UT theoretical chemistry code forum

Hello everyone
I'm trying to obtain voronoi partial charge using bader, from Siesta cube file.

The problem with siesta is alredy known, it uses pseudopotential in order to replace core electron, so the cube file do not contain total charge needed to make bader's analysis. I'm analizing quit large system made of Si(128)H(126) so number of total valence electron is 319, and total electrons 1918. The box is 14x15x27 with 50x50x100 grid.

VORONOI ANALYSIS RESULT
# X Y Z CHARGE ATOMIC VOL
----------------------------------------------------------------------
1 10.2437 2.0650 6.4058 -0.7065 174.0547
2 10.2298 2.0695 10.9111 -0.6558 178.8980
3 8.6489 5.8642 12.7204 -0.5458 187.3737
4 8.6649 5.8512 4.5804 -0.7569 165.5790
5 5.7447 8.7411 6.3897 -0.7200 172.8439
6 5.7485 8.7587 10.8923 -0.6135 181.9250
7 1.9536 10.3377 12.6953 -0.5411 184.3466
8 1.9365 10.2825 4.5801 -0.7560 168.7574
9 -2.1632 10.2741 6.4147 -0.6950 174.5088
10 -2.1660 10.2660 10.9228 -0.6258 185.1034
11 -5.9157 8.6670 12.8196 -0.5957 185.4061
12 -5.9524 8.7175 4.5812 -0.7860 167.6979
13 -8.8507 5.8334 6.4394 -0.7424 170.1196
14 -8.8367 5.8194 10.9552 -0.5968 179.9574
15 -10.3240 2.0450 12.8800 -0.6884 178.7466
16 -10.4256 2.0639 4.5768 -0.8030 164.0655
17 -10.4059 -2.0215 6.4395 -0.7728 169.5142
18 -10.3869 -2.0119 10.9552 -0.5960 179.8061
19 -8.7755 -5.7584 12.8219 -0.6245 184.1953
20 -8.8306 -5.7933 4.5798 -0.7619 166.6385
21 -5.9224 -8.6775 6.4139 -0.7275 173.7520
22 -5.9222 -8.6687 10.9223 -0.5882 185.1034
23 -2.1434 -10.3086 12.6956 -0.5490 185.4061
24 -2.1358 -10.2498 4.5798 -0.7395 168.6060
25 1.9724 -10.2811 6.3895 -0.7328 172.9952
26 1.9671 -10.2997 10.8926 -0.6383 181.9250
27 5.7529 -8.7318 12.7202 -0.5358 187.9791
28 5.7748 -8.7256 4.5798 -0.7556 166.1844
29 8.6796 -5.8301 6.4059 -0.7263 172.2385
30 8.6648 -5.8297 10.9115 -0.6092 181.1683
31 10.2258 -2.0344 12.7328 -0.5549 186.4656
32 10.2495 -2.0385 4.5820 -0.8019 164.2168
33 10.1684 2.0858 19.0425 -0.7626 166.6385
34 10.1200 2.0963 23.5418 -0.6121 173.7520
35 8.5326 5.8924 25.3366 -0.5445 178.4439
36 8.6109 5.8813 17.2240 -0.7706 169.8169
37 5.7161 8.8129 19.0182 -0.7067 167.6979
38 5.6798 8.8453 23.5193 -0.6471 170.8763
39 1.9390 10.5740 25.3132 -0.5429 163.6114
40 1.9504 10.4242 17.1943 -0.8173 163.9141
41 -2.1563 10.4932 18.9937 -0.6883 150.5952
42 -2.1656 10.6593 23.4967 -0.6407 144.6924
43 -5.8064 8.7755 25.2884 -0.5787 125.7734
44 -5.8797 8.6289 17.3334 -0.7047 167.5466
45 -8.3082 5.5256 19.5173 -0.6378 156.8006
46 -7.3736 4.8360 23.8905 -0.6488 123.8059
47 -5.2130 1.0280 25.1232 0.0853 589.3644
48 -10.1581 2.0157 17.3993 -0.6861 161.1898
49 -9.7894 -1.9346 19.5173 -0.7045 153.6222
50 -8.6662 -1.6660 23.8924 -0.6495 121.9896
51 -8.7204 -5.9060 25.2886 -0.5866 126.6816
52 -8.7278 -5.7310 17.3360 -0.7170 165.4277
53 -6.0015 -8.8792 18.9943 -0.7116 150.4438
54 -6.0723 -9.0348 23.4971 -0.6403 143.1789
55 -2.2442 -10.5196 25.3128 -0.5295 164.6709
56 -2.1800 -10.3858 17.1950 -0.7759 164.6709
