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

[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.


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
>>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
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