Atom projected PDOS after GW

Run-time issues concerning Yambo that are not covered in the above forums.

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chwolf
Posts: 44
Joined: Mon Jul 11, 2016 2:11 pm
Location: South Korea
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Atom projected PDOS after GW

Post by chwolf » Sat Sep 10, 2022 8:33 am

Dear all,

I performed a GW calculation to obtain the QP energies. Now I am trying to get the atom projected DOS from ypp via -s s and using

Code: Select all

PROJECT_mode= "ATOM"             # Instruct ypp how to project the DOS. ATOM, LINE, PLANE.
and

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GfnQPdb= "E < SAVE/ndb.QP"                  # [EXTQP G] Database action
However, I get the following error:

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 <---> [01] MPI/OPENMP structure, Files & I/O Directories
 <---> [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> [03] Core DB
 <---> :: Electrons             : 203.0000
 <---> :: Temperature           : 0.000000 [eV]
 <---> :: Lattice factors       : 56.69178  56.69178  28.34589 [a.u.]
 <---> :: K points              : 1
 <---> :: Bands                 :  400
 <---> :: Symmetries            : 2
 <---> :: RL vectors            :  7208583
 <---> [04] K-point grid
 <---> :: Q-points   (IBZ): 1
 <---> :: X K-points (IBZ): 1
 <---> [05] CORE Variables Setup
 <---> [05.01] Unit cells
 <04s> [05.02] Symmetries
 <04s> [05.03] Reciprocal space
 <04s> [05.04] K-grid lattice
 <04s> [05.05] Energies & Occupations
 <04s> [06] Electronic DOS
 <04s> [06.01] External/Internal QP corrections
 <04s> E<SAVE/ndb.QP[ PPA@E  27.21138 * XG 1581 * Xb 1-400 * Scb 1-200]
 <04s> [dE_from_DB-Nearest K] Exact matches       :  100.0000 [o/o]
 <04s> [06.01.01] FIT on E < SAVE/ndb.QP
 <04s> [QP_apply] Action to be applied: E<SAVE/ndb.QP[ PPA@E  27.21138 * XG 1581 * Xb 1-400 * Scb 1-200]
 <04s> [06.02.01]  QP corrections report

[ERROR] STOP signal received while in[06.02.01]  QP corrections report
[ERROR] not enought projections for PDOS
I am not sure what this means .. do I need to define the atoms I want to project on somewhere in the ypp.in file?

Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

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Daniele Varsano
Posts: 3465
Joined: Tue Mar 17, 2009 2:23 pm
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Re: Atom projected PDOS after GW

Post by Daniele Varsano » Sun Sep 11, 2022 7:26 am

Dear Christoph,

yes, you can complete your input file.
ypp -s s -V all
will show you the additional variables to define atoms, kinds etc...

Importantly, be sure to have calculated the projections using projwfc (QE) beforehand.

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/

chwolf
Posts: 44
Joined: Mon Jul 11, 2016 2:11 pm
Location: South Korea
Contact:

Re: Atom projected PDOS after GW

Post by chwolf » Tue Oct 18, 2022 2:09 am

Dear Daniele,

Thank you for your help. Unfortunately I am still struggling with PROJECT_mode= "ATOM". I calculated C6H6 (30 electrons) (scf+nscf+projwfc) and then GW. When I calculate the total DOS (PROJECT_mode= "none") I get a nice DOS - so I think the calculation itself worked well enough. However when I am trying to calculate ATOM projections it does not work and the error is always

Code: Select all

[ERROR] STOP signal received while in[06] Electronic DOS
[ERROR] not enought projections for PDOS
I assume I am doing something wrong in the input block regarding the projections, but even when setting values to -1|-1 (which I assume means "all") it does not work.

Code: Select all

% DOS_bands
   1 | 100 |                         # DOS bands
%
#DOSUsesOcc                    # Weight the DOS with the occupation factors
% PDOS_atoms
-1 |-1 |                             # Select atom number range
%
% PDOS_kinds
-1 |-1 |                             # Select atom kind   range
%
% PDOS_wfcs
-1 |-1 |                             # Select projector   range
%
% PDOS_l
-1 |-1 |                             # Select angular momentum l range
%
% PDOS_j
-1.000000 |-1.000000 |               # Select angular momentum j range
%
% PDOS_m
-10 |-10 |                           # Select angular momentum m range
%
I went back to do it without QP correction (GfnQPdb= "none" ) just in case but the error is the same. I do have a file called atomic_proj.xml, which has the following header:

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<PROJECTIONS>
<HEADER NUMBER_OF_BANDS="100" NUMBER_OF_K-POINTS="1" NUMBER_OF_SPIN_COMPONENTS="1" NUMBER_OF_ATOMIC_WFC="30" NUMBER_OF_ELECTRONS="30.0000000000000" FERMI_ENERGY="-0.418514210562594"/>
<EIGENSTATES>
<K-POINT Weight="2.00000000000000"> 0.000000000000000E+00 0.000000000000000E+00 0.000000000000000E+00 </K-POINT>
<E> -1.511601565001599E+00 -1.307453781633125E+00 -1.307244246191886E+00 -1.042155817877148E+00 -1.041697291167955E+00 -8.990710418682942E-01 -7.746394241781062E-01 -7.538252541865482E-01 -7.038790352618068E-01 -7.034119476955700E-01 -6.188394723013778E-01 -5.580178655044280E-01 -5.571801669787492E-01 -4.186700032480844E-01 -4.185142105625936E-01 -4.414309270647024E-02 -4.337367298079994E-02 -2.183907447882222E-02 6.886223871868206E-02 8.132367683493479E-02 8.556274677668838E-02 8.826522028309439E-02 9.375286822991542E-02 1.351182956360188E-01 1.568800569638477E-01 1.913539363384941E-01 1.920584728411931E-01 1.948652963840791E-01 1.969811682210394E-01 2.022137929372746E-01 2.113080389222470E-01 2.129814918074248E-01 2.144163639697616E-01 2.171994012762322E-01 2.324139686380058E-01 2.325562333816296E-01 2.807440798732166E-01 2.990304592550602E-01 3.052097010613586E-01 3.068666627193030E-01 3.084161781010516E-01 3.095206966952832E-01 3.181168420714406E-01 3.220227793320842E-01 3.320764395859836E-01 3.407985557493390E-01 3.956199234041910E-01 4.035102059306754E-01 4.068425698622668E-01 4.072609573699126E-01 4.217654036720380E-01 4.246023491540938E-01 4.260935292521266E-01 4.472609756041562E-01 4.549711645057816E-01 4.744970848956876E-01 4.754278470553382E-01 4.896919171880122E-01 5.014014610751920E-01 5.028933741940248E-01 5.044587132756638E-01 5.202687712423476E-01 5.238040688416764E-01 5.246778365775112E-01 5.278470425588330E-01 5.329345495716122E-01 5.343020080603600E-01 5.431193183816893E-01 5.448807994137432E-01 5.475888246074062E-01 5.487569079268418E-01 5.606803446851478E-01 5.732399238146982E-01 5.760466657027165E-01 5.840374608144177E-01 5.882560363367190E-01 5.912765072787606E-01 5.945343490322166E-01 6.139402574060792E-01 6.202450580938836E-01 6.275491818542334E-01 6.276468807206758E-01 6.292223452934874E-01 6.393241075996638E-01 6.404132888992468E-01 6.446461979203136E-01 6.490874677926376E-01 6.503793504972700E-01 6.504296844538638E-01 6.545053605771473E-01 6.561957117916986E-01 6.587499111140334E-01 6.597646271404044E-01 6.633485423101178E-01 6.646444599788288E-01 6.719433620649916E-01 6.727172529860442E-01 6.949928817054020E-01 6.972375245466979E-01 7.274785370621388E-01 </E>
<PROJS>
[...]
[..]
So I think yambo can read my atomic wfcs correctly but I don't know how to define the projections.

If I want to project the DOS only for the Carbon s;p orbitals, how would I do that?

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  Cell kind             :  CUB
  Atoms in the cell     :  C  H
  number of C  atoms    :   6
  number of H  atoms    :   6

  List of atomic masses
  Mass of C     :  12.01070
  Mass of H     :  1.000000

  List of atomic coordinates    : [cc]
  C1       :   9.01806  12.79504  16.96375  order 6
  C2       :  13.58069  12.46531  16.97232  order 7
  C3       :  11.01451   8.67728  16.96780  order 8
  C4       :  13.39224   9.82953  16.97200  order 9
  C5       :  11.39405  13.94790  16.96700  order 10
  C6       :   8.82944  10.16115  16.96526  order 12
  H1       :  10.86088   6.61945  16.96583  order 1
  H2       :  15.09868   8.67031  16.97512  order 2
  H3       :  15.43454  13.37115  16.97663  order 3
  H4       :  11.54560  16.00535  16.96577  order 4
  H5       :   7.31043  13.95261  16.95944  order 5
  H6       :   6.97463   9.26003  16.96485  order 11
I assumed it would be:

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% DOS_bands
   1 | 100 |                         # DOS bands
%
#DOSUsesOcc                    # Weight the DOS with the occupation factors
% PDOS_atoms
[b]1 |6 |       [/b]                      # Select atom number range
%
% PDOS_kinds
[b]1 |1 |           [/b]                  # Select atom kind   range
%
% PDOS_wfcs
[b]1 | 4 |        [/b]                     # Select projector   range 1 s + 3 p
%
% PDOS_l
[b]0|1 |    [/b]                         # Select angular momentum l range l=0 + l=1
%
% PDOS_j
-1 |-1 |               # Select angular momentum j range 
%
% PDOS_m
-10 |-10 |                           # Select angular momentum m range
%
but this does not work:

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[ERROR] STOP signal received while in[06] Electronic DOS
[ERROR] not enought projections for PDOS
ypp version is: This is ypp - MPI+HDF5_MPI_IO - Ver. 5.1.0 Revision 21608 Hash b8e986d9e

Thanks again for your help!

Best,
Chris
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr

User avatar
Daniele Varsano
Posts: 3465
Joined: Tue Mar 17, 2009 2:23 pm
Contact:

Re: Atom projected PDOS after GW

Post by Daniele Varsano » Tue Oct 18, 2022 8:03 am

Dear Christoph,

the procedure is the following:

QE--> scf/nscf/projwc
Yambo--> p2y

the p2y procedure should recognize there is an atomic_proj.xml file and convert it in a yambo database (ns.atom_proj_pwscf*)
So, it is important to do the p2y step after the projwfc

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/

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