print("ASE : " + ase.__version__)
Date : 31/03/2018 06:04
Python : 3.5.2
OS : ('Ubuntu', '16.04', 'xenial')
Notebook : 5.4.1
ASE : 3.16.0
Select database (dbname), index (row_id) and supply core_charges¶
In [2]:
# Database name
dbname= "IJQC.116.db"
# Index in the database
row_id= 1
# Core charges
core_charges= {"H": 1., "O": 6., "W": -2., "Al": 3., "N": 5.} # Al(NO3)3.9H2O
#core_charges= {"H": 1., "O": 6., "W": -2., "Mg": 10., "S": 6.} # MgSO4.11H2O, MgSO4.7H2O
#core_charges= {"H": 1., "O": 6., "W": -2., "Na": 1., "C": 4.} # Na2CO3.10H2O
structure= db_read_row(dbname,row_id)
display(Markdown("# " + structure.row.name ))
Al(NO3)3.9H2O¶
In [3]:
#=============================================================
prop_H2O_wannier_dipoles(structure,core_charges)
Origin at atom idx: 88 core_charge: 6.0 ============================================ idx: 213 Chg: -2.0 dist: 0.478127 idx: 286 Chg: -2.0 dist: 0.293650 idx: 5 Chg: 1.0 dist: 1.000710 idx: 302 Chg: -2.0 dist: 0.479148 idx: 337 Chg: -2.0 dist: 0.359560 idx: 4 Chg: 1.0 dist: 0.999393 ============================================ Total Dipole= 3.9117 [Debye] Origin at atom idx: 89 core_charge: 6.0 ============================================ idx: 216 Chg: -2.0 dist: 0.476841 idx: 321 Chg: -2.0 dist: 0.346220 idx: 362 Chg: -2.0 dist: 0.473380 idx: 385 Chg: -2.0 dist: 0.309970 idx: 6 Chg: 1.0 dist: 1.008513 idx: 7 Chg: 1.0 dist: 1.005884 ============================================ Total Dipole= 4.2434 [Debye] Origin at atom idx: 90 core_charge: 6.0 ============================================ idx: 188 Chg: -2.0 dist: 0.481985 idx: 206 Chg: -2.0 dist: 0.471671 idx: 336 Chg: -2.0 dist: 0.292534 idx: 404 Chg: -2.0 dist: 0.363426 idx: 8 Chg: 1.0 dist: 0.994536 idx: 9 Chg: 1.0 dist: 1.014367 ============================================ Total Dipole= 3.9884 [Debye] Origin at atom idx: 91 core_charge: 6.0 ============================================ idx: 349 Chg: -2.0 dist: 0.475838 idx: 378 Chg: -2.0 dist: 0.371750 idx: 392 Chg: -2.0 dist: 0.286843 idx: 428 Chg: -2.0 dist: 0.478127 idx: 10 Chg: 1.0 dist: 1.002876 idx: 11 Chg: 1.0 dist: 1.006199 ============================================ Total Dipole= 4.0216 [Debye] Origin at atom idx: 92 core_charge: 6.0 ============================================ idx: 225 Chg: -2.0 dist: 0.470393 idx: 257 Chg: -2.0 dist: 0.298129 idx: 338 Chg: -2.0 dist: 0.357852 idx: 406 Chg: -2.0 dist: 0.475414 idx: 12 Chg: 1.0 dist: 1.013864 idx: 13 Chg: 1.0 dist: 1.002436 ============================================ Total Dipole= 4.2681 [Debye] Origin at atom idx: 93 core_charge: 6.0 ============================================ idx: 318 Chg: -2.0 dist: 0.473333 idx: 330 Chg: -2.0 dist: 0.289624 idx: 394 Chg: -2.0 dist: 0.482156 idx: 414 Chg: -2.0 dist: 0.372823 idx: 14 Chg: 1.0 dist: 0.994925 idx: 15 Chg: 1.0 dist: 1.010736 ============================================ Total Dipole= 4.0674 [Debye] Origin at atom idx: 94 core_charge: 6.0 ============================================ idx: 228 Chg: -2.0 dist: 0.351342 idx: 289 Chg: -2.0 dist: 0.484676 idx: 347 Chg: -2.0 dist: 0.489517 idx: 398 Chg: -2.0 dist: 0.348581 idx: 17 Chg: 1.0 dist: 0.993212 idx: 16 Chg: 1.0 dist: 1.002251 ============================================ Total Dipole= 3.5975 [Debye] Origin at atom idx: 95 core_charge: 6.0 ============================================ idx: 348 Chg: -2.0 dist: 0.347244 idx: 388 Chg: -2.0 dist: 0.351838 idx: 396 Chg: -2.0 dist: 0.492783 idx: 424 Chg: -2.0 dist: 0.483724 idx: 18 Chg: 1.0 dist: 1.000119 idx: 19 Chg: 1.0 dist: 0.989474 ============================================ Total Dipole= 3.5060 [Debye] Origin at atom idx: 96 core_charge: 6.0 ============================================ idx: 272 Chg: -2.0 dist: 0.497303 idx: 344 Chg: -2.0 dist: 0.331875 idx: 377 Chg: -2.0 dist: 0.491582 idx: 386 Chg: -2.0 dist: 0.342630 idx: 20 Chg: 1.0 dist: 0.979581 idx: 21 Chg: 1.0 dist: 0.991504 ============================================ Total Dipole= 3.2690 [Debye] Origin at atom idx: 106 core_charge: 6.0 ============================================ idx: 204 Chg: -2.0 dist: 0.359563 idx: 229 Chg: -2.0 dist: 0.478132 idx: 335 Chg: -2.0 dist: 0.293643 idx: 352 Chg: -2.0 dist: 0.479147 idx: 22 Chg: 1.0 dist: 0.999399 idx: 23 Chg: 1.0 dist: 1.000710 ============================================ Total Dipole= 3.9116 [Debye] Origin at atom idx: 107 core_charge: 6.0 ============================================ idx: 189 Chg: -2.0 dist: 0.309963 idx: 223 Chg: -2.0 dist: 0.473382 idx: 230 Chg: -2.0 dist: 0.476841 idx: 340 Chg: -2.0 dist: 0.346224 idx: 24 Chg: 1.0 dist: 1.008516 idx: 25 Chg: 1.0 dist: 1.005876 ============================================ Total Dipole= 4.2434 [Debye] Origin at atom idx: 108 core_charge: 6.0 ============================================ idx: 282 Chg: -2.0 dist: 0.471667 idx: 304 Chg: -2.0 dist: 0.481988 idx: 307 Chg: -2.0 dist: 0.363427 idx: 423 Chg: -2.0 dist: 0.292535 idx: 26 Chg: 1.0 dist: 0.994548 idx: 27 Chg: 1.0 dist: 1.014367 ============================================ Total Dipole= 3.9885 [Debye] Origin at atom idx: 109 core_charge: 6.0 ============================================ idx: 409 Chg: -2.0 dist: 0.478128 idx: 434 Chg: -2.0 dist: 0.286838 idx: 28 Chg: 1.0 dist: 1.002876 idx: 29 Chg: 1.0 dist: 1.006199 idx: 334 Chg: -2.0 dist: 0.371753 idx: 442 Chg: -2.0 dist: 0.475837 ============================================ Total Dipole= 4.0216 [Debye] Origin at atom idx: 110 core_charge: 6.0 ============================================ idx: 200 Chg: -2.0 dist: 0.475417 idx: 278 Chg: -2.0 dist: 0.357852 idx: 315 Chg: -2.0 dist: 0.298128 idx: 441 Chg: -2.0 dist: 0.470391 idx: 30 Chg: 1.0 dist: 1.013864 idx: 31 Chg: 1.0 dist: 1.002440 ============================================ Total Dipole= 4.2680 [Debye] Origin at atom idx: 111 core_charge: 6.0 ============================================ idx: 221 Chg: -2.0 dist: 0.482157 idx: 294 Chg: -2.0 dist: 0.473337 idx: 312 Chg: -2.0 dist: 0.289628 idx: 327 Chg: -2.0 dist: 0.372815 idx: 32 Chg: 1.0 dist: 0.994925 idx: 33 Chg: 1.0 dist: 1.010734 ============================================ Total Dipole= 4.0672 [Debye] Origin at atom idx: 112 core_charge: 6.0 ============================================ idx: 222 Chg: -2.0 dist: 0.484679 idx: 231 Chg: -2.0 dist: 0.351337 idx: 296 Chg: -2.0 dist: 0.348584 idx: 351 Chg: -2.0 dist: 0.489516 idx: 34 Chg: 1.0 dist: 1.002256 idx: 35 Chg: 1.0 dist: 0.993213 ============================================ Total Dipole= 3.5974 [Debye] Origin at atom idx: 113 core_charge: 6.0 ============================================ idx: 203 Chg: -2.0 dist: 0.492789 idx: 310 Chg: -2.0 dist: 0.483725 idx: 322 Chg: -2.0 dist: 0.347240 idx: 384 Chg: -2.0 dist: 0.351835 idx: 36 Chg: 1.0 dist: 1.000119 idx: 37 Chg: 1.0 dist: 0.989474 ============================================ Total Dipole= 3.5058 [Debye] Origin at atom idx: 114 core_charge: 6.0 ============================================ idx: 214 Chg: -2.0 dist: 0.491577 idx: 305 Chg: -2.0 dist: 0.331875 idx: 346 Chg: -2.0 dist: 0.342633 idx: 373 Chg: -2.0 dist: 0.497305 idx: 38 Chg: 1.0 dist: 0.979581 idx: 39 Chg: 1.0 dist: 0.991498 ============================================ Total Dipole= 3.2690 [Debye] Origin at atom idx: 124 core_charge: 6.0 ============================================ idx: 195 Chg: -2.0 dist: 0.293644 idx: 205 Chg: -2.0 dist: 0.478130 idx: 40 Chg: 1.0 dist: 0.999399 idx: 41 Chg: 1.0 dist: 1.000712 idx: 285 Chg: -2.0 dist: 0.479149 idx: 415 Chg: -2.0 dist: 0.359562 ============================================ Total Dipole= 3.9117 [Debye] Origin at atom idx: 125 core_charge: 6.0 ============================================ idx: 187 Chg: -2.0 dist: 0.476837 idx: 300 Chg: -2.0 dist: 0.309967 idx: 325 Chg: -2.0 dist: 0.346225 idx: 339 Chg: -2.0 dist: 0.473382 idx: 42 Chg: 1.0 dist: 1.008516 idx: 43 Chg: 1.0 dist: 1.005876 ============================================ Total Dipole= 4.2435 [Debye] Origin at atom idx: 126 core_charge: 6.0 ============================================ idx: 220 Chg: -2.0 dist: 0.471672 idx: 277 Chg: -2.0 dist: 0.481988 idx: 292 Chg: -2.0 dist: 0.363426 idx: 374 Chg: -2.0 dist: 0.292530 idx: 44 Chg: 1.0 dist: 0.994545 idx: 45 Chg: 1.0 dist: 1.014367 ============================================ Total Dipole= 3.9883 [Debye] Origin at atom idx: 127 core_charge: 6.0 ============================================ idx: 190 Chg: -2.0 dist: 0.478130 idx: 219 Chg: -2.0 dist: 0.475839 idx: 332 Chg: -2.0 dist: 0.371750 idx: 361 Chg: -2.0 dist: 0.286838 idx: 46 Chg: 1.0 dist: 1.002876 idx: 47 Chg: 1.0 dist: 1.006199 ============================================ Total Dipole= 4.0215 [Debye] Origin at atom idx: 128 core_charge: 6.0 ============================================ idx: 226 Chg: -2.0 dist: 0.475408 idx: 298 Chg: -2.0 dist: 0.470394 idx: 343 Chg: -2.0 dist: 0.298130 idx: 397 Chg: -2.0 dist: 0.357856 idx: 48 Chg: 1.0 dist: 1.013866 idx: 49 Chg: 1.0 dist: 1.002431 ============================================ Total Dipole= 4.2681 [Debye] Origin at atom idx: 129 core_charge: 6.0 ============================================ idx: 299 Chg: -2.0 dist: 0.482157 idx: 323 Chg: -2.0 dist: 0.372819 idx: 364 Chg: -2.0 dist: 0.473333 idx: 370 Chg: -2.0 dist: 0.289627 idx: 50 Chg: 1.0 dist: 0.994925 idx: 51 Chg: 1.0 dist: 1.010734 ============================================ Total Dipole= 4.0673 [Debye] Origin at atom idx: 130 core_charge: 6.0 ============================================ idx: 291 Chg: -2.0 dist: 0.489513 idx: 350 Chg: -2.0 dist: 0.484678 idx: 371 Chg: -2.0 dist: 0.348583 idx: 421 Chg: -2.0 dist: 0.351341 idx: 52 Chg: 1.0 dist: 1.002256 idx: 53 Chg: 1.0 dist: 0.993212 ============================================ Total Dipole= 3.5975 [Debye] Origin at atom idx: 131 core_charge: 6.0 ============================================ idx: 163 Chg: -2.0 dist: 0.351837 idx: 202 Chg: -2.0 dist: 0.483728 idx: 319 Chg: -2.0 dist: 0.492780 idx: 342 Chg: -2.0 dist: 0.347244 idx: 54 Chg: 1.0 dist: 1.000119 idx: 55 Chg: 1.0 dist: 0.989465 ============================================ Total Dipole= 3.5060 [Debye] Origin at atom idx: 132 core_charge: 6.0 ============================================ idx: 212 Chg: -2.0 dist: 0.491578 idx: 248 Chg: -2.0 dist: 0.497302 idx: 268 Chg: -2.0 dist: 0.342633 idx: 403 Chg: -2.0 dist: 0.331877 idx: 56 Chg: 1.0 dist: 0.979581 idx: 57 Chg: 1.0 dist: 0.991504 ============================================ Total Dipole= 3.2691 [Debye] Origin at atom idx: 142 core_charge: 6.0 ============================================ idx: 207 Chg: -2.0 dist: 0.479151 idx: 246 Chg: -2.0 dist: 0.478130 idx: 329 Chg: -2.0 dist: 0.359556 idx: 345 Chg: -2.0 dist: 0.293650 idx: 58 Chg: 1.0 dist: 0.999393 idx: 59 Chg: 1.0 dist: 1.000715 ============================================ Total Dipole= 3.9116 [Debye] Origin at atom idx: 143 core_charge: 6.0 ============================================ idx: 201 Chg: -2.0 dist: 0.473383 idx: 274 Chg: -2.0 dist: 0.309970 idx: 401 Chg: -2.0 dist: 0.476833 idx: 419 Chg: -2.0 dist: 0.346224 idx: 60 Chg: 1.0 dist: 1.008516 idx: 61 Chg: 1.0 dist: 1.005870 ============================================ Total Dipole= 4.2435 [Debye] Origin at atom idx: 144 core_charge: 6.0 ============================================ idx: 301 Chg: -2.0 dist: 0.481984 idx: 320 Chg: -2.0 dist: 0.363428 idx: 333 Chg: -2.0 dist: 0.292537 idx: 413 Chg: -2.0 dist: 0.471669 idx: 62 Chg: 1.0 dist: 0.994536 idx: 63 Chg: 1.0 dist: 1.014368 ============================================ Total Dipole= 3.9885 [Debye] Origin at atom idx: 145 core_charge: 6.0 ============================================ idx: 217 Chg: -2.0 dist: 0.286832 idx: 358 Chg: -2.0 dist: 0.478132 idx: 65 Chg: 1.0 dist: 1.006202 idx: 331 Chg: -2.0 dist: 0.371754 idx: 420 Chg: -2.0 dist: 0.475839 idx: 64 Chg: 1.0 dist: 1.002876 ============================================ Total Dipole= 4.0215 [Debye] Origin at atom idx: 146 core_charge: 6.0 ============================================ idx: 209 Chg: -2.0 dist: 0.475410 idx: 224 Chg: -2.0 dist: 0.298125 idx: 252 Chg: -2.0 dist: 0.470393 idx: 326 Chg: -2.0 dist: 0.357859 idx: 66 Chg: 1.0 dist: 1.013864 idx: 67 Chg: 1.0 dist: 1.002427 ============================================ Total Dipole= 4.2681 [Debye] Origin at atom idx: 147 core_charge: 6.0 ============================================ idx: 308 Chg: -2.0 dist: 0.482157 idx: 360 Chg: -2.0 dist: 0.289627 idx: 379 Chg: -2.0 dist: 0.473329 idx: 380 Chg: -2.0 dist: 0.372823 idx: 68 Chg: 1.0 dist: 0.994925 idx: 69 Chg: 1.0 dist: 1.010726 ============================================ Total Dipole= 4.0674 [Debye] Origin at atom idx: 148 core_charge: 6.0 ============================================ idx: 208 Chg: -2.0 dist: 0.484673 idx: 287 Chg: -2.0 dist: 0.351344 idx: 324 Chg: -2.0 dist: 0.348580 idx: 425 Chg: -2.0 dist: 0.489518 idx: 71 Chg: 1.0 dist: 0.993212 idx: 70 Chg: 1.0 dist: 1.002251 ============================================ Total Dipole= 3.5975 [Debye] Origin at atom idx: 149 core_charge: 6.0 ============================================ idx: 199 Chg: -2.0 dist: 0.492785 idx: 232 Chg: -2.0 dist: 0.483730 idx: 309 Chg: -2.0 dist: 0.351837 idx: 341 Chg: -2.0 dist: 0.347239 idx: 72 Chg: 1.0 dist: 1.000119 idx: 73 Chg: 1.0 dist: 0.989479 ============================================ Total Dipole= 3.5058 [Debye] Origin at atom idx: 150 core_charge: 6.0 ============================================ idx: 211 Chg: -2.0 dist: 0.497308 idx: 270 Chg: -2.0 dist: 0.491579 idx: 353 Chg: -2.0 dist: 0.331870 idx: 376 Chg: -2.0 dist: 0.342634 idx: 74 Chg: 1.0 dist: 0.979581 idx: 75 Chg: 1.0 dist: 0.991498 ============================================ Total Dipole= 3.2689 [Debye]
