Hi, this is the first time I use this Bader analysis tool and I have found strange results for my kaolinite surface (Al and Si oxide). The volume and charge assigned to Al and Si are zero. Moreover, for some protons also charge and volume is zero. After that I decided to increase FFT grid points, but results were almost the same. Here I present the results. The 8 first atoms are Al and 8 next are Si. The rest are O, H and the last one one U. Are these 0 volumes normal? I know this systems is ionic, hence charges on Al and Si should be almost 0, but also the Bader volumes? The total number of electrons is right for valence elctrons.
1 0.8645 4.3699 3.9816 0.0000 0.0000 0.0000
2 0.8609 7.3813 3.9674 0.0000 0.0000 0.0000
3 3.4692 8.9574 3.9352 0.0000 0.0000 0.0000
4 3.4664 2.8264 3.9826 0.0000 0.0000 0.0000
5 6.0475 4.3218 3.9458 0.0000 0.0000 0.0000
6 5.9846 7.3026 4.0077 0.0000 0.0000 0.0000
7 8.6583 8.8025 3.9665 0.0000 0.0000 0.0000
8 8.6468 2.8563 3.9591 0.0000 0.0000 0.0000
9 0.8426 13.3780 3.9531 0.0000 0.0000 0.0000
10 0.8486 16.4157 3.9710 0.0000 0.0000 0.0000
11 3.5019 17.8900 3.9542 0.0000 0.0000 0.0000
12 3.4431 11.9531 3.9284 0.0000 0.0000 0.0000
13 6.0670 13.4078 3.9576 0.0000 0.0000 0.0000
14 6.0954 16.4228 3.9401 0.0000 0.0000 0.0000
15 8.6415 -0.1548 3.9580 0.0000 0.0000 0.0000
16 8.6413 11.8394 3.9662 0.0000 0.0000 0.0000
17 -0.0243 2.9890 1.2334 0.0000 0.0000 0.0000
18 0.0583 5.9592 1.2437 0.0000 0.0000 0.0000
19 2.5975 7.5102 1.2334 0.0000 0.0000 0.0000
20 2.6456 1.4380 1.2437 0.0000 0.0000 0.0000
21 5.1848 2.9890 1.2334 0.0000 0.0000 0.0000
22 5.2674 5.9592 1.2437 0.0000 0.0000 0.0000
23 7.8067 7.5102 1.2334 0.0000 0.0000 0.0000
24 7.8547 1.4380 1.2437 0.0000 0.0000 0.0000
25 0.0103 12.0314 1.2334 0.0000 0.0000 0.0000
26 0.0929 15.0016 1.2437 0.0000 0.0000 0.0000
27 2.6321 16.5526 1.2334 0.0000 0.0000 0.0000
28 2.6802 10.4804 1.2437 0.0000 0.0000 0.0000
29 5.2194 12.0314 1.2334 0.0000 0.0000 0.0000
30 5.3020 15.0016 1.2437 0.0000 0.0000 0.0000
31 7.8413 16.5526 1.2334 0.0000 0.0000 0.0000
32 7.8893 10.4804 1.2437 0.0000 0.0000 0.0000
33 -0.1462 3.0960 2.8733 8.0002 1.1169 16.4090
34 0.2478 5.8733 2.8720 7.9948 1.1463 16.2149
35 0.1838 4.4705 0.5566 7.9892 1.2176 46.3717
36 1.2116 2.0388 0.7262 7.9932 1.1929 39.9465
37 1.2415 6.8668 0.5570 7.9883 1.2021 46.0240
38 2.4471 7.6483 2.8638 8.0100 1.1307 16.4820
39 2.8058 1.3479 2.8798 7.9992 1.1568 16.2590
40 2.8057 8.9917 0.5566 7.9912 1.2176 68.1747
41 3.8335 6.5600 0.7262 7.9958 1.1929 45.9279
42 3.8288 2.3456 0.5570 7.9881 1.2021 60.9911
43 -0.1683 8.6298 2.9429 8.0027 1.0822 19.0057
44 -1.2627 10.3315 4.9836 8.0080 1.1195 44.9347
45 -0.7402 4.1017 4.9471 8.0096 1.0870 35.0627
