Dear Quan, You may wish to try program I wrote for calculating net atomic charges at ddec.sourceforge.net. One of the people in the research group I work in has used it with very good success for computing atomic charges from Siesta. The current version is written in Matlab (we hope to convert to Fortran in near future) so it runs a bit slow. But if you need accurate atomic charges it is quite reliable.
Sincerely, Tom Manz post-doc Georgia Institute of Technology On Mon, Dec 19, 2011 at 10:24 AM, Quan Phung <[email protected]> wrote: > 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. > >
