Basic questions about BADAR

[kambiz]

Hi all,

I m a newbie using BADAR program. I have two basic questions and I d really appreciate it if you please give me some help.

1. Exactly which output file should be visualized by VMD

2. Regarding the NaCl example, the ACF file is like this:

# X Y Z CHARGE MIN DIST
----------------------------------------------------------------
1 4.2634 1.4211 1.4211 0.1776 1.1369
2 1.4211 4.2634 1.4211 0.1776 1.1369
3 1.4211 1.4211 4.2634 0.1776 1.1369
4 4.2634 4.2634 4.2634 0.1776 1.1369
5 1.4211 1.4211 1.4211 7.8297 1.6580
6 4.2634 4.2634 1.4211 7.8181 1.6580
7 4.2634 1.4211 4.2634 7.8267 1.6580
8 1.4211 4.2634 4.2634 7.8151 1.6580
----------------------------------------------------------------
NUMBER OF ELECTRONS: 32.00000

Does it mean that the partial charges of atom no. 1 and no. 8 are 0.1776 and 7.8151?

Cheers

[graeme]

You can view the BvAtxxxx.dat files to see the Bader volumes.

The charges are 0.1776 and 7.8151; the particles are the valence charge minus these values:

Na: 2-0.2 = 1.8
Cl: 6-7.8 = -1.8

[protonic]

Hi, first of all thanks for sharing the Bader program. I'm a super-newbie to this program and must admit I am very much confused on how to interpret the results in ACF.dat.

I'm having trouble understanding the statement above "The charges are 0.1776 and 7.8151; the particles are the valence charge minus these values.."

Does this statement mean that the net charge on a single Na atom in the cell is +0.1776e, while the Cl atom has a net charge of -7.8151e (which is rather strange)? And what exactly do you mean by "the particles are the valence charge minus these values", which seems dimensionally off (how can a particle derive from a charge?), and why the choice of 2 and 6 above (instead of 1 and 7 for instance, the number of valence electrons of Na and Cl)?

Thanks in advance.

[graeme]

Ah, first, the word "particles" should be "partials" , as in partial charges.

So the issue here is that we are typically interested in the change in charge on atoms. Calculating the change with respect to the valance charge is a natural choice. Thus, we subtract the Bader charge from the valance charge to calculate the partial charge on the atoms.

[protonic]

OK! So the statement "the particles are the valence charge minus these values" then means "the partial charges on the atoms are the valence charges minus the corresponding values in the CHARGE column in ACF.dat", right?

However, I still do not understand why you used 2 and 6 for the valence charges of Na and Cl, respectively. I was under the impression that neutral, isolated Cl atom has 7 valence electrons, and Na has 1?

Lastly, what is the unit of the CHARGE column in ACF.dat? Assuming it's "e", aren't the partial charge values above (Na^+1.8, Cl^-1.8) a bit too large (I'm thinking of obtaining something closer to Na^+1.0, Cl^-1.0)?

Thanks in advance!!

[graeme]

You are absolutely correct, the reference charge for Na should be 1 and Cl should be 7. I have been looking at MgO recently and had those charges in my head.

The unit of charge is the electron charge.

[yasemin]

Dear all,
My system is La2O3 doped with Ce. The ACF.dat results are:
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 1.1342 1.9645 0.7810 8.9141 1.2269 23.3043
2 1.1341 5.9133 0.7801 8.9114 1.2340 23.2495
3 4.5540 3.9388 0.7801 8.9115 1.2340 23.2573
4 4.5488 7.8787 0.8521 8.8976 1.2435 22.4647
5 2.2532 7.8774 4.1741 8.9105 1.2634 24.5960
6 5.6954 5.8901 4.1741 8.9105 1.2634 24.6105
7 5.6962 9.8660 4.1715 8.9097 1.2291 24.5533
8 0.0000 0.0000 0.0000 7.0904 1.0061 105.0262
9 0.0000 3.9390 0.0000 7.0765 1.0190 105.9664
10 3.4113 9.8475 0.0000 7.0765 1.0190 105.8969
11 3.4113 5.9085 0.0000 7.0762 1.0243 105.9467
12 6.8223 11.8166 4.9720 7.1214 1.0043 114.5506
13 0.1643 3.9388 4.9023 7.0573 0.9910 101.3972
14 3.3290 2.1117 4.9023 7.0573 0.9910 101.3883
15 3.3292 5.7663 4.9029 7.0587 0.9580 102.4972
16 1.1605 2.0100 3.2289 7.0144 0.9895 13.2969
17 1.1608 5.8674 3.2278 7.0168 1.0220 13.3078
18 4.5009 3.9390 3.2278 7.0168 1.0220 13.3078
19 4.5494 7.8798 3.3264 7.0715 1.0274 14.2260
20 2.2738 3.9383 1.7447 7.0529 1.0294 13.3227
21 2.2712 7.8776 1.7619 7.0376 1.0400 13.7632
22 5.6866 5.9057 1.7619 7.0376 1.0400 13.7632
23 5.6872 9.8506 1.7604 7.0392 1.0271 13.7583
24 2.2742 3.9390 4.0269 9.7335 1.1709 18.5674
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 185.0000
First 7 atoms are La, until 23 oxygen, and the 24th is Ce. I want to calculate the partial charges of La,O, and Ce. For example, for oxygen 6-7.07=-1.07 is ok. However, I can't decide for La and Ce. Their Bader charges are 8.91 and 9.73, respectively. The results of 3-8.91 and 4-9.73 are not reasonable. Is my Bader analysis corrrect? Or, how can I calculate the partial charges?

[graeme]

Look in your POTCAR file for the valance charges of the elements. My guess is O=6, La=11, Ce=12, making the partial charges for O=-1.07, La=2.09, and Ce=2.27.

[adam2412]

Hello there,
I know this is a stupid question, but I still want to ask to make sure my understanding is correct.
How to make sure that the total charges is correct that we don't have to repeat the calculation?
Is that means the [partial + charges (from BADER analysis) = ~POTCAR valance, should be to the nearest valance value in POTCAR] or the partial charges should be nearest to the expected charge of the atom. For example, if Al3+. So, the partial value should be near to 3?

Thank you in advance.

[graeme]

yes