Asymmetric Charges in 2D C3B and killed when used high density FFT grid

[ringinmay]

Hi, I'm a beginner at bader charge analysis.
I tried to use this to calculate the charge density distribution for 2 dimensional C3B (hexagonal). I used a supercell of 3X3 which have 54 carbon atoms and 18 boron atoms, density-grid of 240X240X224 and expected a symmetric charge distribution among all carbon atoms and all boron atoms, however, the Bader analysis gives a significant asymmetric result. I found a related topic in the forum (viewtopic.php?t=861) and used a higher density FFT grid 360 x 360 x 336.
When I type './bader CHGCAR -ref CHGCAR_sum', it started and then killed giving me as following:
GRID BASED BADER ANALYSIS (Version 1.0 01/11/17)

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 360 x 360 x 336
CLOSE ... CHGCAR
RUN TIME: 24.08 SECONDS

OPEN ... CHGCAR_sum
VASP5-STYLE INPUT FILE
DENSITY-GRID: 360 x 360 x 336
CLOSE ... CHGCAR_sum
RUN TIME: 24.80 SECONDS

CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: ****************Killed

part of ACF.dat displayed below:
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 -1.355542 3.770261 7.500950 4.642859 0.655848 17.858599
2 3.942788 0.711192 7.500950 4.499855 0.655837 17.158990
3 0.000005 1.422385 7.500950 4.644705 0.599167 17.892815
4 2.587241 3.059069 7.500950 4.643322 0.655708 17.869762
5 1.355570 3.770261 7.500950 4.644871 0.599167 17.895727
6 1.231677 0.711192 7.500950 4.787058 0.655710 18.585144
...
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.1287
VACUUM VOLUME: 2088.7176
NUMBER OF ELECTRONS: 270.0000

the charge difference among carbon atoms could reach 0.3e, which is difficult to accept.
how can I solve it please give me some help...
Thank you.

[graeme]

Differences of 0.3 e between identical atoms is very surprising. I would take a careful look at your geometry to make sure that they are indeed identical.
Also try using the "-b weight" flag in your Bader analysis.

[ringinmay]

thx for your reply.
and when I used the "-b weight" flag, it also interrupted with" killed".
I try uploading my C3B poscar file but an error arise as followed:
Invalid file extension: CONTCAR_C3B, how to upload a poscar file, does it necessary to do some change with the file.

[graeme]

There is probably a problem with your input file. Try naming it .txt and upload so I can take a look.

[ringinmay]

I have uploaded the vasp poscar file of C3B and you can check the file.
thx~

[graeme]

Please post the CHGCAR file.

[ringinmay]

this is the CHGCAR file

[graeme]

I'm confused. You posted a CONTCAR file. I need the CHGCAR_sum and the CHGCAR file to reproduce any problems with the Bader analysis.

[ringinmay]

sorry for my mistake and this time should not be wrong

[graeme]

Using the weight method does reduce the asymmetry (see ACF.dat below), but it is still about 0.05 e.

Try using Prec=high and a denser fft grid. Use ediff=1e-8 to get a well-converged electronic structure. You can reduce the size of the cell in z if you need to reduce the cost. Then check to see if the asymmetry gets better. With the -b weight method, the error should drop quadratically with the number of grid points and so double the grid should give you charges to within 0.01 e.


