core dumped (erreur de segmantation)

[halima]

dear user yambo code
I am trying to do GW calculation with Yambo calculation(version 3.3 rev 36)after a DFT with quantum espresso (5.0) following this steps
run scf calculation
then:
halima@halima:~/GaN/Ga.save$ /home/halima/Téléchargements/yambo-3.3.0-rev36/bin/p2y
halima@halima:~/GaN/Ga.save$ /home/halima/Téléchargements/yambo-3.3.0-rev36/bin/yambo -x -F 01HF.in
yambo -p p -g n
yambo
<---> [01] Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [04] Bare local and non-local Exchange-Correlation
<---> [M 1.546 Gb] Alloc WF ( 1.545)
<01s> [FFT-HF/Rho] Mesh size: 30 30 30
<08s> [WF-HF/Rho loader] Wfs (re)loading |####################| [100%] 06s(E) 06s(X)
<08s> EXS | | [000%] --(E) --(X)Erreur de segmentation (core dumped)

&control
calculation = 'scf'
prefix='Ga'
pseudo_dir = '/home/halima/GaN',
outdir= '/home/halima/GaN'
wf_collect=.true.,
verbosity ='high',
tstress=.true.,
tprnfor=.true.,
/
&system
ibrav=4,celldm(1)=6.011,celldm(3)=1,62,celldm(4)=-0.5,nat=4, ntyp=2,
ecutwfc = 15,ecutrho = 240.0,
!nosym = .false.,force_symmorphic = .Ture.
nbnd =10,
!occupations='smearing', smearing='methfessel-paxton', degauss=0.03
/
&electrons
diago_full_acc=.true.,
conv_thr = 1.0d-8
!conv_thr = 1e-12,
!mixing_beta=0.3

/
ATOMIC_SPECIES
Ga 69.723 Ga.pbe-mt_fhi.UPF
N 14.007 N.pbe-mt_fhi.UPF
ATOMIC_POSITIONS
Ga 0.333333333 0.666666667 -0.003561202
Ga 0.666666667 0.333333333 0.496438798
N 0.333333333 0.666666667 0.378561202
N 0.666666667 0.333333333 0.878561202

K_POINTS automatic
8 8 8 1 1 1
01HF.in
# ____ ____ _ ____ ____ ______ ___
# |_ _||_ _| / \ |_ \ / _||_ _ \ ." `.
# \ \ / / / _ \ | \/ | | |_) | / .-. \
# \ \/ / / ___ \ | |\ /| | | __". | | | |
# _| |_ _/ / \ \_ _| |_\/_| |_ _| |__) |\ `-" /
# |______||____| |____||_____||_____||_______/ `.___."
#
# GPL Version 3.3.0 Revision 1887
# http://www.yambo-code.org
#
HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc
EXXRLvcs= 1 RL # [XX] Exchange RL components
%QPkrange # [GW] QP generalized Kpoint/Band indices
1| 50| 1| 10|
%
%QPerange # [GW] QP generalized Kpoint/Energy indices
1| 50| 0.0|-1.0|
%
i have already run the commande yambo -o c for compute the dielctric function it works verry well
but i have problem with Gw in the example of Si it works and i can found the file o.qp in my case of GaN
please any idea can help me to solve this problem
thanks in advance
H.ZAARI
PhD Student in laboratory of magnetism and physics of high energy
Faculty of Sciences in Rabat - Morocco
Email: halimazaari@gmail.com

[Daniele Varsano]

Dear Halima,
it is not very clear at what step you get the error. You posted an HF input (please note that EXXRLvcs= 1 RL does not make much sense), but you assert that you are running the GW calculation input (yambo -p p -g n). Anyway something is going wrong in the HF part. In order to understand what happen I suggest you to remove from you SAVE directory all your data bases (db.* or ndb.*), starting from scratch:
run a setup

Code: Select all

yambo -i

to create the input (yamb.in) and

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yambo

to run iy (it runs the yambo.in by default unless you do not specify another input name by the -F flag).
next the HF run

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yambo -x 

yambo -x to create the input, and

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yambo

to run it.
If you get the error please post the error, standard output, input file together with the reports (r_setup and r_HF**).
Please note that

Code: Select all

yambo -x -F 01HF.in

does not make sense (yambo -x create an HF run while yambo -F 01HF.in run the 01HF.in input, I do not know what the code did with this combination)

Beside that:
common practice is to run a nscf calculation after the scf calculation (this is because in GW implementation you can need a lot of unoccupied bands). Next, think also about also to switch to the 3.4 version.

