Sorry for my naive question.
I am absolute beginner for VASP.
I tried to calculate the bader charge for the elements present on my system.
I used the following comment
bader CHGCAR
and the calculation gave me ACF.DAT, AVF.DAT, BCF.DAT
Now from the previous posts i understand that i need to look at
the ACF.DAT file for charges for individual elements.
The ACF.DAT is in the following format.
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.4826 7.2432 0.4722 105.4766
2 -2.5314 -1.4615 8.4439 7.9985 1.2274 27.1615
3 0.0000 -2.9231 4.0052 7.9932 1.2321 27.0139
4 -2.5232 -0.0071 6.2402 8.0094 1.1802 24.0248
5 -2.5314 -2.9183 10.6759 8.0483 1.1860 27.5518
6 1.2777 -3.6607 1.8145 7.9663 1.1781 23.9748
7 -3.7931 -0.7331 10.6759 8.0451 1.1860 27.3840
8 -1.2596 -2.1959 6.2402 8.0041 1.1843 23.8281
9 1.2595 -2.1959 6.2402 7.9837 1.1843 23.5116
10 -1.2776 -3.6607 1.8145 7.9481 1.1781 23.6708
11 -1.2698 -0.7331 10.6759 8.0371 1.1860 27.5042
12 0.0000 -1.4478 1.8145 7.9723 1.1781 24.3715
13 -5.0629 0.0000 0.4826 7.2432 0.4722 104.4318
14 -7.5943 -1.4615 8.4439 7.9985 1.2274 27.1615
15 -5.0629 -2.9231 4.0052 7.9932 1.2321 27.0139
16 -7.5861 -0.0071 6.2402 8.0094 1.1802 24.0248
17 -7.5943 -2.9183 10.6759 8.0483 1.1860 27.5518
18 -3.7852 -3.6607 1.8145 7.9663 1.1781 23.9748
19 -8.8559 -0.7331 10.6759 8.0451 1.1860 27.3840
20 -6.3224 -2.1959 6.2402 8.0041 1.1843 23.8281
21 -3.8033 -2.1959 6.2402 7.9837 1.1843 23.5116
22 -6.3405 -3.6607 1.8145 7.9481 1.1781 23.6708
23 -6.3327 -0.7331 10.6759 8.0371 1.1860 27.5042
24 -5.0629 -1.4478 1.8145 7.9723 1.1781 24.3715
25 2.5314 -4.3846 0.4826 7.2432 0.4722 104.4318
26 0.0000 -5.8461 8.4439 7.9985 1.2274 27.1615
27 2.5314 -7.3076 4.0052 7.9932 1.2321 27.0139
28 0.0000 -4.3775 6.2402 8.0094 1.1843 24.0248
29 0.0000 -7.3029 10.6759 8.0483 1.1860 27.5518
30 3.8091 -8.0453 1.8145 7.9663 1.1781 23.9748
31 -1.2616 -5.1177 10.6759 8.0451 1.1860 27.3840
32 1.2719 -6.5804 6.2402 8.0041 1.1843 23.8281
33 3.7910 -6.5804 6.2402 7.9837 1.1843 23.5116
34 1.2538 -8.0453 1.8145 7.9481 1.1781 23.6708
35 1.2616 -5.1177 10.6759 8.0371 1.1860 27.5042
36 2.5315 -5.8323 1.8145 7.9723 1.1781 24.3715
37 -2.5314 -4.3846 0.4826 7.2432 0.4722 103.3870
38 -5.0629 -5.8461 8.4439 7.9985 1.2274 27.1615
39 -2.5314 -7.3076 4.0052 7.9932 1.2321 27.0139
40 -5.0629 -4.3775 6.2402 8.0094 1.1843 24.0248
41 -5.0629 -7.3029 10.6759 8.0483 1.1860 27.5518
42 -1.2538 -8.0453 1.8145 7.9663 1.1781 23.9748
43 -6.3245 -5.1177 10.6759 8.0451 1.1860 27.3840
44 -3.7910 -6.5804 6.2402 8.0041 1.1843 23.8281
45 -1.2719 -6.5804 6.2402 7.9837 1.1843 23.5116
46 -3.8091 -8.0453 1.8145 7.9481 1.1781 23.6708
47 -3.8013 -5.1177 10.6759 8.0371 1.1860 27.5042
48 -2.5314 -5.8323 1.8145 7.9723 1.1781 24.3715
49 0.0000 0.0000 11.2773 0.7506 0.0227 81.7430