57 1.9159 -10.3334 19.0177 -0.6977 167.3952
58 1.8732 -10.3502 23.5185 -0.5994 171.4817
59 5.6375 -8.7120 25.3375 -0.5742 177.2331
60 5.7111 -8.7309 17.2235 -0.8040 169.8169
61 8.6019 -5.8201 19.0418 -0.7201 168.7574
62 8.5529 -5.8097 23.5413 -0.5927 174.9628
63 10.1295 -2.0142 25.3376 -0.5527 176.6277
64 10.1855 -2.0255 17.2375 -0.7540 167.6979
65 10.1250 2.0971 31.6369 -0.7204 168.4547
66 10.1755 2.0803 36.1361 -0.6241 180.5628
67 8.6096 5.8725 37.9524 -0.5501 189.1899
68 8.5547 5.9016 29.8358 -0.7829 164.5195
69 5.7034 8.8643 31.6472 -0.7112 169.5142
70 5.7242 8.8089 36.1505 -0.5905 182.2277
71 1.9592 10.4135 37.9807 -0.5744 179.8061
72 1.9656 10.5773 29.8187 -0.8281 151.6546
73 -2.1335 10.6620 31.6509 -0.7067 146.8114
74 -2.1392 10.4764 36.1546 -0.5989 165.2763
75 -5.8838 8.6972 37.8679 -0.5306 182.6818
76 -5.8135 8.9269 29.7763 -0.8005 121.2329
77 -7.6188 5.1635 31.3636 -0.6298 152.1087
78 -8.4182 5.6033 35.7863 -0.6719 176.3250
79 -10.2420 2.0314 37.8155 -0.7595 162.5520
80 -6.7904 1.3448 29.1677 -0.1783 332.3688
81 -9.0104 -1.8682 31.3650 -0.6575 151.5033
82 -9.9157 -1.9668 35.7875 -0.7064 173.1466
83 -8.7529 -5.7946 37.8666 -0.5319 180.7142
84 -8.7847 -6.0377 29.7773 -0.7737 121.3842
85 -6.0483 -9.0512 31.6492 -0.7251 145.9033
86 -5.9752 -8.8729 36.1530 -0.6156 164.6709
87 -2.1639 -10.3807 37.9795 -0.5539 180.5628
88 -2.2245 -10.5351 29.8184 -0.8007 152.5627
89 1.8846 -10.3774 31.6486 -0.7127 169.0601
90 1.9290 -10.3335 36.1516 -0.5869 183.2872
91 5.7157 -8.7211 37.9540 -0.5453 188.8872
92 5.6510 -8.7276 29.8368 -0.7773 165.4277
93 8.5559 -5.8124 31.6385 -0.7049 169.3628
94 8.6108 -5.8151 36.1380 -0.6168 182.8331
95 10.1991 -2.0269 37.9508 -0.5357 184.8007
96 10.1244 -2.0134 29.8377 -0.7591 164.5195
97 10.2298 2.0707 44.2748 -0.7822 168.7574
98 10.2413 2.0665 48.7792 -0.6367 181.1683
99 8.6634 5.8513 50.6046 -0.5641 182.9845
100 8.6454 5.8601 42.4556 -0.7837 168.7574
101 5.7452 8.7523 44.2872 -0.7702 170.4223
102 5.7424 8.7373 48.7904 -0.5706 185.2548
103 1.9366 10.2801 50.6016 -0.5758 186.3142
104 1.9516 10.3292 42.4801 -0.7547 170.5736
105 -2.1621 10.2752 44.2613 -0.7231 173.1466
106 -2.1637 10.2742 48.7685 -0.5790 186.6169
107 -5.9548 8.7208 50.5996 -0.5733 184.4980
108 -5.9242 8.6983 42.3794 -0.8196 169.6655
109 -8.8382 5.8316 44.2238 -0.7111 171.3304
110 -8.8527 5.8388 48.7380 -0.6146 180.7142
111 -10.4303 2.0676 50.5922 -0.6392 180.4115
112 -10.3538 2.0524 42.3306 -0.5948 174.3574
113 -10.3931 -2.0199 44.2224 -0.7387 171.0277
114 -10.4096 -2.0199 48.7368 -0.6104 181.7737
115 -8.8335 -5.7911 50.5981 -0.5668 184.8007
116 -8.7943 -5.7824 42.3783 -0.7993 169.2114
117 -5.9203 -8.6764 44.2611 -0.7404 173.7520
118 -5.9226 -8.6751 48.7683 -0.5913 186.0115
119 -2.1356 -10.2466 50.6019 -0.5754 186.9196
120 -2.1396 -10.2974 42.4788 -0.7510 170.8763
121 1.9685 -10.2912 44.2872 -0.7644 169.9682
122 1.9710 -10.2762 48.7908 -0.5827 184.6493
123 5.7735 -8.7246 50.6039 -0.5788 184.0439
124 5.7535 -8.7246 42.4570 -0.7817 169.3628
