[ase-users] Visualizing problem

[Sepide Araban]

Dear Jakob,
I am running on my own computer.  The SSH is disable or maybe even removed.
I have disabled that before.
Thank you for your reply and the information. I didn't know about that and
It is very useful information.

Best regards
Sepideh

On Fri, 23 Apr 2021, 11:27 Jakob Schiøtz, <schiotz at fysik.dtu.dk> wrote:

>
>
> > 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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