Cannot generate the list of q-points as shown in the tutorial

Deals with issues related to electron-phonon coupling calculations

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lyzhao
Posts: 51
Joined: Tue May 31, 2016 8:02 am

Cannot generate the list of q-points as shown in the tutorial

Post by lyzhao » Tue Nov 28, 2023 2:48 am

Dear all,
I downloaded the file of

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https://www.yambo-code.eu/wiki/index.php/Tutorials_download
and followed the tutorial of "Electron Phonon Coupling"

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https://www.yambo-code.eu/wiki/index.php/Electron_Phonon_Coupling
inputs and partial outputs based on QE 7.2 and yambo 5.2.0:
1. run scf
2. run nscf
3. p2y

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 <---> DBs path set to : .
 <---> detected QE data format : qexsd
 <---> == PWscf v.6.x generated data (QEXSD fmt) ==
 <---> Header/K-points/Energies... done
 <---> Cell data...
 <---> [WARNING] Two or more crystal structures fit the given cell done
 <---> Atomic data... done
 <---> Symmetries...[SI no]...[I yes]...[-I no]...[TR yes]
 <---> XC functional...Perdew, Burke & Ernzerhof SOL(X)+Perdew, Burke & Ernzerhof SOL(C)
 <---> EXX fraction...:  0.000000
 <---> EXX screening...:  0.000000
 <---> K-points mesh... done
 <---> RL vectors... done
 <---> IGK arrays... done
 <---> Energies... done
 <--->  Electrons             :  8.000000
 <--->  Temperature           :  0.000000 [eV]
 <--->  Lattice factors       :  5.132000  5.132000  5.132000 [a.u.]
 <--->  K-points              :   8
 <--->  Bands                 :  12
 <--->  Spinor components     :  1
 <--->  Spin polarizations    :  1
 <--->  Spin orbit coupling    : no
 <--->  Symmetries   [spatial]:  24
 <--->                 [T-rev] : yes
 <--->  Max WF components     :  1174
 <--->  RL vectors        (WF):  1465
 <--->  RL vectors    (CHARGE):   9257
 <--->  XC potential           : Perdew, Burke & Ernzerhof SOL(X)+Perdew, Burke & Ernzerhof SOL(C)
 <--->  Atomic species        :  1
 <--->  Max atoms/species     :  2
 <---> == DB1 (Gvecs and more) ...
 <---> ... Database done
 <---> == DB2 (wavefunctions)  ...
 <---> [p2y] WF I/O |########################################| [100%] --(E) --(X) done ==
 <---> == DB3 (PseudoPotential) ... done ==
 <--->  == P2Y completed ==
4. yambo_ph -i -V all and uncomment the flag BSEscatt then run the setup of yambo_ph

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 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] CORE Variables Setup
 <---> [02.01] Unit cells
 <---> [02.02] Symmetries
 <---> [02.03] Reciprocal space
 <---> Shells finder |########################################| [100%] --(E) --(X)
 <---> [02.04] K-grid lattice
 <---> Grid dimensions      :   4   4   4
 <---> [02.05] Energies & Occupations
 <---> [03] Transferred momenta grid and indexing
 <---> [BZ sampling] Q-grid is User defined and/or read from the database
 <---> [RL indx] Q BZ pts are /= from X grid BS pts. Gamma point only.
 <---> [04] Timing Overview
 <---> [05] Game Over & Game summary
5. ypp_ph -k q, uncomment the flag ListPts and q-point coordinates units in alat, and also change the OutputAlat as explained in tutorial for FCC structure, then ypp_ph

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 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> [03] Core DB
 <---> :: Electrons             : 8.000000
 <---> :: Temperature           : 0.000000 [eV]
 <---> :: Lattice factors       : 5.132000  5.132000  5.132000 [a.u.]
 <---> :: K points              :  8
 <---> :: Bands                 : 12
 <---> :: Symmetries            :  48
 <---> :: RL vectors            :  9257
 <---> :: Lattice constant (used to define "alat" unit) [a.u.]: 5.130000
 <---> [04] K-point grid
 <---> :: Q-points   (IBZ): 1
 <---> :: X K-points (IBZ):  8
 <---> [05] CORE Variables Setup
 <---> [05.01] Unit cells
 <---> [05.02] Symmetries
 <---> [05.03] Reciprocal space
 <---> [05.04] K-grid lattice
 <---> Grid dimensions      :   4   4   4
 <---> [05.05] Energies & Occupations
 <---> [06] BZ grid analyzer/generator
 <---> Q-points  (BZ):  1
 <---> K-points  (BZ):   64
 <---> [07] == Q-grid analyzer ==
 <---> [WARNING] Point already in the grid. Listing internal Q-points.
 <---> [07.01] == Built-in grids [alat] ==
 <---> Q-points (IBZ) formatted
       0.000000000 |  0.000000000 |  0.000000000 |  1.000000000
 <---> Q-points (IBZ) un-formatted
   k1:  0.000000  0.000000  0.000000  1.000000
 <---> Q-points (IBZ) PW-formatted
       0.000000000  0.000000000  0.000000000 1
 <---> [08] Timing Overview
 <---> [09] Game Over & Game summary
I have noticed the hint from yambo_ph: <---> [RL indx] Q BZ pts are /= from X grid BS pts. Gamma point only.
but I don't know how to correct this.
Any help will be appreciated.

