Dear Alex,
I used TOCH file.
Because of the problem with H, I used Alex Voznyy's strategy that add core
to H atom, so that Bader can recognise H.
All C are in the same environment (ruthenocene), so they should have same
charge.
I resized that we have to use a very dense mesh to have better result, but
it's not good enough.
This is the result with 1000 Ry MeshCutOff.
Is there any solution for this, since too high MeshCutOff is very
expensive, for both Siesta and Bader.
Best regards,
Quan
# X Y Z CHARGE MIN DIST
ATOMIC VOL
--------------------------------------------------------------------------------
1 5.7394 5.9700 19.0222 7.1217 1.9164
162.9620
2 7.1772 9.2956 23.2784 0.9733 0.6904
1515.0485
3 10.1828 9.3613 19.0520 0.9614 0.7086
206.5177
4 7.0912 9.4826 14.8891 0.9539 0.6568
1423.0143
5 2.1756 9.4914 16.5428 0.9571 0.6422
519.3928
6 2.2279 9.3754 21.7278 0.9600 0.6460
583.6336
7 7.1137 2.4320 23.1260 0.9609 0.6806
1388.0423
8 2.1654 2.5126 21.5760 0.9651 0.6421
553.5844
9 2.1121 2.6284 16.3909 0.9480 0.6330
550.8159
10 7.0282 2.6198 14.7372 0.9653 0.6817
1548.3185
11 10.1201 2.4990 18.9007 0.9806 0.7433
207.6091
12 6.5122 9.2998 21.3017 4.0981 1.1666
116.7454
13 8.0971 9.3354 19.0727 4.1442 1.2595
118.2341
14 6.4668 9.3995 16.8774 4.1143 1.2306
117.4582
15 3.8744 9.4041 17.7498 4.1722 1.1790
115.8593
16 3.9021 9.3430 20.4840 4.1044 1.2096
116.8574
17 6.4498 2.5266 21.1514 4.1259 1.2099
117.6501
18 3.8400 2.5698 20.3339 4.1403 1.1838
115.6913
19 3.8121 2.6310 17.5996 4.1383 1.2144
117.4715
20 6.4049 2.6265 16.7273 4.1136 1.1977
117.8706
21 8.0352 2.5622 18.9229 4.1013 1.2324
116.2423
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 58.0001
On Mon, Dec 19, 2011 at 4:08 PM, Oleksandr Voznyy <[email protected]> wrote:
> Dear Quan,
> Did you use TOCH or RHO for analysis? (after testing it on my own I see
> that TOCH is not suitable for analysis)
>
> The main problem however usually comes from H (since PSEUDOpotential
> calculations cannot reproduce the charge on H correctly in principle,
> whether in SIESTA or any other program).
>
> I guess, that changes in C in different environments (CH2 vs CH3 vs C-Ru)
> is a normal thing.
>
> Alex.
>
