[Pw_forum] modeling open-shell molecules on metal surfaces

Tue Feb 3 15:40:11 CET 2015

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.
>>>>>
>>>>> ********************************************************
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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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