Errors in yambopy scripts

Post here any question you encounter when running the scripts of the yambo-py suite. Post here problem strictly to the python interface as problem coming from the yambo runs should go in the appropriate subforum.

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sitangshu
Posts: 117
Joined: Thu Jan 05, 2017 8:08 am

Errors in yambopy scripts

Post by sitangshu » Wed Apr 22, 2020 5:45 am

Dear Yambo team,

I hope you are all fine and immune.
I realized that there has been some major changes in the coding structure of yambopy. For example, is this a bug?: When I run gs_si.py, the relax run gives:
rekha@rekha-VirtualBox:~/software/yambopy-master/tutorial/si$ python gs_si.py -rrunning relax:

Traceback (most recent call last):
File "gs_si.py", line 236, in <module>
run_relax(args.nthreads)
File "gs_si.py", line 175, in run_relax
update_positions('relax', 'scf')
File "gs_si.py", line 158, in update_positions
qin = PwIn('%s/%s.scf'%(pathin,prefix))
TypeError: __init__() takes exactly 1 argument (2 given)

Although the program runs, but this message comes. There are several errors such as matdyn is not recognized, elph_pw files are not running, etc. Are these due to recent changes?

Regards,
Sitangshu
Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

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amolina
Posts: 128
Joined: Fri Jul 15, 2011 11:23 am
Location: Valencia, Spain
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Re: Errors in yambopy scripts

Post by amolina » Wed Apr 22, 2020 9:06 am

Dear Sitangshu,

you are right, we have performed many changes in Yambopy. We have changed the reference repository. This is now:

https://github.com/yambo-code/yambopy.git

I recommend you to download this repo and try the tutorial, updated with the new functionalities of the code.

Best,
Alejandro.
Alejandro Molina-Sánchez
Institute of Materials Science (ICMUV)
University of Valencia, Spain

sitangshu
Posts: 117
Joined: Thu Jan 05, 2017 8:08 am

Re: Errors in yambopy scripts

Post by sitangshu » Wed Apr 22, 2020 9:46 am

Dear Alejandro,

Seems there are still some errors:

rekha@rekha-VirtualBox:~/Desktop/yambopy-master/tutorial/bn$ python gs_bn.py -rrunning relax:
Traceback (most recent call last):
File "gs_bn.py", line 210, in <module>
update_positions('relax','scf')
File "gs_bn.py", line 128, in update_positions
e = PwXML(prefix,path=pathin)
File "/usr/local/lib/python2.7/dist-packages/yambopy-0.1-py2.7.egg/qepy/pwxml.py", line 39, in __init__
done_reading = read(path_filename)
File "/usr/local/lib/python2.7/dist-packages/yambopy-0.1-py2.7.egg/qepy/pwxml.py", line 249, in read_datafile_schema
self.ibrav = self.datafile_xml.findall("output/atomic_structure").get('bravais_index')
AttributeError: 'list' object has no attribute 'get'
Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

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amolina
Posts: 128
Joined: Fri Jul 15, 2011 11:23 am
Location: Valencia, Spain
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Re: Errors in yambopy scripts

Post by amolina » Wed Apr 22, 2020 10:23 am

Dear Sitangshu,

I suspect is a question of the installation. Can you be sure you remove previous versions? It happens often with python.
Then install the new version of yambopy.

Cheers,
Alejandro.
Alejandro Molina-Sánchez
Institute of Materials Science (ICMUV)
University of Valencia, Spain

sitangshu
Posts: 117
Joined: Thu Jan 05, 2017 8:08 am

Re: Errors in yambopy scripts

Post by sitangshu » Wed Apr 22, 2020 11:51 am

Yes. This is a python error. Essentially, I managed to recover!

Thank you
Regards,
Sitangshu
Sitangshu Bhattacharya
Indian Institute of Information Technology-Allahabad
India
Web-page: http://profile.iiita.ac.in/sitangshu/
Institute: http://www.iiita.ac.in/

yhypku
Posts: 1
Joined: Wed Sep 02, 2020 11:10 am

Re: Errors in yambopy scripts

Post by yhypku » Wed Sep 02, 2020 12:37 pm

Dear Sitangshu
I just install the latest version of yambopy and meet the same python error as you. Appreciate a lot if you could share your experience to fix it.
Regards,
Huaiyuan

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