125 8.6664 -5.8286 44.2749 -0.7515 169.6655
126 8.6786 -5.8300 48.7795 -0.5657 182.8331
127 10.2480 -2.0378 50.6040 -0.5848 184.3466
128 10.2307 -2.0337 42.4549 -0.7667 169.3628
129 11.0055 7.4353 50.0052 0.6514 152.1087
130 2.4795 13.0553 50.0107 0.5452 88.0868
131 -7.5149 11.0812 50.0164 0.6564 198.2710
132 -13.2065 2.6201 50.0112 0.4993 54.6380
133 -11.1772 -7.3751 50.0119 0.6426 148.7789
134 -2.6955 -13.0186 50.0117 0.5728 89.2976
135 7.3337 -11.0827 50.0055 0.6640 198.8764
136 13.0247 -2.5890 5.1733 0.6159 52.0651
137 13.0182 2.6216 5.8187 0.6273 51.0056
138 13.0013 2.6227 11.5133 0.6301 59.7840
139 11.0032 7.4340 12.1374 0.6617 152.4114
140 11.0093 7.4335 5.1775 0.6384 141.2113
141 7.2998 11.0990 5.7796 0.6444 182.2277
142 7.3189 11.1124 11.4796 0.6545 198.1197
143 2.4832 13.1011 12.0388 0.5623 85.3625
144 2.4823 13.0590 5.1632 0.5076 81.8814
145 -2.7071 13.0508 5.8321 0.5306 82.6381
146 -2.7296 13.0407 11.4962 0.5475 87.4814
147 -7.4769 11.0437 12.3047 0.6541 197.3629
148 -7.5143 11.0792 5.1533 0.6293 183.2872
149 -11.2006 7.4186 5.8759 0.6287 138.7897
150 -11.1892 7.3963 11.5300 0.6469 155.4384
151 -13.1291 2.5997 12.4582 0.5280 59.0272
152 -13.2054 2.6145 5.1435 0.4957 50.7029
153 -13.1832 -2.5901 5.8787 0.5234 52.8218
154 -13.1630 -2.5713 11.5307 0.5104 56.9083
155 -11.1258 -7.3597 12.3105 0.6599 149.5357
156 -11.1764 -7.3799 5.1505 0.6254 137.5789
157 -7.4838 -11.0368 5.8302 0.6453 183.5899
158 -7.5039 -11.0171 11.4947 0.6496 189.6440
159 -2.7083 -13.0652 12.0407 0.6006 88.2382
160 -2.6927 -13.0239 5.1625 0.5458 83.5463
161 2.5084 -13.0545 5.7801 0.5709 82.6381
162 2.5196 -13.0744 11.4798 0.5595 87.3301
163 7.3296 -11.0816 12.1382 0.6629 197.3629
164 7.3382 -11.0822 5.1768 0.6373 183.4385
165 11.0318 -7.4026 5.8171 0.6347 141.3627
166 11.0147 -7.3997 11.5137 0.6500 153.0168
167 13.0031 -2.5856 12.1595 0.6222 54.9407
168 12.9450 2.6369 18.4679 0.5157 51.0056
169 12.8818 2.6601 24.1768 0.5969 103.9788
170 10.8914 7.4472 24.7331 0.6788 184.0439
171 10.9633 7.4435 17.8345 0.6421 160.2817
172 7.3154 11.1435 18.4225 0.6511 182.8331
173 7.3204 11.1494 24.1070 0.6707 198.2710
174 2.6045 13.3193 24.7085 0.5527 85.5138
175 2.5399 13.1964 17.7559 0.5127 83.3949
176 -2.7635 13.2185 18.2454 0.5183 82.6381
177 -2.7645 13.4282 24.0659 0.5316 82.6381
178 -7.8565 10.6351 24.4529 0.6766 215.0711
179 -7.5986 10.8847 17.8811 0.6410 187.5250
180 -10.6792 7.1451 19.8514 0.6523 149.6871
181 -10.0653 4.8658 24.9518 0.6841 115.7842
182 -12.9226 2.5646 18.0212 0.5026 57.3624
183 -12.5999 -2.5251 19.8443 0.4727 77.7949
184 -11.1652 -0.6669 24.9540 0.6252 83.3949
185 -11.3236 -6.8437 24.4510 0.6218 132.2816
186 -11.1781 -7.1584 17.8843 0.6368 131.6762
187 -7.6080 -11.1618 18.2425 0.6541 210.0765
188 -7.6799 -11.3678 24.0644 0.6610 217.9468
189 -2.6796 -13.3103 24.7069 0.5476 80.0652
190 -2.6935 -13.1729 17.7580 0.5171 78.7030
191 2.5022 -13.0987 18.4229 0.5696 80.2165
192 2.5086 -13.1064 24.1052 0.5362 82.4868
193 7.2256 -11.0489 24.7366 0.6739 193.8818