--------
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 -1.355542 3.770261 7.500950 4.647101 0.591090 17.713346
2 3.942788 0.711192 7.500950 4.603380 0.591133 17.519443
3 0.000005 1.422385 7.500950 4.641146 0.551248 17.610174
4 2.587241 3.059069 7.500950 4.608956 0.551120 17.458915
5 1.355570 3.770261 7.500950 4.600415 0.552231 17.980141
6 1.231677 0.711192 7.500950 4.686907 0.552103 18.228772
7 3.819073 3.770261 7.500950 4.647047 0.591109 17.712999
8 9.117558 0.711192 7.500950 4.603394 0.591172 17.519285
9 5.174620 1.422385 7.500950 4.641216 0.551297 17.611141
10 7.762011 3.059069 7.500950 4.608857 0.551217 17.459279
11 6.530185 3.770261 7.500950 4.600485 0.552279 17.981876
12 6.406447 0.711192 7.500950 4.686894 0.552201 18.229787
13 8.993843 3.770261 7.500950 4.647118 0.591070 17.713475
14 14.292173 0.711192 7.500950 4.603373 0.591153 17.519384
15 10.349390 1.422385 7.500950 4.641106 0.551200 17.609630
16 12.936626 3.059069 7.500950 4.608910 0.551169 17.458709
17 11.704955 3.770261 7.500950 4.600438 0.552182 17.980679
18 11.581062 0.711192 7.500950 4.686948 0.552152 18.228869
19 -3.942832 8.251580 7.500950 4.647232 0.591121 17.713474
20 1.355497 5.192512 7.500950 4.603472 0.591102 17.518992
21 -2.587286 5.903704 7.500950 4.640995 0.551209 17.609903
22 -0.000050 7.540388 7.500950 4.608922 0.551160 17.458716
23 -1.231721 8.251580 7.500950 4.600399 0.552191 17.980773
24 -1.355614 5.192512 7.500950 4.686957 0.552142 18.228507
25 1.231782 8.251580 7.500950 4.647179 0.591141 17.713130
26 6.530268 5.192512 7.500950 4.603487 0.591141 17.518846
27 2.587329 5.903704 7.500950 4.641065 0.551257 17.610870
28 5.174721 7.540388 7.500950 4.608824 0.551257 17.459092
29 3.942894 8.251580 7.500950 4.600469 0.552240 17.982028
30 3.819156 5.192512 7.500950 4.686946 0.552240 18.229538
31 6.406553 8.251580 7.500950 4.647250 0.591102 17.713599
32 11.704882 5.192512 7.500950 4.603465 0.591121 17.518940
33 7.762100 5.903704 7.500950 4.690086 0.551160 17.755348
34 10.349336 7.540388 7.500950 4.559780 0.551209 17.313088
35 9.117664 8.251580 7.500950 4.649519 0.552142 18.126251
36 8.993771 5.192512 7.500950 4.637868 0.552191 18.083108
37 -6.530123 12.732900 7.500950 4.647322 0.591153 17.714461
38 -1.231793 9.673831 7.500950 4.603406 0.591070 17.519113
39 -5.174576 10.385023 7.500950 4.690051 0.551169 17.755252
40 -2.587340 12.021707 7.500950 4.559862 0.551200 17.312710
41 -3.819012 12.732900 7.500950 4.649574 0.552152 18.126788
42 -3.942905 9.673831 7.500950 4.637886 0.552182 18.082970
43 -1.355508 12.732900 7.500950 4.647270 0.591172 17.714130
44 3.942977 9.673831 7.500950 4.603419 0.591109 17.518953
45 0.000039 10.385023 7.500950 4.690039 0.551217 17.755988
46 2.587430 12.021707 7.500950 4.559882 0.551297 17.313907
47 1.355603 12.732900 7.500950 4.649526 0.552201 18.127705
48 1.231865 9.673831 7.500950 4.637956 0.552279 18.084226
49 3.819262 12.732900 7.500950 4.647340 0.591133 17.714597
50 9.117592 9.673831 7.500950 4.603398 0.591090 17.519061
51 5.174809 10.385023 7.500950 4.690045 0.551120 17.755295
52 7.762045 12.021707 7.500950 4.559851 0.551248 17.313079
53 6.530373 12.732900 7.500950 4.649562 0.552103 18.126761
54 6.406480 9.673831 7.500950 4.637892 0.552231 18.082484
55 2.587313 1.493773 7.500950 1.098868 0.410808 4.648012
56 0.000011 2.987546 7.500950 1.098856 0.410808 4.647877
57 7.762083 1.493773 7.500950 1.098849 0.410718 4.647914
58 5.174626 2.987546 7.500950 1.098843 0.410763 4.647817
59 12.936698 1.493773 7.500950 1.098862 0.410763 4.647974
60 10.349396 2.987546 7.500950 1.098863 0.410853 4.647916
61 0.000022 5.975092 7.500950 1.098870 0.410763 4.647973
62 -2.587357 7.469000 7.500950 1.098865 0.410718 4.647937
63 5.174792 5.975092 7.500950 1.098851 0.410674 4.647875
64 2.587258 7.469000 7.500950 1.098851 0.410674 4.647874
65 10.349407 5.975092 7.500950 1.098864 0.410718 4.647936
66 7.762028 7.469000 7.500950 1.098870 0.410763 4.647974
67 -2.587346 10.456546 7.500950 1.098862 0.410853 4.647915
68 -5.174648 11.950319 7.500950 1.098863 0.410763 4.647975
69 2.587424 10.456546 7.500950 1.098843 0.410763 4.647816
70 -0.000033 11.950319 7.500950 1.098849 0.410718 4.647915
71 7.762039 10.456546 7.500950 1.098856 0.410808 4.647876
72 5.174737 11.950319 7.500950 1.098868 0.410808 4.648012
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.1287
VACUUM VOLUME: 2088.7176
NUMBER OF ELECTRONS: 270.0000