Dear all,
I calculate a CO2 adsorbed system, and get three files AECCAR0, AECCAR1 and AECCAR2, then what is that in AECCAR1?
I added AECCAR0 to AECCAR2 and get the CHGCAR_sum, then I calculated the charge by bader CHGCAR -ref CHGCAR_sum
Following is my ACF.dat file:
------------------
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.6283600 4.5728367 7.8855617 6.8623795 0.7247496 25.3339456
2 3.6283600 2.4086877 8.7023681 6.9081485 0.6454875 33.4491744
3 3.6283600 3.2956723 7.8609009 2.7197705 0.3156329 7.9653341
4 0.0000000 7.6915954 5.9749023 9.9778625 1.0468872 26.3553210
5 3.6283600 0.0246686 5.9466984 9.9779633 1.0522873 23.1290993
6 0.0000000 2.5779505 5.9836796 10.0567556 1.0596516 26.1496516
7 3.6283600 2.5370183 6.1278598 9.8750677 0.8449093 15.0731312
8 0.0000000 5.1253673 5.9676551 9.9835964 1.0655572 25.4176077
9 3.6283600 5.1639905 6.0970992 9.7573894 0.8138929 15.2700858
10 1.8115095 1.2918500 4.8963893 11.0148450 1.0315405 13.7676530
11 5.4452105 1.2918500 4.8963893 11.0148386 1.0315405 13.7659100
12 1.8298327 3.8439774 4.9013416 10.9914120 1.0267905 13.2186201
13 5.4268873 3.8439774 4.9013416 10.9914072 1.0267905 13.2186201
14 1.8215383 6.4116679 4.8917994 11.0494791 1.0280607 14.1005586
15 5.4351817 6.4116679 4.8917994 11.0494697 1.0280607 14.1005586
16 0.0000000 0.0016933 3.5455405 10.9039885 1.0891445 11.5209756
17 3.6283600 0.0093825 3.5368236 10.9203774 1.0796827 11.5384052
18 0.0000000 2.5706307 3.5564315 10.9709749 1.0899332 11.8451664
19 3.6283600 2.5681292 3.5762004 11.0041714 1.0843171 12.0909240
20 0.0000000 5.1295929 3.5473523 10.9143138 1.1018280 11.5802363
21 3.6283600 5.1361892 3.5806091 10.9583316 1.0905093 11.8347087
22 1.8141800 1.2828216 2.2828263 11.0329790 1.0791111 14.1057875
23 5.4425400 1.2828216 2.2828263 11.0329796 1.0791111 14.1057875
24 1.8141800 3.8484570 2.2828263 10.9640635 1.0826514 13.7136212
25 5.4425400 3.8484570 2.2828263 10.9640642 1.0826514 13.7136212
26 1.8141800 6.4140924 2.2828263 10.9730301 1.0723441 13.7467374
27 5.4425400 6.4140924 2.2828263 10.9730305 1.0723441 13.7467374
28 0.0000000 0.0000000 1.0000010 11.0020439 1.0943010 28.9017878
29 3.6283600 0.0000000 1.0000010 10.9977072 1.0943010 28.6473154
30 0.0000000 2.5656354 1.0000010 11.0700971 1.1055909 30.0190261
31 3.6283600 2.5656354 1.0000010 10.9939112 1.1055909 28.7309776
32 0.0000000 5.1312786 1.0000010 10.9942104 1.1055909 28.6577732
33 3.6283600 5.1312786 1.0000010 11.0544413 1.1055909 29.5327399
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0453
VACUUM VOLUME: 516.0717
NUMBER OF ELECTRONS: 340.0004
--------------------
My questions:
1. what is the meaning of the VACUUM CHARGE?
2. Are the calculated charges the total charge or the valance charge?
Here No.1 and 2 are O atom and No.3 is C atom, if the calculated charges are valance charge, then the O atoms have -0.86e and -0.91e respectively and the C atom has +1.28e. the CO2 get about 0.5e from the surface. am I correct?
about the bader charge
Moderator: moderators
Re: about the bader charge
Yes, that is correct.
By default the code will ignore low density regions of the calculation and assign that charge to a vacuum region. You can include that region in your analysis using the '-vac off' , and the vacuum charge should go to zero.
