[gpaw-users] Major code refactoring of I/O

Thu Nov 3 15:30:33 CET 2016

On 11/03/2016 02:41 PM, Oliver Stauffert wrote:
>
>
>> Jens Jørgen Mortensen <jensj at fysik.dtu.dk> hat am 2. November 2016 um 
>> 14:35 geschrieben:
>>
>>
>> Den 02-11-2016 kl. 14:01 skrev Oliver Stauffert:
>>
>>> Hi,
>>>
>>> I have been working on it and the test are now working and I also put
>>> in a few additional features.
>>>
>>> I will try to finalize it this week and make a merge request.
>>>
>> Thanks! Make that two MR's if that's still possible (one fix and one
>> new feature).
>>
>> Jens Jørgen
>>
> The new features come mainly from the fact, that i use a new, more 
> general Finite difference calculator.
>
> (instead of the currently used one in ase/calculators/test)
>
> So it will be difficult to split it nicely into fix and features.
>
> It was also intended, that the finite difference calculator should be 
> placed in ase. So there is the question, if i should make two MR, one 
> for ase and one for gpaw, or put it into gpaw for the time being.
>

Put it into GPAW for now.  Then we can move it to ASE later.

Thanks!

Jens Jørgen

> Oliver
>
>>> Oliver Stauffert
>>>
>> >> Jens Jørgen Mortensen <jensj at fysik.dtu.dk> hat am 1. November 2016 
>> um >> 09:55 geschrieben:
>> >>
>> >>
>> >> On 10/31/2016 09:53 AM, Jens Jørgen Mortensen wrote:
>> >>
>> >>> On 08/23/2016 09:22 AM, Jens Jørgen Mortensen wrote:
>> >>>
>> >> >> On 08/19/2016 11:12 AM, Michael Walter wrote:>>> Hi,
>> >> >>>
>> >> >>> 2016-08-19 9:09 GMT+02:00 Jens Jørgen Mortensen 
>> <jensj at fysik.dtu.dk
>> >> >>> <mailto:jensj at fysik.dtu.dk>>:
>> >> >>>
>> >> >>> On 08/11/2016 03:11 PM, Jens Jørgen Mortensen wrote:
>> >> >>>
>> >> >>> On 08/09/2016 10:09 AM, Jens Jørgen Mortensen via gpaw-users
>> >> >>> wrote:
>> >> >>>
>> >> >>> Hi!
>> >> >>>
>> >> >>> The last couple of weeks, I have been working hard on
>> >> >>> rewriting the I/O code the reads and writes gpw-files
>> >> >>> (restart files) and also the part of the code that prints
>> >> >>> information to the log file. While doing this I also made
>> >> >>> many other changes to clean up things a bit. This work
>> >> >>> should really have been done 5 years ago, but now is
>> >> >>> better than never! Initially, this broke almost all our
>> >> >>> test, but most of them are working again. Currently
>> >> >>> these 5 are still failing:
>> >> >>>
>> >> >>>
>> >> >>> fdtd/ed_wrapper.py
>> >> >>> fdtd/ed.py
>> >> >>> inducedfield_td.py
>> >> >>> fdtd/ed_shapes.py
>> >> >>> transport.py
>> >> >>>
>> >> >>>
>> >> >>> I also need help fixing the lrtddft/excited_state.py test. It
>> >> >>> works in serial, but not in parallel where it will try to change
>> >> >>> the communicator for a GPAW object which is no longer supported.
>> >> >>>
>> >> >>> Also the Na2_relax_excited.py test is failing. These tests use
>> >> >>> the gpaw.lrtddft.excited_state module and I really need some help
>> >> >>> here.
>> >> >>>
>> >> >>> Michael: Can you take a look at this?
>> >> >>>
>> >> >>> https://gitlab.com/gpaw/gpaw/merge_requests/91
>> >> >>> <https://gitlab.com/gpaw/gpaw/merge_requests/91>
>> >> >>>
>> >> >>>
>> >> >>> I'm currently in vacation and will be back to work early 
>> September.
>> >> >>> Maybe Oliver Stauffert is available and can have a look ?
