[Pw_forum] modeling open-shell molecules on metal surfaces

Tue Feb 3 14:49:43 CET 2015

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
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