By default the code will ignore low density regions of the calculation and assign that charge to a vacuum region. You can include that region in your analysis using the '-vac off' , and the vacuum charge should go to zero.
Re: about the bader charge
Thank you Professor!
the vacuum charge really go to zero if using"vac off", but the charges on each atom seem much different, hear is my ACF.dat(bader -vac off CHGCAR):
--------------------------
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.6283600 4.5728367 7.8855617 7.7738343 0.8495891 88.6505084
2 3.6283600 2.4086877 8.7023681 7.8878492 1.0524395 237.2798084
3 3.6283600 3.2956723 7.8609009 0.9353408 0.0868440 2.9874360
4 0.0000000 7.6915954 5.9749023 9.9779983 1.0468872 42.7565889
5 3.6283600 0.0246686 5.9466984 9.9772846 1.0522873 26.0468168
6 0.0000000 2.5779505 5.9836796 10.0589842 1.0596516 34.0400383
7 3.6283600 2.5370183 6.1278598 9.8128357 0.7844652 14.8413173
8 0.0000000 5.1253673 5.9676551 9.9828865 1.0655572 36.2396558
9 3.6283600 5.1639905 6.0970992 9.7226701 0.7693359 15.3293465
10 1.8115095 1.2918500 4.8963893 11.0184305 1.0315405 13.8652588
11 5.4452105 1.2918500 4.8963893 11.0184259 1.0315405 13.8617729
12 1.8298327 3.8439774 4.9013416 10.9920604 1.0267905 13.2273349
13 5.4268873 3.8439774 4.9013416 10.9920556 1.0267905 13.2273349
14 1.8215383 6.4116679 4.8917994 11.0517385 1.0280607 14.3445732
15 5.4351817 6.4116679 4.8917994 11.0517291 1.0280607 14.3445732
16 0.0000000 0.0016933 3.5455405 10.9024678 1.0891445 11.5140038
17 3.6283600 0.0093825 3.5368236 10.9218740 1.0796827 11.5453771
18 0.0000000 2.5706307 3.5564315 10.9699586 1.0908914 11.8416805
19 3.6283600 2.5681292 3.5762004 11.0049345 1.0843171 12.0944099
20 0.0000000 5.1295929 3.5473523 10.9151270 1.1018280 11.5837222
21 3.6283600 5.1361892 3.5806091 10.9596780 1.0905093 11.8416805
22 1.8141800 1.2828216 2.2828263 11.0304634 1.0723441 14.9302083
23 5.4425400 1.2828216 2.2828263 11.0304640 1.0723441 14.8796624
24 1.8141800 3.8484570 2.2828263 10.9638428 1.0826514 14.3986051
25 5.4425400 3.8484570 2.2828263 10.9638434 1.0826514 14.3881473
26 1.8141800 6.4140924 2.2828263 10.9722041 1.0723441 14.3149429
27 5.4425400 6.4140924 2.2828263 10.9722044 1.0723441 14.3027422
28 0.0000000 0.0000000 1.0000010 11.0055967 1.0943010 66.5532424
29 3.6283600 0.0000000 1.0000010 11.0005572 1.0943010 60.4633349
30 0.0000000 2.5656354 1.0000010 11.0762417 1.1055909 68.4722430
31 3.6283600 2.5656354 1.0000010 10.9981019 1.1055909 61.6834079
32 0.0000000 5.1312786 1.0000010 10.9989257 1.1055909 66.2551960
33 3.6283600 5.1312786 1.0000010 11.0598358 1.1055909 62.3143600
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 340.0004
-----------------------------------
In this case, the two O atoms(No.1 and 2) have -1.77e and -1.89e respectively and the C atom lost +3.07e, CO2 get about 0.6e from surface, this compares the previous value, but the charges on the atom seems too large.
