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

[Jens Jørgen Mortensen]

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
>>
>