50 -2.5314 -1.4615 6.8159 0.0000 0.0000 0.0000
51 0.0000 -2.9231 2.3773 0.0000 0.0000 0.0000
52 0.0000 0.0000 1.1357 0.0000 0.0000 0.0000
53 -2.5314 -1.4615 10.0444 0.0000 0.0000 0.0000
54 0.0000 -2.9231 5.6039 0.0000 0.0000 0.0000
55 -5.0629 0.0000 11.2773 0.7506 0.0227 81.7430
56 -7.5943 -1.4615 6.8159 0.0000 0.0000 0.0000
57 -5.0629 -2.9231 2.3773 0.0000 0.0000 0.0000
58 -5.0629 0.0000 1.1357 0.0000 0.0000 0.0000
59 -7.5943 -1.4615 10.0444 0.0000 0.0000 0.0000
60 -5.0629 -2.9231 5.6039 0.0000 0.0000 0.0000
61 2.5314 -4.3846 11.2773 0.7506 0.0227 81.7430
62 0.0000 -5.8461 6.8159 0.0000 0.0000 0.0000
63 2.5314 -7.3076 2.3773 0.0000 0.0000 0.0000
64 2.5314 -4.3846 1.1357 0.0000 0.0000 0.0000
65 0.0000 -5.8461 10.0444 0.0000 0.0000 0.0000
66 2.5314 -7.3076 5.6039 0.0000 0.0000 0.0000
67 -2.5314 -4.3846 11.2773 0.7506 0.0227 81.7430
68 -5.0629 -5.8461 6.8159 0.0000 0.0000 0.0000
69 -2.5314 -7.3076 2.3773 0.0000 0.0000 0.0000
70 -2.5314 -4.3846 1.1357 0.0000 0.0000 0.0000
71 -5.0629 -5.8461 10.0444 0.0000 0.0000 0.0000
72 -2.5314 -7.3076 5.6039 0.0000 0.0000 0.0000
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 384.0000
(END)
------------------------------------------------------------------------------------
From the values of charge i could find that this programme lists the
total number of electrons on the structure.
So to calculate the charge do we need to substract this value
from the total number of electrons for each element.
For example. element 1 is oxygen.
The charge given is 7.2432
The total number of electrons is 8.
So the charge of element 1 on my system is 8 - 7.2432 = ~0.75.
(am i right). If not please correct me.
Also, I use PAW_PBE psueodopotential, so it gives only 6 electrons for Oxygen.
Does the above value should be substracted from 6 instead?
Please clarify.
Again sorry for the naive questions.
Best regards,
Jeyavimal
Extraction of Charge from ACF.DAT
Moderator: moderators
Re: Extraction of Charge from ACF.DAT
I see that some atoms have Bader charges of zero. You will need to include core charges, as described here:
http://theory.cm.utexas.edu/vtsttools/bader/vasp.php
For O with 6 valance electrons, you need to compare your Bader charge to 6, so the Bader charge is -1.2432
http://theory.cm.utexas.edu/vtsttools/bader/vasp.php
For O with 6 valance electrons, you need to compare your Bader charge to 6, so the Bader charge is -1.2432
Re: Extraction of Charge from ACF.DAT
I added the AECCAR0 and AECCAR2 and got CHGCAR_Sum file.
(chgsum.pl doesnt work for me so i used chgsumF.pl and that worked
and produced the CHGCAR_sum)
Then i ran
bader CHGCAR -ref CHGCAR_sum and ended up
with three files ACF.DAT, AVF.DAT, BCF.DAT.
I think i should look into the ACF.DAT file for the charges.
Here i list the file.