the vacuum charge really go to zero if using"vac off", but the charges on each atom seem much different, hear is my ACF.dat(bader -vac off CHGCAR):
--------------------------
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.6283600 4.5728367 7.8855617 7.7738343 0.8495891 88.6505084
2 3.6283600 2.4086877 8.7023681 7.8878492 1.0524395 237.2798084
3 3.6283600 3.2956723 7.8609009 0.9353408 0.0868440 2.9874360
4 0.0000000 7.6915954 5.9749023 9.9779983 1.0468872 42.7565889
5 3.6283600 0.0246686 5.9466984 9.9772846 1.0522873 26.0468168
6 0.0000000 2.5779505 5.9836796 10.0589842 1.0596516 34.0400383
7 3.6283600 2.5370183 6.1278598 9.8128357 0.7844652 14.8413173
8 0.0000000 5.1253673 5.9676551 9.9828865 1.0655572 36.2396558
9 3.6283600 5.1639905 6.0970992 9.7226701 0.7693359 15.3293465
10 1.8115095 1.2918500 4.8963893 11.0184305 1.0315405 13.8652588
11 5.4452105 1.2918500 4.8963893 11.0184259 1.0315405 13.8617729
12 1.8298327 3.8439774 4.9013416 10.9920604 1.0267905 13.2273349
13 5.4268873 3.8439774 4.9013416 10.9920556 1.0267905 13.2273349
14 1.8215383 6.4116679 4.8917994 11.0517385 1.0280607 14.3445732
15 5.4351817 6.4116679 4.8917994 11.0517291 1.0280607 14.3445732
16 0.0000000 0.0016933 3.5455405 10.9024678 1.0891445 11.5140038
17 3.6283600 0.0093825 3.5368236 10.9218740 1.0796827 11.5453771
18 0.0000000 2.5706307 3.5564315 10.9699586 1.0908914 11.8416805
19 3.6283600 2.5681292 3.5762004 11.0049345 1.0843171 12.0944099
20 0.0000000 5.1295929 3.5473523 10.9151270 1.1018280 11.5837222
21 3.6283600 5.1361892 3.5806091 10.9596780 1.0905093 11.8416805
22 1.8141800 1.2828216 2.2828263 11.0304634 1.0723441 14.9302083
23 5.4425400 1.2828216 2.2828263 11.0304640 1.0723441 14.8796624
24 1.8141800 3.8484570 2.2828263 10.9638428 1.0826514 14.3986051
25 5.4425400 3.8484570 2.2828263 10.9638434 1.0826514 14.3881473
26 1.8141800 6.4140924 2.2828263 10.9722041 1.0723441 14.3149429
27 5.4425400 6.4140924 2.2828263 10.9722044 1.0723441 14.3027422
28 0.0000000 0.0000000 1.0000010 11.0055967 1.0943010 66.5532424
29 3.6283600 0.0000000 1.0000010 11.0005572 1.0943010 60.4633349
30 0.0000000 2.5656354 1.0000010 11.0762417 1.1055909 68.4722430
31 3.6283600 2.5656354 1.0000010 10.9981019 1.1055909 61.6834079
32 0.0000000 5.1312786 1.0000010 10.9989257 1.1055909 66.2551960
33 3.6283600 5.1312786 1.0000010 11.0598358 1.1055909 62.3143600
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 340.0004
-----------------------------------
In this case, the two O atoms(No.1 and 2) have -1.77e and -1.89e respectively and the C atom lost +3.07e, CO2 get about 0.6e from surface, this compares the previous value, but the charges on the atom seems too large.
Re: about the bader charge
Something isn't right. If you can make the charge density files available, I would like to reproduce this.
Re: about the bader charge
Thank you for your kindness, Professor, here are the main files, hope that is ok.
