Generating yambo_ph compatible el-ph matrix elements

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Generating yambo_ph compatible el-ph matrix elements

Postby benjyk » Mon May 06, 2013 12:09 pm

Dear Yambo Developers,

I attended this year's Yambo workshop in Lausanne and learnt about the new electron-phonon capabilities of the yambo_ph package with great interest. Unfortunately I am having some problems converting Quantum Espresso el-ph matrix elements for use with yambo_ph.

The link to the QE 4.0.5 patch, provided in section E of the electron-phonon tutorial, does not appear to work.

Please could you advise on the best way to produce compatible el-ph databases from quantum espresso output.

Many thanks in advance,

Ben
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby andrea marini » Mon May 06, 2013 8:57 pm

Hi Ben. The correct link for the files to replace in the standard distribution of QE is here

http://www.yambo-code.org/tutorials/fil ... _4.0.5.zip

Regarding the documentation we will provide it at the end of the tutorial page as soon as possible. We are working hard on the GPL source to release ASAP.

Thanks

Andrea
Andrea MARINI
Istituto di Struttura della Materia, CNR, (Italy)
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby kazemoor » Mon May 27, 2013 4:22 pm

Dear Andrea

I have compiled many times espresso-4.0.5 with the suggested patched files, but at the end of making espresso I have faced following error while without these patches I make successfully:

../PH/libph.a(allocate_phq.o): In function `allocate_phq_':
allocate_phq.f90:(.text+0x34ba): undefined reference to `yambo_mp_s_elph_'
allocate_phq.f90:(.text+0x3873): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x387f): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x388a): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x389b): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x38a2): undefined reference to `yambo_mp_y_k_'
../PH/libph.a(allocate_phq.o):allocate_phq.f90:(.text+0x38ac): more undefined references to `yambo_mp_y_k_' follow
../PH/libph.a(phq_init.o): In function `phq_init_':
phq_init.f90:(.text+0x9fe): undefined reference to `yambo_mp_y_nk_'
phq_init.f90:(.text+0xb6d): undefined reference to `yambo_mp_y_nk_'
make[1]: *** [d3.x] Error 1
make[1]: Leaving directory `/home/softs/espresso-4.0.5/D3'
make: *** [d3] Error 2

How can I overcome the error?
Moreover, in the tutorial of el_ph you said "The procedure to get the el-ph databases ndb.elph_gkkp_fragment will be described in this section shortly ", but every day I checked I find nothing. Would you please help me how to make the procedure?

Thanks a lot

Ali kazempour, Pnu university , Tehran, Iran
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby andrea marini » Mon May 05, 2014 11:42 am

Dear Ali,

again. I am very sorry for this problem. We are working on it and we will post a news when the new QE + Yambo source will be ready!

Andrea
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby pourya » Wed Dec 03, 2014 10:31 am

Dear all

Hi,

I have faced the same problem when I want to compile QE 4.0.5 with patched file. It will appreciate you if one helps me to find a solution. Plus, is there any possibility to compile other version of QE and Yambo to calculate electron-phonon matrix elements?

!***********************************************************************************

../PH/libph.a(allocate_phq.o): In function `allocate_phq_':
allocate_phq.f90:(.text+0x2faf): undefined reference to `yambo_mp_s_elph_'
allocate_phq.f90:(.text+0x30eb): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x312a): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x3131): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x3138): undefined reference to `yambo_mp_y_k_'
allocate_phq.f90:(.text+0x3143): undefined reference to `yambo_mp_y_k_'
../PH/libph.a(allocate_phq.o):allocate_phq.f90:(.text+0x314a): more undefined references to `yambo_mp_y_k_' follow
../PH/libph.a(phq_init.o): In function `phq_init_':
phq_init.f90:(.text+0xe67): undefined reference to `yambo_mp_y_nk_'
phq_init.f90:(.text+0x116c): undefined reference to `yambo_mp_y_nk_'
make[1]: *** [d3.x] Error 1
make[1]: Leaving directory `/home/students/pourya/package/espresso-4.0.5/D3'
make: *** [d3] Error 2



Best regard,

Pourya Ayria
PhD student Tohoku University Japan
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby myrta gruning » Wed Dec 03, 2014 11:19 am

Dear Pourya Ayria

any version > 4.0.5 will contain the yambo_ph for the electron phonon calculations.
You can look at the qeforge repository
http://qe-forge.org/gf/project/q-e/

Take care that the QE5.1.1 has an issue with the interface between pw and yambo, we are fixing it, so maybe use the 5.0 that should be safe,

Best
m
Dr Myrta GrĂ¼ning
Atomistic Simulation Centre
Queen's University Belfast - Northern Ireland

http://www.researcherid.com/rid/B-1515-2009
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby Davide Sangalli » Wed Feb 04, 2015 6:22 pm

Dear all,
the issue with version QE5.1.1 has now been fixed.

Best,
Davide
Davide Sangalli, PhD
CNR-ISM, Division of Ultrafast Processes in Materials (FLASHit) and MaX Centre
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby r24sudo » Wed Apr 22, 2015 6:20 pm

I am still having difficulty getting the el-ph matrix elements compatible with Yambo in order to calculate the self energy terms as is done in the tutorial on electron-phonon interaction:

http://www.yambo-code.org/tutorials/Ele ... /index.php

Has anyone been able to do this using the p2y interface, or can the needed db.elph_gkkp_fragments be generated in another way? I would appreciate any help in making this work.
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Re: Generating yambo_ph compatible el-ph matrix elements

Postby Daniele Varsano » Sun May 24, 2015 3:33 pm

Dear r24sudo (please fill your signature with your name and affiliation).
We have opened a subforum concerning electron-phonon calculation were you can post there problem you are facing and where we will be posting news about the ongoing development of the interfaces with Quantum Espresso as weil as technical and methodological informations about how to use the code.

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
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