Dear Tom, Thank you, I knew your code. But I don't have a licence for Matlab. Then I'll wait for the Fortran code.
Best regards, Quan On Mon, Dec 19, 2011 at 6:02 PM, Thomas Manz <[email protected]> wrote: > 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. > > > > >