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.0000 5.0470 0.4695 111.7728
2 -2.5314 -1.4615 8.2677 4.1609 0.4686 4.5238
3 0.0000 -2.9231 4.1338 4.1604 0.4671 4.5852
4 -2.5314 0.0000 6.2007 4.2117 0.4632 7.4772
5 -2.5314 -2.9231 10.3346 4.1943 0.4625 13.8682
6 1.2657 -3.6538 2.0669 4.2173 0.4218 7.5044
7 -3.7972 -0.7308 10.3346 4.2212 0.4225 13.0134
8 -1.2657 -2.1923 6.2007 4.2275 0.4227 8.0876
9 1.2657 -2.1923 6.2007 4.2095 0.4632 7.1439
10 -1.2657 -3.6538 2.0669 4.1860 0.4624 6.7458
11 -1.2657 -0.7308 10.3346 4.1926 0.4625 13.4869
12 0.0000 -1.4615 2.0669 4.1873 0.4624 7.0642
13 -5.0629 0.0000 0.0000 5.0470 0.4695 111.7392
14 -7.5943 -1.4615 8.2677 4.1609 0.4686 4.5238
15 -5.0629 -2.9231 4.1338 4.1604 0.4671 4.5852
16 -7.5943 0.0000 6.2007 4.2117 0.4632 7.4770
17 -7.5943 -2.9231 10.3346 4.1943 0.4625 13.8684
18 -3.7972 -3.6538 2.0669 4.2173 0.4218 7.5044
19 -8.8601 -0.7308 10.3346 4.2212 0.4225 13.0160
20 -6.3286 -2.1923 6.2007 4.2275 0.4227 8.0876
21 -3.7972 -2.1923 6.2007 4.2095 0.4632 7.1414
22 -6.3286 -3.6538 2.0669 4.1860 0.4624 6.7461
23 -6.3286 -0.7308 10.3346 4.1926 0.4625 13.4869
24 -5.0629 -1.4615 2.0669 4.1873 0.4624 7.0639
25 2.5314 -4.3846 0.0000 5.0470 0.4695 111.7359
26 0.0000 -5.8461 8.2677 4.1609 0.4686 4.5238
27 2.5314 -7.3076 4.1338 4.1604 0.4671 4.5852
28 0.0000 -4.3846 6.2007 4.2116 0.4632 7.4685
29 0.0000 -7.3076 10.3346 4.1943 0.4625 13.8658
30 3.7972 -8.0384 2.0669 4.2173 0.4218 7.5043
31 -1.2657 -5.1153 10.3346 4.2212 0.4225 13.0111
32 1.2657 -6.5769 6.2007 4.2275 0.4227 8.0876
33 3.7972 -6.5769 6.2007 4.2095 0.4632 7.1389
34 1.2657 -8.0384 2.0669 4.1860 0.4624 6.7491
35 1.2657 -5.1153 10.3346 4.1926 0.4625 13.4895
36 2.5315 -5.8461 2.0669 4.1873 0.4624 7.0607
37 -2.5314 -4.3846 0.0000 5.0470 0.4695 111.7012
38 -5.0629 -5.8461 8.2677 4.1609 0.4686 4.5238
39 -2.5314 -7.3076 4.1338 4.1604 0.4671 4.5852
40 -5.0629 -4.3846 6.2007 4.2116 0.4632 7.4746
41 -5.0629 -7.3076 10.3346 4.1943 0.4625 13.8693
42 -1.2657 -8.0384 2.0669 4.2173 0.4218 7.5044
43 -6.3286 -5.1153 10.3346 4.2212 0.4225 13.0135
44 -3.7972 -6.5769 6.2007 4.2275 0.4227 8.0876
45 -1.2657 -6.5769 6.2007 4.2095 0.4632 7.1428
46 -3.7971 -8.0384 2.0669 4.1860 0.4624 6.7458
47 -3.7972 -5.1153 10.3346 4.1926 0.4625 13.4865
48 -2.5314 -5.8461 2.0669 4.1873 0.4624 7.0641
49 0.0000 0.0000 10.8513 6.6533 0.9447 94.4131
50 -2.5314 -1.4615 6.7175 7.5964 0.9467 32.5760
51 0.0000 -2.9231 2.5837 7.5812 0.9441 32.8922
52 0.0000 0.0000 1.5502 7.7810 0.9441 35.4730
53 -2.5314 -1.4615 9.8178 7.5744 0.9435 32.9969
54 0.0000 -2.9231 5.6840 7.5979 0.9462 32.5876
55 -5.0629 0.0000 10.8513 6.6533 0.9447 94.4133
56 -7.5943 -1.4615 6.7175 7.5964 0.9467 32.5760
57 -5.0629 -2.9231 2.5837 7.5812 0.9441 32.8922
58 -5.0629 0.0000 1.5502 7.7810 0.9441 35.4730
59 -7.5943 -1.4615 9.8178 7.5744 0.9435 32.9969
60 -5.0629 -2.9231 5.6840 7.5979 0.9462 32.5876
61 2.5314 -4.3846 10.8513 6.6533 0.9447 94.4129
62 0.0000 -5.8461 6.7175 7.5964 0.9467 32.5760
63 2.5314 -7.3076 2.5837 7.5812 0.9441 32.8922
64 2.5314 -4.3846 1.5502 7.7810 0.9441 35.4730
65 0.0000 -5.8461 9.8178 7.5744 0.9435 32.9969
66 2.5314 -7.3076 5.6840 7.5979 0.9462 32.5876
67 -2.5314 -4.3846 10.8513 6.6533 0.9447 94.4130
68 -5.0629 -5.8461 6.7175 7.5964 0.9467 32.5760
69 -2.5314 -7.3076 2.5837 7.5812 0.9441 32.8922
70 -2.5314 -4.3846 1.5502 7.7810 0.9441 35.4730
71 -5.0629 -5.8461 9.8178 7.5744 0.9435 32.9969
72 -2.5314 -7.3076 5.6840 7.5979 0.9462 32.5876
Now my question is for the case of oxygen, the valence electrons considered
is 6. So, When i performed Bader CHGCAR you advised me to subtract the
charge in ACF.DAT from 6. Now i considered both core and valence
electron density. So, now do i need to consider 6 or 8 for oxygen.
