Install Yambo, wrong band energies

Having trouble compiling the Yambo source? Using an unusual architecture? Problems with the "configure" script? Problems in GPU architectures? This is the place to look.

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If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
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(3) if the problems occur compiling in serial/in parallel
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(5) the relevant compiler error message
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Nhat Minh Pham
Posts: 14
Joined: Tue Feb 15, 2022 12:07 am
Location: 01 Mac Dinh Chi, Ben Nghe, District 1, Ho Chi Minh City, Viet Nam

Install Yambo, wrong band energies

Post by Nhat Minh Pham » Tue Feb 15, 2022 12:11 pm

Dear Yambo developers, I'm new to Yambo, I've been trying to install Yambo 5.0.4 on my desktop, but after doing the tutorial on obtaining the band structure of a bulk material: h-BN,
I realize Yambo gives wrong band energies and when doing convergence test it usually gives a too large gap or NaN energy. I tried to install it on my laptop and it works well.
I managed to make configure file to use Yambo with internal library and put on --enable dp option (it produces bad results as before without this option) as below, this time I can
produce the band structure on the tutorial, but it still gives slightly different band energies compared to the tutorial which is correctly replicated on my laptop. This is quite annoying to me,
I hope you can help me out, for your information, my desktop is an HP z440 workstation with CPU Xeon E5 v3 2678 and 16Gb ECC ram, the config.log file is attached below.

The gap I get from my desktop

Code: Select all

#    K-point	Band	Eo [eV]		E-Eo [eV]	Sc|Eo [eV]
#
         7       8      -0.411876      -0.576270       2.313213
         7       9       3.877976        2.392646       -2.254435
and from the tutorial

Code: Select all

#  K-point    Band       Eo         E-Eo       Sc|Eo
#
 7.000000   8.000000  -0.411876  -0.567723   2.322443
 7.000000   9.000000   3.877976   2.413773  -2.232241
My configure input file

Code: Select all

#!/bin/sh
YAMBO_EXT_LIBS="/home/minh/yambo-5.0.4/lib"

./configure FC=gfortran \
 --with-hdf5-path=$YAMBO_EXT_LIBS \
 --with-netcdf-path=$YAMBO_EXT_LIBS \
 --with-netcdff-path=$YAMBO_EXT_LIBS \
 --with-iotk-path=$YAMBO_EXT_LIBS \
 --with-libxc-path=$YAMBO_EXT_LIBS \
 --with-fft-path=$YAMBO_EXT_LIBS \
 --enable-dp \
 --enable-keep-extlibs \
 --enable-time-profile \
 --enable-msgs-comps \
 --enable-keep-src \
 --enable-netcdf-output \
 --enable-memory-profile\
 --enable-int-linalg
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Pham Nhat Minh
MS student, Ho Chi Minh University of Science,
Ho Chi Minh City Institute of Physics
https://www.hcmus.edu.vn/

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Daniele Varsano
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Re: Install Yambo, wrong band energies

Post by Daniele Varsano » Tue Feb 15, 2022 12:22 pm

Dear Nhat Minh Pham ,

please sign your post with your name and affiliation, this is a rule of the forum and you can do once for all by filling the signature in your user profile.

The tutorial example are run in single precision, so the small difference you are finding are probably due to the DP usage.
What do you get when compiling in single precision?

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/

Nhat Minh Pham
Posts: 14
Joined: Tue Feb 15, 2022 12:07 am
Location: 01 Mac Dinh Chi, Ben Nghe, District 1, Ho Chi Minh City, Viet Nam

Re: Install Yambo, wrong band energies

Post by Nhat Minh Pham » Tue Feb 15, 2022 1:41 pm

Dear Daniele,

Thank you for your reply, within single-precision I got the same result as double-precision but when changing variables like EXXRLvcs, BndsRnXp, NGsBlkXp, GbndRnge (as convergence test on the tutorial) Yambo gives E-E0 =NaN or huge numbers about 20eV for conduction band and -20eV for valance band.
Using double-precision the code gives reasonable energies on convergence test and I can plot the band structure like the tutorial.
I tried doing GW correction for 2D MoS2 following the low dimension tutorial but my desktop with DP mode gives E-E0= NaN, meanwhile, my laptop gives a correction of about 1eV for the gap.
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Last edited by Nhat Minh Pham on Tue Feb 15, 2022 2:38 pm, edited 1 time in total.
Pham Nhat Minh
MS student, Ho Chi Minh University of Science,
Ho Chi Minh City Institute of Physics
https://www.hcmus.edu.vn/

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Daniele Varsano
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Re: Install Yambo, wrong band energies

Post by Daniele Varsano » Tue Feb 15, 2022 2:36 pm

Dear Pham,
as you said there should be a problem of compilation but it is not easy to spot, your config.log files does not show evident errors.
I would try to do a make distclean and then recompile the code and all the libraries, i.e. by running the configure without indicating libs option, something like
./configure

and see what happen.

Other possibilities could be related to the gfortran release which is very new. Do you have the possibility to try another compiler?

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/

Nhat Minh Pham
Posts: 14
Joined: Tue Feb 15, 2022 12:07 am
Location: 01 Mac Dinh Chi, Ben Nghe, District 1, Ho Chi Minh City, Viet Nam

Re: Install Yambo, wrong band energies

Post by Nhat Minh Pham » Wed Feb 16, 2022 3:04 am

Dear Daniele,

Thanks for your suggestion, I changed gfortran-11.2.0 to gfortran-8.5.0 and I got a closer band correction energy (not exact).
This time I'm able to do convergence tests for my 2D-MoS2 system without NaN error.

Best,
Minh
Pham Nhat Minh
MS student, Ho Chi Minh University of Science,
Ho Chi Minh City Institute of Physics
https://www.hcmus.edu.vn/

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Daniele Varsano
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Re: Install Yambo, wrong band energies

Post by Daniele Varsano » Thu Feb 17, 2022 9:36 am

Dear Minh,

thanks for reporting, we will inspect what is causing problem with the gfortran-11.2.0

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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claudio
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Re: Install Yambo, wrong band energies

Post by claudio » Thu Feb 17, 2022 11:03 am

Dear Minh,

gfortran 11 is not a stable release of gfortran

https://gcc.gnu.org/wiki/GFortran/News

you should not use it for production.

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

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