[ase-users] Visualizing problem

[Albert Bruix Fusté]

Dear Sepideh,

I don´t know what your problem could be due to, but I still would advise you to create a fresh installation of ase. If you don't want to destroy previous installations, you always have the option to use virtual environments. This would be useful even if you use the fresher version just to visualize whatever structure you have constructed. Also, keep in mind that you can control the rotation of the images you generate with the write function.

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 <sepide.araban at gmail.com<mailto:sepide.araban at gmail.com>> del dia dj., 22 d’abr. 2021 a les 19:07:
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<mailto: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<mailto: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

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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.

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