UT theoretical chemistry code forum

These days I have done some reaserch about the Bader charge analysis in CASTEP files and the cuncrete plans as follow:
Firstly, the CASTEP setting: Functional,(GGA-PW91), Pseudopotentials, (Ultrasoft)
Secondly, make the cube files. Here two different approaches are use here,(den_fmt---cube and check2xsf---cube).
Thirdly, Bader analysis. Now the files are follow:
den_fmt way: ACF

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.9982 3.8003 0.9202 0.3722 1.8504 122.6644
2 10.2239 10.5195 0.9202 0.3878 1.6705 130.1727
3 1.2920 12.5515 0.9202 0.3880 1.7423 130.0417
4 11.5159 5.1568 7.4342 0.3466 1.7716 110.7472
5 5.2902 -1.5624 7.4342 0.3611 1.6705 117.1205
6 14.2221 -3.5944 7.4342 0.3613 1.7064 117.2951
7 11.5159 5.1568 12.1077 0.3660 1.8505 118.3864
8 5.2902 -1.5624 12.1077 0.3830 1.6705 127.0733
9 14.2221 -3.5944 12.1077 0.3829 1.7423 126.5058
10 3.9982 3.8003 5.5938 0.3404 1.7716 106.4692
11 10.2239 10.5195 5.5938 0.3562 1.6705 114.0211
12 1.2920 12.5515 5.5938 0.3563 1.7064 113.7592
13 7.5013 1.5483 3.2570 0.3420 1.6550 105.3342
14 7.2176 6.3261 3.2570 0.3425 1.7440 101.5801
15 10.4226 -3.2350 3.2570 0.3423 1.6235 105.5961
16 6.4267 12.0447 3.2570 0.3509 1.7816 106.6438
17 13.1044 1.6866 3.2570 0.3460 1.8848 109.0884
18 1.8697 8.5004 3.2570 0.3477 1.7201 105.6835
19 8.0128 7.4088 9.7710 0.3420 1.6550 105.4215
20 8.2965 2.6310 9.7710 0.3425 1.7441 101.5364
21 5.0915 12.1920 9.7710 0.3423 1.6235 105.5088
22 9.0874 -3.0876 9.7710 0.3509 1.7816 106.6438
23 2.4097 7.2704 9.7710 0.3460 1.8848 109.0884
24 13.6444 0.4566 9.7710 0.3477 1.7201 105.6835
25 0.0000 0.0000 3.2570 0.4953 1.7103 139.6017
26 0.0000 0.0000 9.7710 0.4953 1.8661 139.6017
27 5.7163 3.8333 3.2570 0.0000 0.0000 0.0000
28 9.3362 11.9909 3.2570 0.0000 0.0000 0.0000
29 0.4616 11.0470 3.2570 0.0000 0.0000 0.0000
30 9.7978 5.1237 9.7710 0.0000 0.0000 0.0000
31 6.1779 -3.0338 9.7710 0.0000 0.0000 0.0000
32 15.0525 -2.0899 9.7710 0.0000 0.0000 0.0000
33 10.3427 -0.0000 0.0745 0.4287 1.6832 94.2464
34 5.1714 8.9571 6.5885 0.3668 1.6832 84.0753
35 5.1714 8.9571 12.9534 0.4287 1.6832 94.2464
36 10.3427 -0.0000 6.4394 0.3668 1.6832 84.0753
37 15.4618 -4.5842 3.2570 0.4211 1.7817 91.6272
38 11.7533 6.7254 3.2570 0.3656 1.7318 84.6428
39 3.8131 -2.1412 3.2570 0.4216 1.7612 93.7662
40 0.0523 13.5413 9.7710 0.4211 1.7817 91.6272
41 3.7609 2.2317 9.7710 0.3656 1.7318 84.6428
42 11.7010 11.0982 9.7710 0.4216 1.7612 93.7662
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 13.5427
The main problem :1. the wrong coordinates even after coordinate transformation,2. the charge are so small I can't imagine this is Ca10(PO4)6F2
3. the number of electrons also wrong.


the check2xsf way: ACF

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.9982 3.8003 0.9202 52.8835 1.7716 107.3859
2 -5.2902 1.5624 0.9202 53.1890 1.6705 109.0884
3 1.2920 -5.3627 0.9202 52.5780 1.7064 106.3819
4 -3.9982 -3.8003 7.4342 52.8835 1.7716 107.3859
5 5.2902 -1.5624 7.4342 53.1880 1.6705 109.0447
6 -1.2920 5.3627 7.4342 52.5780 1.7064 106.3819
7 -3.9982 -3.8003 -0.9202 53.3303 1.7716 109.8305
8 5.2902 -1.5624 -0.9202 52.9087 1.6705 107.8661
9 -1.2920 5.3627 -0.9202 53.4782 1.7064 110.1797
10 3.9982 3.8003 5.5938 53.3303 1.7715 109.8305
11 -5.2902 1.5624 5.5938 52.9097 1.6705 107.9097
12 1.2920 -5.3627 5.5938 53.4782 1.7064 110.1797
13 7.5013 1.5483 3.2570 52.8627 1.6550 105.1596
14 7.2176 6.3261 3.2570 52.9389 1.7440 101.1436
15 -5.0915 5.7221 3.2570 52.8072 1.6235 104.1556
16 -9.0874 3.0876 3.2570 52.9773 1.7816 100.7070
17 -2.4097 -7.2704 3.2570 53.0177 1.8848 107.0367
18 1.8697 -9.4137 3.2570 52.9694 1.7201 101.0563
19 -7.5013 -1.5483 9.7710 52.8569 1.6550 105.0723
20 -7.2176 -6.3261 9.7710 52.9409 1.7440 101.2309
21 5.0915 -5.7221 9.7710 52.8130 1.6235 104.2429
22 9.0874 -3.0876 9.7710 52.9773 1.7816 100.7070
23 2.4097 7.2704 9.7710 53.0177 1.8848 107.0367
24 -1.8697 9.4137 9.7710 52.9714 1.7201 101.1436
25 0.0000 0.0000 3.2570 52.8138 1.7103 117.2514
26 0.0000 0.0000 9.7710 52.8138 1.7103 117.2514
27 5.7163 3.8333 3.2570 0.0000 0.0000 0.0000
28 -6.1779 3.0338 3.2570 0.0000 0.0000 0.0000
29 0.4616 -6.8672 3.2570 0.0000 0.0000 0.0000
30 -5.7163 -3.8333 9.7710 0.0000 0.0000 0.0000
31 6.1779 -3.0338 9.7710 0.0000 0.0000 0.0000
32 -0.4616 6.8672 9.7710 0.0000 0.0000 0.0000
33 10.3427 -0.0000 0.0745 56.6973 1.6832 84.0753
34 -10.3427 0.0000 6.5885 56.6973 1.6832 84.0753
35 -10.3427 0.0000 -0.0745 56.6973 1.6832 84.0753
36 10.3427 -0.0000 6.4394 56.6973 1.6832 84.0753
37 -0.0523 4.3729 3.2570 56.4893 1.7612 83.9880
38 -3.7609 -2.2317 3.2570 56.5253 1.7318 84.5991
39 3.8131 -2.1411 3.2570 56.5910 1.7429 86.3016
40 0.0523 -4.3729 9.7710 56.4893 1.7612 83.9880
41 3.7609 2.2317 9.7710 56.5253 1.7318 84.5991
42 -3.8131 2.1411 9.7710 56.5910 1.7429 86.3016
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 1943.5138
the main problem:the charge may be wrong, I can distinguish the Ca, O and F. most of the charge distribute between 52-57, but the P are 0?