Abinit to yambo

Forum for discussing issues arising with interfacing the Abinit code (KSS) file with Yambo.

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FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Abinit to yambo

Post by FGH » Sat May 22, 2021 9:25 am

Hello dears,
I calculated the SCF and NSCF calculations of Silicon with Abinit, which I wrote the input file of Abinit below.Then I converted it by "a2y" command. After, in the simultaneous convergence calculations of "BndsRnXs" and "NGsBlkXs" all the gaps are the same and for an example I put one of my calculation at the attach. On the other hand the report file says the the direct gap is in k-point 19(gamma), while in the output file the gamma point is in k-point 1. Unfortunately, I do not know where the problem is.
Thank you for answering me.
Sincerely Yours,

Code: Select all

# Crystalline silicon
# Calculation of the GW corrections
# Dataset 1: ground state calculation to get the density 
# Dataset 2: NSCF run to produce the WFK file for 10 k-points in IBZ

iomode 3
prtkbff 1
ndtset      2

############
# Dataset 1
############
# SCF-GS run 
nband1  8
tolvrs1 1.0e-10

############
# Dataset 2
############
# Definition of parameters for the calculation of the WFK file
nband2      50       # Number of (occ and empty) bands to be computed
nbdbuf2      5
iscf2       -2
getden2     -1
tolwfr2  1.0d-18     # Will stop when this tolerance is achieved 

############


# Data common to the three different datasets

# Definition of the unit cell: fcc
acell  3*10.26        # This is equivalent to   10.217 10.217 10.217
rprim  0.0  0.5  0.5   # FCC primitive vectors (to be scaled by acell)
       0.5  0.0  0.5   
       0.5  0.5  0.0

# Definition of the atom types
ntypat  1         # There is only one type of atom
znucl 14          # The keyword "znucl" refers to the atomic number of the 
                  # possible type(s) of atom. The pseudopotential(s) 
                  # mentioned in the "files" file must correspond
                  # to the type(s) of atom. Here, the only type is Silicon.
                         
# Definition of the atoms
natom 2           # There are two atoms
typat  1 1        # They both are of type 1, that is, Silicon.
xred              # Reduced coordinate of atoms
      0.0  0.0  0.0
      0.25 0.25 0.25


# Definition of the k-point grid
ngkpt   4 4 4  
nshiftk 4
shiftk  0.0 0.0 0.0  # These shifts will be the same for all grids
        0.0 0.5 0.5
        0.5 0.0 0.5
        0.5 0.5 0.0
istwfk  *1         # This is mandatory in all the GW steps.

# Definition of the planewave basis set (at convergence 16 Rydberg 8 Hartree)
ecut 8.0          # Maximal kinetic energy cut-off, in Hartree

# Definition of the SCF procedure
nstep   30        # Maximal number of SCF cycles
#toldfe  1.0d-6    # Will stop when this tolerance is achieved on total energy
diemac  12.0      # Although this is not mandatory, it is worth to
                  # precondition the SCF cycle. The model dielectric
                  # function used as the standard preconditioner
                  # is described in the "dielng" input variable section.
                  # Here, we follow the prescription for bulk silicon.


pseudos = "14si.pspnc"
symmorphi2 0
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Sincerely yours,
Farzaneh
UCL

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Daniele Varsano
Posts: 4043
Joined: Tue Mar 17, 2009 2:23 pm
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Re: Abinit to yambo

Post by Daniele Varsano » Sat May 22, 2021 10:15 am

Dear FGH,
please sign your posts with your full name and affiliation, this is a rule of the forum. You can do once for all filling the signature in your user profile.

Note that GW needs dynamical screening so the variable to converge are "BndsRnXp" and "NGsBlkXp" and not the static ones.

I do not know if what you posted is just as an example, anyway the values you used for BndsRnXp and NGsBlkXp are extremely low and I have doubt the gap is converged.