Best regards.
Youzhao Lan
College of Chemistry and Materials Science,
Zhejiang Normal University,
Jinhua, Zhejiang, China.
HomePage: http://blog.sciencenet.cn/u/lyzhao

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claudio
Posts: 461
Joined: Tue Mar 31, 2009 11:33 pm
Location: Marseille
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Re: Cannot generate the list of q-points as shown in the tutorial

Post by claudio » Thu Nov 30, 2023 10:51 am

Dear Youzhao

there were some errors in the Tutorial. I fixed it now, and I added all input files.

https://www.yambo-code.eu/wiki/index.ph ... n_Coupling

Now you should be able to run the tutorial from the beginning to the end

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com

lyzhao
Posts: 51
Joined: Tue May 31, 2016 8:02 am

Re: Cannot generate the list of q-points as shown in the tutorial

Post by lyzhao » Fri Dec 01, 2023 3:57 am

Dear Claudio,
It works now, thank you very much.
But I have two questions about the tutorial
1. I notice in the tutorial that
For particular cells, like the FCC, there could be an inconsistency between Yambo and QE definition of alat,
in this case you can specify OutputAlat equal to the celldm(1) of QE.
Can you tell me, besides FCC, what else are there?
2. For 2D structure, if I use "assume_isolated='2D'" for truncation of the Coulomb interaction in PW_PH calculation.
Shall I use the "Coulomb cut technique" in GW and BSE calculations either?

Best regards.
Youzhao Lan
College of Chemistry and Materials Science,
Zhejiang Normal University,
Jinhua, Zhejiang, China.
HomePage: http://blog.sciencenet.cn/u/lyzhao

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claudio
Posts: 461
Joined: Tue Mar 31, 2009 11:33 pm
Location: Marseille
Contact:

Re: Cannot generate the list of q-points as shown in the tutorial

Post by claudio » Mon Dec 04, 2023 9:51 am

Dear Youzhao

> Can you tell me, besides FCC, what else are there?
at the end it is only FCC, all the other works. This is due to the different definition
of lattice constant between QE and Yambo

>2. For 2D structure, if I use "assume_isolated='2D'" for truncation of the Coulomb interaction in PW_PH calculation.
>Shall I use the "Coulomb cut technique" in GW and BSE calculations either?

Yes, in both calculation phonons and excitons (GW +BSE) you should truncate the Coulomb interaction

best
Claudio
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com

lyzhao
Posts: 51
Joined: Tue May 31, 2016 8:02 am

Re: Cannot generate the list of q-points as shown in the tutorial

Post by lyzhao » Fri Jan 05, 2024 4:01 pm

Dear Claudio,
In the tutorial, I notice that
...Then you can prepare an input file for phonons using the q-points list you generated in the previous step multiplied by -1, the final input will be...
Could you tell me why the q-points generated in the previous step should be multiplied by -1?
Is this only required for the system (i.e., Si) used in this tutorial or for all other systems?

Best regards.
Youzhao Lan
College of Chemistry and Materials Science,
Zhejiang Normal University,
Jinhua, Zhejiang, China.
HomePage: http://blog.sciencenet.cn/u/lyzhao

User avatar
claudio
Posts: 461
Joined: Tue Mar 31, 2009 11:33 pm
Location: Marseille
Contact:

Re: Cannot generate the list of q-points as shown in the tutorial

Post by claudio » Fri Jan 12, 2024 5:31 pm

Dear Youzhao

the -1 is due to the different convention between Yambo and QE on the electron-phoon coupling.
One code calculates g(k,k+q) and another g(k,k-1). I know it is stupid, but it was not me that implemented it in the code
You need to put -1 for all systems

best regards
Claudio Attaccalite
Claudio Attaccalite
[CNRS/ Aix-Marseille Université/ CINaM laborarory / TSN department
Campus de Luminy – Case 913
13288 MARSEILLE Cedex 09
web site: http://www.attaccalite.com

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