[ase-users] Visualizing problem

[Jakob Schiøtz]

> On 22 Apr 2021, at 19.07, Sepide Araban via ase-users <ase-users at listserv.fysik.dtu.dk> wrote:
> 
> 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.

Are you running on your own computer, or do you log on to another computer with ssh?

The default ssh setup only forwards new windows for the first 20 minutes after you log in, for "security reasons".  Most linux distributions fix that in a configuration file, but some Linux distributions and MacOS leaves it that way (I do not know about Windows).

If that is the case, find (or create) the file $HOME/.ssh/config and add these lines to it:

Host *
    ForwardX11 yes
    ForwardX11Timeout 36000

Note that I have no clue whether this is related to your problem, but it could be.


Best regards

Jakob



> 
> 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
> 
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