[halima]

Dear Daniele Varsano
thank you for your reply
I redid the calculation with the commands that you proposed to me, but I still get the same error:

halima@halima:~$ cd GaN/
halima@halima:~/GaN$
halima@halima:~/GaN$ halima@halima:~/GaN$ halima@halima:~/GaN$
halima@halima:~/GaN$ /home/halima/Documents/quantum/espresso-5.0/bin/pw.x<GaN.scf.in >scf.out
halima@halima:~/GaN$ /home/halima/Documents/quantum/espresso-5.0/bin/pw.x<GaN.nscf.in >nscf.out
halima@halima:~/GaN$ cd Ga.save/
halima@halima:~/GaN/Ga.save$ /home/halima/Tأ©lأ©chargements/yambo-3.3.0-rev36/bin/p2y
<--->
P(W) 2 Y(ambo) Ver. 5.0 <---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...done
<---> Atomic data...done
<---> Symmetries...[SI no]......[-I no]...[TR yes]
<---> XC functional...Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<---> K-points mesh...done <---> RL vectors...done
<---> IGK arrays...done <---> Energies...done
<---> :: Electrons : 16.00000
<---> :: Temperature [ev]: 0.000000
<---> :: Lattice factors [a.u.]: 6.011000 5.205679 6.011000
<---> :: K-points : 24
<---> :: Bands : 10
<---> :: Spinor components : 1
<---> :: Spin polarizations : 1
<---> :: Spin orbit coupling : no
<---> :: Symmetries [spatial]: 1 <---> :: [T-rev]: yes
<---> :: Max WF components : 188
<---> :: RL vectors (WF): 332
<---> :: RL vectors (CHARGE): 11747
<---> :: XC potential : Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
<---> :: Atomic species : 2
<---> :: Max atoms/species : 2

<---> == Writing DB1 ...done == <---> == DB2 (wavefunctions) ...done ==
<---> == P2Y completed ==
halima@halima:~/GaN/Ga.save$ /home/halima/Tأ©lأ©chargements/yambo-3.3.0-rev36/bin/yambo -i
halima@halima:~/GaN/Ga.save$ /home/halima/Tأ©lأ©chargements/yambo-3.3.0-rev36/bin/yambo

<---> [01] Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> Shells finder |####################| [100%] --(E) --(X)
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [WARNING][RL indx] 2 equivalent points in the rlu grid found
<---> [RL indx] X grid is not uniform. Gamma point only.
<---> [04] Game Over & Game summary
halima@halima:~/GaN/Ga.save$ /home/halima/Tأ©lأ©chargements/yambo-3.3.0-rev36/bin/yambo -x
halima@halima:~/GaN/Ga.save$ /home/halima/Tأ©lأ©chargements/yambo-3.3.0-rev36/bin/yambo
<---> [01] Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells <---> [02.02] Symmetries
<---> [02.03] RL shells <---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [04] Bare local and non-local Exchange-Correlation
<---> [FFT-HF/Rho] Mesh size: 30 30 30
<---> [WF-HF/Rho loader] Wfs (re)loading |####################| [100%] --(E) --(X)
<---> EXS | | [000%] --(E) --(X)Erreur de segmentation (core dumped) halima@halima:~/GaN/Ga.save$

[Daniele Varsano]

Dear Halima,
I think the problem is related to the fact your k-point grid it is not uniform, you can see it from the r_setup report file:

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[WARNING][RL indx] 2 equivalent points in the rlu grid found

 [RL indx] X grid is not uniform.  Gamma point only.
 [WR./SAVE//db.kindx]----------------------------------------
  Polarization last K   : 24
  QP states             :  1  24
  X grid is uniform     :no
  BS scattering         :no

In order to overcome this problem you need to change your qe input files *both scf and nscf):
try to add:

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force_symmorphic=.true.

into the SYSTEM namelist of qe inputs. Yambo does not accept non uniform grid, and does not support non symmorphic symmetries.
Not sure this is the problem, as I do not have access to your qe output.

Moreover, even if not related to your problem, note that your cutoff are not much meaningful. The cutoff for the wfs look me quite low (it depends on your pseudo) and the cutoff for the density too high (there is not reason to set it bigger that 4*ecutwfc).
Hope it helps,
Daniele

[halima]

sorry but i can't solve this problem
how i can do to have xgrid=uniform??

[Daniele Varsano]

Dear Halima,
sorry but it is impossible to help you if you do not provide any relevant information.
Please post your qe input/output (scf and nscf), yambo input , report and standard output (setup and HF).
Best,
Daniele

[halima]

ok thank you for your help
in attached you find the scf nscf.in and .out
cordially

[Daniele Varsano]

Dear Halima,
looking at your ground state output, it looks that something it is not working properly.
The pw run does not recognize any symmetry and your band structure it is not reliable: have a look at the occupation numbers!!!!
It has a metallica behavior, as you can also see from the r_setup.
Please check carefully your set up and start a Many Body calculations once you are sure you have a reliable ground state.
Best,
Daniele

[halima]

thank you for your help i solve the problem and i get the file O.qp
now how i can get the band struture and dos files?

[Daniele Varsano]

Dear Halima,
please fill your signature with your complete name and affiliation. You can edit it from your profile once for all.
For the band structure and the DOS, there is a documentation in the yambo web page I invite you to read.
In general, even if you do not find the info you need in the web page, before posting I invite you to make a search in the forum if the question has been already answer. This is the case for your question.
These are the pages of the manual:
http://www.yambo-code.org/input_file/ypp/index.php
http://www.yambo-code.org/input_file/ypp/ypp_bands.php

Other info you can find by making searches in the forum.
Use this variable in input file if you want to look at QP dos and bands:

GfnQPdb= "E < ./SAVE/ndb.QP"

ndb.QP have to be substituted with db.QP if you are not using netcdf library.

Best,
Daniele