Zero Charge even with LAECHG

Bader charge density analysis

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ibrahim
Posts: 7
Joined: Fri Jun 01, 2018 1:46 am

Zero Charge even with LAECHG

Post by ibrahim » Fri Jun 01, 2018 2:00 am

Dear All,

I am doing bader analysis. Even when I use LAECHG = True, then get CHGCAR_SUM and doing bader analysis I got zero charge, volume, and distance for atom number 108 (attached CHGCAR, AECCAR0, AECCAR2).

How to fix that?
Attachments
files.zip
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graeme
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Re: Zero Charge even with LAECHG

Post by graeme » Sat Jun 02, 2018 1:06 am

It looks fine to me. Here is ACF.dat from the command

bader CHGCAR -ref CHGCAR_sum


GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 80 x 80 x 336
CLOSE ... CHGCAR
RUN TIME: 0.89 SECONDS

OPEN ... CHGCAR_sum
VASP5-STYLE INPUT FILE
DENSITY-GRID: 80 x 80 x 336
CLOSE ... CHGCAR_sum
RUN TIME: 0.87 SECONDS

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

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 1089066
REASSIGNED POINTS: 99577

RUN TIME: 4.80 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 0.44 SECONDS

WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat

NUMBER OF BADER MAXIMA FOUND: 861
SIGNIFICANT MAXIMA FOUND: 472
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 871.00003