194 7.2863 -11.0740 17.8347 0.6394 179.9574
195 10.9574 -7.3906 18.4675 0.6450 143.7843
196 10.8898 -7.3857 24.1763 0.6603 159.5249
197 12.9010 -2.5643 24.7281 0.6590 80.3679
198 12.9525 -2.5742 17.8608 0.7200 70.5300
199 12.8914 2.6480 31.0073 0.5732 97.9247
200 12.9502 2.6423 36.7116 0.5651 53.1245
201 10.9627 7.4348 37.3456 0.6649 165.5790
202 10.9258 7.4469 30.4173 0.6468 170.2709
203 7.3435 11.1746 31.0795 0.6544 183.1358
204 7.3224 11.1361 36.7660 0.6655 197.9683
205 2.5429 13.1892 37.4286 0.5396 86.7247
206 2.6065 13.3299 30.4140 0.5170 78.2489
207 -2.7046 13.4450 31.1257 0.5373 75.6760
208 -2.7445 13.2089 36.8759 0.5344 86.2706
209 -7.5799 10.9651 37.2931 0.6443 194.6386
210 -7.7756 10.8948 30.5714 0.6415 213.1035
211 -10.3313 5.2655 30.3231 0.6465 116.5410
212 -10.8042 7.2205 35.5901 0.6578 152.2600
213 -13.0049 2.5784 37.1699 0.4467 52.3678
214 -11.5566 -0.9260 30.3268 0.5340 72.8003
215 -12.7382 -2.5529 35.5945 0.4550 75.2219
216 -11.1887 -7.2387 37.2901 0.6398 135.1573
217 -11.3526 -7.0996 30.5708 0.6212 142.4222
218 -7.6390 -11.4069 31.1286 0.6529 201.9035
219 -7.5807 -11.1637 36.8803 0.6549 198.2710
220 -2.6826 -13.1696 37.4277 0.5496 84.3030
221 -2.6818 -13.3245 30.4120 0.5070 73.5570
222 2.5188 -13.1387 31.0811 0.5393 76.7354
223 2.5205 -13.0937 36.7667 0.5395 85.9679
224 7.2938 -11.0635 37.3474 0.6572 195.0926
225 7.2518 -11.0610 30.4194 0.6390 179.0493
226 10.9026 -7.3778 31.0109 0.6459 142.4222
227 10.9601 -7.3947 36.7146 0.6601 153.1681
228 12.9688 -2.5767 37.3345 0.7129 71.7408
229 12.8942 -2.5624 30.4529 0.6638 74.1624
230 13.0015 2.6284 43.6772 0.6531 55.2435
231 13.0156 2.6215 49.3675 0.6552 54.3353
232 10.9963 7.4377 43.0332 0.6443 141.5140
233 7.3077 11.1099 43.6949 0.6475 182.3791
234 7.2955 11.0987 49.3943 0.6579 196.9089
235 2.4807 13.0943 43.1333 0.5240 82.1841
236 -2.7295 13.0463 43.6741 0.5661 82.9409
237 -2.7082 13.0524 49.3442 0.5443 90.2057
238 -7.4933 11.0647 42.9173 0.6389 190.4007
239 -11.1896 7.4039 43.6355 0.6438 148.9303
240 -11.2053 7.4247 49.2870 0.6570 150.2925
241 -13.1552 2.6078 42.7780 0.5105 61.9029
242 -13.1668 -2.5761 43.6344 0.5499 53.8813
243 -13.1895 -2.5870 49.2862 0.5986 56.4543
244 -11.1492 -7.3700 42.9132 0.6509 146.8114
245 -7.5027 -11.0207 43.6729 0.6503 184.8007
246 -7.4871 -11.0344 49.3449 0.6584 197.9683
247 -2.7071 -13.0541 43.1339 0.5661 83.5463
248 2.5134 -13.0666 43.6955 0.5660 81.5787
249 2.5045 -13.0510 49.3974 0.5743 88.9949
250 7.3250 -11.0799 43.0336 0.6437 183.2872
251 11.0152 -7.4015 43.6754 0.6498 142.5735
252 11.0306 -7.4022 49.3695 0.6435 151.8060
253 13.0234 -2.5875 50.0137 0.5881 58.5732
254 13.0065 -2.5836 43.0373 0.5674 48.8867
-----------------------------------------------------------------------
NUMBER OF ELECTRONS: -8.10415

Something has gone very wrong. The file should contain the charge density, which is a positive quantity. Your files seems to have negative values. That, or it is not being read properly. If you make the file available, we'll take a look at it.