About the position of the gap in the BZ, note Silicon is an indirect gap, here Yambo is reporting also the direct gap at gamma, labeled with index 19:

Code: Select all

QP [eV] @ K [19] (iku):  0.000000  0.000000  0.000000
I do not know if there are discrepancy with the abinit output, in order to inspect them you should post the abinit output and the r_setup.

Also, please note that there are problem with the calculation of the <Vxc> term as they are set to zero:

Code: Select all

[xc] E_xc :  -0.495498E-7 [Ha]
      E_xc :  -0.990997E-7 [Ry]

  Local XC kind (lXC) : Teter 93(XC)
  Non-Local XC kind (nlXC) : Hartree-Fock

  Corrections @ K [19] :  [eV]
 <4|nlXC|4> = -1.570241  0.000000 <4|lXC|4> =  0.000000  0.000000
 <5|nlXC|5> =  0.000000  0.000000 <5|lXC|5> =  0.000000  0.000000
I also noticed in your abinit input:

Code: Select all

ecut 8.0
which seems to me very low.

Anyway, someone else more proficient with abinit can advise on that.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Re: Abinit to yambo

Post by FGH » Sat May 22, 2021 11:32 am

Dear Daniele,

Thank you so much for your answering.
Here is my output of Abinit and yambo r_setup.

Sincerely yours,
You do not have the required permissions to view the files attached to this post.
Sincerely yours,
Farzaneh
UCL

FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Re: Abinit to yambo

Post by FGH » Sat May 22, 2021 11:34 am

and the ecut=8 Ha is converged value by Abinit.
Sincerely yours,
Farzaneh
UCL

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Daniele Varsano
Posts: 4043
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Re: Abinit to yambo

Post by Daniele Varsano » Sat May 22, 2021 12:01 pm

Dear,

please sign your posts with your full name and affiliation, this is a rule of the forum. You can do once for all filling the signature in your user profile.

Unfortunately abinit print only the first k points eigenvalues (I think you should add more verbosity if you want to see all of them). Anyway for what I see:

Abinit (Ha)

Code: Select all

Kpt=1   kpt= -0.1250 -0.1250  0.0000 
-0.21820    0.16278    0.18259    0.18259    0.28424 
gap for kpt=1
.10165 Ha = 2.7659 eV
Yambo (eV):

Code: Select all

 kpt=1 ( K [ 1]: -0.125000 -0.125000  0.000000)
 -11.72575  -1.35870  -0.81957  -0.81957   1.94634 
gap for kpt=1
2.7659 eV
Note yambo shift the zero to the VBM.

All seems ok.
You have the gamma points at nkpt=19 in both Abinit and Yambo.
All seems to me coherent.

It seems you are using a shorter grid, do not get confused between K grid and Q grid Q=(K-K'), where the Q=0 is the first point.

Finally note, as said before, that in your calculation there are problems with the evaluation of <Vxc>, someone more experts than me with abinit probably can tell you more about that.


Best,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Re: Abinit to yambo

Post by FGH » Sun May 23, 2021 11:01 am

Dear Daniele,

But the kpoint you wrote is not gamma point.
Sincerely yours,
Farzaneh
UCL

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Daniele Varsano
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Re: Abinit to yambo

Post by Daniele Varsano » Mon May 24, 2021 8:05 am

Dear Farzaneh,

if you look at the list of the k point in the r_setup:

Code: Select all

  IBZ K-points :  19
  BZ  K-points :  256

  K/Q-points units:
  rlu = crystal or reduced units; cc = cartesian coordinates; iku = interal k-units