46 -0.7479 7.5697 4.9711 8.0027 1.0801 35.9286
47 2.4724 4.1156 2.9990 8.0160 1.1055 19.2674
48 1.4180 5.8747 4.9695 8.0173 1.1358 25.1355
49 1.8356 8.7529 4.9488 7.9875 1.1366 37.8249
50 1.8389 2.9938 5.0471 7.9649 1.1191 22.4904
51 5.0488 3.0700 2.8630 8.0161 1.1245 16.2456
52 5.4206 5.8535 2.8736 8.0135 1.1487 16.3706
53 5.3929 4.4705 0.5566 7.9890 1.2176 60.7837
54 6.4208 2.0388 0.7262 7.9939 1.1929 43.2078
55 6.4506 6.8668 0.5570 7.9904 1.2021 53.4652
56 7.6470 7.5686 2.8779 8.0072 1.1370 16.7874
57 8.0553 1.3563 2.8674 7.9982 1.1454 16.0995
58 8.0148 8.9917 0.5566 7.9933 1.2176 48.5888
59 9.0427 6.5600 0.7262 7.9960 1.1929 37.1927
60 9.0379 2.3456 0.5570 7.9872 1.2021 47.5874
61 5.0735 8.6430 2.9387 7.9961 1.0497 19.1536
62 4.0903 1.2844 4.9783 8.0008 1.1849 24.9307
63 4.4729 4.0085 5.0481 7.5403 0.8840 14.7530
64 4.4242 7.7535 4.9499 8.0378 1.0561 20.0391
65 7.6387 4.1312 2.9316 8.0049 1.0742 19.3720
66 6.3482 5.7815 5.1507 7.5952 0.9100 17.4666
67 7.0891 8.4842 5.0792 7.9877 1.1404 24.4933
68 7.0249 2.9618 4.8896 8.0215 1.1013 20.8264
69 4.7488 5.1514 9.4226 7.9366 1.1163 143.5979
70 6.5526 7.0248 7.5432 7.9689 1.1021 95.9455
71 3.3402 3.1416 7.4031 7.9761 1.0854 84.5298
72 3.5891 6.0859 6.8374 6.9999 0.7850 40.5184
73 6.3695 3.7568 7.3931 6.9574 0.7922 68.0577
74 -0.1586 12.1183 2.8687 8.0052 1.1117 16.4135
75 0.2376 14.9086 2.8775 7.9955 1.1394 16.1649
76 0.2184 13.5129 0.5566 7.9927 1.2176 74.8576
77 1.2462 11.0812 0.7262 7.9950 1.1929 41.2973
78 1.2761 15.9092 0.5570 7.9900 1.2021 74.1404
79 2.4763 16.6443 2.8683 8.0061 1.1201 16.3126
80 2.8284 10.4224 2.8696 8.0115 1.1393 16.0709
81 2.8402 18.0341 0.5566 7.9910 1.2176 78.6297
82 3.8681 15.6024 0.7262 7.9964 1.1929 76.1325
83 3.8633 11.3880 0.5570 7.9906 1.2021 76.2155
84 -0.1193 17.6728 2.9276 8.0047 1.0837 18.9201
85 -1.1319 1.3339 4.9289 7.9966 1.1214 41.7227
86 -0.7625 13.0987 4.9475 8.0081 1.0909 49.0062
87 -0.7683 16.6172 4.9720 8.0083 1.1093 46.5384
88 2.4305 13.1772 2.9105 8.0056 1.0813 18.8907
89 1.3846 14.8799 4.9619 8.0036 1.1158 50.0402
90 1.8921 17.6868 4.9483 8.0010 1.1121 41.2294
91 1.8596 12.1077 4.9604 8.0067 1.0998 44.9176
92 5.0566 12.1690 2.8654 8.0122 1.1289 16.2229
93 5.4973 14.9132 2.8723 8.0031 1.1518 15.9618
94 5.4275 13.5129 0.5566 7.9905 1.2176 144.5659
95 6.4554 11.0812 0.7262 7.9967 1.1929 48.0870
96 6.4852 15.9092 0.5570 7.9897 1.2021 133.7166
97 7.6920 16.6581 2.8675 8.0053 1.1183 16.2762
98 8.0323 10.3688 2.8792 7.9944 1.1343 16.3508
99 8.0494 18.0341 0.5566 7.9897 1.2176 55.8547
100 9.0772 15.6024 0.7262 7.9952 1.1929 57.2278
101 9.0725 11.3880 0.5570 7.9899 1.2021 53.8252
102 5.0777 17.6628 2.9142 8.0075 1.0836 18.8026