Out[3]:
{88: [array([-3.02923381, 2.46655442, 0.20299813])],
89: [array([-1.69659655, -2.07146666, -3.29199891])],
90: [array([-2.49556635, -2.58701062, 1.72831028])],
91: [array([-3.3802184 , 2.16315416, 0.26112024])],
92: [array([-2.33286895, -1.53507373, -3.22764346])],
93: [array([-1.26388107, -2.5276067 , 2.92529232])],
94: [array([ 1.2275097 , -2.06969332, -2.67421386])],
95: [array([ 0.51025006, -2.67201754, -2.21175154])],
96: [array([3.17010761, 0.38071436, 0.70112757])],
106: [array([ 3.0290667 , 2.46667364, -0.20300877])],
107: [array([ 1.69664852, -2.07129769, 3.29198363])],
108: [array([ 2.4955432 , -2.58712983, -1.72828723])],
109: [array([ 3.38012671, 2.16332132, -0.26110172])],
110: [array([ 2.33279748, -1.53495067, 3.22766633])],
111: [array([ 1.26369288, -2.52738941, -2.9253075 ])],
112: [array([-1.22758098, -2.06957238, 2.67423692])],
113: [array([-0.51010212, -2.67180005, 2.21173685])],
114: [array([-3.17017898, 0.38087709, -0.70110461])],
124: [array([ 3.02917626, -2.46655644, -0.20299409])],
125: [array([1.69673152, 2.07141671, 3.29200256])],
126: [array([ 2.49546039, 2.58696067, -1.72830625])],
127: [array([ 3.38006489, -2.16320383, -0.26111659])],
128: [array([2.33300325, 1.53506998, 3.2276475 ])],
129: [array([ 1.26377549, 2.52755675, -2.9252879 ])],
130: [array([-1.22761527, 2.06964356, 2.67421799])],
131: [array([-0.51035563, 2.6719671 , 2.21175596])],
132: [array([-3.17026122, -0.38076432, -0.70112344])],
142: [array([-3.02917199, -2.46643521, 0.20301262])],
143: [array([-1.69680222, 2.07153593, -3.2919795 ])],
144: [array([-2.49560103, 2.58712791, 1.72829107])],
145: [array([-3.37994399, -2.16332257, 0.26110537])],
146: [array([-2.33290325, 1.5351892 , -3.22766229])],
147: [array([-1.26379874, 2.52767596, 2.92531125])],
148: [array([ 1.22742727, 2.06981071, -2.67423336])],
149: [array([ 0.51033277, 2.67179793, -2.211733 ])],
150: [array([ 3.17002528, -0.38092694, 0.70110816])]}
In [4]:
#=============================================================
prop_H2O_bader_dipoles(structure,core_charges)
Origin at atom idx: 88 core_charge: 6.0 ========================================== idx: 164 Chg: -0.3572 dist: 0.999387 idx: 248 Chg: -7.3174 dist: 0.000008 idx: 5 Chg: 1.0000 dist: 1.000710 idx: 165 Chg: -0.3630 dist: 1.000718 idx: 4 Chg: 1.0000 dist: 0.999393 ========================================== Total Dipole= 2.8789 [Debye] Total Charge= -0.0375 [e] Origin at atom idx: 89 core_charge: 6.0 ========================================== idx: 166 Chg: -0.3560 dist: 1.008518 idx: 167 Chg: -0.3638 dist: 1.005874 idx: 249 Chg: -7.3243 dist: 0.000005 idx: 6 Chg: 1.0000 dist: 1.008513 idx: 7 Chg: 1.0000 dist: 1.005884 ========================================== Total Dipole= 3.1690 [Debye] Total Charge= -0.0442 [e] Origin at atom idx: 90 core_charge: 6.0 ========================================== idx: 168 Chg: -0.3648 dist: 0.994530 idx: 169 Chg: -0.3543 dist: 1.014369 idx: 250 Chg: -7.3190 dist: 0.000015 idx: 8 Chg: 1.0000 dist: 0.994536 idx: 9 Chg: 1.0000 dist: 1.014367 ========================================== Total Dipole= 2.8990 [Debye] Total Charge= -0.0382 [e] Origin at atom idx: 91 core_charge: 6.0 ========================================== idx: 170 Chg: -0.3630 dist: 1.002870 idx: 171 Chg: -0.3597 dist: 1.006198 idx: 251 Chg: -7.3219 dist: 0.000002 idx: 10 Chg: 1.0000 dist: 1.002876 idx: 11 Chg: 1.0000 dist: 1.006199 ========================================== Total Dipole= 2.9338 [Debye] Total Charge= -0.0447 [e] Origin at atom idx: 92 core_charge: 6.0 ========================================== idx: 172 Chg: -0.3583 dist: 1.013867 idx: 173 Chg: -0.3606 dist: 1.002434 idx: 252 Chg: -7.3296 dist: 0.000011 idx: 12 Chg: 1.0000 dist: 1.013864 idx: 13 Chg: 1.0000 dist: 1.002436 ========================================== Total Dipole= 3.1772 [Debye] Total Charge= -0.0485 [e] Origin at atom idx: 93 core_charge: 6.0 ========================================== idx: 174 Chg: -0.3654 dist: 0.994927 idx: 175 Chg: -0.3560 dist: 1.010735 idx: 253 Chg: -7.3122 dist: 0.000011 idx: 14 Chg: 1.0000 dist: 0.994925 idx: 15 Chg: 1.0000 dist: 1.010736 ========================================== Total Dipole= 3.0269 [Debye] Total Charge= -0.0336 [e] Origin at atom idx: 94 core_charge: 6.0 ========================================== idx: 176 Chg: -0.3778 dist: 1.002244 idx: 254 Chg: -7.2094 dist: 0.000013 idx: 17 Chg: 1.0000 dist: 0.993212 idx: 177 Chg: -0.3809 dist: 0.993214 idx: 16 Chg: 1.0000 dist: 1.002251 ========================================== Total Dipole= 2.0557 [Debye] Total Charge= 0.0320 [e] Origin at atom idx: 95 core_charge: 6.0 ========================================== idx: 178 Chg: -0.3733 dist: 1.000118 idx: 179 Chg: -0.3846 dist: 0.989477 idx: 255 Chg: -7.2021 dist: 0.000010 idx: 18 Chg: 1.0000 dist: 1.000119 idx: 19 Chg: 1.0000 dist: 0.989474 ========================================== Total Dipole= 1.9481 [Debye] Total Charge= 0.0401 [e] Origin at atom idx: 96 core_charge: 6.0 ========================================== idx: 180 Chg: -0.3904 dist: 0.979579 idx: 181 Chg: -0.3889 dist: 0.991506 idx: 256 Chg: -7.1870 dist: 0.000002 idx: 20 Chg: 1.0000 dist: 0.979581 idx: 21 Chg: 1.0000 dist: 0.991504 ========================================== Total Dipole= 1.9396 [Debye] Total Charge= 0.0336 [e] Origin at atom idx: 106 core_charge: 6.0 ========================================== idx: 182 Chg: -0.3572 dist: 0.999399 idx: 183 Chg: -0.3630 dist: 1.000717 idx: 266 Chg: -7.3174 dist: 0.000007 idx: 22 Chg: 1.0000 dist: 0.999399 idx: 23 Chg: 1.0000 dist: 1.000710 ========================================== Total Dipole= 2.8786 [Debye] Total Charge= -0.0375 [e] Origin at atom idx: 107 core_charge: 6.0 ========================================== idx: 184 Chg: -0.3560 dist: 1.008524 idx: 185 Chg: -0.3638 dist: 1.005879 idx: 267 Chg: -7.3243 dist: 0.000006 idx: 24 Chg: 1.0000 dist: 1.008516 idx: 25 Chg: 1.0000 dist: 1.005876 ========================================== Total Dipole= 3.1686 [Debye] Total Charge= -0.0442 [e] Origin at atom idx: 108 core_charge: 6.0 ========================================== idx: 186 Chg: -0.3648 dist: 0.994537 idx: 187 Chg: -0.3543 dist: 1.014365 idx: 268 Chg: -7.3190 dist: 0.000009 idx: 26 Chg: 1.0000 dist: 0.994548 idx: 27 Chg: 1.0000 dist: 1.014367 ========================================== Total Dipole= 2.8989 [Debye] Total Charge= -0.0382 [e] Origin at atom idx: 109 core_charge: 6.0 ========================================== idx: 188 Chg: -0.3630 dist: 1.002877 idx: 269 Chg: -7.3219 dist: 0.000007 idx: 28 Chg: 1.0000 dist: 1.002876 idx: 29 Chg: 1.0000 dist: 1.006199 idx: 189 Chg: -0.3597 dist: 1.006194 ========================================== Total Dipole= 2.9336 [Debye] Total Charge= -0.0447 [e] Origin at atom idx: 110 core_charge: 6.0 ========================================== idx: 190 Chg: -0.3583 dist: 1.013867 idx: 191 Chg: -0.3606 dist: 1.002443 idx: 270 Chg: -7.3296 dist: 0.000009 idx: 30 Chg: 1.0000 dist: 1.013864 idx: 31 Chg: 1.0000 dist: 1.002440 ========================================== Total Dipole= 3.1769 [Debye] Total Charge= -0.0485 [e] Origin at atom idx: 111 core_charge: 6.0 ========================================== idx: 192 Chg: -0.3654 dist: 0.994924 idx: 193 Chg: -0.3560 dist: 1.010739 idx: 271 Chg: -7.3122 dist: 0.000012 idx: 32 Chg: 1.0000 dist: 0.994925 idx: 33 Chg: 1.0000 dist: 1.010734 ========================================== Total Dipole= 3.0268 [Debye] Total Charge= -0.0336 [e] Origin at atom idx: 112 core_charge: 6.0 ========================================== idx: 194 Chg: -0.3778 dist: 1.002253 idx: 272 Chg: -7.2094 dist: 0.000005 idx: 34 Chg: 1.0000 dist: 1.002256 idx: 35 Chg: 1.0000 dist: 0.993213 idx: 195 Chg: -0.3809 dist: 0.993208 ========================================== Total Dipole= 2.0557 [Debye] Total Charge= 0.0320 [e] Origin at atom idx: 113 core_charge: 6.0 ========================================== idx: 196 Chg: -0.3733 dist: 1.000126 idx: 197 Chg: -0.3846 dist: 0.989481 idx: 273 Chg: -7.2021 dist: 0.000006 idx: 36 Chg: 1.0000 dist: 1.000119 idx: 37 Chg: 1.0000 dist: 0.989474 ========================================== Total Dipole= 1.9478 [Debye] Total Charge= 0.0401 [e] Origin at atom idx: 114 core_charge: 6.0 ========================================== idx: 199 Chg: -0.3889 dist: 0.991497 idx: 274 Chg: -7.1870 dist: 0.000010 idx: 38 Chg: 1.0000 dist: 0.979581 idx: 39 Chg: 1.0000 dist: 0.991498 idx: 198 Chg: -0.3904 dist: 0.979576 ========================================== Total Dipole= 1.9399 [Debye] Total Charge= 0.0336 [e] Origin at atom idx: 124 core_charge: 6.0 ========================================== idx: 200 Chg: -0.3572 dist: 0.999396 idx: 284 Chg: -7.3174 dist: 0.000006 idx: 40 Chg: 1.0000 dist: 0.999399 idx: 41 Chg: 1.0000 dist: 1.000712 idx: 201 Chg: -0.3630 dist: 1.000714 ========================================== Total Dipole= 2.8788 [Debye] Total Charge= -0.0375 [e] Origin at atom idx: 125 core_charge: 6.0 ========================================== idx: 202 Chg: -0.3560 dist: 1.008522 idx: 203 Chg: -0.3638 dist: 1.005876 idx: 285 Chg: -7.3243 dist: 0.000002 idx: 42 Chg: 1.0000 dist: 1.008516 idx: 43 Chg: 1.0000 dist: 1.005876 ========================================== Total Dipole= 3.1687 [Debye] Total Charge= -0.0442 [e] Origin at atom idx: 126 core_charge: 6.0 ========================================== idx: 204 Chg: -0.3648 dist: 0.994536 idx: 205 Chg: -0.3543 dist: 1.014372 idx: 286 Chg: -7.3190 dist: 0.000009 idx: 44 Chg: 1.0000 dist: 0.994545 idx: 45 Chg: 1.0000 dist: 1.014367 ========================================== Total Dipole= 2.8988 [Debye] Total Charge= -0.0382 [e] Origin at atom idx: 127 core_charge: 6.0 ========================================== idx: 206 Chg: -0.3630 dist: 1.002880 idx: 207 Chg: -0.3597 dist: 1.006195 idx: 287 Chg: -7.3219 dist: 0.000010 idx: 46 Chg: 1.0000 dist: 1.002876 idx: 47 Chg: 1.0000 dist: 1.006199 ========================================== Total Dipole= 2.9336 [Debye] Total Charge= -0.0447 [e] Origin at atom idx: 128 core_charge: 6.0 ========================================== idx: 208 Chg: -0.3583 dist: 1.013871 idx: 209 Chg: -0.3606 dist: 1.002434 idx: 288 Chg: -7.3296 dist: 0.000014 idx: 48 Chg: 1.0000 dist: 1.013866 idx: 49 Chg: 1.0000 dist: 1.002431 ========================================== Total Dipole= 3.1770 [Debye] Total Charge= -0.0485 [e] Origin at atom idx: 129 core_charge: 6.0 ========================================== idx: 210 Chg: -0.3654 dist: 0.994926 idx: 211 Chg: -0.3560 dist: 1.010737 idx: 289 Chg: -7.3122 dist: 0.000009 idx: 50 Chg: 1.0000 