Dear all, I'm just curious about Xiaochuan's solution. It would be Interesting and useful to be able to specify the initial configuration in such a flexible way. As I understand from experience in other codes, it's trivial to set up the occupation for the whole system, however rather than for separate parts.
Is there a way to make this setting? 2015 年 2 月 3 日 下午 9:38于 "xiaochuan Ge" <[email protected]>写道： > Dear Sergi Vela, > > I have encountered similar problems before. To solve your trouble I think > the main question is: what is the converged electronic configuration you > are expecting? > > I notice that your system is made by a gold slab plus a C2S3N3 molecule. > The latter being isolated contains odd number of electrons. I believe if > you run the ground-state calculation for only the C2S3N3 molecule without > special care you will end up with similar problems with convergence. Using > smearing does not solve your problem is probably because the band gap of > C2S3N3 is too large for the smearing parameter you used to make a > difference. > > The trick is, if somehow C2S3N3 can take one electron from the slab, then > an even electron configuration can be achieved for the molecule, and most > probably you will achieve the convergence. However, the initial electron > configuration is generated based on the overlap of atomic orbitals. Since > the molecule is pretty far away from the metal slab, a large barrier may > hinder the electron from metal to transfer to the molecule. Therefore > during the SCF iteration the system can not find its energy minimum. > > I have some suggestions that you may want to try. First, you may want to > put the molecule closer to the slab, so the barrier between the initial > electronic configuration and the reasonable final configuration is low > enough for SCF to overcome. Second, you could try to set the initial > configuration by hand, say let the system start with ( C2S3N3 - ) + ( Slab > + ), I believe this is possible in QE. Third, maybe you can add a little > magnetic filed to breakdown the degeneracy of spin up and down. > > Hope this can solve your problem! > > =================== > Dr. Xiaochuan Ge (Giovanni) > Center for Functional Nanomaterials > Brookhaven national laboratory > =================== > > On 3 February 2015 at 08:02, Sergi Vela <[email protected]> wrote: > >> Dear Guido and Giuseppe, >> >> Thank you both for your replies. >> >> The structure should be ok, it represents an organic molecule between 2 >> gold electrodes. You should get something like the image I attach (do >> you?). It is a rather standard scheme, as you may also see in: >> >> http://pubs.acs.org/doi/abs/10.1021/ja2090096 >> >> although my structure is simplified for testing. >> >> I don't know whether ibrav=0 is strictly necessary but, anyway, it should >> not affect the outcome of the calculation, right? >> >> I have tested other k-point meshes without improvement. Anyway, I'll try >> denser meshes together with Giuseppe's suggestions and let you know the >> outcome. >> >> Cheers, >> Sergi >> >> 2015-02-03 13:56 GMT+01:00 Giuseppe Mattioli < >> [email protected]>: >> >>> >>> Dear Sergi >>> It seems that you bounce between more than one electronic configuration >>> at every scf step. This is far from uncommon in the case of molecular open >>> shell systems. :-( >>> I can add one or two things to Guido's good advice. >>> >>> > I've tried several tricks to try to improve electronic structure's >>> > convergence. Changing the 'mixing_beta', the 'type of mixing', >>> removing the >>> > smearing, >>> >>> Use always the more robust gaussian smearing (at least 0.01 Ry, but also >>> more if you struggle for convergence) for geometry optimizations. If it does >>> not converge, then m-p and m-v will also fail 99.9% . You can use other >>> schemes after you tamed the system. Reduce also the mixing_beta down to 0.05 >>> or 0.02 (with davidson). >>> >>> Maybe your starting configuration is horribly unlucky. Try (carefully) >>> to use something like >>> >>> conv_thr=1.0d-5~1.0d-6 >>> electron_maxstep=50~100 >>> scf_must_converge=.false. >>> >>> and see if your convergence problem improves after few bfgs steps >>> without showing unphysical behavior. >>> >>> If your SOMO is higher than the Ag Fermi energy, then there is probably >>> no way to have an integer value for the magnetization of the system because >>> of >>> the molecule-to-surface charge transfer. You may try not to bias the >>> tot_magnetization variable. >>> >>> Finally, ecutwfc=25.0 seems a bit too low. It could be a source of >>> instability. I would use something around 35/280 Ry for ecutwfc and ecutrho. >>> >>> HTH >>> Giuseppe >>> >>> >>> On Tuesday, February 03, 2015 10:57:23 AM Sergi Vela wrote: >>> > Hi all, >>> > >>> > I'm having a lot of troubles in modeling the adsorption of molecules on >>> > surfaces. I've quite a lot of experience with QE when working with >>> crystals >>> > made of open-shell molecules but I'm not familiar with the description >>> of >>> > metal surfaces. >>> > >>> > First of all, I'm using Qespresso v.5.1.1 >>> > >>> > I succeed in simulating 4 layers of a 111 Gold surface with Quantum >>> > Espresso (QE). However, using the same surface and unit cell, when I >>> > include a magnetic (open-shell) molecule on top of that surface, even >>> if >>> > its far away from it, I cannot reach convergence. I'm 99% sure that the >>> > input is fine in terms of the unit cell definition (see input file >>> > attached) and the problem is just the convergence of the electronic >>> > structure. >>> > >>> > I believe the problem is the fact that the system is highly >>> inhomogeneous >>> > as it has a metal surface and an open-shell molecule. I take as an >>> example >>> > the smearing, since, although it is mandatory when modeling the metal >>> > alone, it seems to hinder the description of an open-shell molecule. >>> > Originally, I used methfessel-paxton smearing with a 'degauss' of 0.2 >>> eV. >>> > The convergence seems to be even worse as the value is increased, and >>> > changing the type of smearing doesn't help neither. >>> > >>> > I've tried several tricks to try to improve electronic structure's >>> > convergence. Changing the 'mixing_beta', the 'type of mixing', >>> removing the >>> > smearing, switching to 'cg' algorith, increasing number K points ... >>> all of >>> > them with identical output (take Summary.out as an example of the >>> typical >>> > evolution of the SCF energy, you'll see that is awful). >>> > >>> > Anyone has experience on modeling such king of systems? >>> > >>> > Any help is appreciated, thanks in advance >>> > >>> > Dr. Sergi Vela, >>> > University of Strasbourg, France. >>> >>> ******************************************************** >>> - Article premier - Les hommes naissent et demeurent >>> libres et ègaux en droits. Les distinctions sociales >>> ne peuvent être fondèes que sur l'utilitè commune >>> - Article 2 - Le but de toute association politique >>> est la conservation des droits naturels et >>> imprescriptibles de l'homme. Ces droits sont la libertè, >>> la propriètè, la sùretè et la rèsistance à l'oppression. >>> ******************************************************** >>> >>> Giuseppe Mattioli >>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >>> v. Salaria Km 29,300 - C.P. 10 >>> I 00015 - Monterotondo Stazione (RM) >>> Tel + 39 06 90672836 - Fax +39 06 90672316 >>> E-mail: <[email protected]> >>> http://www.ism.cnr.it/english/staff/mattiolig >>> ResearcherID: F-6308-2012 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> [email protected] >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> _______________________________________________ >> Pw_forum mailing list >> [email protected] >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum >
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