103 4.0906 10.5021 4.9478 8.0126 1.1601 39.5395
104 4.4206 13.2907 4.9442 7.9955 1.1387 46.0687
105 4.4757 16.5440 4.9496 8.0114 1.1219 43.3468
106 7.6446 13.1085 2.9562 8.0043 1.1007 18.9191
107 6.7461 14.8989 4.9531 7.9973 1.1486 46.9546
108 7.0763 17.6974 4.9252 8.0037 1.0892 43.8230
109 6.9494 11.9954 4.9677 7.9799 1.1024 47.4726
110 0.2472 9.3918 2.5099 0.0000 0.0000 0.0000
111 -0.5000 10.2465 5.5718 0.0000 3.6765 1.1677
112 -0.9127 4.4124 5.8457 0.0000 4.3754 0.2889
113 -1.1763 6.7744 5.3229 0.0000 0.0000 0.0000
114 2.9357 4.9152 2.6982 0.0000 0.0000 0.0000
115 2.1434 5.8746 5.6251 0.0000 0.0000 0.0000
116 1.9361 8.6247 5.9056 0.0000 3.7471 2.0679
117 1.3176 2.1675 5.0889 0.0000 0.0000 0.0000
118 5.4636 9.2051 2.2531 0.0000 0.0000 0.0000
119 5.0679 1.3019 5.0129 0.0000 0.0000 0.0000
120 4.0128 7.2166 5.6559 0.0000 0.0000 0.0000
121 8.0712 4.8934 2.5157 0.0000 0.0000 0.0000
122 6.6667 9.3228 5.3296 0.0000 0.0000 0.0000
123 6.9839 2.9961 5.8654 0.0000 0.0000 0.0000
124 5.1714 4.4576 9.9601 0.0000 3.0799 40.8567
125 3.8319 5.2333 9.7406 0.0000 3.0959 34.2444
126 6.8271 7.5199 6.7221 0.0000 0.0000 0.0000
127 6.3455 7.6779 8.2326 0.0000 3.1553 18.7131
128 2.6694 3.2128 6.6582 0.0000 0.0000 0.0000
129 3.7961 2.3097 7.1548 0.0000 3.7767 4.0359
130 0.2598 0.3533 2.5331 0.0000 0.0000 0.0000
131 -0.9647 1.3159 5.8804 0.0000 4.0661 1.7167
132 -0.8443 13.3528 5.8757 0.0000 3.5861 12.3991
133 -1.2739 15.8013 5.1334 0.0000 0.0000 0.0000
134 2.8229 13.9149 2.4180 0.0000 0.0000 0.0000
135 2.0231 14.8178 5.6839 0.0000 3.6283 10.7235
136 1.8913 17.7180 5.9154 0.0000 3.6705 5.3429
137 1.4816 11.2398 5.1798 0.0000 0.0000 0.0000
138 5.4123 0.3002 2.4070 0.0000 0.0000 0.0000
139 5.0586 10.5765 5.0222 0.0000 0.0000 0.0000
140 4.0518 15.6660 4.9827 0.0000 0.0000 0.0000
141 8.1178 13.8751 2.5937 0.0000 0.0000 0.0000
142 6.8904 -0.1640 5.8578 0.0000 3.7026 3.1056
143 7.0422 12.0410 5.9312 0.0000 3.6761 2.5822
144 4.4311 13.0844 5.8919 0.0000 3.6789 4.3992
145 6.5917 14.9675 5.9071 0.0000 3.6783 4.0970
146 5.1010 4.9852 6.8386 11.0454 0.8829 15.7460
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NUMBER OF ELECTRONS: 624.00000
Tahnk you very much!
Strange results in Bader volumes
Moderator: moderators
Re: Strange results in Bader volumes
If you are using vasp, did you follow these instructions: http://theory.cm.utexas.edu/bader/vasp.php
Re: Strange results in Bader volumes
Thank you very much for your answer.
I had not taken into account the instructions presents in this webpage.
Now my problem is solved and now all atoms "exist".
Thanks once again
I had not taken into account the instructions presents in this webpage.
Now my problem is solved and now all atoms "exist".