Thanks graeme,
the problem is that siesta gives total charge as the sum of ionic+valence instead of core+valence. Now I've tried to run Bader only on valence charges using vozny's util rho2cube that adds artifical core for H, so I should have core+valence for H, and only valence for Si. Maybe it should work since Bader is able to find peak on Si atoms. I paste my results:

VORONOI ANALYSIS RESULT
# X Y Z CHARGE ATOMIC VOL
----------------------------------------------------------------------
1 10.2437 2.0650 6.4058 3.2620 174.0547
2 10.2298 2.0695 10.9111 3.3127 178.8980
3 8.6489 5.8642 12.7204 3.4262 187.3737
4 8.6649 5.8512 4.5804 3.1517 165.5790
5 5.7447 8.7411 6.3897 3.2498 172.8439
6 5.7485 8.7587 10.8923 3.3661 181.9250
7 1.9536 10.3377 12.6953 3.4233 184.3466
8 1.9365 10.2825 4.5801 3.1605 168.7574
9 -2.1632 10.2741 6.4147 3.2714 174.5088
10 -2.1660 10.2660 10.9228 3.3441 185.1034
11 -5.9157 8.6670 12.8196 3.3714 185.4061
12 -5.9524 8.7175 4.5812 3.1392 167.6979
13 -8.8507 5.8334 6.4394 3.2274 170.1196
14 -8.8367 5.8194 10.9552 3.3740 179.9574
15 -10.3240 2.0450 12.8800 3.2867 178.7466
16 -10.4256 2.0639 4.5768 3.1230 164.0655
17 -10.4059 -2.0215 6.4395 3.1970 169.5142
18 -10.3869 -2.0119 10.9552 3.3894 179.8061
19 -8.7755 -5.7584 12.8219 3.3424 184.1953
20 -8.8306 -5.7933 4.5798 3.1456 166.6385
21 -5.9224 -8.6775 6.4139 3.2437 173.7520
22 -5.9222 -8.6687 10.9223 3.3838 185.1034
23 -2.1434 -10.3086 12.6956 3.4132 185.4061
24 -2.1358 -10.2498 4.5798 3.1757 168.6060
25 1.9724 -10.2811 6.3895 3.2369 172.9952
26 1.9671 -10.2997 10.8926 3.3304 181.9250
27 5.7529 -8.7318 12.7202 3.4357 187.9791
28 5.7748 -8.7256 4.5798 3.1687 166.1844
29 8.6796 -5.8301 6.4059 3.2404 172.2385
30 8.6648 -5.8297 10.9115 3.3692 181.1683
31 10.2258 -2.0344 12.7328 3.4025 186.4656
32 10.2495 -2.0385 4.5820 3.1290 164.2168
33 10.1684 2.0858 19.0425 3.1910 166.6385
34 10.1200 2.0963 23.5418 3.3541 173.7520
35 8.5326 5.8924 25.3366 3.4276 178.4439
36 8.6109 5.8813 17.2240 3.1995 169.8169
37 5.7161 8.8129 19.0182 3.2657 167.6979
38 5.6798 8.8453 23.5193 3.3275 170.8763
39 1.9390 10.5740 25.3132 3.4328 163.6114
40 1.9504 10.4242 17.1943 3.1464 163.9141
41 -2.1563 10.4932 18.9937 3.2586 150.5952
42 -2.1656 10.6593 23.4967 3.3400 144.6924
43 -5.8064 8.7755 25.2884 3.4030 125.7734
44 -5.8797 8.6289 17.3334 3.2673 167.5466
45 -8.3082 5.5256 19.5173 3.3326 156.8006
46 -7.3736 4.8360 23.8905 3.3187 123.8059
47 -5.2130 1.0280 25.1232 4.0814 589.3644
48 -10.1581 2.0157 17.3993 3.2750 161.1898
49 -9.7894 -1.9346 19.5173 3.2704 153.6222
50 -8.6662 -1.6660 23.8924 3.3148 121.9896
51 -8.7204 -5.9060 25.2886 3.3902 126.6816
52 -8.7278 -5.7310 17.3360 3.2496 165.4277
53 -6.0015 -8.8792 18.9943 3.2634 150.4438
54 -6.0723 -9.0348 23.4971 3.3395 143.1789
55 -2.2442 -10.5196 25.3128 3.4337 164.6709
56 -2.1800 -10.3858 17.1950 3.1827 164.6709
57 1.9159 -10.3334 19.0177 3.2478 167.3952
58 1.8732 -10.3502 23.5185 3.3734 171.4817
59 5.6375 -8.7120 25.3375 3.3995 177.2331
60 5.7111 -8.7309 17.2235 3.1718 169.8169
61 8.6019 -5.8201 19.0418 3.2411 168.7574
62 8.5529 -5.8097 23.5413 3.3841 174.9628
