[ase-users] [ase-developers] Genetic algorithm added to ase
Jens Jørgen Mortensen
jensj at fysik.dtu.dk
Mon Mar 10 14:20:32 CET 2014
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
>>>
>>>
>>>
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>>
>>
>
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