[ase-users] [ase-developers] Genetic algorithm added to ase
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Mon Mar 10 15:20:40 CET 2014
Den 10-03-2014 15:19, Lasse Vilhelmsen skrev:
> In principle it should be possible to change it to using the ase.db
> interface. All data communication happens through the module data.py,
> so the change is fairly isolated. I will try looking into it.
Great! The ase.db module is quite new so we may need to add some new
features or look at performance for ga stuff. Let me know if you run
into problems.
Jens Jørgen
>
> /Lasse
>
> On 10/03/2014, at 14.20, Jens Jørgen Mortensen <jensj at fysik.dtu.dk
> <mailto:jensj at fysik.dtu.dk>> wrote:
>
>> Den 27-02-2014 15:38, Lasse Vilhelmsen skrev:
>>> Hi Marcin,
>>>
>>> Thank you for adding the branch to the test build system. I have
>>> added a number of tests to the folder you suggested which verifies
>>> that essential parts of the GA work as intended. I have just
>>> committed the tests to the svn and the buildbot has given them the
>>> all clear :)
>>>
>>> Concerning your comment about how to refer to py scripts in the
>>> documentation and the location for these I am a bit confused. If I
>>> look through the other tutorials in doc/tutorials most of them
>>> reference py scripts located in doc/tutorials using the ..
>>> literalinclude:: syntax. I therefore take it that is the correct way
>>> to include py samples in the tutorials?
>>>
>>> The tutorial scripts I have created serve as full examples of the GA
>>> and they therefore take quite some time to execute and they should
>>> therefore not be considered tests.
>>
>> I see that the new GA stuff uses an SQLite database. Could the new
>> ase.db module be used instead?
>>
>> https://wiki.fysik.dtu.dk/ase/ase/db/db.html
>>
>> Jens Jørgen
>>
>>>
>>> Best Regards
>>> Lasse
>>>
>>> On 27/02/2014, at 11.40, Marcin Dulak <Marcin.Dulak at fysik.dtu.dk
>>> <mailto:Marcin.Dulak at fysik.dtu.dk>> wrote:
>>>
>>>> Hi,
>>>>
>>>> On 02/27/2014 11:22 AM, Lasse Vilhelmsen wrote:
>>>>> Hi Michael,
>>>>>
>>>>> It was Jens Jørgens suggestion to first put it in a separate
>>>>> branch to let people test it out before moving it into the trunk
>>>>> version.
>>>>>
>>>>> I have already updated the optimize.rst file in the ga branch with
>>>>> a short description of the method and a reference to the tutorial.
>>>>>
>>>>> I am unsure when it is an appropriate step to move the code from
>>>>> the branch to the trunk, but I assume that a few need to test it
>>>>> out first to ensure the high quality of the code in the trunk.
>>>> your branch is now added to automatic testing
>>>> athttps://ase-buildbot.fysik.dtu.dk/waterfall
>>>> Please do not add python scripts to documentation - they should be
>>>> part of the running tests,
>>>> and only referred to in the rst file using :svn:.
>>>> Seehttps://wiki.fysik.dtu.dk/ase/ase/calculators/abinit.htmlfor an
>>>> example.
>>>> Consider also creating a special ase/test/ga subdirectory.
>>>> The tests must be fast - few seconds max.
>>>>
>>>> Best regards,
>>>>
>>>> Marcin
>>>>
>>>>>
>>>>> Best Regards
>>>>> Lasse
>>>>>
>>>>> On 27/02/2014, at 10.59, Michael Walter
>>>>> <Michael.Walter at fmf.uni-freiburg.de
>>>>> <mailto:Michael.Walter at fmf.uni-freiburg.de>> wrote:
>>>>>
>>>>>> Dear Lasse,
>>>>>>
>>>>>> great that there is a genetic algorith in ase now !
>>>>>>
>>>>>> I suggest to put the algorithm to trunk and add the explanation
>>>>>> (or the link) to the list of global optimization agorithms:
>>>>>> https://wiki.fysik.dtu.dk/ase/ase/optimize.html#global-optimization
>>>>>>
>>>>>> Best,
>>>>>> Michael
>>>>>>
>>>>>>
>>>>>> 2014-02-27 9:50 GMT+01:00 Lasse Vilhelmsen<lassebv at phys.au.dk
>>>>>> <mailto:lassebv at phys.au.dk>>:
>>>>>>
>>>>>> Dear ase-users and ase-developers,
>>>>>>
>>>>>> I have in the past couple of years developed and used a
>>>>>> genetic algorithm for global structure optimization within
>>>>>> ase. The method has been used for the optimization of metal
>>>>>> clusters and oxide structures both on supported surfaces, in
>>>>>> metal organic frameworks and in vacuum. The method implements
>>>>>> the cut-and-splice pairing operator by Deaven and Ho, a set
>>>>>> of different mutations, a way to verify if two structures are
>>>>>> equal, a starting population generator and a population that
>>>>>> can propose structures to pair. The method works with all
>>>>>> calculators in ase and it has especially been developed for
>>>>>> parallel execution of multiple local relaxations
>>>>>> simultaneously using first principles calculations.
>>>>>>
>>>>>> The code is currently located in the svn branch ga of ase.
>>>>>> The entire genetic algorithm code is located in
>>>>>> ase/optimiize/genetic_algorithm with a tutorial describing
>>>>>> the method in the documentations section.
>>>>>>
>>>>>> My hope is that some of you might have an interest in trying
>>>>>> the method and giving some feedback on what aspects of the
>>>>>> implementation you find intuitive and easy to use, and which
>>>>>> parts of the method you find counter intuitive and weird. The
>>>>>> reporting any sorts of bugs are of course also very much
>>>>>> appreciated!
>>>>>>
>>>>>> I have compiled the current version of the tutorial and
>>>>>> published it on the following link for easy reference. This
>>>>>> tutorial is the optimal way to start using the method, since
>>>>>> it includes full test examples:
>>>>>> http://users-phys.au.dk/lassebv/ga_optimize.html
>>>>>>
>>>>>> The ga branch of ase can easily be obtained using the
>>>>>> following command
>>>>>> svn co https://svn.fysik.dtu.dk/projects/ase/branches/ga
>>>>>>
>>>>>> I look forward to any feedback you might have!
>>>>>>
>>>>>> Best Regards
>>>>>> Lasse
>>>>>>
>>>>>> _______________________________________________
>>>>>> ase-users mailing list
>>>>>> ase-users at listserv.fysik.dtu.dk
>>>>>> <mailto:ase-users at listserv.fysik.dtu.dk>
>>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------
>>>>>> PD Dr Michael Walter
>>>>>> Address: Fraunhofer IWM
>>>>>> Wöhlerstrasse 11
>>>>>> D-79108 Freiburg i. Br.
>>>>>> Germany
>>>>>> Tel.: +49 761 5142 296
>>>>>> email:Michael.Walter at fmf.uni-freiburg.de
>>>>>> <mailto:Michael.Walter at fmf.uni-freiburg.de>
>>>>>> www:http://omnibus.uni-freiburg.de/~mw767
>>>>>> <http://omnibus.uni-freiburg.de/%7Emw767>
>>>>>> publications:http://scholar.google.com/citations?user=vlmryKEAAAAJ&hl=en
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ase-users mailing list
>>>>> ase-users at listserv.fysik.dtu.dk
>>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>>>
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ase-developers mailing list
>>> ase-developers at listserv.fysik.dtu.dk
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-developers
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20140310/b733502f/attachment.html>
More information about the ase-users
mailing list