63 10.1295 -2.0142 25.3376 3.4076 176.6277
64 10.1855 -2.0255 17.2375 3.2092 167.6979
65 10.1250 2.0971 31.6369 3.2418 168.4547
66 10.1755 2.0803 36.1361 3.3516 180.5628
67 8.6096 5.8725 37.9524 3.4182 189.1899
68 8.5547 5.9016 29.8358 3.1846 164.5195
69 5.7034 8.8643 31.6472 3.2557 169.5142
70 5.7242 8.8089 36.1505 3.3820 182.2277
71 1.9592 10.4135 37.9807 3.3979 179.8061
72 1.9656 10.5773 29.8187 3.1461 151.6546
73 -2.1335 10.6620 31.6509 3.2687 146.8114
74 -2.1392 10.4764 36.1546 3.3659 165.2763
75 -5.8838 8.6972 37.8679 3.4417 182.6818
76 -5.8135 8.9269 29.7763 3.1831 121.2329
77 -7.6188 5.1635 31.3636 3.3376 152.1087
78 -8.4182 5.6033 35.7863 3.2977 176.3250
79 -10.2420 2.0314 37.8155 3.2205 162.5520
80 -6.7904 1.3448 29.1677 3.8141 332.3688
81 -9.0104 -1.8682 31.3650 3.3117 151.5033
82 -9.9157 -1.9668 35.7875 3.2732 173.1466
83 -8.7529 -5.7946 37.8666 3.4355 180.7142
84 -8.7847 -6.0377 29.7773 3.1901 121.3842
85 -6.0483 -9.0512 31.6492 3.2491 145.9033
86 -5.9752 -8.8729 36.1530 3.3609 164.6709
87 -2.1639 -10.3807 37.9795 3.4152 180.5628
88 -2.2245 -10.5351 29.8184 3.1686 152.5627
89 1.8846 -10.3774 31.6486 3.2433 169.0601
90 1.9290 -10.3335 36.1516 3.3843 183.2872
91 5.7157 -8.7211 37.9540 3.4244 188.8872
92 5.6510 -8.7276 29.8368 3.1946 165.4277
93 8.5559 -5.8124 31.6385 3.2435 169.3628
94 8.6108 -5.8151 36.1380 3.3507 182.8331
95 10.1991 -2.0269 37.9508 3.4311 184.8007
96 10.1244 -2.0134 29.8377 3.2163 164.5195
97 10.2298 2.0707 44.2748 3.1916 168.7574
98 10.2413 2.0665 48.7792 3.3232 181.1683
99 8.6634 5.8513 50.6046 3.4014 182.9845
100 8.6454 5.8601 42.4556 3.1867 168.7574
101 5.7452 8.7523 44.2872 3.2013 170.4223
102 5.7424 8.7373 48.7904 3.4072 185.2548
103 1.9366 10.2801 50.6016 3.3828 186.3142
104 1.9516 10.3292 42.4801 3.2123 170.5736
105 -2.1621 10.2752 44.2613 3.2414 173.1466
106 -2.1637 10.2742 48.7685 3.3844 186.6169
107 -5.9548 8.7208 50.5996 3.4019 184.4980
108 -5.9242 8.6983 42.3794 3.1574 169.6655
109 -8.8382 5.8316 44.2238 3.2589 171.3304
110 -8.8527 5.8388 48.7380 3.3434 180.7142
111 -10.4303 2.0676 50.5922 3.3374 180.4115
112 -10.3538 2.0524 42.3306 3.3892 174.3574
113 -10.3931 -2.0199 44.2224 3.2331 171.0277
114 -10.4096 -2.0199 48.7368 3.3699 181.7737
115 -8.8335 -5.7911 50.5981 3.3970 184.8007
116 -8.7943 -5.7824 42.3783 3.1725 169.2114
117 -5.9203 -8.6764 44.2611 3.2329 173.7520
118 -5.9226 -8.6751 48.7683 3.3779 186.0115
119 -2.1356 -10.2466 50.6019 3.3849 186.9196
120 -2.1396 -10.2974 42.4788 3.2153 170.8763
121 1.9685 -10.2912 44.2872 3.2049 169.9682
122 1.9710 -10.2762 48.7908 3.3778 184.6493
123 5.7735 -8.7246 50.6039 3.3967 184.0439
124 5.7535 -8.7246 42.4570 3.1906 169.3628
125 8.6664 -5.8286 44.2749 3.2137 169.6655
126 8.6786 -5.8300 48.7795 3.4010 182.8331
127 10.2480 -2.0378 50.6040 3.3732 184.3466
128 10.2307 -2.0337 42.4549 3.2132 169.3628
129 11.0055 7.4353 50.0052 1.6705 152.1087
130 2.4795 13.0553 50.0107 1.5847 88.0868
131 -7.5149 11.0812 50.0164 1.6931 198.2710
132 -13.2065 2.6201 50.0112 1.2678 54.6380
133 -11.1772 -7.3751 50.0119 1.6742 148.7789
134 -2.6955 -13.0186 50.0117 1.6094 89.2976
135 7.3337 -11.0827 50.0055 1.7003 198.8764