> cat ACF.dat

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 5.515535 2.401829 20.365527 7.369118 1.000190 18.521835
2 2.505186 4.118910 17.663756 6.476173 0.620309 15.041937
3 1.751371 6.065972 20.875608 7.474892 1.027654 19.097788
4 3.310569 3.285855 23.870287 7.310145 1.009407 30.700135
5 4.014366 3.498143 5.939541 8.426465 1.168326 15.904522
6 0.045471 0.237448 6.115885 8.924789 1.135664 15.274826
7 0.801820 0.128713 14.326016 8.109879 0.380458 18.463613
8 0.482522 3.854819 6.260185 8.979217 1.116772 15.994095
9 3.760389 0.082531 5.758081 8.928348 1.060166 15.019544
10 0.195842 0.044609 10.465876 9.096241 0.831290 16.601397
11 0.066910 3.601772 10.167078 8.964513 1.084746 15.258703
12 3.522592 0.246397 10.404245 8.999227 0.845804 15.443223
13 3.558260 3.482726 10.283676 8.973221 1.087130 15.196002
14 3.962063 3.763989 14.167142 8.985404 1.137173 16.258334
15 0.407873 3.739533 14.074342 9.042096 1.115593 17.496228
16 3.251534 0.023435 14.534673 9.012878 0.990007 18.254013
17 0.000000 0.000000 1.455046 8.947157 1.125036 14.768741
18 0.000000 3.782349 1.932981 8.880441 1.136608 15.679695
19 3.782349 0.000000 1.932981 8.866419 1.136608 14.946990
20 3.782349 3.782349 2.034129 8.876769 1.122410 14.835025
21 1.947115 2.041417 6.212724 7.200736 0.901579 11.368562
22 2.369188 5.334557 6.317137 7.111211 0.797436 12.045732
23 5.545892 1.360261 6.550265 6.960999 0.680718 11.801198
24 5.320055 5.703888 6.079768 7.196504 0.849123 12.179195
25 2.514316 0.007996 7.961082 7.107679 0.846184 11.900624
26 5.382903 0.098341 9.017394 7.045368 0.812992 10.552555
27 0.012731 1.274984 8.358571 7.008182 0.761295 10.694080
28 0.214089 5.959182 7.631956 7.095180 0.806965 11.150005
29 1.618997 3.632704 8.507683 7.111638 0.805619 10.896515
30 6.343892 3.549008 7.904365 7.084561 0.797972 11.375728
31 3.940133 2.377259 8.319963 7.029240 0.794929 11.414244
32 3.658235 5.387827 8.949569 7.091303 0.839491 10.752303
33 1.845733 1.524045 10.386978 7.137840 0.783150 11.081930
34 1.455629 5.973365 10.162265 7.166497 0.915344 11.655195
35 5.777818 2.307566 10.304141 7.126541 0.823141 11.425889
36 6.164707 5.341705 10.410977 7.072671 0.775706 11.399017
37 1.511124 3.651291 11.971042 7.135234 0.821725 10.564200
38 5.905162 3.758028 12.874774 7.064522 0.843697 11.399017
39 3.701195 2.213272 12.178992 7.066666 0.866341 10.319667
40 3.825316 5.282618 11.816610 7.095605 0.857673 10.848145
41 2.305947 0.033867 12.525284 7.045566 0.815616 10.371619
42 5.447089 0.133464 11.862421 7.064210 0.687508 10.432528
43 0.007232 1.417488 12.576548 7.070302 0.857877 11.200166
44 0.092161 5.860470 12.794529 7.067270 0.762272 11.139256
45 2.052620 2.105081 14.226013 7.208455 0.927761 14.948782
46 2.164631 5.284229 14.305349 7.293278 0.985355 15.344693
47 5.160168 1.403985 14.415214 7.271071 0.955433 16.958792
48 5.082917 5.968622 14.105814 7.745596 0.912460 14.073657
49 1.994001 0.000000 0.000000 7.080383 0.940685 36.501756
50 5.570696 0.000000 0.000000 7.103764 0.908374 36.954994
51 0.000000 1.994001 0.000000 7.103585 0.908374 37.357175
52 0.000000 5.570696 0.000000 7.084825 0.940685 38.340683
53 1.934074 3.782349 0.582887 7.098457 0.856045 18.804885
54 5.630624 3.782349 0.582887 7.103076 0.852303 19.304700
55 3.782349 1.934074 0.582887 7.107215 0.852303 19.180194
56 3.782349 5.630624 0.582887 7.101657 0.856045 19.513405
57 1.568124 1.568124 2.224913 7.160311 0.882363 11.806573
58 1.568124 5.996574 2.224913 7.127516 0.882363 11.728645
59 5.996574 1.568124 2.224913 7.052330 0.824143 11.057745
60 5.996574 5.996574 2.224913 7.141657 0.882363 11.624740
61 2.148011 3.710605 3.852937 7.172129 0.868640 11.781492
62 5.452400 3.680642 3.741455 7.136921 0.845206 11.842402
63 3.902847 1.468217 3.898815 7.148591 0.836802 11.341691
64 3.786010 5.971777 3.846036 7.146757 0.856981 11.407974
65 1.730553 0.016680 4.553128 7.114787 0.838175 11.209123
66 5.990371 0.054504 4.459217 7.025099 0.820816 10.937718
67 0.075987 2.219112 4.537038 7.061670 0.776846 11.321985
68 0.062083 5.346418 4.493382 7.080583 0.822174 11.866586
69 6.390369 0.719599 16.620807 7.292728 0.054826 17.120919
70 4.311908 3.977745 16.454494 8.099957 0.968880 23.416086
71 2.246004 0.253591 16.718790 7.579768 0.827073 23.533426
72 0.532736 3.872074 16.366406 10.979786 1.032734 26.238520
73 0.379627 5.630049 18.708623 9.479282 0.709325 17.011640
74 0.738012 2.288268 18.396530 6.964569 0.323954 15.965432
75 3.113009 5.871045 18.827341 6.778721 0.550527 12.162176
76 3.174942 2.454979 19.112575 7.820423 0.938193 19.018068
77 5.551754 0.205790 19.527196 7.013110 0.740336 13.252276
78 5.443678 4.404530 19.509053 9.882087 0.514779 18.048892
79 1.585727 0.435311 19.652411 6.984947 0.640786 11.326463
80 0.370436 5.759383 21.685665 7.150160 0.295404 14.057534
81 0.240330 2.671208 21.562638 6.915982 0.422941 15.086724
82 3.979651 6.423722 21.546650 6.884989 0.549394 13.231674
83 3.978388 2.007709 22.134181 7.132889 0.802013 13.363346
84 6.229445 0.403675 23.944439 7.078743 0.832217 34.525783
85 1.768853 0.300545 22.392689 7.292405 0.887617 16.443750
86 2.077455 4.119091 22.134754 7.067736 0.760453 12.979975
87 0.969658 5.989448 24.457044 7.108921 0.862379 57.472508
88 0.946752 2.726015 24.267573 7.194074 0.863691 43.336150
89 5.214331 4.399409 23.952114 7.195175 0.894127 55.934545
90 3.150152 1.111746 24.702963 7.170991 0.797632 66.563238
91 2.020236 1.747294 8.209222 7.614718 0.774703 8.267557
92 1.965482 5.689167 8.225042 7.671176 0.749426 8.022128
93 5.713125 1.819885 8.347833 7.719812 0.736602 7.759680
94 5.624171 6.031946 20.544900 8.174465 0.786228 13.544282
95 1.897521 1.786789 12.330899 7.720149 0.774076 7.510668
96 1.863223 5.616070 12.278759 7.735710 0.863493 8.747666
97 5.585644 1.825914 12.369675 7.747117 0.859538 8.830969
98 5.631804 5.588247 12.289733 7.690973 0.769383 7.651297
99 1.924111 1.924111 0.166111 7.530818 0.851702 25.999361
100 1.924111 5.640587 0.166111 7.559838 0.851702 26.402438
101 5.640587 1.924111 0.166111 7.632587 0.851702 29.289365
102 5.640587 5.640587 0.166111 7.534462 0.851702 27.073338
103 1.853979 1.873216 4.121205 7.532633 0.834785 7.868063
104 1.911168 5.651873 4.121609 7.550096 0.846895 7.965697
105 5.776403 1.842836 4.008748 7.634760 0.768022 7.910162
106 5.779459 5.669877 4.115281 7.508606 0.844596 7.946887
107 0.019993 0.207840 18.098607 10.127435 1.063131 20.411819
108 1.181901 4.389204 17.580919 0.000000 0.000000 0.000000
109 3.572519 0.287557 18.344323 9.499214 0.813449 16.525261
110 5.664945 5.633839 8.196600 9.829868 1.064960 15.091202
111 1.795284 2.142269 21.124354 9.438995 0.788897 15.548919
112 0.764564 0.512168 24.385416 9.729859 1.076650 30.968853
113 4.247949 0.041122 23.315775 10.169411 0.965177 23.234253
114 0.263766 4.396913 23.361048 10.111260 0.811434 21.577159
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 871.0000

ibrahim
Posts: 7
Joined: Fri Jun 01, 2018 1:46 am

Re: Zero Charge even with LAECHG

Post by ibrahim » Sat Jun 02, 2018 8:42 am

Thank you.

Is it normal that CHARGE, MIN DIST, and ATOMIC VOL are zero for atom number 108?

graeme
Site Admin
Posts: 1864
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
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Re: Zero Charge even with LAECHG

Post by graeme » Sat Jun 02, 2018 2:22 pm

Ah, my bad, I didn't read your post carefully.

Ok, I took a closer look and it seems that the atoms are not in the same locations in your AECCAR? files as in your CHGCAR file.

ibrahim
Posts: 7
Joined: Fri Jun 01, 2018 1:46 am

Re: Zero Charge even with LAECHG

Post by ibrahim » Sun Jun 03, 2018 7:31 am

Thank you.

It is strange, the files are from the same converged job.

How can that happen?

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