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

Wed Nov 2 14:35:51 CET 2016

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

>
> 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
>> >>
>> >
>>