[Pw_forum] modeling open-shell molecules on metal surfaces

xiaochuan Ge ustc.scgyer at gmail.com
Tue Feb 3 15:00:19 CET 2015 

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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