bader on a Li system demonstrates nonphysical charge&volume

[nikolai]

Dear Graeme,

I came across some nonphysical results upon bader analysis of a simple bcc Li metal structure. My ACF.dat file suggests that atom 1 has a zero charge and volume, whereas atom 2 has a charge of 2 and a volume of ~42.

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 1.7212 1.7212 1.7212 2.0000 0.0000 42.4282
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 2.00000

AVF.dat file suggests that bader volume of atom 2 is constructed by both atom 1 and 2:
Atom Volume(s)
------------------------------------------------------------------------
2 ... 1 2
------------------------------------------------------------------------

When I performed bader on both valence and core charge, I got
the net charge on atom 1=1-2.28=-1.28 and
the net charge on atom 2=1-3.78=-2.78, which are both nonphysical (results presented below).

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.0000 2.2829 0.9062 5.7771
2 1.7212 1.7212 1.7212 3.7845 1.6867 36.6511
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 6.06746

I'd appreciate an explanation on the issue. My understanding is that the zero flux surfaces, where the charge density is a minimum, is not located between the two Li atoms. However, I don't understand why this is so. If this is a bug, is there a way to get rid of the error?

Thanks in advance,
~m

[graeme]

Try doing the partitioning using the total charge and the integration on the valence charge, as described here:
http://theory.cm.utexas.edu/bader/vasp.php

[nikolai]

This is what I get with bader CHGCAR -ref CHGCAR_sum:

This is what I am getting:
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 0.0000 0.0000 0.0000 0.2219 0.9062 5.7771
2 1.7212 1.7212 1.7212 1.7781 1.6867 36.6511
--------------------------------------------------------------------------------
NUMBER OF ELECTRONS: 2.00000

Although the charges are corrected, the atomic volume still doesn't seem right. Can I fix this somehow?

Thank you,
~m

[graeme]

The volumes are consistent with atom 1 having a diameter of about 1.7 Ang and the other of 3.3 Ang; why do you think this is wrong?

[nikolai]

The reason this is confusing to me is because I'd anticipate the zero flux surface to reach a minimum half way between the to Li atoms, as this would be a natural place to separate atoms from each other. Also, the main reason I ran bader on the simple Li system, is because I am trying to understand why I am getting negative net charges on amorphous Li for a Cu-Li slab system (after I do the bader CHGCAR -ref CHGCAR_sum):

