[Pw_forum] modeling open-shell molecules on metal surfaces

Wed Feb 4 09:41:30 CET 2015

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 <sergi.vela at gmail.com>:

> 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 <ustc.scgyer at gmail.com>:
>
>> 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 <puzhang0702 at gmail.com> 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" <ustc.scgyer at gmail.com>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 <sergi.vela at gmail.com> 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 <
>>>>> giuseppe.mattioli at ism.cnr.it>:
>>>>>
>>>>>>
>>>>>> 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
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>>>>>> ********************************************************
>>>>>>
>>>>>>    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: <giuseppe.mattioli at ism.cnr.it>
>>>>>>    http://www.ism.cnr.it/english/staff/mattiolig
>>>>>>    ResearcherID: F-6308-2012
>>>>>>
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