Hi, I worked at the same field, to find out which atoms could be doped with look https://www.researchgate.net/publication/285619763_Doping_graphene_with_a_monovacancy_bonding_and_magnetism You can use faster codes loke SIESTA to find most stable configurations of the molecule on the graphene surface, and then use QE for refined calcs
2016-08-09 20:46 GMT+04:00 Rolly Ng <roll...@gmail.com>: > Dear QE experts, > > I am trying to refine computation of 3-NT adsorption on metal doped > graphene using QE. This is according to our previous work > http://dx.doi.org/10.1016/j.commatsci.2011.07.045 > > With the help of Dr. Guido Fratesi, I am exploring molecularpdos.x to > find the change of HOMO and LUMO of the nitrated tyrosine molecule on > adsorption to metal-doped graphene. > > There are my questions and answers, your comments are welcome. > > Q1) Spin polarization. The full system contains a metal doped graphene > with single metallic atom of Au and Ni at the center and a 3-NT molecule > adsorbed onto the graphene sheet, so I included nspin=2 for the full > system. But the adsorbate (3-NT) molecule is likely to be nonmagnetic, > so I did nspin=1 for its gas phase. Can molecularpdos.x cope with > different nspin for the full system and adsorbate? > A1) Yes, since nspin=2 can handle a nonmagnetic case > R1) So, I am adding nspin=2 to the 3-NT molecules > > Q2) K-points. I used smearing for the full system since it is > semi-metallic. Should I use smearing for the molecule in gas phase? I > believe this is not a good idea but can molecularpdos.x works with > k-point and non k-point? > A2) Smearing: no problem, K-points: should be the same > R2) So, I am using the same K-points for both full system and single > molecule. > > Q3) I would like to evaluate the change of the HOMO-LUMO gap of the > adsorbate (3-NT) on adsorption to the metal-doped graphene. Can > molecularpdos.x do that? > A3) Dr. Fratesi and his team used that code also to study > molecules/graphene... > http://dx.doi.org/10.1038/srep24603 > R3) Very useful and thank you! > > Q4) I would like to determine if physisorption or chemisorption occurs as > with DMol3, can molecularpdos.x do the same job? For the physisorption > vs. chemisorption, the adsorption energy may be a good indicator. > However, I believe the electronic structure of the bond may also > indicate which type of adsorption it suppose to be? > > With regards, > Rolly > > -- > PhD. Research Fellow, > Dept. of Physics & Materials Science, > City University of Hong Kong > Tel: +852 3442 4000 > Fax: +852 3442 0538 > > _______________________________________________ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Best wishes, Maxim Arsent'ev, Ph.D. (Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS
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