Dear Quan, There are a lot of free MatLab clones (e.g. http://www.dspguru.com/dsp/links/matlab-clones), you can try to use them for executing the code
2011/12/19 Quan Phung <[email protected]>: > 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. >> > >> > > > -- Sincerely yours, Pavel B. Sorokin
