I managed to converge the calculation. There was an error on the structure caused by the software that I used. Without your help I couldn't have seen it. Your advices regarding convergence will also be very helpful.
Thanks, Sergi 2015-02-03 15:40 GMT+01:00 Sergi Vela <[email protected]>: > Thank you all for your suggestions, you've given me a lot to work on! > > I'll let you know about the results. > > Cheers, > Sergi > > 2015-02-03 15:00 GMT+01:00 xiaochuan Ge <[email protected]>: > >> There is another easier solution but I have never tested. The default >> startingwfc is "atomic + random", instead one could try to use "random". >> >> =================== >> Dr. Xiaochuan Ge (Giovanni) >> Center for Functional Nanomaterials >> Brookhaven national laboratory >> =================== >> >> On 3 February 2015 at 08:49, Pu ZHANG <[email protected]> wrote: >> >>> 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 >>>> >>> >>> _______________________________________________ >>> 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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