- Attachments
-
- atomic-charge.tar.gz
- (11.88 MiB) Downloaded 9477 times
Re: about the bader charge
anyone catch it? thanks
Re: about the bader charge
I think there is something wrong with the second calculation. See my output below, which gives results that are quite similar between the calculation with and without a vacuum region:
graeme@guelph:~/Desktop/tmp> bader -vac off CHGCAR -ref CHGCAR_sum
GRID BASED BADER ANALYSIS (Version 0.95a 02/26/16)
OPEN ... CHGCAR
VASP4-STYLE INPUT FILE
DENSITY-GRID: 60 x 64 x 168
CLOSE ... CHGCAR
RUN TIME: 0.26 SECONDS
OPEN ... CHGCAR_sum
VASP4-STYLE INPUT FILE
DENSITY-GRID: 60 x 64 x 168
CLOSE ... CHGCAR_sum
RUN TIME: 0.25 SECONDS
CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************
REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 299700
REASSIGNED POINTS: 13370
ITERATION: 2
CHECKED POINTS: 159224
REASSIGNED POINTS: 3
ITERATION: 3
CHECKED POINTS: 69
REASSIGNED POINTS: 0
RUN TIME: 1.62 SECONDS
CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 0.12 SECONDS
WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat
NUMBER OF BADER MAXIMA FOUND: 1769
SIGNIFICANT MAXIMA FOUND: 33
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 340.00044
graeme@guelph:~/Desktop/tmp> cat ACF.dat
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.6283600 4.5728367 7.8855617 6.8669971 0.7247496 86.0569817
2 3.6283600 2.4086877 8.7023681 6.9165981 0.6454875 232.7324219
3 3.6283600 3.2956723 7.8609009 2.7199178 0.3156329 8.5579410
4 0.0000000 7.6915954 5.9749023 9.9808843 1.0468872 42.6851274
5 3.6283600 0.0246686 5.9466984 9.9790369 1.0522873 26.0712183
6 0.0000000 2.5779505 5.9836796 10.0586220 1.0596516 34.1271864
7 3.6283600 2.5370183 6.1278598 9.8750757 0.8449093 15.0835889
8 0.0000000 5.1253673 5.9676551 9.9859260 1.0655572 36.2413987
9 3.6283600 5.1639905 6.0970992 9.7574735 0.8138929 15.5280441
10 1.8115095 1.2918500 4.8963893 11.0148736 1.0315405 13.8338855
11 5.4452105 1.2918500 4.8963893 11.0148690 1.0315405 13.8338855
12 1.8298327 3.8439774 4.9013416 10.9914129 1.0267905 13.2203631
13 5.4268873 3.8439774 4.9013416 10.9914081 1.0267905 13.2203631
14 1.8215383 6.4116679 4.8917994 11.0495578 1.0280607 14.3254007
15 5.4351817 6.4116679 4.8917994 11.0495484 1.0280607 14.3254007
16 0.0000000 0.0016933 3.5455405 10.9039885 1.0891445 11.5209756
17 3.6283600 0.0093825 3.5368236 10.9203774 1.0796827 11.5384052
18 0.0000000 2.5706307 3.5564315 10.9709749 1.0899332 11.8451664
19 3.6283600 2.5681292 3.5762004 11.0041714 1.0843171 12.0909240
20 0.0000000 5.1295929 3.5473523 10.9143138 1.1018280 11.5802363
21 3.6283600 5.1361892 3.5806091 10.9583316 1.0905093 11.8347087
22 1.8141800 1.2828216 2.2828263 11.0331197 1.0791111 14.8936061
23 5.4425400 1.2828216 2.2828263 11.0331203 1.0791111 14.8936061
24 1.8141800 3.8484570 2.2828263 10.9642046 1.0826514 14.3776895
25 5.4425400 3.8484570 2.2828263 10.9642052 1.0826514 14.3776895
26 1.8141800 6.4140924 2.2828263 10.9731747 1.0723441 14.3480592
27 5.4425400 6.4140924 2.2828263 10.9731751 1.0723441 14.3498021
28 0.0000000 0.0000000 1.0000010 11.0057732 1.0943010 66.7101089
29 3.6283600 0.0000000 1.0000010 11.0013967 1.0943010 62.0651165
30 0.0000000 2.5656354 1.0000010 11.0740101 1.1055909 67.5519593
31 3.6283600 2.5656354 1.0000010 10.9977011 1.1055909 60.4633349
32 0.0000000 5.1312786 1.0000010 10.9979457 1.1055909 67.2591418