If i take 8 for oxygen (atom number 1),
i end up with the following charge.
8-5.0470 ==> 2.953
Is this correct.
If i take 6 for oxygen (atom number 1),
6-5.0470 ==> 0.953.
But for Atom number 72, which is Si,
14 - 7.5979 = 6.4021 (which is wrong).
8 - 7.5979 = 0.4021 (which is reasonable i presume)
Which method is correct.
So, please advice me on this little calculation.
Best regards,
Vimal
(chgsum.pl doesnt work for me so i used chgsumF.pl and that worked
and produced the CHGCAR_sum)
Then i ran
bader CHGCAR -ref CHGCAR_sum and ended up
with three files ACF.DAT, AVF.DAT, BCF.DAT.
I think i should look into the ACF.DAT file for the charges.
Here i list the file.
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.0000 5.0470 0.4695 111.7728
2 -2.5314 -1.4615 8.2677 4.1609 0.4686 4.5238
3 0.0000 -2.9231 4.1338 4.1604 0.4671 4.5852
4 -2.5314 0.0000 6.2007 4.2117 0.4632 7.4772
5 -2.5314 -2.9231 10.3346 4.1943 0.4625 13.8682
6 1.2657 -3.6538 2.0669 4.2173 0.4218 7.5044
7 -3.7972 -0.7308 10.3346 4.2212 0.4225 13.0134
8 -1.2657 -2.1923 6.2007 4.2275 0.4227 8.0876
9 1.2657 -2.1923 6.2007 4.2095 0.4632 7.1439
10 -1.2657 -3.6538 2.0669 4.1860 0.4624 6.7458
11 -1.2657 -0.7308 10.3346 4.1926 0.4625 13.4869
12 0.0000 -1.4615 2.0669 4.1873 0.4624 7.0642
13 -5.0629 0.0000 0.0000 5.0470 0.4695 111.7392
14 -7.5943 -1.4615 8.2677 4.1609 0.4686 4.5238
15 -5.0629 -2.9231 4.1338 4.1604 0.4671 4.5852
16 -7.5943 0.0000 6.2007 4.2117 0.4632 7.4770
17 -7.5943 -2.9231 10.3346 4.1943 0.4625 13.8684
18 -3.7972 -3.6538 2.0669 4.2173 0.4218 7.5044
19 -8.8601 -0.7308 10.3346 4.2212 0.4225 13.0160
20 -6.3286 -2.1923 6.2007 4.2275 0.4227 8.0876
21 -3.7972 -2.1923 6.2007 4.2095 0.4632 7.1414
22 -6.3286 -3.6538 2.0669 4.1860 0.4624 6.7461
23 -6.3286 -0.7308 10.3346 4.1926 0.4625 13.4869
24 -5.0629 -1.4615 2.0669 4.1873 0.4624 7.0639
25 2.5314 -4.3846 0.0000 5.0470 0.4695 111.7359
26 0.0000 -5.8461 8.2677 4.1609 0.4686 4.5238
27 2.5314 -7.3076 4.1338 4.1604 0.4671 4.5852
28 0.0000 -4.3846 6.2007 4.2116 0.4632 7.4685
29 0.0000 -7.3076 10.3346 4.1943 0.4625 13.8658
30 3.7972 -8.0384 2.0669 4.2173 0.4218 7.5043
31 -1.2657 -5.1153 10.3346 4.2212 0.4225 13.0111
32 1.2657 -6.5769 6.2007 4.2275 0.4227 8.0876
33 3.7972 -6.5769 6.2007 4.2095 0.4632 7.1389
34 1.2657 -8.0384 2.0669 4.1860 0.4624 6.7491
35 1.2657 -5.1153 10.3346 4.1926 0.4625 13.4895
36 2.5315 -5.8461 2.0669 4.1873 0.4624 7.0607
37 -2.5314 -4.3846 0.0000 5.0470 0.4695 111.7012
38 -5.0629 -5.8461 8.2677 4.1609 0.4686 4.5238
39 -2.5314 -7.3076 4.1338 4.1604 0.4671 4.5852
40 -5.0629 -4.3846 6.2007 4.2116 0.4632 7.4746
