[ase-users] Visualizing problem

[Sepide Araban]

Dear Albert,
Thank you very much for your reply. Earlier, when I closed the terminal and
reopened it , It worked but now, I have to restart the computer. It seems
that some variables are not removed from the RAM memory properly. Is there
any code that clean all variables produced by python and ASE and ... of
RAM. I think something remains in RAM even if I close the windows. These
days because of a university project (as a student) I can't risk to
reinstall ASE and gpaw so I need a simpler or replacements solutions or
repairing that mentioned library for example without any main changes. I
can write the structure to a PNG file but it just covers one angle of view,
I need to rotate the structure. Please help me with this.

Best regards
Sepideh

On Thu, 22 Apr 2021, 12:03 Albert Bruix Fusté, <abruix at ub.edu> wrote:

> Dear Sepideh Araban,
>
> I have copied and run your script (removing all gpaw imports) and it works
> fine, showin the three images every time.
> I do not think this is a problem with ASE. There is probably a problem
> with the tkinter library. I would just try to do a fresh install of ase and
> its dependencies with the latest versions for all.
>
> Best wishes,
>
> Albert
>
> Albert Bruix - Beatriu de Pinós Fellow
> Institut de Química Teòrica i Computacional (IQTC-UB)
> Departament de Química-Física. Universitat de Barcelona
>
>
> Missatge de Sepide Araban via ase-users <ase-users at listserv.fysik.dtu.dk>
> del dia dj., 22 d’abr. 2021 a les 2:40:
>
>> Dear ASE users,
>> I have a problem with visualizing I would appreciate if you solve it.
>> When I using "view" it sometimes works and sometimes does not work. It
>> sometimes shows one image less than what I used in my script. Here is the
>> one script for example(I created it from a part of a bigger script and run
>> it), I turned on the computer and run the script, it worked and showed 3
>> images. I closed the windows and  run the script for the second time, it
>> showed nothing (no windows, no errors, no messages). It seems that I have
>> to restart the computer every time in order for it to work. I run the
>> script in serial mode.
>> Does 'view' work in parallel mode? And how can I solve the problem?
>>
>> «««««««««
>> from ase import Atoms, io, o ptimize
>> from gpaw import GPAW, FermiDirac
>> from gpaw.cluster import Cluster
>> from gpaw.lrtddft import LrTDDFT
>> from ase.cluster.cubic import BodyCenteredCubic
>> from ase.visualize import view
>> import numpy as np
>> a0=.53#.053nm
>> n=20
>> d = n*a0 # starting distance
>> #Na particle
>> surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)]
>> layers = [1, 5, 5]
>> lc = 4.28#0.428nm
>> atoms1 = BodyCenteredCubic('Na', surfaces, layers, latticeconstant=lc)
>> view(atoms1)
>> positions1=atoms1.get_positions()
>> positions2=positions1
>> positions2[:,2]=positions2[:,2]+d
>> positions1=atoms1.get_positions()
>> d=Atoms('Na9',positions2)
>> dp=d.get_positions()
>> view(d)
>> positions3=np.vstack((positions1,positions2))
>> c=Atoms('Na18',positions3)
>> cp=c.get_positions()
>> view(c)
>> #s = Cluster(symbols='Na18',positions=cp)
>> #view(s)
>> ««««««««
>>
>> I don't know if the information is enough or  there are some other
>> necessary professional Linux or python scripts. I hope that it would be
>> enough. Please let me know if it's not.
>>
>> Best regards
>> Sepideh Araban
>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>
>
> Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir
> informació confidencial o protegida legalment i s’adreça exclusivament a la
> persona o entitat destinatària. Si no consteu com a destinatari final o no
> teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo,
> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si
> l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant
> el missatge com els fitxers adjunts que hi pugui haver.
>
> Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener
> información confidencial o legalmente protegida y está exclusivamente
> dirigido a la persona o entidad destinataria. Si usted no consta como
> destinatario final ni es la persona encargada de recibirlo, no está
> autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a
> revelar su contenido. Si lo ha recibido por error, informe de ello al
> remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos
> que pueda contener.
>
> This email message and any attachments it carries may contain confidential
> or legally protected material and are intended solely for the individual or
> organization to whom they are addressed. If you are not the intended
> recipient of this message or the person responsible for processing it, then
> you are not authorized to read, save, modify, send, copy or disclose any
> part of it. If you have received the message by mistake, please inform the
> sender of this and eliminate the message and any attachments it carries
> from your account.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20210422/6f5448a4/attachment.htm>