[gpaw-users] non standard crystal structures in band_Structure()

Thu Feb 2 14:56:18 CET 2017

Hi Ask,

It is proving to take  more time finding a simple example, the pw cut-off and k-popint sampling mess up the convergence and forces, and in order to get this example to converge a largish cut-off with specific rmm-diis settings seems necessary.

Anyhow:

It was quicker to write a script to dump the k-points into a file  by hand and then write a script to reorder and turn them into a band structure. I can now write a script to extract the info I want from the band structure (e.g. effective mass).

Thanks

Glenn

-----Original Message-----
From: Ask Hjorth Larsen [mailto:asklarsen at gmail.com] 
Sent: 31 January 2017 05:29 PM
To: Glenn Jones
Subject: Re: [gpaw-users] non standard crystal structures in band_Structure()

Hi

Is there not a minimal script that reproduces the problem?  (Like with
5 atoms which runs in 60 seconds.)

Best regards
Ask

2017-01-31 16:25 GMT+01:00 Glenn Jones <gjones at matthey.com>:
> Hi.
>
>
>
>
>
> I sent the scripts and outputs as attachments. I wasn’t sure if the 
> list would keep attachments.
>
>
>
> I can resend them tomorrow, the script requires a .gpw file which is 
> too big to attach so there is another script to generate it – I guess 
> I could lump it into one.
>
>
>
> Cheers
>
>
>
> Glenn
>
>
>
> Sent from my Windows 10 phone
>
>
>
> From: Ask Hjorth Larsen
> Sent: Tuesday, 31 January 2017 5:08 PM
> To: Glenn Jones
>
>
> Subject: Re: [gpaw-users] non standard crystal structures in
> band_Structure()
>
>
>
> Hi Glenn
>
> I cannot see that I have received a script.  (Let us keep things on 
> the list so others can follow as well.)
>
> Best regards
> Ask
>
> 2017-01-31 12:56 GMT+01:00 Glenn Jones <gjones at matthey.com>:
>> Hi Ask,
>>
>> I sent you a script on Friday afternoon, perhaps it didn’t come through?
>>
>> Cheers,
>>
>> Glenn
>>
>> -----Original Message-----
>> From: Ask Hjorth Larsen [mailto:asklarsen at gmail.com]
>> Sent: 31 January 2017 01:54 PM
>> To: Korina Kuhar
>> Cc: Glenn Jones; gpaw-users at listserv.fysik.dtu.dk
>> Subject: Re: [gpaw-users] non standard crystal structures in
>> band_Structure()
>>
>> Dear Glenn,
>>
>> A script is still needed if we should somehow consider this.
>>
>> Best regards
>> Ask
>>
>> 2017-01-31 8:50 GMT+01:00 Korina Kuhar <Kokuha at fysik.dtu.dk>:
>>> Dear Glenn,
>>>
>>> I still stand behind my last email, you should to it the 'old' way, 
>>> as I described in the previous email.
>>>
>>>
>>> \Korina
>>>
>>> Korina Kuhar
>>> PhD student
>>> DTU Physics
>>>
>>>
>>> Technical University of Denmark
>>>
>>>
>>> Department of Physics
>>> Fysikvej
>>> Building 307
>>> 2800 Kgs. Lyngby
>>> Denmark
>>> Direct +45 45253293
>>> kokuha at fysik.dtu.dk
>>> www.fysik.dtu.dk
>>>
>>> ________________________________________
>>> From: Glenn Jones [gjones at matthey.com]
>>> Sent: Tuesday, January 31, 2017 8:17 AM
>>> To: Ask Hjorth Larsen
>>> Cc: Korina Kuhar; gpaw-users at listserv.fysik.dtu.dk
>>> Subject: RE: [gpaw-users] non standard crystal structures in
>>> band_Structure()
>>>
>>> Hi Ask/Korina,
>>>
>>> I have rerun the calculation, just using one core (just to rule out 
>>> that making some undue influence):
>>>
>>> The error still persists, but as you can see the DFT part is 
>>> running, it seems the error comes from the final part of the script:
>>>
>>> band_structure = calc.band_structure() 
>>> band_structure.plot(filename='bandstructure.png', show=False)
>>>
>>> Unit cell:
>>>            periodic     x           y           z      points  spacing