dist: 0.994925 idx: 51 Chg: 1.0000 dist: 1.010734 ========================================== Total Dipole= 3.0268 [Debye] Total Charge= -0.0336 [e] Origin at atom idx: 130 core_charge: 6.0 ========================================== idx: 212 Chg: -0.3778 dist: 1.002254 idx: 290 Chg: -7.2094 dist: 0.000002 idx: 52 Chg: 1.0000 dist: 1.002256 idx: 53 Chg: 1.0000 dist: 0.993212 idx: 213 Chg: -0.3809 dist: 0.993207 ========================================== Total Dipole= 2.0556 [Debye] Total Charge= 0.0320 [e] Origin at atom idx: 131 core_charge: 6.0 ========================================== idx: 214 Chg: -0.3733 dist: 1.000129 idx: 215 Chg: -0.3846 dist: 0.989473 idx: 291 Chg: -7.2021 dist: 0.000012 idx: 54 Chg: 1.0000 dist: 1.000119 idx: 55 Chg: 1.0000 dist: 0.989465 ========================================== Total Dipole= 1.9479 [Debye] Total Charge= 0.0401 [e] Origin at atom idx: 132 core_charge: 6.0 ========================================== idx: 216 Chg: -0.3904 dist: 0.979573 idx: 217 Chg: -0.3889 dist: 0.991499 idx: 292 Chg: -7.1870 dist: 0.000011 idx: 56 Chg: 1.0000 dist: 0.979581 idx: 57 Chg: 1.0000 dist: 0.991504 ========================================== Total Dipole= 1.9400 [Debye] Total Charge= 0.0336 [e] Origin at atom idx: 142 core_charge: 6.0 ========================================== idx: 218 Chg: -0.3572 dist: 0.999390 idx: 219 Chg: -0.3630 dist: 1.000721 idx: 302 Chg: -7.3174 dist: 0.000006 idx: 58 Chg: 1.0000 dist: 0.999393 idx: 59 Chg: 1.0000 dist: 1.000715 ========================================== Total Dipole= 2.8788 [Debye] Total Charge= -0.0375 [e] Origin at atom idx: 143 core_charge: 6.0 ========================================== idx: 220 Chg: -0.3560 dist: 1.008523 idx: 221 Chg: -0.3638 dist: 1.005869 idx: 303 Chg: -7.3243 dist: 0.000009 idx: 60 Chg: 1.0000 dist: 1.008516 idx: 61 Chg: 1.0000 dist: 1.005870 ========================================== Total Dipole= 3.1689 [Debye] Total Charge= -0.0442 [e] Origin at atom idx: 144 core_charge: 6.0 ========================================== idx: 222 Chg: -0.3648 dist: 0.994529 idx: 223 Chg: -0.3543 dist: 1.014372 idx: 304 Chg: -7.3190 dist: 0.000016 idx: 62 Chg: 1.0000 dist: 0.994536 idx: 63 Chg: 1.0000 dist: 1.014368 ========================================== Total Dipole= 2.8989 [Debye] Total Charge= -0.0382 [e] Origin at atom idx: 145 core_charge: 6.0 ========================================== idx: 224 Chg: -0.3630 dist: 1.002874 idx: 305 Chg: -7.3219 dist: 0.000011 idx: 65 Chg: 1.0000 dist: 1.006202 idx: 225 Chg: -0.3597 dist: 1.006195 idx: 64 Chg: 1.0000 dist: 1.002876 ========================================== Total Dipole= 2.9337 [Debye] Total Charge= -0.0447 [e] Origin at atom idx: 146 core_charge: 6.0 ========================================== idx: 226 Chg: -0.3583 dist: 1.013864 idx: 227 Chg: -0.3606 dist: 1.002433 idx: 306 Chg: -7.3296 dist: 0.000010 idx: 66 Chg: 1.0000 dist: 1.013864 idx: 67 Chg: 1.0000 dist: 1.002427 ========================================== Total Dipole= 3.1772 [Debye] Total Charge= -0.0485 [e] Origin at atom idx: 147 core_charge: 6.0 ========================================== idx: 228 Chg: -0.3654 dist: 0.994925 idx: 229 Chg: -0.3560 dist: 1.010736 idx: 307 Chg: -7.3122 dist: 0.000010 idx: 68 Chg: 1.0000 dist: 0.994925 idx: 69 Chg: 1.0000 dist: 1.010726 ========================================== Total Dipole= 3.0269 [Debye] Total Charge= -0.0336 [e] Origin at atom idx: 148 core_charge: 6.0 ========================================== idx: 230 Chg: -0.3778 dist: 1.002242 idx: 308 Chg: -7.2094 dist: 0.000015 idx: 71 Chg: 1.0000 dist: 0.993212 idx: 231 Chg: -0.3809 dist: 0.993216 idx: 70 Chg: 1.0000 dist: 1.002251 ========================================== Total Dipole= 2.0557 [Debye] Total Charge= 0.0320 [e] Origin at atom idx: 149 core_charge: 6.0 ========================================== idx: 232 Chg: -0.3733 dist: 1.000127 idx: 233 Chg: -0.3846 dist: 0.989482 idx: 309 Chg: -7.2021 dist: 0.000004 idx: 72 Chg: 1.0000 dist: 1.000119 idx: 73 Chg: 1.0000 dist: 0.989479 ========================================== Total Dipole= 1.9478 [Debye] Total Charge= 0.0401 [e] Origin at atom idx: 150 core_charge: 6.0 ========================================== idx: 235 Chg: -0.3889 dist: 0.991499 idx: 310 Chg: -7.1870 dist: 0.000011 idx: 74 Chg: 1.0000 dist: 0.979581 idx: 234 Chg: -0.3904 dist: 0.979586 idx: 75 Chg: 1.0000 dist: 0.991498 ========================================== Total Dipole= 1.9396 [Debye] Total Charge= 0.0336 [e]
Out[4]:
({88: array([-2.20541438, 1.84832408, 0.08738486]),
89: array([-1.29290694, -1.47568555, -2.48861482]),
90: array([-1.76657884, -1.90533086, 1.28573377]),
91: array([-2.42183426, 1.65013022, 0.13667826]),
92: array([-1.74330385, -1.19268728, -2.37337498]),
93: array([-0.96998128, -1.95057609, 2.10161152]),
94: array([ 0.71522038, -1.11878677, -1.56933694]),
95: array([ 0.23092409, -1.55944252, -1.14459109]),
96: array([1.8942698 , 0.1866887 , 0.37297182]),
106: array([ 2.20506102, 1.84837125, -0.08762802]),
107: array([ 1.2927759 , -1.47544249, 2.48833985]),
108: array([ 1.76634947, -1.90537804, -1.28581001]),
109: array([ 2.42153702, 1.65022644, -0.1367498 ]),
110: array([ 1.74300655, -1.19251073, 2.37331727]),
111: array([ 0.96960851, -1.95030396, -2.10188523]),
112: array([-0.71549633, -1.11859449, 1.56927981]),
113: array([-0.2309587 , -1.55915542, 1.14431906]),
114: array([-1.89454571, 0.18691551, -0.3730482 ]),
124: array([ 2.20517055, -1.84845126, -0.08753199]),
125: array([1.29283848, 1.47548974, 2.48844803]),
126: array([ 1.76626833, 1.90513612, -1.28590044]),
127: array([ 2.42149314, -1.65032513, -0.13684506]),
128: array([1.74323539, 1.19255803, 2.37320901]),
129: array([ 0.96967098, 1.95040095, -2.1017781 ]),
130: array([-0.71551032, 1.11859377, 1.56917173]),
131: array([-0.23123102, 1.5592497 , 1.14442605]),
132: array([-1.89460677, -0.18688162, -0.37313699]),
142: array([-2.20537147, -1.8482574 , 0.08746137]),
143: array([-1.2931347 , 1.47555744, -2.48850664]),
144: array([-1.76659331, 1.90524994, 1.28564335]),
145: array([-2.42155654, -1.6503733 , 0.136583 ]),
146: array([-1.74331842, 1.19260625, -2.37346551]),
147: array([-0.96990112, 1.95044808, 2.10171958]),
148: array([ 0.71514099, 1.11868912, -1.56944405]),
149: array([ 0.23100435, 1.559028 , -1.1444841 ]),
150: array([ 1.89418948, -0.18709017, 0.37288302])},
{88: -0.037470000000000114,
89: -0.044159999999999755,
90: -0.03815999999999953,
91: -0.0446800000000005,
92: -0.04846000000000039,
93: -0.033639999999999226,
94: 0.03196999999999972,
95: 0.04005000000000081,
96: 0.03362000000000087,
106: -0.03746999999999989,
107: -0.044159999999999755,
108: -0.03815999999999953,
109: -0.04468000000000072,
110: -0.04846000000000039,
111: -0.033639999999999226,
112: 0.03196999999999972,
113: 0.04005000000000081,
114: 0.03362000000000065,
124: -0.037470000000000114,
125: -0.044159999999999755,
126: -0.03815999999999953,
127: -0.0446800000000005,
128: -0.04846000000000039,
129: -0.033639999999999226,
130: 0.03196999999999972,
131: 0.04005000000000081,
132: 0.03362000000000087,
142: -0.03746999999999989,
143: -0.044159999999999755,
144: -0.03815999999999953,
145: -0.04468000000000072,
146: -0.04846000000000039,
147: -0.033639999999999226,
148: 0.03196999999999972,
149: 0.04005000000000081,
150: 0.03362000000000065})
In [5]:
#=============================================================
EF_H2O_wannier(structure,core_charges)
Running Ewald ...
Done
Ow idx: 88
==================================================
H4 H4 dist: 0.000000 chg4 1.0000
H4 H5 dist: 1.661998 chg5 1.0000
H4 W213 dist: 0.521994 chg213 -2.0000
H4 W286 dist: 1.119922 chg286 -2.0000
H4 W302 dist: 1.252862 chg302 -2.0000
H4 W337 dist: 1.190344 chg337 -2.0000
--------------------------------------------------
H4 rOH= 0.999393 EF@H_along_bisector= 0.068833 a.u.
EF@H_along_OH_bond= 0.104850 a.u.
H5 H5 dist: 0.000000 chg5 1.0000
H5 H4 dist: 1.661998 chg4 1.0000
H5 W213 dist: 1.255014 chg213 -2.0000
H5 W286 dist: 1.116823 chg286 -2.0000
H5 W302 dist: 0.522386 chg302 -2.0000
H5 W337 dist: 1.185104 chg337 -2.0000
--------------------------------------------------
H5 rOH= 1.000710 EF@H_along_bisector= 0.112705 a.u.
EF@H_along_OH_bond= 0.116978 a.u.
Ow idx: 89
==================================================
H6 H6 dist: 0.000000 chg6 1.0000
H6 H7 dist: 1.632131 chg7 1.0000
H6 W216 dist: 1.241445 chg216 -2.0000
H6 W321 dist: 1.191205 chg321 -2.0000
H6 W362 dist: 0.535256 chg362 -2.0000
H6 W385 dist: 1.153142 chg385 -2.0000
--------------------------------------------------
H6 rOH= 1.008513 EF@H_along_bisector= 0.106675 a.u.
EF@H_along_OH_bond= 0.116253 a.u.
H7 H7 dist: 0.000000 chg7 1.0000
H7 H6 dist: 1.632131 chg6 1.0000
H7 W216 dist: 0.529217 chg216 -2.0000
H7 W321 dist: 1.182884 chg321 -2.0000
H7 W362 dist: 1.241590 chg362 -2.0000
H7 W385 dist: 1.140782 chg385 -2.0000
--------------------------------------------------
H7 rOH= 1.005884 EF@H_along_bisector= 0.122974 a.u.
EF@H_along_OH_bond= 0.122691 a.u.
Ow idx: 90
==================================================
H8 H8 dist: 0.000000 chg8 1.0000
H8 H9 dist: 1.672475 chg9 1.0000
H8 W188 dist: 0.513496 chg188 -2.0000
H8 W206 dist: 1.245042 chg206 -2.0000
H8 W336 dist: 1.108959 chg336 -2.0000
H8 W404 dist: 1.185726 chg404 -2.0000
--------------------------------------------------
H8 rOH= 0.994536 EF@H_along_bisector= 0.078163 a.u.
EF@H_along_OH_bond= 0.108656 a.u.
H9 H9 dist: 0.000000 chg9 1.0000
H9 H8 dist: 1.672475 chg8 1.0000
H9 W188 dist: 1.272380 chg188 -2.0000
H9 W206 dist: 0.543411 chg206 -2.0000
H9 W336 dist: 1.135564 chg336 -2.0000
H9 W404 dist: 1.201781 chg404 -2.0000
--------------------------------------------------
H9 rOH= 1.014367 EF@H_along_bisector= 0.089613 a.u.
EF@H_along_OH_bond= 0.131249 a.u.
Ow idx: 91
==================================================
H10 H10 dist: 0.000000 chg10 1.0000
H10 H11 dist: 1.652785 chg11 1.0000
H10 W349 dist: 1.247449 chg349 -2.0000
H10 W378 dist: 1.201275 chg378 -2.0000
H10 W392 dist: 1.114703 chg392 -2.0000
H10 W428 dist: 0.525688 chg428 -2.0000
--------------------------------------------------
H10 rOH= 1.002876 EF@H_along_bisector= 0.079714 a.u.
EF@H_along_OH_bond= 0.117575 a.u.
H11 H11 dist: 0.000000 chg11 1.0000
H11 H10 dist: 1.652785 chg10 1.0000
H11 W349 dist: 0.531184 chg349 -2.0000
H11 W378 dist: 1.203271 chg378 -2.0000
H11 W392 dist: 1.119641 chg392 -2.0000
H11 W428 dist: 1.251521 chg428 -2.0000
--------------------------------------------------
H11 rOH= 1.006199 EF@H_along_bisector= 0.116549 a.u.
EF@H_along_OH_bond= 0.127440 a.u.
Ow idx: 92
==================================================
H12 H12 dist: 0.000000 chg12 1.0000
H12 H13 dist: 1.635166 chg13 1.0000
H12 W225 dist: 0.544093 chg225 -2.0000
H12 W257 dist: 1.142426 chg257 -2.0000
H12 W338 dist: 1.213012 chg338 -2.0000
H12 W406 dist: 1.246268 chg406 -2.0000
--------------------------------------------------
H12 rOH= 1.013864 EF@H_along_bisector= 0.115031 a.u.
EF@H_along_OH_bond= 0.131631 a.u.
H13 H13 dist: 0.000000 chg13 1.0000
H13 H12 dist: 1.635166 chg12 1.0000
H13 W225 dist: 1.237598 chg225 -2.0000
H13 W257 dist: 1.127959 chg257 -2.0000
H13 W338 dist: 1.185442 chg338 -2.0000
H13 W406 dist: 0.527277 chg406 -2.0000
--------------------------------------------------
H13 rOH= 1.002436 EF@H_along_bisector= 0.126634 a.u.
EF@H_along_OH_bond= 0.129112 a.u.
Ow idx: 93
==================================================
H14 H14 dist: 0.000000 chg14 1.0000
H14 H15 dist: 1.623866 chg15 1.0000
H14 W318 dist: 1.223170 chg318 -2.0000
H14 W330 dist: 1.111077 chg330 -2.0000
H14 W394 dist: 0.513417 chg394 -2.0000
H14 W414 dist: 1.197694 chg414 -2.0000
--------------------------------------------------
H14 rOH= 0.994925 EF@H_along_bisector= 0.081558 a.u.
EF@H_along_OH_bond= 0.098089 a.u.
H15 H15 dist: 0.000000 chg15 1.0000
H15 H14 dist: 1.623866 chg14 1.0000
H15 W318 dist: 0.538274 chg318 -2.0000
H15 W330 dist: 1.123483 chg330 -2.0000
H15 W394 dist: 1.248871 chg394 -2.0000
H15 W414 dist: 1.211773 chg414 -2.0000
--------------------------------------------------
H15 rOH= 1.010736 EF@H_along_bisector= 0.093430 a.u.
EF@H_along_OH_bond= 0.123480 a.u.