# X Y Z CHARGE MIN DIST ATOMIC VOL
-------------------------------------------------------------------------------
-
1 6.4752 3.7934 6.8522 0.6407 0.7437 13.3294
2 9.9199 4.0624 6.8761 0.2034 0.7369 4.6489
3 5.1900 4.2609 17.0381 0.2457 0.8846 22.0537
4 1.3324 8.1391 17.2759 3.8882 1.7524 192.4859
5 8.7652 1.8603 14.1342 0.2213 0.9002 5.3896
6 0.3437 5.4185 9.3504 2.3457 0.9038 48.6847
7 4.5832 1.2356 17.1306 3.4017 1.6214 149.5337
8 5.7623 8.6567 14.6000 0.2183 0.9032 5.5745
9 4.1134 7.1223 16.7043 0.2478 0.8860 13.9791
10 8.0483 6.1629 6.9177 0.2005 0.7346 4.7808
11 9.8171 6.2315 15.8298 0.2462 0.8900 8.5179
12 1.3662 1.7174 6.9418 0.1992 0.7434 4.8143
13 6.7970 1.3391 9.2902 0.2157 0.8996 5.4835
14 0.4714 6.7975 12.1410 0.2102 0.9141 5.9547
15 2.7533 4.1917 6.9539 0.2021 0.7489 4.8143
16 6.9827 6.4479 16.2133 5.3394 1.6992 213.6232
17 3.0486 6.2576 9.5187 0.2197 0.9134 5.7028
18 7.9018 4.7513 13.9804 2.5144 0.8952 52.3874
19 8.1986 0.3055 16.5009 0.2195 0.9021 13.9874
20 6.2079 8.7316 11.7588 4.2439 0.9317 85.7844
21 1.9227 4.7754 17.1790 2.9752 0.9145 108.0333
22 8.2050 1.7930 6.7473 1.3229 0.7130 26.0836
23 0.8384 1.9961 16.2895 1.5467 0.9082 67.7913
24 5.6869 7.1454 9.3171 2.0377 0.9180 42.1352
25 7.0521 2.7149 11.8494 0.2228 0.8997 5.5151
26 9.6887 8.4963 6.9400 0.2020 0.7421 4.9240
27 3.9408 0.6948 9.7054 0.2166 0.9162 5.7242
28 1.4972 1.5899 12.4066 0.2065 0.9056 5.7688
29 4.5128 1.8803 6.9226 0.2010 0.7371 4.8087
30 8.4464 3.5614 16.6724 0.2228 0.9035 15.8146
31 3.4227 7.8355 12.2385 0.2061 0.9177 5.8775
32 4.8563 3.7796 9.5335 0.2112 0.9151 5.7046
33 2.2351 6.3950 14.7175 0.2206 0.8850 5.3459
34 5.0025 5.6407 14.2547 0.2157 0.9013 5.5662
35 8.1558 7.4967 13.4859 0.2219 0.8953 5.7372
36 9.1779 0.6850 11.5980 1.0414 0.9028 22.5686
37 6.1102 5.6065 11.6990 0.2217 0.9205 6.1266
38 4.3688 2.2035 12.3824 0.2161 0.9112 5.7595
39 0.5427 4.0077 14.2955 0.2209 0.8980 5.5104
40 8.5157 7.5220 9.7329 0.2129 0.9131 5.8887
41 1.2336 6.5065 6.8424 0.2088 0.7410 4.6935
42 3.2382 8.3358 6.9548 0.2008 0.7363 4.8236
43 2.0189 2.9897 9.6997 1.4709 0.9144 31.8365
44 6.0890 2.6041 14.8482 0.2210 0.8937 5.5634
45 7.7593 4.4734 9.4079 0.2194 0.9074 5.6387
46 9.7342 3.9261 11.6641 0.2179 0.9094 5.7446
47 2.7773 4.7048 12.1066 0.2093 0.9205 5.8143
48 9.5959 2.1438 9.2496 4.8148 0.9182 96.3675
49 3.0589 0.4346 14.8245 0.2233 0.8991 5.4379
50 0.3221 8.6668 14.4961 1.5377 0.8880 31.2008
51 1.1569 8.6127 9.5907 0.2117 0.9189 5.8431
52 6.3577 8.4785 6.8681 0.2034 0.7285 4.7102
53 3.2558 3.3101 14.9580 0.2245 0.8864 5.5671
54 4.8275 5.9846 6.8617 0.2068 0.7364 4.6925
55 10.2472 8.9014 0.5481 11.0222 1.1429 37.9985
56 2.5358 0.0015 0.5703 11.0250 1.1286 37.5458
57 5.1065 0.0080 0.5878 11.0248 1.1206 37.4817
58 7.6759 0.0058 0.5696 11.0218 1.1351 38.2392
59 1.2526 2.2223 0.5600 11.0332 1.1326 37.9176
60 3.8192 2.2265 0.5744 11.0310 1.1314 37.5923
61 6.3878 2.2385 0.5748 11.0269 1.1242 38.1592
62 8.9643 2.2282 0.5535 11.0274 1.1250 38.6890
63 10.2538 4.4467 0.5580 11.0252 1.1363 38.0514
64 2.5345 4.4504 0.5644 11.0276 1.1358 37.7484
65 5.1024 4.4637 0.5793 11.0218 1.1269 37.6090
66 7.6783 4.4570 0.5763 11.0217 1.1273 37.9706
67 1.2544 6.6762 0.5549 11.0299 1.1323 37.4919
68 3.8226 6.6867 0.5788 11.0310 1.1322 37.3386
69 6.3947 6.6887 0.5947 11.0290 1.1211 37.5681
70 8.9653 6.6709 0.5625 11.0300 1.1414 38.2615
71 10.2635 1.4425 2.6195 10.9904 1.1123 11.8889
72 2.5241 1.4386 2.6504 10.9831 1.1250 11.8917
73 5.0974 1.4896 2.6478 10.9751 1.1102 11.8842
74 7.6866 1.4863 2.6185 10.9698 1.1154 11.8192
75 1.2539 3.6570 2.6456 10.9862 1.1263 11.8954
76 3.7966 3.6875 2.6379 10.9836 1.1226 11.8972
77 6.3821 3.7276 2.6324 10.9715 1.1130 11.8480
78 8.9822 3.6874 2.6249 10.9754 1.1068 11.8238
79 10.2617 5.8841 2.6303 10.9875 1.1262 11.8814
80 2.5240 5.8998 2.6319 10.9822 1.1312 11.8443
81 5.0961 5.9401 2.6553 10.9691 1.1124 11.8833
82 7.6877 5.9337 2.6488 10.9699 1.1244 11.8786
83 1.2527 8.1104 2.6299 10.9775 1.1212 11.8322
84 3.8184 8.1455 2.6467 10.9843 1.1213 11.8805
85 6.3970 8.1765 2.6582 10.9738 1.1117 11.9325
86 8.9793 8.1275 2.6145 10.9738 1.1176 11.8285
87 1.2632 0.5678 4.7529 11.3533 1.1528 18.3407
88 3.8303 0.6786 4.7406 11.4136 1.1192 18.5499
89 6.4031 0.8033 4.7406 11.3824 1.1351 18.3500
90 8.9727 0.6643 4.6735 11.4196 1.1214 18.2302
91 10.2571 2.8120 4.7423 11.4024 1.1258 18.4179
92 2.5415 2.8443 4.7688 11.3969 1.1365 18.6883
93 5.1084 2.9831 4.7297 11.3858 1.1293 18.1837
94 7.6829 2.9862 4.6729 11.3949 1.1133 17.6930
95 1.2354 5.0474 4.7567 11.4319 1.1432 18.7422
96 3.8019 5.1270 4.7226 11.3670 1.1283 17.7710
97 6.3909 5.2252 4.7532 11.4420 1.1409 18.9551
98 8.9583 5.1256 4.7271 11.3772 1.1311 17.9578
99 10.2280 7.2967 4.7248 11.4225 1.1297 18.6623
100 2.5415 7.2946 4.7266 11.3637 1.1298 17.8826
101 5.1069 7.4255 4.7605 11.4396 1.1324 18.6939
102 7.6691 7.4291 4.7493 11.3890 1.1306 18.6121

As you can see, atoms 4,6,7,16,18,20, 21 and 48 demonstrate great volumes accompanied by nonphysical net charges of
at 4=-2.88
at 6=-1.33
at 7=-2.4
at 16=-4.33
at 18=-1.5
at 20=-3.29
at 21=-1.9
at 48=-3.8

How can this be happening when Li has only 1 valence electron to give? Is there some correlation between the very negative charges and the large volumes?Can I trust this result?

Thank you very much,
~m

[graeme]

If you have a slab geometry, the vacuum above the slab will be associated with some of the surface atoms.

If you check this carefully and really think that there is something wrong with the analysis, I'll take a look at your file if you post it.