Post
by elena.mol » Tue Mar 07, 2023 10:24 am
Hello,
I have just encountered a p2y error similar to the one found by Bo Peng: also in my case it looks like a problem in parsing the pseudopotential files, but in my case it is not completely harmless: p2y does not create the ns.kb_pp* files in the SAVE folder.
More in detail:
I am using yambo 5.1.1. on CINECA Marconi100, and I find a p2y error when in the QE run I use norm-conserving TM pseudopotentials from the pslibrary.1.0.0.
The last lines of the l_p2y file are like this:
<31s> ... Database done
<31s> == DB2 (wavefunctions) ...
<31s> [p2y] WF I/O | | [000%] --(E) --(X)
<35s> [p2y] WF I/O |########################################| [100%] 03s(E) 03s(X)
i.e. p2y stops when it should read the PsP.
The output of the slurm batch script I use to submit the p2y run gives this error:
# WARNING: there are pending errors
# PENDING ERROR (ierr=1)
# ERROR IN: iotk_open_read (iotk_files.spp:487)
# CVS Revision: 1.20
# unit
file=./data-file.xml
binary=F
iostat=209
# PENDING ERROR (ierr=2)
# ERROR IN: iotk_scan_empty (iotk_scan.spp:364)
# CVS Revision: 1.23
# Tag not found
namel=fft_grid
# PENDING ERROR (ierr=3)
# ERROR IN: iotk_scan_empty (iotk_scan.spp:364)
# CVS Revision: 1.23
# Tag not found
namel=fft_smooth
# FROM IOTK LIBRARY, VERSION 1.2.0
# UNRECOVERABLE ERROR (ierr=4)
# ERROR IN: iotk_tag_parse (iotk_misc.spp:625)
# CVS Revision: 1.39
# Wrong syntax in tag
tag=![CDATA[ Generated using "atomic" code by A. Dal Corso v.6.6 Author: TM Generation date: 28Feb2023 Pseudopotential
# ERROR IN: iotk_scan (iotk_scan.spp:719)
# CVS Revision: 1.23
# direction
control=2
# ERROR IN: iotk_scan_end (iotk_scan.spp:211)
# CVS Revision: 1.23
# foundl
The p2y run has created a SAVE folder, with ns.db1, ns.wf* files, but without ns.kb_pp* files.
Then I have run the yambo setup and it runs correctly, creating the ndb.gops and ndb.kindx files in the SAVE,
but then an Independent Particle optics run creates all the expected files (including spectra), but it gives the following warning in the report file:
[WARNING] [r,Vnl^pseudo] not included in position and velocity dipoles
The system is bulk nickel oxide, the QE scf run is with Hubbard correction, but I have removed the Hubbard-related lines in the data-file-schema.xml (and previously verified in other tests that yambo optics runs with Covariant Dipoles, which should somehow take into account the otherwise missing Hubbard part, yield spectra similar to runs with G space dipoles), and the same system runs smoothly when using different NC PsP, i.e. those from the DoJo library.
I am attaching a .zip containing the following files:
bulk_NiO_4L_unitcell_EM_feb2023.scf.in --> QE scf input
Ni.pbe-n-nc.UPF --> the PsP used for Ni (the one for O is of the same type and format)
l_p2y --> p2y log file
yambo_IP_test.in --> yambo IP optics input
r-test_IP_optics_dipoles_bse --> report file of the IP run
Is there a way to allow yambo to correctly read the above-mentioned pseudpotentials, e.g. by somehow creating them with a different format (if the format is the problem...) ...?
Thanks a lot in advance
Best
Elena Molteni
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