Ow idx: 94
==================================================
H16 H16 dist: 0.000000 chg16 1.0000
H16 H17 dist: 1.597805 chg17 1.0000
H16 W228 dist: 1.157856 chg228 -2.0000
H16 W289 dist: 0.517770 chg289 -2.0000
H16 W347 dist: 1.226942 chg347 -2.0000
H16 W398 dist: 1.167363 chg398 -2.0000
--------------------------------------------------
H16 rOH= 1.002251 EF@H_along_bisector= 0.077584 a.u.
EF@H_along_OH_bond= 0.100421 a.u.
H17 H17 dist: 0.000000 chg17 1.0000
H17 H16 dist: 1.597805 chg16 1.0000
H17 W228 dist: 1.151298 chg228 -2.0000
H17 W289 dist: 1.214673 chg289 -2.0000
H17 W347 dist: 0.503833 chg347 -2.0000
H17 W398 dist: 1.156405 chg398 -2.0000
--------------------------------------------------
H17 rOH= 0.993212 EF@H_along_bisector= 0.065867 a.u.
EF@H_along_OH_bond= 0.079954 a.u.
Ow idx: 95
==================================================
H18 H18 dist: 0.000000 chg18 1.0000
H18 H19 dist: 1.608759 chg19 1.0000
H18 W348 dist: 1.166421 chg348 -2.0000
H18 W388 dist: 1.154016 chg388 -2.0000
H18 W396 dist: 1.234666 chg396 -2.0000
H18 W424 dist: 0.516792 chg424 -2.0000
--------------------------------------------------
H18 rOH= 1.000119 EF@H_along_bisector= 0.091437 a.u.
EF@H_along_OH_bond= 0.105777 a.u.
H19 H19 dist: 0.000000 chg19 1.0000
H19 H18 dist: 1.608759 chg18 1.0000
H19 W348 dist: 1.164399 chg348 -2.0000
H19 W388 dist: 1.128145 chg388 -2.0000
H19 W396 dist: 0.497424 chg396 -2.0000
H19 W424 dist: 1.217406 chg424 -2.0000
--------------------------------------------------
H19 rOH= 0.989474 EF@H_along_bisector= 0.066705 a.u.
EF@H_along_OH_bond= 0.068783 a.u.
Ow idx: 96
==================================================
H20 H20 dist: 0.000000 chg20 1.0000
H20 H21 dist: 1.573506 chg21 1.0000
H20 W272 dist: 0.482478 chg272 -2.0000
H20 W344 dist: 1.129552 chg344 -2.0000
H20 W377 dist: 1.203528 chg377 -2.0000
H20 W386 dist: 1.137923 chg386 -2.0000
--------------------------------------------------
H20 rOH= 0.979581 EF@H_along_bisector= 0.049019 a.u.
EF@H_along_OH_bond= 0.037226 a.u.
H21 H21 dist: 0.000000 chg21 1.0000
H21 H20 dist: 1.573506 chg20 1.0000
H21 W272 dist: 1.217976 chg272 -2.0000
H21 W344 dist: 1.151344 chg344 -2.0000
H21 W377 dist: 0.500206 chg377 -2.0000
H21 W386 dist: 1.135731 chg386 -2.0000
--------------------------------------------------
H21 rOH= 0.991504 EF@H_along_bisector= 0.041562 a.u.
EF@H_along_OH_bond= 0.074756 a.u.
Ow idx: 106
==================================================
H22 H22 dist: 0.000000 chg22 1.0000
H22 H23 dist: 1.662002 chg23 1.0000
H22 W204 dist: 1.190344 chg204 -2.0000
H22 W229 dist: 0.521996 chg229 -2.0000
H22 W335 dist: 1.119924 chg335 -2.0000
H22 W352 dist: 1.252864 chg352 -2.0000
--------------------------------------------------
H22 rOH= 0.999399 EF@H_along_bisector= 0.068944 a.u.
EF@H_along_OH_bond= 0.104717 a.u.
H23 H23 dist: 0.000000 chg23 1.0000
H23 H22 dist: 1.662002 chg22 1.0000
H23 W204 dist: 1.185107 chg204 -2.0000
H23 W229 dist: 1.255015 chg229 -2.0000
H23 W335 dist: 1.116822 chg335 -2.0000
H23 W352 dist: 0.522388 chg352 -2.0000
--------------------------------------------------
H23 rOH= 1.000710 EF@H_along_bisector= 0.112758 a.u.
EF@H_along_OH_bond= 0.116671 a.u.
Ow idx: 107
==================================================
H24 H24 dist: 0.000000 chg24 1.0000
H24 H25 dist: 1.632127 chg25 1.0000
H24 W189 dist: 1.153145 chg189 -2.0000
H24 W223 dist: 0.535258 chg223 -2.0000
H24 W230 dist: 1.241447 chg230 -2.0000
H24 W340 dist: 1.191205 chg340 -2.0000
--------------------------------------------------
H24 rOH= 1.008516 EF@H_along_bisector= 0.106464 a.u.
EF@H_along_OH_bond= 0.115929 a.u.
H25 H25 dist: 0.000000 chg25 1.0000
H25 H24 dist: 1.632127 chg24 1.0000
H25 W189 dist: 1.140773 chg189 -2.0000
H25 W223 dist: 1.241583 chg223 -2.0000
H25 W230 dist: 0.529209 chg230 -2.0000
H25 W340 dist: 1.182877 chg340 -2.0000
--------------------------------------------------
H25 rOH= 1.005876 EF@H_along_bisector= 0.122675 a.u.
EF@H_along_OH_bond= 0.122790 a.u.
Ow idx: 108
==================================================
H26 H26 dist: 0.000000 chg26 1.0000
H26 H27 dist: 1.672489 chg27 1.0000
H26 W282 dist: 1.245052 chg282 -2.0000
H26 W304 dist: 0.513505 chg304 -2.0000
H26 W307 dist: 1.185734 chg307 -2.0000
H26 W423 dist: 1.108967 chg423 -2.0000
--------------------------------------------------
H26 rOH= 0.994548 EF@H_along_bisector= 0.078951 a.u.
EF@H_along_OH_bond= 0.111783 a.u.
H27 H27 dist: 0.000000 chg27 1.0000
H27 H26 dist: 1.672489 chg26 1.0000
H27 W282 dist: 0.543416 chg282 -2.0000
H27 W304 dist: 1.272385 chg304 -2.0000
H27 W307 dist: 1.201785 chg307 -2.0000
H27 W423 dist: 1.135567 chg423 -2.0000
--------------------------------------------------
H27 rOH= 1.014367 EF@H_along_bisector= 0.089514 a.u.
EF@H_along_OH_bond= 0.131012 a.u.
Ow idx: 109
==================================================
H28 H28 dist: 0.000000 chg28 1.0000
H28 H29 dist: 1.652787 chg29 1.0000
H28 W334 dist: 1.201276 chg334 -2.0000
H28 W409 dist: 0.525687 chg409 -2.0000
H28 W434 dist: 1.114701 chg434 -2.0000
H28 W442 dist: 1.247448 chg442 -2.0000
--------------------------------------------------
H28 rOH= 1.002876 EF@H_along_bisector= 0.079510 a.u.
EF@H_along_OH_bond= 0.117607 a.u.
H29 H29 dist: 0.000000 chg29 1.0000
H29 H28 dist: 1.652787 chg28 1.0000
H29 W334 dist: 1.203272 chg334 -2.0000
H29 W409 dist: 1.251523 chg409 -2.0000
H29 W434 dist: 1.119639 chg434 -2.0000
H29 W442 dist: 0.531185 chg442 -2.0000
--------------------------------------------------
H29 rOH= 1.006199 EF@H_along_bisector= 0.116371 a.u.
EF@H_along_OH_bond= 0.127451 a.u.
Ow idx: 110
==================================================
H30 H30 dist: 0.000000 chg30 1.0000
H30 H31 dist: 1.635166 chg31 1.0000
H30 W200 dist: 1.246268 chg200 -2.0000
H30 W278 dist: 1.213021 chg278 -2.0000
H30 W315 dist: 1.142418 chg315 -2.0000
H30 W441 dist: 0.544095 chg441 -2.0000
--------------------------------------------------
H30 rOH= 1.013864 EF@H_along_bisector= 0.115265 a.u.
EF@H_along_OH_bond= 0.131847 a.u.
H31 H31 dist: 0.000000 chg31 1.0000
H31 H30 dist: 1.635166 chg30 1.0000
H31 W200 dist: 0.527277 chg200 -2.0000
H31 W278 dist: 1.185449 chg278 -2.0000
H31 W315 dist: 1.127951 chg315 -2.0000
H31 W441 dist: 1.237597 chg441 -2.0000
--------------------------------------------------
H31 rOH= 1.002440 EF@H_along_bisector= 0.126754 a.u.
EF@H_along_OH_bond= 0.129019 a.u.
Ow idx: 111
==================================================
H32 H32 dist: 0.000000 chg32 1.0000
H32 H33 dist: 1.623862 chg33 1.0000
H32 W221 dist: 0.513416 chg221 -2.0000
H32 W294 dist: 1.223172 chg294 -2.0000
H32 W312 dist: 1.111079 chg312 -2.0000
H32 W327 dist: 1.197691 chg327 -2.0000
--------------------------------------------------
H32 rOH= 0.994925 EF@H_along_bisector= 0.081666 a.u.
EF@H_along_OH_bond= 0.098225 a.u.
H33 H33 dist: 0.000000 chg33 1.0000
H33 H32 dist: 1.623862 chg32 1.0000
H33 W221 dist: 1.248865 chg221 -2.0000
H33 W294 dist: 0.538268 chg294 -2.0000
H33 W312 dist: 1.123476 chg312 -2.0000
H33 W327 dist: 1.211768 chg327 -2.0000
--------------------------------------------------
H33 rOH= 1.010734 EF@H_along_bisector= 0.093487 a.u.
EF@H_along_OH_bond= 0.123413 a.u.
Ow idx: 112
==================================================
H34 H34 dist: 0.000000 chg34 1.0000
H34 H35 dist: 1.597805 chg35 1.0000
H34 W222 dist: 0.517772 chg222 -2.0000
H34 W231 dist: 1.157859 chg231 -2.0000
H34 W296 dist: 1.167363 chg296 -2.0000
H34 W351 dist: 1.226943 chg351 -2.0000
--------------------------------------------------
H34 rOH= 1.002256 EF@H_along_bisector= 0.077653 a.u.
EF@H_along_OH_bond= 0.100398 a.u.
H35 H35 dist: 0.000000 chg35 1.0000
H35 H34 dist: 1.597805 chg34 1.0000
H35 W222 dist: 1.214674 chg222 -2.0000
H35 W231 dist: 1.151302 chg231 -2.0000
H35 W296 dist: 1.156407 chg296 -2.0000
H35 W351 dist: 0.503835 chg351 -2.0000
--------------------------------------------------
H35 rOH= 0.993213 EF@H_along_bisector= 0.066128 a.u.
EF@H_along_OH_bond= 0.080432 a.u.
Ow idx: 113
==================================================
H36 H36 dist: 0.000000 chg36 1.0000
H36 H37 dist: 1.608759 chg37 1.0000
H36 W203 dist: 1.234668 chg203 -2.0000
H36 W310 dist: 0.516792 chg310 -2.0000
H36 W322 dist: 1.166418 chg322 -2.0000
H36 W384 dist: 1.154017 chg384 -2.0000
--------------------------------------------------
H36 rOH= 1.000119 EF@H_along_bisector= 0.091147 a.u.
EF@H_along_OH_bond= 0.105158 a.u.
H37 H37 dist: 0.000000 chg37 1.0000
H37 H36 dist: 1.608759 chg36 1.0000
H37 W203 dist: 0.497418 chg203 -2.0000
H37 W310 dist: 1.217401 chg310 -2.0000
H37 W322 dist: 1.164391 chg322 -2.0000
H37 W384 dist: 1.128141 chg384 -2.0000
--------------------------------------------------
H37 rOH= 0.989474 EF@H_along_bisector= 0.066603 a.u.
EF@H_along_OH_bond= 0.068887 a.u.
Ow idx: 114
==================================================
H38 H38 dist: 0.000000 chg38 1.0000
H38 H39 dist: 1.573500 chg39 1.0000
H38 W214 dist: 1.203525 chg214 -2.0000
H38 W305 dist: 1.129552 chg305 -2.0000
H38 W346 dist: 1.137921 chg346 -2.0000
H38 W373 dist: 0.482477 chg373 -2.0000
--------------------------------------------------
H38 rOH= 0.979581 EF@H_along_bisector= 0.050998 a.u.
EF@H_along_OH_bond= 0.040268 a.u.
H39 H39 dist: 0.000000 chg39 1.0000
H39 H38 dist: 1.573500 chg38 1.0000
H39 W214 dist: 0.500205 chg214 -2.0000
H39 W305 dist: 1.151347 chg305 -2.0000
H39 W346 dist: 1.135727 chg346 -2.0000
H39 W373 dist: 1.217974 chg373 -2.0000
--------------------------------------------------
H39 rOH= 0.991498 EF@H_along_bisector= 0.041803 a.u.
EF@H_along_OH_bond= 0.074213 a.u.
Ow idx: 124
==================================================
H40 H40 dist: 0.000000 chg40 1.0000
H40 H41 dist: 1.662001 chg41 1.0000
H40 W195 dist: 1.119924 chg195 -2.0000
H40 W205 dist: 0.521997 chg205 -2.0000
H40 W285 dist: 1.252866 chg285 -2.0000
H40 W415 dist: 1.190347 chg415 -2.0000
--------------------------------------------------
H40 rOH= 0.999399 EF@H_along_bisector= 0.068618 a.u.
EF@H_along_OH_bond= 0.104680 a.u.
H41 H41 dist: 0.000000 chg41 1.0000
H41 H40 dist: 1.662001 chg40 1.0000
H41 W195 dist: 1.116823 chg195 -2.0000
H41 W205 dist: 1.255013 chg205 -2.0000
H41 W285 dist: 0.522388 chg285 -2.0000
H41 W415 dist: 1.185109 chg415 -2.0000
--------------------------------------------------
H41 rOH= 1.000712 EF@H_along_bisector= 0.112574 a.u.
EF@H_along_OH_bond= 0.117060 a.u.
Ow idx: 125
==================================================
H42 H42 dist: 0.000000 chg42 1.0000
H42 H43 dist: 1.632131 chg43 1.0000
H42 W187 dist: 1.241448 chg187 -2.0000
H42 W300 dist: 1.153144 chg300 -2.0000
H42 W325 dist: 1.191205 chg325 -2.0000
H42 W339 dist: 0.535257 chg339 -2.0000
--------------------------------------------------
H42 rOH= 1.008516 EF@H_along_bisector= 0.106695 a.u.
EF@H_along_OH_bond= 0.116343 a.u.
H43 H43 dist: 0.000000 chg43 1.0000
H43 H42 dist: 1.632131 chg42 1.0000
H43 W187 dist: 0.529213 chg187 -2.0000
H43 W300 dist: 1.140779 chg300 -2.0000
H43 W325 dist: 1.182880 chg325 -2.0000
H43 W339 dist: 1.241586 chg339 -2.0000
--------------------------------------------------
H43 rOH= 1.005876 EF@H_along_bisector= 0.122801 a.u.
EF@H_along_OH_bond= 0.122423 a.u.
Ow idx: 126
==================================================
H44 H44 dist: 0.000000 chg44 1.0000
H44 H45 dist: 1.672482 chg45 1.0000
H44 W220 dist: 1.245047 chg220 -2.0000
H44 W277 dist: 0.513502 chg277 -2.0000
H44 W292 dist: 1.185732 chg292 -2.0000
H44 W374 dist: 1.108964 chg374 -2.0000
--------------------------------------------------
H44 rOH= 0.994545 EF@H_along_bisector= 0.078169 a.u.
EF@H_along_OH_bond= 0.108663 a.u.
H45 H45 dist: 0.000000 chg45 1.0000
H45 H44 dist: 1.672482 chg44 1.0000
H45 W220 dist: 0.543411 chg220 -2.0000
H45 W277 dist: 1.272381 chg277 -2.0000
H45 W292 dist: 1.201781 chg292 -2.0000
H45 W374 dist: 1.135561 chg374 -2.0000
--------------------------------------------------
H45 rOH= 1.014367 EF@H_along_bisector= 0.089557 a.u.