Thanks once again
Re: Strange results in Bader volumes
I am definitely new with VASP and Bader,
then I am trying to get some ideas on how to use Bader in charge analysis
By reading this message I deduce, please correct me if I am wrong, that for previous versions of vasp (i.e., 4.5) I can expect "strange" results for Volume values. Moreover this means, that charge analysis (i.e. charge transfer) is performable only for the valence since the use of Pseudos.
Thanks,
G
then I am trying to get some ideas on how to use Bader in charge analysis
By reading this message I deduce, please correct me if I am wrong, that for previous versions of vasp (i.e., 4.5) I can expect "strange" results for Volume values. Moreover this means, that charge analysis (i.e. charge transfer) is performable only for the valence since the use of Pseudos.
Thanks,
G
Re: Strange results in Bader volumes
There needs to be a charge density maximum at the atomic centers for the Bader analysis to work properly. This is ensured when the total charge is written in vasp > 4.6.31. It will not always fail when used on the valance charge, particularly when some core electrons are treated as valance using the _pv and _sv US potentials, but some of the elements are problematic (e.g. Si and H). The safest way to go is to use the latest vasp with the PAW potentials where the core charges can be included to calculate the Bader volumes. The integration of the charge over the volumes is best done on the valance electrons to avoid large errors in the density near the atomic centers.
Re: Strange results in Bader volumes
Thank you very much for the very quick answer!
Let me stress a last point.... You said that not always Bader fails especially when treating core electrons as valence.
I am using PAW/LDA for Ge-doped GaAs, and I use all d-electrons in the valence (for the case of Ge and Ga). I am studying charged Ge substitutional and I am quite confident (I hope) that the charges I evaluate via Bader (the redistribution after the optimization) are well reproduced.
For example if I replace 1 Ga with 1Ge and I charge my supercell (i.e., +1 or -1) I observe a redistribution of the charge which is not strictly localized in Ge but at odds quite enough delocalized in the first 4NN (4 As atoms).
In few words, I would like to observe "how much" and "where" the extra charge (electron or hole) is redistributed. Is this one the corrected procedure? Can I still perform it with VASP 4.5 version?
When you warn that some atoms (and you bring Si and H as example) are problematic, would you include also the ones I have mentioned (Ga,As, and Ge)?
Thanks in advance!
My very best,
Giacomo
Let me stress a last point.... You said that not always Bader fails especially when treating core electrons as valence.
I am using PAW/LDA for Ge-doped GaAs, and I use all d-electrons in the valence (for the case of Ge and Ga). I am studying charged Ge substitutional and I am quite confident (I hope) that the charges I evaluate via Bader (the redistribution after the optimization) are well reproduced.
For example if I replace 1 Ga with 1Ge and I charge my supercell (i.e., +1 or -1) I observe a redistribution of the charge which is not strictly localized in Ge but at odds quite enough delocalized in the first 4NN (4 As atoms).
In few words, I would like to observe "how much" and "where" the extra charge (electron or hole) is redistributed. Is this one the corrected procedure? Can I still perform it with VASP 4.5 version?
When you warn that some atoms (and you bring Si and H as example) are problematic, would you include also the ones I have mentioned (Ga,As, and Ge)?
Thanks in advance!
My very best,
Giacomo
Re: Strange results in Bader volumes
The delocalization of additional electrons in semiconductors is something that I have seen as well. Given that GGA has a tendency to delocalize electronic states, this may be an artifact. But it is still very interesting, and makes many of the published calculations of charged clusters in semiconductors a little suspect (in my view). If you add a delocalized electron and then subtract off a uniform background, the overall energy change may not have anything to do with the energy of a charged defect.
With respect to the Bader analysis: I would be particularly worried about Ga As and Ge -- any elements in which most of the valance electrons are used for bonding. Since this can now be treated properly in the current versions of vasp, we have not made much effort to figure out exactly when the analysis fails when you only use the valance electrons. I do not recommend using vasp 4.5 for these calculations.
With respect to the Bader analysis: I would be particularly worried about Ga As and Ge -- any elements in which most of the valance electrons are used for bonding. Since this can now be treated properly in the current versions of vasp, we have not made much effort to figure out exactly when the analysis fails when you only use the valance electrons. I do not recommend using vasp 4.5 for these calculations.