a2y processing the *.WFK file error

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Roman
Posts: 8
Joined: Wed Jan 23, 2019 1:40 pm

a2y processing the *.WFK file error

Post by Roman » Thu Jul 02, 2020 3:49 pm

I used a2y from yambo 4.5.1 to process the wave function file tbase3_xo_WFK from the DFT calculation using the Abinit 8.10.3. There is an error: __ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/


<---> E(TSF) 2 Y(ambo)
<---> Checking input file ...
<---> ETSF file tbase3_xo_WFK
<---> DBs path set to :.
[ERROR] NetCDF: Unknown file format

That shows the a2y could not identify the NetCDF format file. But in D Sangalli et al 2019 J. Phys.: Condens. Matter 31 325902, the authors said " Starting with yambo 4.4, we will release a new version of the a2y interface, which is based on the direct reading of the Abinit wave-function files (WFK files) written in NetCDF format. " I don't know what caused this error.
Dongxiao Liu
PhD Student
Graduate School of CAEP,China

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Davide Sangalli
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Re: a2y processing the *.WFK file error

Post by Davide Sangalli » Thu Jul 02, 2020 10:21 pm

Dear Dongxiao Liu,
I suspect the reason is that your WFK file is not in NETCDF format.

To get files in NETCDF format with abinit you need to compile it with --enable-netcdf-default and --enable-mpi-io
After that it should work.

See also these related posts in the abinit forum for more details:
https://forum.abinit.org/viewtopic.php?f=14&t=4321
https://forum.abinit.org/viewtopic.php?p=12797#p12797


Best,
D.
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
https://sites.google.com/view/davidesangalli
http://www.max-centre.eu/

Roman
Posts: 8
Joined: Wed Jan 23, 2019 1:40 pm

Re: a2y processing the *.WFK file error

Post by Roman » Fri Jul 03, 2020 5:52 am

Dear Davide,

Thank you very much for your prompt reply. It works after I compiled the Abinit with --enable-netcdf-default and --enable-mpi-io.
But there is another error:
[liudx@localhost yambo]$ a2y -F t01_out_WFK.nc


__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/


<---> E(TSF) 2 Y(ambo)
<---> Checking input file ...
<---> ETSF file t01_out_WFK.nc
<---> DBs path set to :.
<---> Header/K-points/Energies...done
<---> Cell data...[SI yes]......[-I no]...[TR yes]...done
<---> Eigenvalues data...done
<---> K-points mesh...done
<---> Pseudopotential...
[ERROR] variable: lmnmax NetCDF: Invalid dimension ID or name

I want to know how to deal with this problem.
Dongxiao Liu
PhD Student
Graduate School of CAEP,China

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