EF@H_along_OH_bond= 0.131278 a.u.
Ow idx: 127
==================================================
H46 H46 dist: 0.000000 chg46 1.0000
H46 H47 dist: 1.652785 chg47 1.0000
H46 W190 dist: 0.525685 chg190 -2.0000
H46 W219 dist: 1.247447 chg219 -2.0000
H46 W332 dist: 1.201274 chg332 -2.0000
H46 W361 dist: 1.114698 chg361 -2.0000
--------------------------------------------------
H46 rOH= 1.002876 EF@H_along_bisector= 0.079463 a.u.
EF@H_along_OH_bond= 0.117569 a.u.
H47 H47 dist: 0.000000 chg47 1.0000
H47 H46 dist: 1.652785 chg46 1.0000
H47 W190 dist: 1.251521 chg190 -2.0000
H47 W219 dist: 0.531184 chg219 -2.0000
H47 W332 dist: 1.203271 chg332 -2.0000
H47 W361 dist: 1.119638 chg361 -2.0000
--------------------------------------------------
H47 rOH= 1.006199 EF@H_along_bisector= 0.116324 a.u.
EF@H_along_OH_bond= 0.127361 a.u.
Ow idx: 128
==================================================
H48 H48 dist: 0.000000 chg48 1.0000
H48 H49 dist: 1.635168 chg49 1.0000
H48 W226 dist: 1.246270 chg226 -2.0000
H48 W298 dist: 0.544095 chg298 -2.0000
H48 W343 dist: 1.142419 chg343 -2.0000
H48 W397 dist: 1.213019 chg397 -2.0000
--------------------------------------------------
H48 rOH= 1.013866 EF@H_along_bisector= 0.115091 a.u.
EF@H_along_OH_bond= 0.131717 a.u.
H49 H49 dist: 0.000000 chg49 1.0000
H49 H48 dist: 1.635168 chg48 1.0000
H49 W226 dist: 0.527277 chg226 -2.0000
H49 W298 dist: 1.237596 chg298 -2.0000
H49 W343 dist: 1.127950 chg343 -2.0000
H49 W397 dist: 1.185450 chg397 -2.0000
--------------------------------------------------
H49 rOH= 1.002431 EF@H_along_bisector= 0.126684 a.u.
EF@H_along_OH_bond= 0.128958 a.u.
Ow idx: 129
==================================================
H50 H50 dist: 0.000000 chg50 1.0000
H50 H51 dist: 1.623862 chg51 1.0000
H50 W299 dist: 0.513415 chg299 -2.0000
H50 W323 dist: 1.197691 chg323 -2.0000
H50 W364 dist: 1.223169 chg364 -2.0000
H50 W370 dist: 1.111077 chg370 -2.0000
--------------------------------------------------
H50 rOH= 0.994925 EF@H_along_bisector= 0.081567 a.u.
EF@H_along_OH_bond= 0.098119 a.u.
H51 H51 dist: 0.000000 chg51 1.0000
H51 H50 dist: 1.623862 chg50 1.0000
H51 W299 dist: 1.248868 chg299 -2.0000
H51 W323 dist: 1.211772 chg323 -2.0000
H51 W364 dist: 0.538272 chg364 -2.0000
H51 W370 dist: 1.123479 chg370 -2.0000
--------------------------------------------------
H51 rOH= 1.010734 EF@H_along_bisector= 0.093360 a.u.
EF@H_along_OH_bond= 0.123434 a.u.
Ow idx: 130
==================================================
H52 H52 dist: 0.000000 chg52 1.0000
H52 H53 dist: 1.597814 chg53 1.0000
H52 W291 dist: 1.226947 chg291 -2.0000
H52 W350 dist: 0.517773 chg350 -2.0000
H52 W371 dist: 1.167364 chg371 -2.0000
H52 W421 dist: 1.157858 chg421 -2.0000
--------------------------------------------------
H52 rOH= 1.002256 EF@H_along_bisector= 0.077380 a.u.
EF@H_along_OH_bond= 0.099921 a.u.
H53 H53 dist: 0.000000 chg53 1.0000
H53 H52 dist: 1.597814 chg52 1.0000
H53 W291 dist: 0.503836 chg291 -2.0000
H53 W350 dist: 1.214677 chg350 -2.0000
H53 W371 dist: 1.156409 chg371 -2.0000
H53 W421 dist: 1.151301 chg421 -2.0000
--------------------------------------------------
H53 rOH= 0.993212 EF@H_along_bisector= 0.066004 a.u.
EF@H_along_OH_bond= 0.080519 a.u.
Ow idx: 131
==================================================
H54 H54 dist: 0.000000 chg54 1.0000
H54 H55 dist: 1.608749 chg55 1.0000
H54 W163 dist: 1.154015 chg163 -2.0000
H54 W202 dist: 0.516788 chg202 -2.0000
H54 W319 dist: 1.234662 chg319 -2.0000
H54 W342 dist: 1.166417 chg342 -2.0000
--------------------------------------------------
H54 rOH= 1.000119 EF@H_along_bisector= 0.091228 a.u.
EF@H_along_OH_bond= 0.105169 a.u.
H55 H55 dist: 0.000000 chg55 1.0000
H55 H54 dist: 1.608749 chg54 1.0000
H55 W163 dist: 1.128140 chg163 -2.0000
H55 W202 dist: 1.217400 chg202 -2.0000
H55 W319 dist: 0.497418 chg319 -2.0000
H55 W342 dist: 1.164393 chg342 -2.0000
--------------------------------------------------
H55 rOH= 0.989465 EF@H_along_bisector= 0.066867 a.u.
EF@H_along_OH_bond= 0.069147 a.u.
Ow idx: 132
==================================================
H56 H56 dist: 0.000000 chg56 1.0000
H56 H57 dist: 1.573506 chg57 1.0000
H56 W212 dist: 1.203528 chg212 -2.0000
H56 W248 dist: 0.482480 chg248 -2.0000
H56 W268 dist: 1.137926 chg268 -2.0000
H56 W403 dist: 1.129553 chg403 -2.0000
--------------------------------------------------
H56 rOH= 0.979581 EF@H_along_bisector= 0.051066 a.u.
EF@H_along_OH_bond= 0.040354 a.u.
H57 H57 dist: 0.000000 chg57 1.0000
H57 H56 dist: 1.573506 chg56 1.0000
H57 W212 dist: 0.500209 chg212 -2.0000
H57 W248 dist: 1.217978 chg248 -2.0000
H57 W268 dist: 1.135735 chg268 -2.0000
H57 W403 dist: 1.151347 chg403 -2.0000
--------------------------------------------------
H57 rOH= 0.991504 EF@H_along_bisector= 0.041881 a.u.
EF@H_along_OH_bond= 0.074249 a.u.
Ow idx: 142
==================================================
H58 H58 dist: 0.000000 chg58 1.0000
H58 H59 dist: 1.661999 chg59 1.0000
H58 W207 dist: 1.252861 chg207 -2.0000
H58 W246 dist: 0.521992 chg246 -2.0000
H58 W329 dist: 1.190341 chg329 -2.0000
H58 W345 dist: 1.119920 chg345 -2.0000
--------------------------------------------------
H58 rOH= 0.999393 EF@H_along_bisector= 0.068777 a.u.
EF@H_along_OH_bond= 0.104740 a.u.
H59 H59 dist: 0.000000 chg59 1.0000
H59 H58 dist: 1.661999 chg58 1.0000
H59 W207 dist: 0.522389 chg207 -2.0000
H59 W246 dist: 1.255015 chg246 -2.0000
H59 W329 dist: 1.185109 chg329 -2.0000
H59 W345 dist: 1.116825 chg345 -2.0000
--------------------------------------------------
H59 rOH= 1.000715 EF@H_along_bisector= 0.112595 a.u.
EF@H_along_OH_bond= 0.116929 a.u.
Ow idx: 143
==================================================
H60 H60 dist: 0.000000 chg60 1.0000
H60 H61 dist: 1.632127 chg61 1.0000
H60 W201 dist: 0.535256 chg201 -2.0000
H60 W274 dist: 1.153144 chg274 -2.0000
H60 W401 dist: 1.241445 chg401 -2.0000
H60 W419 dist: 1.191204 chg419 -2.0000
--------------------------------------------------
H60 rOH= 1.008516 EF@H_along_bisector= 0.106488 a.u.
EF@H_along_OH_bond= 0.115957 a.u.
H61 H61 dist: 0.000000 chg61 1.0000
H61 H60 dist: 1.632127 chg60 1.0000
H61 W201 dist: 1.241586 chg201 -2.0000
H61 W274 dist: 1.140776 chg274 -2.0000
H61 W401 dist: 0.529212 chg401 -2.0000
H61 W419 dist: 1.182879 chg419 -2.0000
--------------------------------------------------
H61 rOH= 1.005870 EF@H_along_bisector= 0.122848 a.u.
EF@H_along_OH_bond= 0.122645 a.u.
Ow idx: 144
==================================================
H62 H62 dist: 0.000000 chg62 1.0000
H62 H63 dist: 1.672482 chg63 1.0000
H62 W301 dist: 0.513497 chg301 -2.0000
H62 W320 dist: 1.185728 chg320 -2.0000
H62 W333 dist: 1.108960 chg333 -2.0000
H62 W413 dist: 1.245042 chg413 -2.0000
--------------------------------------------------
H62 rOH= 0.994536 EF@H_along_bisector= 0.078091 a.u.
EF@H_along_OH_bond= 0.108574 a.u.
H63 H63 dist: 0.000000 chg63 1.0000
H63 H62 dist: 1.672482 chg62 1.0000
H63 W301 dist: 1.272386 chg301 -2.0000
H63 W320 dist: 1.201784 chg320 -2.0000
H63 W333 dist: 1.135566 chg333 -2.0000
H63 W413 dist: 0.543416 chg413 -2.0000
--------------------------------------------------
H63 rOH= 1.014368 EF@H_along_bisector= 0.089483 a.u.
EF@H_along_OH_bond= 0.131296 a.u.
Ow idx: 145
==================================================
H64 H64 dist: 0.000000 chg64 1.0000
H64 H65 dist: 1.652788 chg65 1.0000
H64 W217 dist: 1.114693 chg217 -2.0000
H64 W331 dist: 1.201272 chg331 -2.0000
H64 W358 dist: 0.525683 chg358 -2.0000
H64 W420 dist: 1.247447 chg420 -2.0000
--------------------------------------------------
H64 rOH= 1.002876 EF@H_along_bisector= 0.079350 a.u.
EF@H_along_OH_bond= 0.117710 a.u.
H65 H65 dist: 0.000000 chg65 1.0000
H65 H64 dist: 1.652788 chg64 1.0000
H65 W217 dist: 1.119640 chg217 -2.0000
H65 W331 dist: 1.203277 chg331 -2.0000
H65 W358 dist: 1.251523 chg358 -2.0000
H65 W420 dist: 0.531187 chg420 -2.0000
--------------------------------------------------
H65 rOH= 1.006202 EF@H_along_bisector= 0.116139 a.u.
EF@H_along_OH_bond= 0.127296 a.u.
Ow idx: 146
==================================================
H66 H66 dist: 0.000000 chg66 1.0000
H66 H67 dist: 1.635159 chg67 1.0000
H66 W209 dist: 1.246267 chg209 -2.0000
H66 W224 dist: 1.142418 chg224 -2.0000
H66 W252 dist: 0.544094 chg252 -2.0000
H66 W326 dist: 1.213019 chg326 -2.0000
--------------------------------------------------
H66 rOH= 1.013864 EF@H_along_bisector= 0.115331 a.u.
EF@H_along_OH_bond= 0.131973 a.u.
H67 H67 dist: 0.000000 chg67 1.0000
H67 H66 dist: 1.635159 chg66 1.0000
H67 W209 dist: 0.527271 chg209 -2.0000
H67 W224 dist: 1.127946 chg224 -2.0000
H67 W252 dist: 1.237591 chg252 -2.0000
H67 W326 dist: 1.185443 chg326 -2.0000
--------------------------------------------------
H67 rOH= 1.002427 EF@H_along_bisector= 0.126884 a.u.
EF@H_along_OH_bond= 0.128878 a.u.
Ow idx: 147
==================================================
H68 H68 dist: 0.000000 chg68 1.0000
H68 H69 dist: 1.623858 chg69 1.0000
H68 W308 dist: 0.513415 chg308 -2.0000
H68 W360 dist: 1.111078 chg360 -2.0000
H68 W379 dist: 1.223168 chg379 -2.0000
H68 W380 dist: 1.197692 chg380 -2.0000
--------------------------------------------------
H68 rOH= 0.994925 EF@H_along_bisector= 0.081773 a.u.
EF@H_along_OH_bond= 0.097989 a.u.
H69 H69 dist: 0.000000 chg69 1.0000
H69 H68 dist: 1.623858 chg68 1.0000
H69 W308 dist: 1.248865 chg308 -2.0000
H69 W360 dist: 1.123477 chg360 -2.0000
H69 W379 dist: 0.538268 chg379 -2.0000
H69 W380 dist: 1.211766 chg380 -2.0000
--------------------------------------------------
H69 rOH= 1.010726 EF@H_along_bisector= 0.093462 a.u.
EF@H_along_OH_bond= 0.123566 a.u.
Ow idx: 148
==================================================
H70 H70 dist: 0.000000 chg70 1.0000
H70 H71 dist: 1.597805 chg71 1.0000
H70 W208 dist: 0.517773 chg208 -2.0000
H70 W287 dist: 1.157860 chg287 -2.0000
H70 W324 dist: 1.167364 chg324 -2.0000
H70 W425 dist: 1.226945 chg425 -2.0000
--------------------------------------------------
H70 rOH= 1.002251 EF@H_along_bisector= 0.077669 a.u.
EF@H_along_OH_bond= 0.100315 a.u.
H71 H71 dist: 0.000000 chg71 1.0000
H71 H70 dist: 1.597805 chg70 1.0000
H71 W208 dist: 1.214671 chg208 -2.0000
H71 W287 dist: 1.151298 chg287 -2.0000
H71 W324 dist: 1.156403 chg324 -2.0000
H71 W425 dist: 0.503831 chg425 -2.0000
--------------------------------------------------
H71 rOH= 0.993212 EF@H_along_bisector= 0.066148 a.u.
EF@H_along_OH_bond= 0.080535 a.u.
Ow idx: 149
==================================================
H72 H72 dist: 0.000000 chg72 1.0000
H72 H73 dist: 1.608759 chg73 1.0000
H72 W199 dist: 1.234663 chg199 -2.0000
H72 W232 dist: 0.516787 chg232 -2.0000
H72 W309 dist: 1.154013 chg309 -2.0000
H72 W341 dist: 1.166413 chg341 -2.0000
--------------------------------------------------
H72 rOH= 1.000119 EF@H_along_bisector= 0.091218 a.u.
EF@H_along_OH_bond= 0.105146 a.u.
H73 H73 dist: 0.000000 chg73 1.0000
H73 H72 dist: 1.608759 chg72 1.0000
H73 W199 dist: 0.497427 chg199 -2.0000
H73 W232 dist: 1.217408 chg232 -2.0000
H73 W309 dist: 1.128149 chg309 -2.0000
H73 W341 dist: 1.164402 chg341 -2.0000
--------------------------------------------------
H73 rOH= 0.989479 EF@H_along_bisector= 0.066656 a.u.
EF@H_along_OH_bond= 0.068957 a.u.
Ow idx: 150
==================================================
H74 H74 dist: 0.000000 chg74 1.0000
H74 H75 dist: 1.573500 chg75 1.0000
H74 W211 dist: 0.482474 chg211 -2.0000
H74 W270 dist: 1.203524 chg270 -2.0000
H74 W353 dist: 1.129546 chg353 -2.0000
H74 W376 dist: 1.137921 chg376 -2.0000
--------------------------------------------------
H74 rOH= 0.979581 EF@H_along_bisector= 0.051038 a.u.