>>>   1. axis:    yes    4.980825   -0.003369   -0.003369    30     0.1660
>>>   2. axis:    yes   -0.003369    4.980825   -0.003369    30     0.1660
>>>   3. axis:    yes   -0.003369   -0.003369    4.980825    30     0.1660
>>>
>>>                      log10-error:    total        iterations:
>>>            time      wfs    density  energy       fermi  poisson
>>> iter:   1  10:49:48  +1.49          -48.874673    3
>>> iter:   2  10:50:23  -0.16          -49.503395    3
>>> iter:   3  10:50:59  +0.90          -49.824318    3
>>> ..............
>>> iter:  40  11:12:43  -7.26          -50.215558    3
>>> iter:  41  11:13:19  -6.82          -50.215558    3
>>> iter:  42  11:13:54  -7.57          -50.215558    3
>>>
>>> Converged after 42 iterations.
>>>
>>> Energy contributions relative to reference atoms: (reference =
>>> -211812.275828)
>>>
>>> Kinetic:       +108.608022
>>> Potential:      -95.992394
>>> External:        +0.000000
>>> XC:             -64.427694
>>> Entropy (-ST):   -0.000008
>>> Local:           +1.596512
>>> --------------------------
>>> Free energy:    -50.215562
>>> Extrapolated:   -50.215558
>>>
>>> Fixed Fermi level: 6.20709
>>>
>>> Warning: Showing only first 2 kpts
>>>  Kpt  Band  Eigenvalues  Occupancy
>>>   0    46      5.13996    0.02000
>>>   0    47      5.13996    0.02000
>>>   0    48      7.92327    0.00000
>>>   0    49      8.45121    0.00000
>>>
>>>   1    46      5.13748    0.02000
>>>   1    47      5.13915    0.02000
>>>   1    48      7.91186    0.00000
>>>   1    49      8.45097    0.00000
>>>
>>>
>>> Traceback (most recent call last):
>>>   File "band.py", line 27, in <module>
>>>     band_structure = calc.band_structure()
>>>   File "/home/gjones/ase/ase/calculators/calculator.py", line 576, 
>>> in band_structure
>>>     return BandStructure(calc=self)
>>>   File "/home/gjones/ase/ase/dft/band_structure.py", line 32, in __init__
>>>     x, X, labels = labels_from_kpts(self.kpts, self.cell)
>>>   File "/home/gjones/ase/ase/dft/kpoints.py", line 182, in 
>>> labels_from_kpts
>>>     crystal_structure = crystal_structure_from_cell(cell)
>>>   File "/home/gjones/ase/ase/geometry/cell.py", line 156, in 
>>> crystal_structure_from_cell
>>>     raise ValueError('Cannot find crystal structure')
>>> ValueError: Cannot find crystal structure
>>>
>>>
>>>
>>> Glenn
>>>
>>>
>>>
>>> If the reader of this email is not the intended recipient(s), please 
>>> be advised that any dissemination, distribution or copying of this 
>>> information is strictly prohibited. Johnson Matthey Plc has its main 
>>> place of business at 5th Floor, 25 Farringdon Street, London (020 7269 8400).
>>>
>>> Johnson Matthey Public Limited Company Registered Office: 5th Floor,
>>> 25 Farringdon Street, London EC4A 4AB Registered in England No 33774
>>>
>>> Whilst Johnson Matthey aims to keep its network free from viruses 
>>> you should note that we are unable to scan certain emails, 
>>> particularly if any part is encrypted or password-protected, and 
>>> accordingly you are strongly advised to check this email and any 
>>> attachments for viruses. The company shall not accept any liability 
>>> with regard to computer viruses transferred by way of email.
>>>
>>> Please note that your communication may be monitored in accordance 
>>> with Johnson Matthey internal policy documentation.
>>
>>
>> This message has been scanned for viruses by MailControl - 
>> http://www.websense.com/
>>
>> Click
>> https://www.mailcontrol.com/sr/6cR2uGHk0OHGX2PQPOmvUuRWCrKzB2y3P3e3GW
>> SPChNStimKw7HQkYGF7MGQcSza+HRhnupCX4UzGm2rSK1dVQ==
>> to report this email as spam
>>