obtained the Fermi energy as,
The molecule NTNO2 Fermi energy reads -3.5478 eV,
the full-system Fermi energy reads -2.1546 eV.
So I suppose the HOMO is located at the first band to the left of the
Fermi energy, and the LUMO is at the first band to the right of the
Fermi eenrgy. From the scf output at K = 0 0 0, I collect these number
for spin up and down as,
1) Molecule Up, HOMO -5.5984 eV, LUMO -3.2161 eV, so |delta| HOMO-LUMO
gap is 2.3823 eV
2) Molecule Down, HOMO -5.5981 eV, LUMO -3.2159 eV, so |delta| HOMO-LUMO
gap is 2.3822 eV
3) Full-system Up, HOMO -2.1696 eV, LUMO -2.1449 eV, so |delta|
HOMO-LUMO gap is 0.0247 eV
4) Full-system Down, HOMO -2.1935 eV, LUMO -2.1177 eV, so |delta|
HOMO-LUMO gap is 0.0758 eV
I can see the substantial drop in the H0MO-LUMO gap on the full-system
particularly for the Up spin configuration. Does this help to explain my
previous questions Q3+Q4 on physisorption vs. chemisorption?
I am running molecularpdos.x but it seems run for more than 10 hours on
a 12 cores/24 thread system without stopping and output as shown in the
attached screenshot?
However can I select fewer bands so it may help to reduce the
computation time? Is this i_bnd_beg_full = 1 refers to -28.1982 eV the
first one? or 2.1629 eV the last one?
Thank you for your patient.
Regards,
Rolly
-------- 原始邮件 --------
主题：Re: [Pw_forum] Using molecularpdos.x for adsorption on metal-doped
graphene
发件人：Guido Fratesi
收件人：PWSCF Forum
抄送：
Dear Rolly,
let me try to expand a bit my previous concise answers to your questions
(Q1-Q2):
As it is implemented, molecularpdos.x needs the two systems (full &
part) to be described by the very same parameters as of:
(1) unit cell dimensions
(2) k-point sampling
(3) number spin populations considered
(4) dimension of the localized basis set (atomic functions)
In principle, such close correspondence could be avoided in some cases
like where your reference (i.e., part) system is an isolated molecule.
Its states could be computed at the gamma point for a cell of your
choice, then the Bloch states (as would be obtained by computing them
for the same cell as for the full system) could be reconstructed
analytically. This is not implemented so far, so an explicit calculation
with the very same k-grid is needed (I generally copy the k-points as
given in output by pw.x for the full system).
Similarly, the spin-up states of the full system will be projected on
the spin-up states of the part (same for spin down); this requires you
to make a calculation with nspin=2 (but no magnetization) also when the
molecule by itself is not spin-polarized if it is embedded in a
spin-polarized system.
Smearing / not smearing is not relevant to molecularpdos.x : just use
the one adequate to each of the two calculations (full & part).
As for the dimension of the localized basis set, molecularpdos.x assumes
that the atomic orbitals of the full & part calculation correspond 1-1
to each other, keeping the same order. The range of the orbitals to be
considered is specified by input variables
i_atmwfc_{beg,end}_{full,part} so the atoms to be considered have to be
consecutive and listed in the same order in the full & part systems.
BEWARE (common mistake) this range specifies the atomic wavefunctions
(see the output of projwfc.x for a list), not the atoms. You may want to
add atoms to the "part" calculation, e.g., add H to saturate a dangling
bond: in that case, just do not include the corresponding atomic states
in the range for molecularpdos.x.
Hope this helps,
Guido
On 09/08/2016 18:46, Rolly Ng wrote:
> Dear QE experts,
>
> I am trying to refine computation of 3-NT adsorption on metal doped
> graphene using QE. This is according to our previous work
> http://dx.doi.org/10.1016/j.commatsci.2011.07.045
>
> With the help of Dr. Guido Fratesi, I am exploring molecularpdos.x to
> find the change of HOMO and LUMO of the nitrated tyrosine molecule on
> adsorption to metal-doped graphene.
>
> There are my questions and answers, your comments are welcome.
>
> Q1) Spin polarization. The full system contains a metal doped graphene
> with single metallic atom of Au and Ni at the center and a 3-NT molecule
> adsorbed onto the graphene sheet, so I included nspin=2 for the full
> system. But the adsorbate (3-NT) molecule is likely to be nonmagnetic,
> so I did nspin=1 for its gas phase. Can molecularpdos.x cope with
> different nspin for the full system and adsorbate?
> A1) Yes, since nspin=2 can handle a nonmagnetic case
> R1) So, I am adding nspin=2 to the 3-NT molecules
>
> Q2) K-points. I used smearing for the full system since it is
> semi-metallic. Should I use smearing for the molecule in gas phase? I
> believe this is not a good idea but can molecularpdos.x works with
> k-point and non k-point?
> A2) Smearing: no problem, K-points: should be the same
> R2) So, I am using the same K-points for both full system and single
> molecule.
>
> Q3) I would like to evaluate the change of the HOMO-LUMO gap of the
> adsorbate (3-NT) on adsorption to the metal-doped graphene. Can
> molecularpdos.x do that?
> A3) Dr. Fratesi and his team used that code also to study
> molecules/graphene...
> http://dx.doi.org/10.1038/srep24603
> R3) Very useful and thank you!
>
> Q4) I would like to determine if physisorption or chemisorption occurs as
> with DMol3, can molecularpdos.x do the same job? For the physisorption
> vs. chemisorption, the adsorption energy may be a good indicator.
> However, I believe the electronic structure of the bond may also
> indicate which type of adsorption it suppose to be?
>
> With regards,
> Rolly
>
--
Guido Fratesi
Dipartimento di Fisica
Universita` degli Studi di Milano Italy
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