EF@H_along_OH_bond= 0.040262 a.u.
H75 H75 dist: 0.000000 chg75 1.0000
H75 H74 dist: 1.573500 chg74 1.0000
H75 W211 dist: 1.217974 chg211 -2.0000
H75 W270 dist: 0.500202 chg270 -2.0000
H75 W353 dist: 1.151342 chg353 -2.0000
H75 W376 dist: 1.135727 chg376 -2.0000
--------------------------------------------------
H75 rOH= 0.991498 EF@H_along_bisector= 0.041888 a.u.
EF@H_along_OH_bond= 0.074327 a.u.
In [6]:
#=============================================================
EF_H2O_bader(structure,core_charges)
Running Ewald ...
Done
Ow idx: 88
==================================================
H4 H4 dist: 0.000000 chg4 0.6428
H4 O88 dist: 0.999393 chg88 -1.3174
H4 H5 dist: 1.661998 chg5 0.6370
--------------------------------------------------
H4 rOH= 0.999393 EF@H_along_bisector= 0.048039 a.u.
EF@H_along_OH_bond= 0.063004 a.u.
H5 H5 dist: 0.000000 chg5 0.6370
H5 O88 dist: 1.000710 chg88 -1.3174
H5 H4 dist: 1.661998 chg4 0.6428
--------------------------------------------------
H5 rOH= 1.000710 EF@H_along_bisector= 0.046210 a.u.
EF@H_along_OH_bond= 0.063271 a.u.
Ow idx: 89
==================================================
H6 H6 dist: 0.000000 chg6 0.6440
H6 O89 dist: 1.008513 chg89 -1.3243
H6 H7 dist: 1.632131 chg7 0.6362
--------------------------------------------------
H6 rOH= 1.008513 EF@H_along_bisector= 0.083824 a.u.
EF@H_along_OH_bond= 0.095432 a.u.
H7 H7 dist: 0.000000 chg7 0.6362
H7 O89 dist: 1.005884 chg89 -1.3243
H7 H6 dist: 1.632131 chg6 0.6440
--------------------------------------------------
H7 rOH= 1.005884 EF@H_along_bisector= 0.061299 a.u.
EF@H_along_OH_bond= 0.063774 a.u.
Ow idx: 90
==================================================
H8 H8 dist: 0.000000 chg8 0.6352
H8 O90 dist: 0.994536 chg90 -1.3190
H8 H9 dist: 1.672475 chg9 0.6457
--------------------------------------------------
H8 rOH= 0.994536 EF@H_along_bisector= 0.051897 a.u.
EF@H_along_OH_bond= 0.054365 a.u.
H9 H9 dist: 0.000000 chg9 0.6457
H9 O90 dist: 1.014367 chg90 -1.3190
H9 H8 dist: 1.672475 chg8 0.6352
--------------------------------------------------
H9 rOH= 1.014367 EF@H_along_bisector= 0.069973 a.u.
EF@H_along_OH_bond= 0.099288 a.u.
Ow idx: 91
==================================================
H10 H10 dist: 0.000000 chg10 0.6370
H10 O91 dist: 1.002876 chg91 -1.3219
H10 H11 dist: 1.652785 chg11 0.6403
--------------------------------------------------
H10 rOH= 1.002876 EF@H_along_bisector= 0.059421 a.u.
EF@H_along_OH_bond= 0.066950 a.u.
H11 H11 dist: 0.000000 chg11 0.6403
H11 O91 dist: 1.006199 chg91 -1.3219
H11 H10 dist: 1.652785 chg10 0.6370
--------------------------------------------------
H11 rOH= 1.006199 EF@H_along_bisector= 0.053592 a.u.
EF@H_along_OH_bond= 0.067094 a.u.
Ow idx: 92
==================================================
H12 H12 dist: 0.000000 chg12 0.6418
H12 O92 dist: 1.013864 chg92 -1.3296
H12 H13 dist: 1.635166 chg13 0.6394
--------------------------------------------------
H12 rOH= 1.013864 EF@H_along_bisector= 0.083872 a.u.
EF@H_along_OH_bond= 0.094820 a.u.
H13 H13 dist: 0.000000 chg13 0.6394
H13 O92 dist: 1.002436 chg92 -1.3296
H13 H12 dist: 1.635166 chg12 0.6418
--------------------------------------------------
H13 rOH= 1.002436 EF@H_along_bisector= 0.062456 a.u.
EF@H_along_OH_bond= 0.068858 a.u.
Ow idx: 93
==================================================
H14 H14 dist: 0.000000 chg14 0.6346
H14 O93 dist: 0.994925 chg93 -1.3122
H14 H15 dist: 1.623866 chg15 0.6440
--------------------------------------------------
H14 rOH= 0.994925 EF@H_along_bisector= 0.064580 a.u.
EF@H_along_OH_bond= 0.057257 a.u.
H15 H15 dist: 0.000000 chg15 0.6440
H15 O93 dist: 1.010736 chg93 -1.3122
H15 H14 dist: 1.623866 chg14 0.6346
--------------------------------------------------
H15 rOH= 1.010736 EF@H_along_bisector= 0.081823 a.u.
EF@H_along_OH_bond= 0.096876 a.u.
Ow idx: 94
==================================================
H16 H16 dist: 0.000000 chg16 0.6222
H16 O94 dist: 1.002251 chg94 -1.2094
H16 H17 dist: 1.597805 chg17 0.6191
--------------------------------------------------
H16 rOH= 1.002251 EF@H_along_bisector= 0.065034 a.u.
EF@H_along_OH_bond= 0.072093 a.u.
H17 H17 dist: 0.000000 chg17 0.6191
H17 O94 dist: 0.993212 chg94 -1.2094
H17 H16 dist: 1.597805 chg16 0.6222
--------------------------------------------------
H17 rOH= 0.993212 EF@H_along_bisector= 0.058109 a.u.
EF@H_along_OH_bond= 0.064351 a.u.
Ow idx: 95
==================================================
H18 H18 dist: 0.000000 chg18 0.6267
H18 O95 dist: 1.000119 chg95 -1.2021
H18 H19 dist: 1.608759 chg19 0.6154
--------------------------------------------------
H18 rOH= 1.000119 EF@H_along_bisector= 0.037965 a.u.
EF@H_along_OH_bond= 0.055437 a.u.
H19 H19 dist: 0.000000 chg19 0.6154
H19 O95 dist: 0.989474 chg95 -1.2021
H19 H18 dist: 1.608759 chg18 0.6267
--------------------------------------------------
H19 rOH= 0.989474 EF@H_along_bisector= 0.036389 a.u.
EF@H_along_OH_bond= 0.045720 a.u.
Ow idx: 96
==================================================
H20 H20 dist: 0.000000 chg20 0.6096
H20 O96 dist: 0.979581 chg96 -1.1870
H20 H21 dist: 1.573506 chg21 0.6111
--------------------------------------------------
H20 rOH= 0.979581 EF@H_along_bisector= 0.033998 a.u.
EF@H_along_OH_bond= 0.039209 a.u.
H21 H21 dist: 0.000000 chg21 0.6111
H21 O96 dist: 0.991504 chg96 -1.1870
H21 H20 dist: 1.573506 chg20 0.6096
--------------------------------------------------
H21 rOH= 0.991504 EF@H_along_bisector= 0.043982 a.u.
EF@H_along_OH_bond= 0.043819 a.u.
Ow idx: 106
==================================================
H22 H22 dist: 0.000000 chg22 0.6428
H22 O106 dist: 0.999399 chg106 -1.3174
H22 H23 dist: 1.662002 chg23 0.6370
--------------------------------------------------
H22 rOH= 0.999399 EF@H_along_bisector= 0.048029 a.u.
EF@H_along_OH_bond= 0.063016 a.u.
H23 H23 dist: 0.000000 chg23 0.6370
H23 O106 dist: 1.000710 chg106 -1.3174
H23 H22 dist: 1.662002 chg22 0.6428
--------------------------------------------------
H23 rOH= 1.000710 EF@H_along_bisector= 0.046205 a.u.
EF@H_along_OH_bond= 0.063299 a.u.
Ow idx: 107
==================================================
H24 H24 dist: 0.000000 chg24 0.6440
H24 O107 dist: 1.008516 chg107 -1.3243
H24 H25 dist: 1.632127 chg25 0.6362
--------------------------------------------------
H24 rOH= 1.008516 EF@H_along_bisector= 0.083843 a.u.
EF@H_along_OH_bond= 0.095462 a.u.
H25 H25 dist: 0.000000 chg25 0.6362
H25 O107 dist: 1.005876 chg107 -1.3243
H25 H24 dist: 1.632127 chg24 0.6440
--------------------------------------------------
H25 rOH= 1.005876 EF@H_along_bisector= 0.061326 a.u.
EF@H_along_OH_bond= 0.063764 a.u.
Ow idx: 108
==================================================
H26 H26 dist: 0.000000 chg26 0.6352
H26 O108 dist: 0.994548 chg108 -1.3190
H26 H27 dist: 1.672489 chg27 0.6457
--------------------------------------------------
H26 rOH= 0.994548 EF@H_along_bisector= 0.051824 a.u.
EF@H_along_OH_bond= 0.054078 a.u.
H27 H27 dist: 0.000000 chg27 0.6457
H27 O108 dist: 1.014367 chg108 -1.3190
H27 H26 dist: 1.672489 chg26 0.6352
--------------------------------------------------
H27 rOH= 1.014367 EF@H_along_bisector= 0.069981 a.u.
EF@H_along_OH_bond= 0.099310 a.u.
Ow idx: 109
==================================================
H28 H28 dist: 0.000000 chg28 0.6370
H28 O109 dist: 1.002876 chg109 -1.3219
H28 H29 dist: 1.652787 chg29 0.6403
--------------------------------------------------
H28 rOH= 1.002876 EF@H_along_bisector= 0.059439 a.u.
EF@H_along_OH_bond= 0.066947 a.u.
H29 H29 dist: 0.000000 chg29 0.6403
H29 O109 dist: 1.006199 chg109 -1.3219
H29 H28 dist: 1.652787 chg28 0.6370
--------------------------------------------------
H29 rOH= 1.006199 EF@H_along_bisector= 0.053608 a.u.
EF@H_along_OH_bond= 0.067093 a.u.
Ow idx: 110
==================================================
H30 H30 dist: 0.000000 chg30 0.6418
H30 O110 dist: 1.013864 chg110 -1.3296
H30 H31 dist: 1.635166 chg31 0.6394
--------------------------------------------------
H30 rOH= 1.013864 EF@H_along_bisector= 0.083850 a.u.
EF@H_along_OH_bond= 0.094800 a.u.
H31 H31 dist: 0.000000 chg31 0.6394
H31 O110 dist: 1.002440 chg110 -1.3296
H31 H30 dist: 1.635166 chg30 0.6418
--------------------------------------------------
H31 rOH= 1.002440 EF@H_along_bisector= 0.062444 a.u.
EF@H_along_OH_bond= 0.068867 a.u.
Ow idx: 111
==================================================
H32 H32 dist: 0.000000 chg32 0.6346
H32 O111 dist: 0.994925 chg111 -1.3122
H32 H33 dist: 1.623862 chg33 0.6440
--------------------------------------------------
H32 rOH= 0.994925 EF@H_along_bisector= 0.064570 a.u.
EF@H_along_OH_bond= 0.057245 a.u.
H33 H33 dist: 0.000000 chg33 0.6440
H33 O111 dist: 1.010734 chg111 -1.3122
H33 H32 dist: 1.623862 chg32 0.6346
--------------------------------------------------
H33 rOH= 1.010734 EF@H_along_bisector= 0.081818 a.u.
EF@H_along_OH_bond= 0.096882 a.u.
Ow idx: 112
==================================================
H34 H34 dist: 0.000000 chg34 0.6222
H34 O112 dist: 1.002256 chg112 -1.2094
H34 H35 dist: 1.597805 chg35 0.6191
--------------------------------------------------
H34 rOH= 1.002256 EF@H_along_bisector= 0.065027 a.u.
EF@H_along_OH_bond= 0.072095 a.u.
H35 H35 dist: 0.000000 chg35 0.6191
H35 O112 dist: 0.993213 chg112 -1.2094
H35 H34 dist: 1.597805 chg34 0.6222
--------------------------------------------------
H35 rOH= 0.993213 EF@H_along_bisector= 0.058085 a.u.
EF@H_along_OH_bond= 0.064307 a.u.
Ow idx: 113
==================================================
H36 H36 dist: 0.000000 chg36 0.6267
H36 O113 dist: 1.000119 chg113 -1.2021
H36 H37 dist: 1.608759 chg37 0.6154
--------------------------------------------------
H36 rOH= 1.000119 EF@H_along_bisector= 0.037991 a.u.
EF@H_along_OH_bond= 0.055494 a.u.
H37 H37 dist: 0.000000 chg37 0.6154
H37 O113 dist: 0.989474 chg113 -1.2021
H37 H36 dist: 1.608759 chg36 0.6267
--------------------------------------------------
H37 rOH= 0.989474 EF@H_along_bisector= 0.036398 a.u.
EF@H_along_OH_bond= 0.045710 a.u.
Ow idx: 114
==================================================
H38 H38 dist: 0.000000 chg38 0.6096
H38 O114 dist: 0.979581 chg114 -1.1870
H38 H39 dist: 1.573500 chg39 0.6111
--------------------------------------------------
H38 rOH= 0.979581 EF@H_along_bisector= 0.033816 a.u.
EF@H_along_OH_bond= 0.038929 a.u.
H39 H39 dist: 0.000000 chg39 0.6111
H39 O114 dist: 0.991498 chg114 -1.1870
H39 H38 dist: 1.573500 chg38 0.6096
--------------------------------------------------
H39 rOH= 0.991498 EF@H_along_bisector= 0.043960 a.u.
EF@H_along_OH_bond= 0.043869 a.u.
Ow idx: 124
==================================================
H40 H40 dist: 0.000000 chg40 0.6428
H40 O124 dist: 0.999399 chg124 -1.3174
H40 H41 dist: 1.662001 chg41 0.6370
--------------------------------------------------
H40 rOH= 0.999399 EF@H_along_bisector= 0.048058 a.u.
EF@H_along_OH_bond= 0.063019 a.u.
H41 H41 dist: 0.000000 chg41 0.6370
H41 O124 dist: 1.000712 chg124 -1.3174
H41 H40 dist: 1.662001 chg40 0.6428
--------------------------------------------------
H41 rOH= 1.000712 EF@H_along_bisector= 0.046221 a.u.
EF@H_along_OH_bond= 0.063263 a.u.
Ow idx: 125
==================================================
H42 H42 dist: 0.000000 chg42 0.6440
H42 O125 dist: 1.008516 chg125 -1.3243
H42 H43 dist: 1.632131 chg43 0.6362
--------------------------------------------------
H42 rOH= 1.008516 EF@H_along_bisector= 0.083822 a.u.
EF@H_along_OH_bond= 0.095423 a.u.
H43 H43 dist: 0.000000 chg43 0.6362
H43 O125 dist: 1.005876 chg125 -1.3243
H43 H42 dist: 1.632131 chg42 0.6440
--------------------------------------------------
H43 rOH= 1.005876 EF@H_along_bisector= 0.061314 a.u.
EF@H_along_OH_bond= 0.063798 a.u.
Ow idx: 126
==================================================
H44 H44 dist: 0.000000 chg44 0.6352
H44 O126 dist: 0.994545 chg126 -1.3190
H44 H45 dist: 1.672482 chg45 0.6457
--------------------------------------------------
H44 rOH= 0.994545 EF@H_along_bisector= 0.051896 a.u.
EF@H_along_OH_bond= 0.054364 a.u.
H45 H45 dist: 0.000000 chg45 0.6457
H45 O126 dist: 1.014367 chg126 -1.3190
H45 H44 dist: 1.672482 chg44 0.6352
--------------------------------------------------
H45 rOH= 1.014367 EF@H_along_bisector= 0.069978 a.u.
