[Pw_forum] modeling open-shell molecules on metal surfaces

xiaochuan Ge ustc.scgyer at gmail.com
Tue Feb 3 14:36:59 CET 2015

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

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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