136 13.0247 -2.5890 5.1733 1.1810 52.0651
137 13.0182 2.6216 5.8187 1.1295 51.0056
138 13.0013 2.6227 11.5133 1.2171 59.7840
139 11.0032 7.4340 12.1374 1.6724 152.4114
140 11.0093 7.4335 5.1775 1.6699 141.2113
141 7.2998 11.0990 5.7796 1.6809 182.2277
142 7.3189 11.1124 11.4796 1.6952 198.1197
143 2.4832 13.1011 12.0388 1.5873 85.3625
144 2.4823 13.0590 5.1632 1.5493 81.8814
145 -2.7071 13.0508 5.8321 1.5579 82.6381
146 -2.7296 13.0407 11.4962 1.5872 87.4814
147 -7.4769 11.0437 12.3047 1.6905 197.3629
148 -7.5143 11.0792 5.1533 1.6769 183.2872
149 -11.2006 7.4186 5.8759 1.6548 138.7897
150 -11.1892 7.3963 11.5300 1.6894 155.4384
151 -13.1291 2.5997 12.4582 1.3127 59.0272
152 -13.2054 2.6145 5.1435 1.2777 50.7029
153 -13.1832 -2.5901 5.8787 1.2480 52.8218
154 -13.1630 -2.5713 11.5307 1.3194 56.9083
155 -11.1258 -7.3597 12.3105 1.6866 149.5357
156 -11.1764 -7.3799 5.1505 1.6697 137.5789
157 -7.4838 -11.0368 5.8302 1.6787 183.5899
158 -7.5039 -11.0171 11.4947 1.6976 189.6440
159 -2.7083 -13.0652 12.0407 1.6311 88.2382
160 -2.6927 -13.0239 5.1625 1.5853 83.5463
161 2.5084 -13.0545 5.7801 1.6029 82.6381
162 2.5196 -13.0744 11.4798 1.6144 87.3301
163 7.3296 -11.0816 12.1382 1.6936 197.3629
164 7.3382 -11.0822 5.1768 1.6815 183.4385
165 11.0318 -7.4026 5.8171 1.6574 141.3627
166 11.0147 -7.3997 11.5137 1.6746 153.0168
167 13.0031 -2.5856 12.1595 1.1497 54.9407
168 12.9450 2.6369 18.4679 1.2385 51.0056
169 12.8818 2.6601 24.1768 1.2352 103.9788
170 10.8914 7.4472 24.7331 1.6902 184.0439
171 10.9633 7.4435 17.8345 1.6680 160.2817
172 7.3154 11.1435 18.4225 1.6840 182.8331
173 7.3204 11.1494 24.1070 1.7143 198.2710
174 2.6045 13.3193 24.7085 1.5223 85.5138
175 2.5399 13.1964 17.7559 1.5441 83.3949
176 -2.7635 13.2185 18.2454 1.5324 82.6381
177 -2.7645 13.4282 24.0659 1.4714 82.6381
178 -7.8565 10.6351 24.4529 1.7035 215.0711
179 -7.5986 10.8847 17.8811 1.6901 187.5250
180 -10.6792 7.1451 19.8514 1.6678 149.6871
181 -10.0653 4.8658 24.9518 1.7010 115.7842
182 -12.9226 2.5646 18.0212 1.3504 57.3624
183 -12.5999 -2.5251 19.8443 1.5077 77.7949
184 -11.1652 -0.6669 24.9540 1.6429 83.3949
185 -11.3236 -6.8437 24.4510 1.6577 132.2816
186 -11.1781 -7.1584 17.8843 1.6798 131.6762
187 -7.6080 -11.1618 18.2425 1.6878 210.0765
188 -7.6799 -11.3678 24.0644 1.7099 217.9468
189 -2.6796 -13.3103 24.7069 1.5528 80.0652
190 -2.6935 -13.1729 17.7580 1.5639 78.7030
191 2.5022 -13.0987 18.4229 1.6109 80.2165
192 2.5086 -13.1064 24.1052 1.5818 82.4868
193 7.2256 -11.0489 24.7366 1.7043 193.8818
194 7.2863 -11.0740 17.8347 1.6815 179.9574
195 10.9574 -7.3906 18.4675 1.6572 143.7843
196 10.8898 -7.3857 24.1763 1.6790 159.5249
197 12.9010 -2.5643 24.7281 1.2719 80.3679
198 12.9525 -2.5742 17.8608 1.2914 70.5300
199 12.8914 2.6480 31.0073 1.1940 97.9247
200 12.9502 2.6423 36.7116 1.1930 53.1245
201 10.9627 7.4348 37.3456 1.6856 165.5790
202 10.9258 7.4469 30.4173 1.6732 170.2709
203 7.3435 11.1746 31.0795 1.6933 183.1358
204 7.3224 11.1361 36.7660 1.7076 197.9683
205 2.5429 13.1892 37.4286 1.5509 86.7247
206 2.6065 13.3299 30.4140 1.4996 78.2489
207 -2.7046 13.4450 31.1257 1.4392 75.6760
208 -2.7445 13.2089 36.8759 1.5586 86.2706