EF@H_along_OH_bond= 0.099285 a.u.
Ow idx: 127
==================================================
H46 H46 dist: 0.000000 chg46 0.6370
H46 O127 dist: 1.002876 chg127 -1.3219
H46 H47 dist: 1.652785 chg47 0.6403
--------------------------------------------------
H46 rOH= 1.002876 EF@H_along_bisector= 0.059444 a.u.
EF@H_along_OH_bond= 0.066951 a.u.
H47 H47 dist: 0.000000 chg47 0.6403
H47 O127 dist: 1.006199 chg127 -1.3219
H47 H46 dist: 1.652785 chg46 0.6370
--------------------------------------------------
H47 rOH= 1.006199 EF@H_along_bisector= 0.053613 a.u.
EF@H_along_OH_bond= 0.067101 a.u.
Ow idx: 128
==================================================
H48 H48 dist: 0.000000 chg48 0.6418
H48 O128 dist: 1.013866 chg128 -1.3296
H48 H49 dist: 1.635168 chg49 0.6394
--------------------------------------------------
H48 rOH= 1.013866 EF@H_along_bisector= 0.083867 a.u.
EF@H_along_OH_bond= 0.094812 a.u.
H49 H49 dist: 0.000000 chg49 0.6394
H49 O128 dist: 1.002431 chg128 -1.3296
H49 H48 dist: 1.635168 chg48 0.6418
--------------------------------------------------
H49 rOH= 1.002431 EF@H_along_bisector= 0.062451 a.u.
EF@H_along_OH_bond= 0.068872 a.u.
Ow idx: 129
==================================================
H50 H50 dist: 0.000000 chg50 0.6346
H50 O129 dist: 0.994925 chg129 -1.3122
H50 H51 dist: 1.623862 chg51 0.6440
--------------------------------------------------
H50 rOH= 0.994925 EF@H_along_bisector= 0.064580 a.u.
EF@H_along_OH_bond= 0.057255 a.u.
H51 H51 dist: 0.000000 chg51 0.6440
H51 O129 dist: 1.010734 chg129 -1.3122
H51 H50 dist: 1.623862 chg50 0.6346
--------------------------------------------------
H51 rOH= 1.010734 EF@H_along_bisector= 0.081830 a.u.
EF@H_along_OH_bond= 0.096881 a.u.
Ow idx: 130
==================================================
H52 H52 dist: 0.000000 chg52 0.6222
H52 O130 dist: 1.002256 chg130 -1.2094
H52 H53 dist: 1.597814 chg53 0.6191
--------------------------------------------------
H52 rOH= 1.002256 EF@H_along_bisector= 0.065053 a.u.
EF@H_along_OH_bond= 0.072139 a.u.
H53 H53 dist: 0.000000 chg53 0.6191
H53 O130 dist: 0.993212 chg130 -1.2094
H53 H52 dist: 1.597814 chg52 0.6222
--------------------------------------------------
H53 rOH= 0.993212 EF@H_along_bisector= 0.058096 a.u.
EF@H_along_OH_bond= 0.064299 a.u.
Ow idx: 131
==================================================
H54 H54 dist: 0.000000 chg54 0.6267
H54 O131 dist: 1.000119 chg131 -1.2021
H54 H55 dist: 1.608749 chg55 0.6154
--------------------------------------------------
H54 rOH= 1.000119 EF@H_along_bisector= 0.037984 a.u.
EF@H_along_OH_bond= 0.055493 a.u.
H55 H55 dist: 0.000000 chg55 0.6154
H55 O131 dist: 0.989465 chg131 -1.2021
H55 H54 dist: 1.608749 chg54 0.6267
--------------------------------------------------
H55 rOH= 0.989465 EF@H_along_bisector= 0.036374 a.u.
EF@H_along_OH_bond= 0.045686 a.u.
Ow idx: 132
==================================================
H56 H56 dist: 0.000000 chg56 0.6096
H56 O132 dist: 0.979581 chg132 -1.1870
H56 H57 dist: 1.573506 chg57 0.6111
--------------------------------------------------
H56 rOH= 0.979581 EF@H_along_bisector= 0.033810 a.u.
EF@H_along_OH_bond= 0.038921 a.u.
H57 H57 dist: 0.000000 chg57 0.6111
H57 O132 dist: 0.991504 chg132 -1.1870
H57 H56 dist: 1.573506 chg56 0.6096
--------------------------------------------------
H57 rOH= 0.991504 EF@H_along_bisector= 0.043953 a.u.
EF@H_along_OH_bond= 0.043866 a.u.
Ow idx: 142
==================================================
H58 H58 dist: 0.000000 chg58 0.6428
H58 O142 dist: 0.999393 chg142 -1.3174
H58 H59 dist: 1.661999 chg59 0.6370
--------------------------------------------------
H58 rOH= 0.999393 EF@H_along_bisector= 0.048044 a.u.
EF@H_along_OH_bond= 0.063014 a.u.
H59 H59 dist: 0.000000 chg59 0.6370
H59 O142 dist: 1.000715 chg142 -1.3174
H59 H58 dist: 1.661999 chg58 0.6428
--------------------------------------------------
H59 rOH= 1.000715 EF@H_along_bisector= 0.046219 a.u.
EF@H_along_OH_bond= 0.063275 a.u.
Ow idx: 143
==================================================
H60 H60 dist: 0.000000 chg60 0.6440
H60 O143 dist: 1.008516 chg143 -1.3243
H60 H61 dist: 1.632127 chg61 0.6362
--------------------------------------------------
H60 rOH= 1.008516 EF@H_along_bisector= 0.083841 a.u.
EF@H_along_OH_bond= 0.095460 a.u.
H61 H61 dist: 0.000000 chg61 0.6362
H61 O143 dist: 1.005870 chg143 -1.3243
H61 H60 dist: 1.632127 chg60 0.6440
--------------------------------------------------
H61 rOH= 1.005870 EF@H_along_bisector= 0.061311 a.u.
EF@H_along_OH_bond= 0.063778 a.u.
Ow idx: 144
==================================================
H62 H62 dist: 0.000000 chg62 0.6352
H62 O144 dist: 0.994536 chg144 -1.3190
H62 H63 dist: 1.672482 chg63 0.6457
--------------------------------------------------
H62 rOH= 0.994536 EF@H_along_bisector= 0.051903 a.u.
EF@H_along_OH_bond= 0.054372 a.u.
H63 H63 dist: 0.000000 chg63 0.6457
H63 O144 dist: 1.014368 chg144 -1.3190
H63 H62 dist: 1.672482 chg62 0.6352
--------------------------------------------------
H63 rOH= 1.014368 EF@H_along_bisector= 0.069985 a.u.
EF@H_along_OH_bond= 0.099284 a.u.
Ow idx: 145
==================================================
H64 H64 dist: 0.000000 chg64 0.6370
H64 O145 dist: 1.002876 chg145 -1.3219
H64 H65 dist: 1.652788 chg65 0.6403
--------------------------------------------------
H64 rOH= 1.002876 EF@H_along_bisector= 0.059455 a.u.
EF@H_along_OH_bond= 0.066938 a.u.
H65 H65 dist: 0.000000 chg65 0.6403
H65 O145 dist: 1.006202 chg145 -1.3219
H65 H64 dist: 1.652788 chg64 0.6370
--------------------------------------------------
H65 rOH= 1.006202 EF@H_along_bisector= 0.053629 a.u.
EF@H_along_OH_bond= 0.067108 a.u.
Ow idx: 146
==================================================
H66 H66 dist: 0.000000 chg66 0.6418
H66 O146 dist: 1.013864 chg146 -1.3296
H66 H67 dist: 1.635159 chg67 0.6394
--------------------------------------------------
H66 rOH= 1.013864 EF@H_along_bisector= 0.083845 a.u.
EF@H_along_OH_bond= 0.094789 a.u.
H67 H67 dist: 0.000000 chg67 0.6394
H67 O146 dist: 1.002427 chg146 -1.3296
H67 H66 dist: 1.635159 chg66 0.6418
--------------------------------------------------
H67 rOH= 1.002427 EF@H_along_bisector= 0.062434 a.u.
EF@H_along_OH_bond= 0.068880 a.u.
Ow idx: 147
==================================================
H68 H68 dist: 0.000000 chg68 0.6346
H68 O147 dist: 0.994925 chg147 -1.3122
H68 H69 dist: 1.623858 chg69 0.6440
--------------------------------------------------
H68 rOH= 0.994925 EF@H_along_bisector= 0.064561 a.u.
EF@H_along_OH_bond= 0.057267 a.u.
H69 H69 dist: 0.000000 chg69 0.6440
H69 O147 dist: 1.010726 chg147 -1.3122
H69 H68 dist: 1.623858 chg68 0.6346
--------------------------------------------------
H69 rOH= 1.010726 EF@H_along_bisector= 0.081821 a.u.
EF@H_along_OH_bond= 0.096869 a.u.
Ow idx: 148
==================================================
H70 H70 dist: 0.000000 chg70 0.6222
H70 O148 dist: 1.002251 chg148 -1.2094
H70 H71 dist: 1.597805 chg71 0.6191
--------------------------------------------------
H70 rOH= 1.002251 EF@H_along_bisector= 0.065026 a.u.
EF@H_along_OH_bond= 0.072103 a.u.
H71 H71 dist: 0.000000 chg71 0.6191
H71 O148 dist: 0.993212 chg148 -1.2094
H71 H70 dist: 1.597805 chg70 0.6222
--------------------------------------------------
H71 rOH= 0.993212 EF@H_along_bisector= 0.058083 a.u.
EF@H_along_OH_bond= 0.064297 a.u.
Ow idx: 149
==================================================
H72 H72 dist: 0.000000 chg72 0.6267
H72 O149 dist: 1.000119 chg149 -1.2021
H72 H73 dist: 1.608759 chg73 0.6154
--------------------------------------------------
H72 rOH= 1.000119 EF@H_along_bisector= 0.037985 a.u.
EF@H_along_OH_bond= 0.055495 a.u.
H73 H73 dist: 0.000000 chg73 0.6154
H73 O149 dist: 0.989479 chg149 -1.2021
H73 H72 dist: 1.608759 chg72 0.6267
--------------------------------------------------
H73 rOH= 0.989479 EF@H_along_bisector= 0.036393 a.u.
EF@H_along_OH_bond= 0.045704 a.u.
Ow idx: 150
==================================================
H74 H74 dist: 0.000000 chg74 0.6096
H74 O150 dist: 0.979581 chg150 -1.1870
H74 H75 dist: 1.573500 chg75 0.6111
--------------------------------------------------
H74 rOH= 0.979581 EF@H_along_bisector= 0.033812 a.u.
EF@H_along_OH_bond= 0.038930 a.u.
H75 H75 dist: 0.000000 chg75 0.6111
H75 O150 dist: 0.991498 chg150 -1.1870
H75 H74 dist: 1.573500 chg74 0.6096
--------------------------------------------------
H75 rOH= 0.991498 EF@H_along_bisector= 0.043952 a.u.
EF@H_along_OH_bond= 0.043859 a.u.
Results from the DVR calculations for the OH stretches¶
In [7]:
# Take only the rows that contain data
DVR_data= structure.row.data.DVR_data[ ~np.all(structure.row.data.DVR_data == 0, axis=1) ]
# Calculate the anharmonic frequency E1-E2, then add it to the DVR_data
def calc_anhfreq(x):
return np.append(x,x[2]-x[1])
DVR_data= np.apply_along_axis(calc_anhfreq, axis=1, arr=DVR_data)
# Print extracted and calculated data
print(tabulate(DVR_data, headers=["Harmonic [cm-1]", "E0 [eV]","E1 [eV]","E2 [eV]", "Anharmonic [cm-1]"]))
Harmonic [cm-1] E0 [eV] E1 [eV] E2 [eV] Anharmonic [cm-1]
----------------- --------- --------- --------- -------------------
3179.2 1550.78 4414.91 6933.87 2864.13
3137.25 1527.16 4330.91 6770.09 2803.75
3022.41 1469.35 4154.44 6474.03 2685.09
3060.48 1487.08 4202.43 6543.59 2715.34
3278.03 1604.6 4597.52 7285.14 2992.91
2926.6 1418.18 3984.3 6165.43 2566.12
3115.3 1516.64 4301.4 6721.81 2784.76
3057.02 1485.43 4197.83 6533.89 2712.4
2937.51 1423.5 4001.69 6208.73 2578.19
3114.22 1516.41 4302.9 6736.06 2786.49
3268.95 1599.41 4578.67 7244.98 2979.26
2997.85 1456.58 4114.13 6404.96 2657.55
3167.22 1547.77 4419.71 6976.39 2871.95
3336.44 1637.7 4715.44 7520.78 3077.74
3192.08 1558.6 4445.61 7002.42 2887.01
3391.72 1666.18 4804.79 7677.14 3138.6
3616.24 1788.05 5213.32 8447.18 3425.27
3360.2 1648.92 4746.1 7563.39 3097.17
PES data example¶
In [8]:
# Collect all PES data
print ("=== Labels for OH_PES associated with the structure ===")
all_PES_keys= ([key for key, value in structure.row.data.items() if 'OH_PES' in key])
print(all_PES_keys)
all_PES= [{key:value} for key, value in structure.row.data.items() if 'OH_PES' in key]
all_PES
=== Labels for OH_PES associated with the structure === ['OH_PES_O91.H11', 'OH_PES_O89.H07', 'OH_PES_O89.H06', 'OH_PES_O95.H18', 'OH_PES_O90.H09', 'OH_PES_O91.H10', 'OH_PES_O90.H08', 'OH_PES_O93.H14', 'OH_PES_O92.H13', 'OH_PES_O88.H04', 'OH_PES_O95.H19', 'OH_PES_O93.H15', 'OH_PES_O92.H12', 'OH_PES_O94.H16', 'OH_PES_O94.H17', 'OH_PES_O88.H05', 'OH_PES_O96.H21', 'OH_PES_O96.H20']
Out[8]:
[{'OH_PES_O91.H11': array([[ 6.31203000e-01, -8.74305181e+02],
[ 6.46203000e-01, -8.75330831e+02],
[ 6.61203000e-01, -8.76242815e+02],
[ 6.76203000e-01, -8.77052612e+02],
[ 6.91203000e-01, -8.77770556e+02],
[ 7.06203000e-01, -8.78405950e+02],
[ 7.21203000e-01, -8.78967191e+02],
[ 7.36203000e-01, -8.79461842e+02],
[ 7.51203000e-01, -8.79896708e+02],
[ 7.66203000e-01, -8.80277924e+02],
[ 7.81203000e-01, -8.80611022e+02],
[ 7.96203000e-01, -8.80900985e+02],
[ 8.11203000e-01, -8.81152313e+02],
[ 8.26203000e-01, -8.81369058e+02],
[ 8.41203000e-01, -8.81554858e+02],
[ 8.56203000e-01, -8.81712994e+02],
[ 8.71203000e-01, -8.81846418e+02],
[ 8.86203000e-01, -8.81957788e+02],
[ 9.01203000e-01, -8.82049496e+02],