41 -5.0629 -7.3076 10.3346 4.1943 0.4625 13.8693
42 -1.2657 -8.0384 2.0669 4.2173 0.4218 7.5044
43 -6.3286 -5.1153 10.3346 4.2212 0.4225 13.0135
44 -3.7972 -6.5769 6.2007 4.2275 0.4227 8.0876
45 -1.2657 -6.5769 6.2007 4.2095 0.4632 7.1428
46 -3.7971 -8.0384 2.0669 4.1860 0.4624 6.7458
47 -3.7972 -5.1153 10.3346 4.1926 0.4625 13.4865
48 -2.5314 -5.8461 2.0669 4.1873 0.4624 7.0641
49 0.0000 0.0000 10.8513 6.6533 0.9447 94.4131
50 -2.5314 -1.4615 6.7175 7.5964 0.9467 32.5760
51 0.0000 -2.9231 2.5837 7.5812 0.9441 32.8922
52 0.0000 0.0000 1.5502 7.7810 0.9441 35.4730
53 -2.5314 -1.4615 9.8178 7.5744 0.9435 32.9969
54 0.0000 -2.9231 5.6840 7.5979 0.9462 32.5876
55 -5.0629 0.0000 10.8513 6.6533 0.9447 94.4133
56 -7.5943 -1.4615 6.7175 7.5964 0.9467 32.5760
57 -5.0629 -2.9231 2.5837 7.5812 0.9441 32.8922
58 -5.0629 0.0000 1.5502 7.7810 0.9441 35.4730
59 -7.5943 -1.4615 9.8178 7.5744 0.9435 32.9969
60 -5.0629 -2.9231 5.6840 7.5979 0.9462 32.5876
61 2.5314 -4.3846 10.8513 6.6533 0.9447 94.4129
62 0.0000 -5.8461 6.7175 7.5964 0.9467 32.5760
63 2.5314 -7.3076 2.5837 7.5812 0.9441 32.8922
64 2.5314 -4.3846 1.5502 7.7810 0.9441 35.4730
65 0.0000 -5.8461 9.8178 7.5744 0.9435 32.9969
66 2.5314 -7.3076 5.6840 7.5979 0.9462 32.5876
67 -2.5314 -4.3846 10.8513 6.6533 0.9447 94.4130
68 -5.0629 -5.8461 6.7175 7.5964 0.9467 32.5760
69 -2.5314 -7.3076 2.5837 7.5812 0.9441 32.8922
70 -2.5314 -4.3846 1.5502 7.7810 0.9441 35.4730
71 -5.0629 -5.8461 9.8178 7.5744 0.9435 32.9969
72 -2.5314 -7.3076 5.6840 7.5979 0.9462 32.5876
Now my question is for the case of oxygen, the valence electrons considered
is 6. So, When i performed Bader CHGCAR you advised me to subtract the
charge in ACF.DAT from 6. Now i considered both core and valence
electron density. So, now do i need to consider 6 or 8 for oxygen.
If i take 8 for oxygen (atom number 1),
i end up with the following charge.
8-5.0470 ==> 2.953
Is this correct.
If i take 6 for oxygen (atom number 1),
6-5.0470 ==> 0.953.
But for Atom number 72, which is Si,
14 - 7.5979 = 6.4021 (which is wrong).
8 - 7.5979 = 0.4021 (which is reasonable i presume)
Which method is correct.
So, please advice me on this little calculation.
Best regards,
Vimal
Re: Extraction of Charge from ACF.DAT
The total number of electrons reported by the bader analysis should be equal to the total number of valence electrons in your system. If there are 6 valence electrons for oxygen, you should that as your reference. So if the first atom is O, the charge on that is 6-5.0470=+0.953, saying that ~1 electron has transferred to other atoms in the system.