209 -7.5799 10.9651 37.2931 1.6810 194.6386
210 -7.7756 10.8948 30.5714 1.6830 213.1035
211 -10.3313 5.2655 30.3231 1.6787 116.5410
212 -10.8042 7.2205 35.5901 1.6861 152.2600
213 -13.0049 2.5784 37.1699 1.3100 52.3678
214 -11.5566 -0.9260 30.3268 1.5666 72.8003
215 -12.7382 -2.5529 35.5945 1.4792 75.2219
216 -11.1887 -7.2387 37.2901 1.6746 135.1573
217 -11.3526 -7.0996 30.5708 1.6681 142.4222
218 -7.6390 -11.4069 31.1286 1.6793 201.9035
219 -7.5807 -11.1637 36.8803 1.7026 198.2710
220 -2.6826 -13.1696 37.4277 1.5702 84.3030
221 -2.6818 -13.3245 30.4120 1.5364 73.5570
222 2.5188 -13.1387 31.0811 1.5629 76.7354
223 2.5205 -13.0937 36.7667 1.5851 85.9679
224 7.2938 -11.0635 37.3474 1.6977 195.0926
225 7.2518 -11.0610 30.4194 1.6834 179.0493
226 10.9026 -7.3778 31.0109 1.6730 142.4222
227 10.9601 -7.3947 36.7146 1.6868 153.1681
228 12.9688 -2.5767 37.3345 1.2572 71.7408
229 12.8942 -2.5624 30.4529 1.2791 74.1624
230 13.0015 2.6284 43.6772 1.1914 55.2435
231 13.0156 2.6215 49.3675 1.1841 54.3353
232 10.9963 7.4377 43.0332 1.6708 141.5140
233 7.3077 11.1099 43.6949 1.6820 182.3791
234 7.2955 11.0987 49.3943 1.6957 196.9089
235 2.4807 13.0943 43.1333 1.5686 82.1841
236 -2.7295 13.0463 43.6741 1.5973 82.9409
237 -2.7082 13.0524 49.3442 1.5760 90.2057
238 -7.4933 11.0647 42.9173 1.6734 190.4007
239 -11.1896 7.4039 43.6355 1.6743 148.9303
240 -11.2053 7.4247 49.2870 1.6931 150.2925
241 -13.1552 2.6078 42.7780 1.2952 61.9029
242 -13.1668 -2.5761 43.6344 1.3127 53.8813
243 -13.1895 -2.5870 49.2862 1.2418 56.4543
244 -11.1492 -7.3700 42.9132 1.6789 146.8114
245 -7.5027 -11.0207 43.6729 1.6824 184.8007
246 -7.4871 -11.0344 49.3449 1.7037 197.9683
247 -2.7071 -13.0541 43.1339 1.6114 83.5463
248 2.5134 -13.0666 43.6955 1.6015 81.5787
249 2.5045 -13.0510 49.3974 1.6223 88.9949
250 7.3250 -11.0799 43.0336 1.6879 183.2872
251 11.0152 -7.4015 43.6754 1.6746 142.5735
252 11.0306 -7.4022 49.3695 1.6680 151.8060
253 13.0234 -2.5875 50.0137 1.2406 58.5732
254 13.0065 -2.5836 43.0373 1.1225 48.8867
-----------------------------------------------------------------------
NUMBER OF ELECTRONS: 619.76855

This is a SiH system in which Si atoms #47 and #80 host a defect due of the lack of H. In fact charges #47 and #80 are larger than other. My question now is if the oscillation of charge on other atoms is normal, and if you think these values could be reliable. This is my first work, so I am quite newbie.

I would suggest looking for convergence in these charges with respect to an increasing lattice.

Also, why don't you use the Bader volumes? The Voronoi partitioning is simply geometric and does not take into account the relative sizes of atoms. It is only in our code as a sanity check.

As far as how to interpret the charges - that is up to the user. (in your question for example, are the charges reliable in what sense?) We generally use the Bader charges to understand changes in the electronic structure of materials. I personally don't read much into the Bader definition itself, but it is a nice consistent way to partition the total charge when you only have a charge density.