[gpaw-users] non standard crystal structures in band_Structure()
Ask Hjorth Larsen
asklarsen at gmail.com
Thu Feb 2 15:18:51 CET 2017
Hi
2017-02-02 14:56 GMT+01:00 Glenn Jones <gjones at matthey.com>:
> 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).
Just set calc.scf.converged = True after one iteration and it will
immediately "converge". You can use an observer which runs every N
iterations to do anything in step N.
Either that or set very coarse convergence parameters.
Best regards
Ask
>
> 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
>>>>
>>>>
>>>>
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