[ 9.16203000e-01, -8.82123709e+02],
[ 9.31203000e-01, -8.82182376e+02],
[ 9.46203000e-01, -8.82227247e+02],
[ 9.61203000e-01, -8.82259877e+02],
[ 9.76203000e-01, -8.82281681e+02],
[ 9.91203000e-01, -8.82293947e+02],
[ 1.00620000e+00, -8.82297821e+02],
[ 1.02120000e+00, -8.82294348e+02],
[ 1.03620000e+00, -8.82284460e+02],
[ 1.05120000e+00, -8.82269014e+02],
[ 1.06620000e+00, -8.82248783e+02],
[ 1.08120000e+00, -8.82224463e+02],
[ 1.09620000e+00, -8.82196684e+02],
[ 1.11120000e+00, -8.82166005e+02],
[ 1.12620000e+00, -8.82132939e+02],
[ 1.14120000e+00, -8.82097953e+02],
[ 1.15620000e+00, -8.82061460e+02],
[ 1.17120000e+00, -8.82023845e+02],
[ 1.18620000e+00, -8.81985430e+02],
[ 1.20120000e+00, -8.81946519e+02],
[ 1.21620000e+00, -8.81907388e+02],
[ 1.23120000e+00, -8.81868268e+02],
[ 1.24620000e+00, -8.81829366e+02],
[ 1.26120000e+00, -8.81790875e+02],
[ 1.27620000e+00, -8.81752935e+02],
[ 1.29120000e+00, -8.81715683e+02],
[ 1.30620000e+00, -8.81679230e+02],
[ 1.32120000e+00, -8.81643660e+02],
[ 1.33620000e+00, -8.81609050e+02],
[ 1.35120000e+00, -8.81575452e+02],
[ 1.36620000e+00, -8.81542893e+02],
[ 1.38120000e+00, -8.81511394e+02],
[ 1.39620000e+00, -8.81480942e+02],
[ 1.41120000e+00, -8.81451512e+02],
[ 1.42620000e+00, -8.81423051e+02],
[ 1.44120000e+00, -8.81395501e+02],
[ 1.45620000e+00, -8.81368786e+02],
[ 1.47120000e+00, -8.81342803e+02],
[ 1.48620000e+00, -8.81317440e+02],
[ 1.50120000e+00, -8.81292554e+02],
[ 1.51620000e+00, -8.81267976e+02],
[ 1.53120000e+00, -8.81243515e+02],
[ 1.54620000e+00, -8.81218963e+02],
[ 1.56120000e+00, -8.81194055e+02],
[ 1.57620000e+00, -8.81168521e+02],
[ 1.59120000e+00, -8.81142061e+02],
[ 1.60620000e+00, -8.81114327e+02],
[ 1.62120000e+00, -8.81084929e+02],
[ 1.63620000e+00, -8.81053445e+02],
[ 1.65120000e+00, -8.81019395e+02],
[ 1.66620000e+00, -8.80982251e+02],
[ 1.68120000e+00, -8.80941429e+02]])},
{'OH_PES_O89.H07': array([[ 6.30877000e-01, -8.74288218e+02],
[ 6.45877000e-01, -8.75316308e+02],
[ 6.60877000e-01, -8.76230454e+02],
[ 6.75877000e-01, -8.77042155e+02],
[ 6.90877000e-01, -8.77761762e+02],
[ 7.05877000e-01, -8.78398619e+02],
[ 7.20877000e-01, -8.78961133e+02],
[ 7.35877000e-01, -8.79456884e+02],
[ 7.50877000e-01, -8.79892700e+02],
[ 7.65877000e-01, -8.80274740e+02],
[ 7.80877000e-01, -8.80608547e+02],
[ 7.95877000e-01, -8.80899109e+02],
[ 8.10877000e-01, -8.81150937e+02],
[ 8.25877000e-01, -8.81368089e+02],
[ 8.40877000e-01, -8.81554217e+02],
[ 8.55877000e-01, -8.81712609e+02],
[ 8.70877000e-01, -8.81846229e+02],
[ 8.85877000e-01, -8.81957749e+02],
[ 9.00877000e-01, -8.82049582e+02],
[ 9.15877000e-01, -8.82123876e+02],
[ 9.30877000e-01, -8.82182576e+02],
[ 9.45877000e-01, -8.82227433e+02],
[ 9.60877000e-01, -8.82260039e+02],
[ 9.75877000e-01, -8.82281802e+02],
[ 9.90877000e-01, -8.82294015e+02],
[ 1.00588000e+00, -8.82297821e+02],
[ 1.02088000e+00, -8.82294274e+02],
[ 1.03588000e+00, -8.82284314e+02],
[ 1.05088000e+00, -8.82268797e+02],
[ 1.06588000e+00, -8.82248496e+02],
[ 1.08088000e+00, -8.82224095e+02],
[ 1.09588000e+00, -8.82196230e+02],
[ 1.11088000e+00, -8.82165476e+02],
[ 1.12588000e+00, -8.82132334e+02],
[ 1.14088000e+00, -8.82097279e+02],
[ 1.15588000e+00, -8.82060727e+02],
[ 1.17088000e+00, -8.82023049e+02],
[ 1.18588000e+00, -8.81984579e+02],
[ 1.20088000e+00, -8.81945620e+02],
[ 1.21588000e+00, -8.81906440e+02],
[ 1.23088000e+00, -8.81867266e+02],
[ 1.24588000e+00, -8.81828301e+02],
[ 1.26088000e+00, -8.81789738e+02],
[ 1.27588000e+00, -8.81751720e+02],
[ 1.29088000e+00, -8.81714383e+02],
[ 1.30588000e+00, -8.81677831e+02],
[ 1.32088000e+00, -8.81642148e+02],
[ 1.33588000e+00, -8.81607405e+02],
[ 1.35088000e+00, -8.81573641e+02],
[ 1.36588000e+00, -8.81540882e+02],
[ 1.38088000e+00, -8.81509132e+02],
[ 1.39588000e+00, -8.81478371e+02],
[ 1.41088000e+00, -8.81448565e+02],
[ 1.42588000e+00, -8.81419661e+02],
[ 1.44088000e+00, -8.81391582e+02],
[ 1.45588000e+00, -8.81364220e+02],
[ 1.47088000e+00, -8.81337461e+02],
[ 1.48588000e+00, -8.81311165e+02],
[ 1.50088000e+00, -8.81285166e+02],
[ 1.51588000e+00, -8.81259266e+02],
[ 1.53088000e+00, -8.81233243e+02],
[ 1.54588000e+00, -8.81206842e+02],
[ 1.56088000e+00, -8.81179772e+02],
[ 1.57588000e+00, -8.81151717e+02],
[ 1.59088000e+00, -8.81122300e+02],
[ 1.60588000e+00, -8.81091134e+02],
[ 1.62088000e+00, -8.81057733e+02],
[ 1.63588000e+00, -8.81021612e+02],
[ 1.65088000e+00, -8.80982209e+02],
[ 1.66588000e+00, -8.80938891e+02],
[ 1.68088000e+00, -8.80890954e+02]])},
{'OH_PES_O89.H06': array([[ 6.33519000e-01, -8.74451732e+02],
[ 6.48519000e-01, -8.75459286e+02],
[ 6.63519000e-01, -8.76355079e+02],
[ 6.78519000e-01, -8.77150400e+02],
[ 6.93519000e-01, -8.77855411e+02],
[ 7.08519000e-01, -8.78479277e+02],
[ 7.23519000e-01, -8.79030251e+02],
[ 7.38519000e-01, -8.79515773e+02],
[ 7.53519000e-01, -8.79942555e+02],
[ 7.68519000e-01, -8.80316636e+02],
[ 7.83519000e-01, -8.80643456e+02],
[ 7.98519000e-01, -8.80927919e+02],
[ 8.13519000e-01, -8.81174438e+02],
[ 8.28519000e-01, -8.81386993e+02],
[ 8.43519000e-01, -8.81569166e+02],
[ 8.58519000e-01, -8.81724200e+02],
[ 8.73519000e-01, -8.81855009e+02],
[ 8.88519000e-01, -8.81964193e+02],
[ 9.03519000e-01, -8.82054120e+02],
[ 9.18519000e-01, -8.82126901e+02],
[ 9.33519000e-01, -8.82184430e+02],
[ 9.48519000e-01, -8.82228433e+02],
[ 9.63519000e-01, -8.82260440e+02],
[ 9.78519000e-01, -8.82281862e+02],
[ 9.93519000e-01, -8.82293945e+02],
[ 1.00852000e+00, -8.82297821e+02],
[ 1.02352000e+00, -8.82294506e+02],
[ 1.03852000e+00, -8.82284912e+02],
[ 1.05352000e+00, -8.82269872e+02],
[ 1.06852000e+00, -8.82250130e+02],
[ 1.08352000e+00, -8.82226363e+02],
[ 1.09852000e+00, -8.82199186e+02],
[ 1.11352000e+00, -8.82169149e+02],
[ 1.12852000e+00, -8.82136756e+02],
[ 1.14352000e+00, -8.82102454e+02],
[ 1.15852000e+00, -8.82066647e+02],
[ 1.17352000e+00, -8.82029685e+02],
[ 1.18852000e+00, -8.81991893e+02],
[ 1.20352000e+00, -8.81953563e+02],
[ 1.21852000e+00, -8.81914950e+02],
[ 1.23352000e+00, -8.81876305e+02],
[ 1.24852000e+00, -8.81837824e+02],
[ 1.26352000e+00, -8.81799685e+02],
[ 1.27852000e+00, -8.81762046e+02],
[ 1.29352000e+00, -8.81725034e+02],
[ 1.30852000e+00, -8.81688758e+02],
[ 1.32352000e+00, -8.81653310e+02],
[ 1.33852000e+00, -8.81618772e+02],
[ 1.35352000e+00, -8.81585211e+02],
[ 1.36852000e+00, -8.81552653e+02],
[ 1.38352000e+00, -8.81521122e+02],
[ 1.39852000e+00, -8.81490617e+02],
[ 1.41352000e+00, -8.81461098e+02],
[ 1.42852000e+00, -8.81432538e+02],
[ 1.44352000e+00, -8.81404870e+02],
[ 1.45852000e+00, -8.81378030e+02],
[ 1.47352000e+00, -8.81351922e+02],
[ 1.48852000e+00, -8.81326427e+02],
[ 1.50352000e+00, -8.81301415e+02],
[ 1.51852000e+00, -8.81276722e+02],
[ 1.53352000e+00, -8.81252155e+02],
[ 1.54852000e+00, -8.81227506e+02],
[ 1.56352000e+00, -8.81202546e+02],
[ 1.57852000e+00, -8.81177012e+02],
[ 1.59352000e+00, -8.81150613e+02],
[ 1.60852000e+00, -8.81123028e+02],
[ 1.62352000e+00, -8.81093893e+02],
[ 1.63852000e+00, -8.81062824e+02],
[ 1.65352000e+00, -8.81029371e+02],
[ 1.66852000e+00, -8.80993048e+02],
[ 1.68352000e+00, -8.80953334e+02]])},
{'OH_PES_O95.H18': array([[ 6.25121000e-01, -8.73848802e+02],
[ 6.40121000e-01, -8.74927356e+02],
[ 6.55121000e-01, -8.75886996e+02],
[ 6.70121000e-01, -8.76739680e+02],
[ 6.85121000e-01, -8.77496192e+02],
[ 7.00121000e-01, -8.78166253e+02],
[ 7.15121000e-01, -8.78758611e+02],
[ 7.30121000e-01, -8.79281158e+02],
[ 7.45121000e-01, -8.79741001e+02],
[ 7.60121000e-01, -8.80144537e+02],
[ 7.75121000e-01, -8.80497526e+02],
[ 7.90121000e-01, -8.80805185e+02],
[ 8.05121000e-01, -8.81072197e+02],
[ 8.20121000e-01, -8.81302782e+02],
[ 8.35121000e-01, -8.81500731e+02],
[ 8.50121000e-01, -8.81669457e+02],
[ 8.65121000e-01, -8.81812060e+02],
[ 8.80121000e-01, -8.81931310e+02],
[ 8.95121000e-01, -8.82029703e+02],
[ 9.10121000e-01, -8.82109487e+02],
[ 9.25121000e-01, -8.82172699e+02],
[ 9.40121000e-01, -8.82221150e+02],
[ 9.55121000e-01, -8.82256483e+02],
[ 9.70121000e-01, -8.82280166e+02],
[ 9.85121000e-01, -8.82293543e+02],
[ 1.00012000e+00, -8.82297821e+02],
[ 1.01512000e+00, -8.82294077e+02],
[ 1.03012000e+00, -8.82283291e+02],
[ 1.04512000e+00, -8.82266366e+02],
[ 1.06012000e+00, -8.82244109e+02],
[ 1.07512000e+00, -8.82217243e+02],
[ 1.09012000e+00, -8.82186437e+02],
[ 1.10512000e+00, -8.82152282e+02],
[ 1.12012000e+00, -8.82115333e+02],
[ 1.13512000e+00, -8.82076082e+02],
[ 1.15012000e+00, -8.82034983e+02],
[ 1.16512000e+00, -8.81992425e+02],
[ 1.18012000e+00, -8.81948784e+02],
[ 1.19512000e+00, -8.81904384e+02],
[ 1.21012000e+00, -8.81859521e+02],
[ 1.22512000e+00, -8.81814455e+02],
[ 1.24012000e+00, -8.81769425e+02],
[ 1.25512000e+00, -8.81724649e+02],
[ 1.27012000e+00, -8.81680297e+02],
[ 1.28512000e+00, -8.81636528e+02],
[ 1.30012000e+00, -8.81593489e+02],
[ 1.31512000e+00, -8.81551309e+02],
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{'OH_PES_O94.H17': array([[ 6.18210000e-01, -8.73345731e+02],
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{'OH_PES_O88.H05': array([[ 6.25716000e-01, -8.73955408e+02],
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{'OH_PES_O96.H21': array([[ 6.16500000e-01, -8.73241702e+02],
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[ 1.65150000e+00, -8.80592544e+02],
[ 1.66650000e+00, -8.80570194e+02]])},
{'OH_PES_O96.H20': array([[ 6.04582000e-01, -8.72300216e+02],
[ 6.19582000e-01, -8.73561937e+02],
[ 6.34582000e-01, -8.74686005e+02],
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[ 1.63958000e+00, -8.79741158e+02],
[ 1.65458000e+00, -8.79692874e+02]])}]
In [9]:
# Make plot of all PES in the row
plt.rcParams['figure.figsize'] = (10,7)
plt.xlabel("$R_{OH}$ [Å]")
plt.ylabel("$E_{total}$ [eV]")
for i in range(len(all_PES)):
D=[value for key,value in all_PES[i].items()]
plt.plot(D[0][:,0],D[0][:,1])
In [10]:
# Plot for selected OH_PES
PES= structure.row.data[all_PES_keys[0]]
plt.xlabel("$R_{OH}$ [Å]")
plt.ylabel("$E_{total}$ [eV]")
plt.title(all_PES_keys[0])
plt.plot(PES[:,0],PES[:,1])
Out[10]:
[<matplotlib.lines.Line2D at 0x7f40ee986cf8>]
Anharmonicity and harmonic frequency calculations (see link)¶
http://www.theochem.unito.it/crystal_tuto/mssc2008_cd/tutorials/vibfreq/vibfreq_tut.html#anharm
In [11]:
# Take only the rows that contain data
DVR_data= structure.row.data.DVR_data[ ~np.all(structure.row.data.DVR_data == 0, axis=1) ]
# Calculate harmonic frequecies from the energy levels
def calc_harm(x):
return [3*(x[2]-x[1])-(x[3]-x[1])]
harmonic= np.apply_along_axis(calc_harm, axis=1, arr=DVR_data)
print (harmonic)
[[3209.298] [3168.328] [3050.583] [3089.524] [3298.198] [2951.102] [3149.124] [3088.742] [2949.342] [3139.833] [3292.214] [3024.27 ] [3187.219] [3350.137] [3217.215] [3404.848] [3616.687] [3377.052]]
In [12]:
# Take only the rows that contain data
DVR_data= structure.row.data.DVR_data[ ~np.all(structure.row.data.DVR_data == 0, axis=1) ]
# Calculate anharmonicity
def anharm_corr(x):
w01= x[2]-x[1]
w02= x[3]-x[1]
return [(2*w01-w02)/2.]
anharmonicity= np.apply_along_axis(anharm_corr, axis=1, arr=DVR_data)
print (anharmonicity)
[[172.5855] [182.288 ] [182.748 ] [187.091 ] [152.6435] [192.493 ] [182.18 ] [188.171 ] [185.575 ] [176.6705] [156.4765] [183.36 ] [157.636 ] [136.1995] [165.103 ] [133.123 ] [ 95.708 ] [139.94 ]]