33 3.6283600 5.1312786 1.0000010 11.0582593 1.1055909 62.8755936
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 340.0004
graeme@guelph:~/Desktop/tmp> bader -vac off CHGCAR -ref CHGCAR_sum
GRID BASED BADER ANALYSIS (Version 0.95a 02/26/16)
OPEN ... CHGCAR
VASP4-STYLE INPUT FILE
DENSITY-GRID: 60 x 64 x 168
CLOSE ... CHGCAR
RUN TIME: 0.26 SECONDS
OPEN ... CHGCAR_sum
VASP4-STYLE INPUT FILE
DENSITY-GRID: 60 x 64 x 168
CLOSE ... CHGCAR_sum
RUN TIME: 0.25 SECONDS
CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************
REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 299700
REASSIGNED POINTS: 13370
ITERATION: 2
CHECKED POINTS: 159224
REASSIGNED POINTS: 3
ITERATION: 3
CHECKED POINTS: 69
REASSIGNED POINTS: 0
RUN TIME: 1.62 SECONDS
CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 0.12 SECONDS
WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat
NUMBER OF BADER MAXIMA FOUND: 1769
SIGNIFICANT MAXIMA FOUND: 33
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 340.00044
graeme@guelph:~/Desktop/tmp> cat ACF.dat
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.6283600 4.5728367 7.8855617 6.8669971 0.7247496 86.0569817
2 3.6283600 2.4086877 8.7023681 6.9165981 0.6454875 232.7324219
3 3.6283600 3.2956723 7.8609009 2.7199178 0.3156329 8.5579410
4 0.0000000 7.6915954 5.9749023 9.9808843 1.0468872 42.6851274
5 3.6283600 0.0246686 5.9466984 9.9790369 1.0522873 26.0712183
6 0.0000000 2.5779505 5.9836796 10.0586220 1.0596516 34.1271864
7 3.6283600 2.5370183 6.1278598 9.8750757 0.8449093 15.0835889
8 0.0000000 5.1253673 5.9676551 9.9859260 1.0655572 36.2413987
9 3.6283600 5.1639905 6.0970992 9.7574735 0.8138929 15.5280441
10 1.8115095 1.2918500 4.8963893 11.0148736 1.0315405 13.8338855
11 5.4452105 1.2918500 4.8963893 11.0148690 1.0315405 13.8338855
12 1.8298327 3.8439774 4.9013416 10.9914129 1.0267905 13.2203631
13 5.4268873 3.8439774 4.9013416 10.9914081 1.0267905 13.2203631
14 1.8215383 6.4116679 4.8917994 11.0495578 1.0280607 14.3254007
15 5.4351817 6.4116679 4.8917994 11.0495484 1.0280607 14.3254007
16 0.0000000 0.0016933 3.5455405 10.9039885 1.0891445 11.5209756
17 3.6283600 0.0093825 3.5368236 10.9203774 1.0796827 11.5384052
18 0.0000000 2.5706307 3.5564315 10.9709749 1.0899332 11.8451664
19 3.6283600 2.5681292 3.5762004 11.0041714 1.0843171 12.0909240
20 0.0000000 5.1295929 3.5473523 10.9143138 1.1018280 11.5802363
21 3.6283600 5.1361892 3.5806091 10.9583316 1.0905093 11.8347087
22 1.8141800 1.2828216 2.2828263 11.0331197 1.0791111 14.8936061
23 5.4425400 1.2828216 2.2828263 11.0331203 1.0791111 14.8936061
24 1.8141800 3.8484570 2.2828263 10.9642046 1.0826514 14.3776895
25 5.4425400 3.8484570 2.2828263 10.9642052 1.0826514 14.3776895
26 1.8141800 6.4140924 2.2828263 10.9731747 1.0723441 14.3480592
27 5.4425400 6.4140924 2.2828263 10.9731751 1.0723441 14.3498021
28 0.0000000 0.0000000 1.0000010 11.0057732 1.0943010 66.7101089
29 3.6283600 0.0000000 1.0000010 11.0013967 1.0943010 62.0651165
30 0.0000000 2.5656354 1.0000010 11.0740101 1.1055909 67.5519593
31 3.6283600 2.5656354 1.0000010 10.9977011 1.1055909 60.4633349
32 0.0000000 5.1312786 1.0000010 10.9979457 1.1055909 67.2591418
33 3.6283600 5.1312786 1.0000010 11.0582593 1.1055909 62.8755936
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 340.0004
Re: about the bader charge
thank you professor, now I know the problem since I remove the vacuum charge but not reference the CHGCAR_sum