>> >> >>> Anyway we will keep care in September.
>> >>
>> >>> Any progress? I really need some help fixing this.
>> >>>
>> >> About the gpaw.transport module. It seems that no one is able to
>> >> maintain that so I'll go ahead and remove that.
>> >>
>> >> Jens Jørgen
>> >>
>> >>> Jens Jørgen
>> >>>
>> >> >>>> Great! Have a nice vacation.
>> >> >>
>> >> >> Jens Jørgen
>> >> >>
>> >> >>>
>> >> >>> Best,
>> >> >>> Michael
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> Jens Jørgen
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> I can maybe fix the transport.py test myself, but I could
>> >> >>> use some help with the others - please! The major
>> >> >>> problem is the reading and writing done by the fdtd and
>> >> >>> inducedfields modules. Typically, I have found that the
>> >> >>> code for I/O can be expressed in 3-4 times fewer lines of
>> >> >>> code with the new approach. That's good, but there is
>> >> >>> still a lot of work to be done and I'm not so familiar
>> >> >>> with these parts of the code.
>> >> >>>
>> >> >>> We are dropping the old tar-file format for gpw-files in
>> >> >>> favour of the much more flexible and simple-to-use
>> >> >>> aff-file format from ASE (which is also used for
>> >> >>> ASE-trajectories). Reading of old gpw-files will be sort
>> >> >>> of supported, but it will impossible to test all use
>> >> >>> cases. So, if you have old gpw-files that you want to
>> >> >>> reuse, then I would like you to test reading of those!
>> >> >>>
>> >> >>>
>> >> >>> I forgot to mention that you can use:
>> >> >>>
>> >> >>> $ alias aff="python -m ase.io.aff"
>> >> >>> $ aff my.gpw
>> >> >>>
>> >> >>> to look inside a gpw-file.
>> >> >>>
>> >> >>> I also forgot to say that writing to hdf-file will no longer
>> >> >>> work. If someone wants to work on making that work again then
>> >> >>> let me know.
>> >> >>>
>> >> >>> Jens Jørgen
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> You can find the work-in-progress code here:
>> >> >>>
>> >> >>>
>> >> >>> https://gitlab.com/gpaw/gpaw/merge_requests/83
>> >> >>> <https://gitlab.com/gpaw/gpaw/merge_requests/83>
>> >> >>>
>> >> >>>
>> >> >>> Help, question and comments are very welcome.
>> >> >>>
>> >> >>>
>> >> >>> Jens Jørgen
>> >> >>>
>> >> >>>
>> >> >>> _______________________________________________
>> >> >>> gpaw-users mailing list
>> >> >>> gpaw-users at listserv.fysik.dtu.dk
>> >> >>> <mailto:gpaw-users at listserv.fysik.dtu.dk>
>> >> >>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>> >> >>> <https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> --
>> >> >>> ------------------------------------------
>> >> >>> PD Dr Michael Walter
>> >> >>> Addresses:
>> >> >>> - Fraunhofer IWM, Wöhlerstrasse 11, D-79108 Freiburg i. Br., 
>> Germany
>> >> >>> Tel.: +49 761 5142 296
>> >> >>> - FIT Freiburg Centre for Interactive Materials and Bioinspired
>> >> >>> Technologies, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
>> >> >>> Tel: +49 761 203 95072
>> >> >>> email: Michael.Walter at fmf.uni-freiburg.de
>> >> >>> <mailto:Michael.Walter at fmf.uni-freiburg.de>
>> >> >>> www:
>> >> >>>
>> >> 
>> http://www.functional-nanosystems.uni-freiburg.de/People/PDWalter/group
>> >> >>> publications:
>> >> >>> http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
>> >> >>
>> >> >
>> >>
>>