  K [ 1]: -0.125000 -0.125000  0.000000 [rlu]
        : wf components:  295
        : BZ grid      : X S
  K [ 2]: -0.125000 -0.375000  0.000000 [rlu]
        : wf components:  296
        : BZ grid      : X S
  K [ 3]: -0.250000 -0.250000  0.000000 [rlu]
        : wf components:  303
        : BZ grid      : X S
  K [ 4]: -0.125000 -0.250000  0.125000 [rlu]
        : wf components:  296
        : BZ grid      : X S
  K [ 5]: -0.125000  0.375000  0.000000 [rlu]
        : wf components:  290
        : BZ grid      : X S
  K [ 6]: -0.250000  0.500000  0.000000 [rlu]
        : wf components:  290
        : BZ grid      : X S
  K [ 7]: -0.125000  0.500000  0.125000 [rlu]
        : wf components:  284
        : BZ grid      : X S
  K [ 8]: -0.375000 -0.375000  0.000000 [rlu]
        : wf components:  298
        : BZ grid      : X S
  K [ 9]: -0.250000 -0.375000  0.125000 [rlu]
        : wf components:  296
        : BZ grid      : X S
  K [10]: -0.125000 -0.375000  0.250000 [rlu]
        : wf components:  286
        : BZ grid      : X S
  K [11]: -0.125000  0.125000  0.000000 [rlu]
        : wf components:  297
        : BZ grid      : X S
  K [12]: -0.250000  0.250000  0.000000 [rlu]
        : wf components:  295
        : BZ grid      : X S
  K [13]: -0.375000  0.375000  0.000000 [rlu]
        : wf components:  288
        : BZ grid      : X S
  K [14]:  0.500000  0.500000  0.000000 [rlu]
        : wf components:  302
        : BZ grid      : X S
  K [15]: -0.375000  0.500000  0.125000 [rlu]
        : wf components:  290
        : BZ grid      : X S
  K [16]: -0.250000  0.500000  0.250000 [rlu]
        : wf components:  280
        : BZ grid      : X S
  K [17]: -0.250000  0.000000  0.000000 [rlu]
        : wf components:  296
        : BZ grid      : X S
  K [18]:  0.500000  0.000000  0.000000 [rlu]
        : wf components:  272
        : BZ grid      : X S
  K [19]:  0.000000  0.000000  0.000000 [rlu]
        : wf components:  283
        : BZ grid      : X S
The gamma point is the number 19:

and here you can find the info about the direct band gap minimum, which is located at gamma:

Code: Select all

[02.05] Energies & Occupations
  ==============================

  [X] === Gaps and Widths ===
  [X] Conduction Band Min                           :  0.519739 [eV]
  [X] Valence Band Max                              :  0.000000 [eV]
  [X] Filled Bands                                  :   4
  [X] Empty Bands                                   :    5   60
  [X] Direct Gap                                    :  2.524044 [eV]
  [X] Direct Gap localized at k-point               :  19
  [X] Indirect Gap                                  :  0.519739 [eV]
  [X] Indirect Gap between k-points                 :  19   8
  [X] Last valence band width                       :  3.900747 [eV]
  [X] 1st conduction band width                     :  3.704579 [eV]
What part it is not clear on the report?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Re: Abinit to yambo

Post by FGH » Mon May 24, 2021 11:13 am

Dear Daniele,
The report file is clear. But in the convergence calculations all the gaps are the same. This is my main problem. And one of my calculation I send you before and now for 2Ry I have attached. These files have the same band gap.
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Sincerely yours,
Farzaneh
UCL

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Daniele Varsano
Posts: 4043
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Re: Abinit to yambo

Post by Daniele Varsano » Tue May 25, 2021 8:50 am

Dera Farzaneh,

as I told you before, your calculation have problems, you have zero <Vxc> term, zero <HF> for the CBM and negligible self energy correction. There is something not working properly, possibly something odd in your compilation. Can you post your config.log file?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/

FGH
Posts: 13
Joined: Thu Apr 22, 2021 9:28 am

Re: Abinit to yambo

Post by FGH » Wed May 26, 2021 9:41 am

Dear Daniele,

Here is my Abinit log file.
You do not have the required permissions to view the files attached to this post.
Sincerely yours,
Farzaneh
UCL

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