[ase-users] Some glitches in ASE-3.15.x

[Jens Jørgen Mortensen]

Den 23-01-2018 kl. 16:20 skrev Chang Liu:
> Hi,
>
> Here is a sample of the input:
> "
> ...
> slab = fcc100('Cu', a = 3.67, size = (2,2,4), vacuum = 7.)
> slab.pbc = 1
>
> add_adsorbate(slab,'O',-1.84,'ontop')
>
> CO =Atoms('CO',positions = [(0,0,0),(0,0,d)])
> add_adsorbate(slab,CO,2.05,'ontop')
>
> c = FixAtoms(mask=[atom.tag > 2 for atom in slab])
> slab.set_constraint(c)
>
> mixer = Mixer(0.1, 5, weight = 100.0)
> calc = GPAW(h=0.2,
>          kpts = (4,4,1),
>          xc = 'RBPE',
>          txt = '%s_%s_%s_gpaw.out' % (name,surf,task),
>          poissonsolver = PoissonSolver(nn = 3),
>          stencils = (3,3),
>          symmetry = {'point_group':False},
>          #eigensolver = 'rmm-diis',
>          mixer = mixer,
>          maxiter = 250,
>          occupations = FermiDirac(0.1)
> )
>
> slab.set_calculator(calc)
> dyn = MDMin(slab, trajectory='%s_%s_%s.traj' % (name,surf,task), dt=0.05, logfile='%s_%s_%s.log' % (name,surf,task))
> dyn.run(fmax=0.05)
> ...
> "
> After running this calculation, when reading the trajectory file produced by the optimizer with ase gui (3.15.x), I cannot use the repeat function in it. Nothing happens if I try and there is no error message. If I try with 3.9.1, it works fine. Thanks.

Hmm.  I can't reproduce this.  Can you send me the trajectory file? And 
"Help->About" says 3.15.0 ?

Jens Jørgen

>
>
> Best wishes,
> Chang Liu
> ----------------------------------------------------------
>                          Chang Liu
>                         PhD student
> Fysikum, Albanova, Stockholm University
>         S-106 91 Stockholm, Sweden
>                   +46 767159891
>      http://xsolasgroup.fysik.su.se/
>
> ________________________________________
> From: Jens Jørgen Mortensen <jjmo at dtu.dk>
> Sent: Tuesday, January 23, 2018 4:05 PM
> To: Ask Hjorth Larsen
> Cc: Chang Liu; ase-users at listserv.fysik.dtu.dk
> Subject: Re: [ase-users] Some glitches in ASE-3.15.x
>
> On 01/22/2018 04:33 PM, Ask Hjorth Larsen wrote:
>> Hi,
>>
>> 2018-01-22 13:16 GMT+01:00 Jens Jørgen Mortensen via ase-users
>> <ase-users at listserv.fysik.dtu.dk>:
>>> On 01/22/2018 11:33 AM, Chang Liu via ase-users wrote:
>>>> Hello again,
>>>>
>>>>
>>>> I am sorry for expressing the second problem in a wrong way. It is
>>>> actually "the non-pickle trajectory files created with the 3.15.x versions
>>>> cannot be visualized by older versions like 3.9.1."
>>>>
>>> Thanks you for your feedback.
>>>
>>> We are working on your glitch number 1 here:
>>>
>>>       https://gitlab.com/ase/ase/merge_requests/682
>> I did not quite understand this one - so this is only when there are
>> cached results on the calculator?  Repetition in 'normal' cases seems
>> to work.
> OK, I see.  Chang:  How exactly do you get it to fail?  And what is the
> error message if any?
>
> Jens Jørgen
>
>>> Glitch number 2: We could try to fix that in the next release, but I can't
>>> promise anything.
>> Is it a big problem that new trajectories are not readable with old
>> versions?  This is a difference of 6 releases after all.
>>
>> Best regards
>> Ask
>>
>>> Jens  Jørgen
>>>
>>>> Best wishes,
>>>> Chang Liu
>>>> ----------------------------------------------------------
>>>>                           Chang Liu
>>>>                          PhD student
>>>> Fysikum, Albanova, Stockholm University
>>>>          S-106 91 Stockholm, Sweden
>>>>    +46 767159891
>>>> http://xsolasgroup.fysik.su.se/
>>>> ------------------------------------------------------------------------
>>>> *From:* ase-users-bounces at listserv.fysik.dtu.dk
>>>> <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Chang Liu via
>>>> ase-users <ase-users at listserv.fysik.dtu.dk>
>>>> *Sent:* Monday, January 22, 2018 9:52 AM
>>>> *To:* ase-users
>>>> *Subject:* [ase-users] Some glitches in ASE-3.15.x
>>>>
>>>> Hello,
>>>>
>>>>
>>>> There are 2 glitches in the ASE-3.15.x versions (both stable and dev):
>>>>
>>>>
>>>> 1. The ase gui cannot repeat the visualized structure as previous version.
>>>> (-r x,y,z can do the same thing though)
>>>>
>>>>
>>>> 2. The non-pickle trajectory files created with older versions like 3.9.1
>>>> cannot be visualized by 3.15.x. When doing so, the following error pops out:
>>>>
>>>> "
>>>>
>>>> /IndexError: list index out of range/
>>>> /To get a full traceback, use: ase-gui --verbose/
>>>> /"/
>>>> Thank you very much!
>>>>
>>>>
>>>>
>>>> Best wishes,
>>>> Chang Liu
>>>> ----------------------------------------------------------
>>>>                           Chang Liu
>>>>                          PhD student
>>>> Fysikum, Albanova, Stockholm University
>>>>          S-106 91 Stockholm, Sweden
>>>>        +46 767159891
>>>> http://xsolasgroup.fysik.su.se/
>>>>
>>>>
>>>> _______________________________________________
>>>> ase-users mailing list
>>>> ase-users at listserv.fysik.dtu.dk
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