Have you tried with the larger mesh-cutoff? The one you have attached in the forum have a smaller mesh than the one you supply here.
2017-01-12 15:46 GMT+01:00 Seyed Mohammad Tabatabaei <smt...@gmail.com>: > Can this core charge fragmentation issue be attributed to some parts of > the SIESTA code functioning *inappropriately*? > > On Thu, Jan 12, 2017 at 3:45 PM, Seyed Mohammad Tabatabaei < > smt...@gmail.com> wrote: > >> Dear all, >> >> I went through a useful set of BADER-related questions and answers >> which I hope you take time to read at: >> >> http://theory.cm.utexas.edu/forum/viewtopic.php?f=1&t=2806&p=8619#p8619 >> >> Meanwhile, I also became aware of the "fragmented" nature of core >> charges in the Systemlabel.BADER file that directly influences some >> aspects of BADER charge transfer analysis. Also, my >> Systemlabel.BADER.cube file contains negative values and I do not know >> why there should be negative values. >> >> I would be really grateful if someone guides me on this issue. >> Specifically, is it possible to get a BADER file which is not >> fragmented with SIESTA? I have used vdW+BH in my calculations. >> >> I quote from the above thread for BADER: >> >> "The core charge is indeed very fragmented near the S and Mo core (see >> attached picture). This will lead to a Bader maximum at each of the >> blue islands (plotted in vesta with an isosurface cutoff of 0.2). >> There are similar problems at all the atomic cores." >> >> Bests, >> Mohammad, >> You can also download my output files from the above thread. >> > > -- Kind regards Nick
