bader analyse

Asked by chenhao on 2017-10-13

For the H4SiO4 molecule calculation ,adding 'save-bader-charge T' to the H4SiO4.fdf file,and I get the H4SiO4.BADER file in the output files.The input file for grid2cube is then edited like this:
H4SiO4
bader
4.0 6.0 5.0
2
unformatted
And then run the grid2cube script,I get H4SiO4.BADER.cube file.Using 'bader H4SiO4.BADER.cube' ,I get ACF.dat AVF.dat and BCF.dat.
The ACF.dat shows like this:
    # X Y Z CHARGE MIN DIST ATOMIC VOL
 --------------------------------------------------------------------------------
    1 12.985385 15.505082 14.949571 10.104598 0.673976 4.119593
    2 11.820778 12.624454 15.381916 9.492838 1.147713 136.273362
    3 11.819069 16.513933 12.215859 9.509975 1.169969 136.910854
    4 12.192240 17.652769 17.094154 9.508529 1.175731 136.717999
    5 16.105429 15.234390 15.095061 9.506354 1.145698 136.412646
    6 10.033790 12.340021 15.156147 1.440040 0.178384 23.421147
    7 16.944937 13.928174 14.142571 1.428232 0.165856 23.362219
    8 12.184941 18.209324 11.654619 1.427285 0.228300 23.019366
    9 12.922251 17.565752 18.762887 1.428608 0.187773 23.137222
 --------------------------------------------------------------------------------
    VACUUM CHARGE: 0.1557
    VACUUM VOLUME: 6105.0016
    NUMBER OF ELECTRONS: 54.0022
The charge for the Si and O is normal ,but H atoms have an extra electron.There are 4 H atoms,and the total number of electrons is 4 more.

Using the same method ,I calculate H2O molecule.The ACF.dat for the H2O shows like this :
    # X Y Z CHARGE MIN DIST ATOMIC VOL
 --------------------------------------------------------------------------------
    1 5.920812 5.973094 5.974975 9.044021 1.074720 130.011325
    2 7.351335 7.080474 5.974975 1.475151 0.158616 22.674547
    3 4.490288 7.080474 5.974975 1.475151 0.158606 22.674547
 --------------------------------------------------------------------------------
    VACUUM CHARGE: 0.0525
    VACUUM VOLUME: 1413.0492
    NUMBER OF ELECTRONS: 12.0468
The same thing happened´╝îThe charge for the O is normal ,but H atoms have an extra electron.
I really do not konw why ,please help me ,thank you .

Question information

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Status:
Solved
For:
Siesta Edit question
Assignee:
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Solved by:
chenhao
Solved:
2017-10-17
Last query:
2017-10-17
Last reply:
2017-10-13
Nick Papior (nickpapior) said : #1

Have you looked in the documentation for 4.0.1? There is an explicit remark about bader charge analysis using Hydrogen atoms.

There are two flags to control the "range" of the model charge:

bader-core-radius-standard 1. Bohr
bader-core-radius-hydrogen 0.6 Bohr

where the defaults are as written here. These values have an effect of the bader charges.

chenhao (guofudyiyasuo) said : #2

Thank you very much,I read the manual,and I tried to change the value of the range
bader-core-radius-standard 1. Bohr
bader-core-radius-hydrogen 0.6 Bohr
but it did not work .
However ,when I used
bader h2o-pop.RHO.cube -ref h2o-pop.BADER.cube. It works.The ACF.dat shows like this:
    # X Y Z CHARGE MIN DIST ATOMIC VOL
 --------------------------------------------------------------------------------
    1 3.993106 5.973094 4.912757 7.043854 1.074722 130.011325
    2 5.423629 7.080474 4.912757 0.451814 0.158616 22.674547
    3 2.562582 7.080474 4.912757 0.451814 0.158609 22.674547
 --------------------------------------------------------------------------------
    VACUUM CHARGE: 0.0525
    VACUUM VOLUME: 1413.0492
    NUMBER OF ELECTRONS: 8.0000

And the same as H4SiO4 .The ACF.dat shows like this:
    # X Y Z CHARGE MIN DIST ATOMIC VOL
 --------------------------------------------------------------------------------
    1 12.733684 14.613695 15.385960 0.074406 0.468900 5.785595
    2 11.384629 11.642392 16.257708 7.377257 0.909602 157.196763
    3 11.402304 15.428985 12.392228 7.365812 0.915768 154.153968
    4 12.075586 16.776087 17.893391 7.274328 0.743156 152.953993
    5 16.083204 14.584161 14.953689 7.490442 0.918361 158.396738
    6 9.600861 15.389174 12.146170 0.557142 0.222658 29.099401
    7 12.739665 18.468786 17.873003 0.650136 0.307175 31.842201
    8 11.670133 10.928612 17.905493 0.557767 0.156987 28.885119
    9 16.811116 13.632854 13.584434 0.434216 0.066751 25.285194
 --------------------------------------------------------------------------------
    VACUUM CHARGE: 0.2183
    VACUUM VOLUME: 6004.7192
    NUMBER OF ELECTRONS: 31.9998

chenhao (guofudyiyasuo) said : #3

My problem solved