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Topics - leila

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1
Support Forum / Calculating the area of Voronoi faces
« on: June 12, 2019, 03:58:03 PM »
Hi all,

I need to calculate the surface area of Voronoi faces for all neighbors for every single atom. I was wondering whether I can use OVITOS.
Since VoronoiAnalysisModifier ignores any faces smaller than a threshold, it seems to me the algorithm calculates the surface area of each face. However, I am not sure how to dump these values.

Thanks
Leila

2
Support Forum / issue with importing matplot and ovito
« on: November 19, 2018, 05:27:19 PM »
Hi all,

I am trying to run a code using ovitos which has "import matplotlib.pyplot as plt" . However,  I get this error:

ImportError: /lib/x86_64-linux-gnu/libz.so.1: version `ZLIB_1.2.9' not found (required by /home/leila/anaconda3/lib/python3.6/site-packages/matplotlib/../../../libpng16.so.16)

Then I tried to add "export LD_LIBRARY_PATH=/home/leila/anaconda3/lib:$LD_LIBRARY_PATH" to my bashrc. But this time,  I got this error:

This application failed to start because it could not find or load the Qt platform plugin "xcb"
in "".
Available platform plugins are: minimal, offscreen, vnc, xcb.

Reinstalling the application may fix this problem.
Aborted

Thank you in advance,
Leila

3
Support Forum / sort_particles
« on: October 20, 2018, 11:18:38 PM »
Hi all,

I am using import_file (filename, sort_particles=True). However it is giving me this error:

node_1 = import_file (filename, sort_particles=True)
  File "/home/leila/Downloads/ovito-3.0.0-dev200-x86_64/bin/../lib/ovito/plugins/python/ovito/io/import_file.py", line 118, in import_file
    raise RuntimeError("Invalid keyword parameter. Object %s doesn't have a parameter named '%s'." % (repr(importer), key))
RuntimeError: Invalid keyword parameter. Object LAMMPSTextDumpImporter() doesn't have a parameter named 'sort_particles'.

I appreciate your help.

Regards,
Leila

4
Support Forum / Problem with export_file
« on: June 14, 2018, 04:21:03 PM »
Hi OVITO users,

I am very new to ovito. I tried to export the displacement magnitude of about 16000 atoms into txt file with this command:
export_file(node, "msd_data.%i.txt"%i,format = "txt", columns = ["Timestep", "MSD"], frame=i)

The problem is that it is just dumping 3 first and last numbers. For example:

# "Timestep" "MSD"
100 [ 0.2056347   0.39410666  0.37800705 ...,  0.33246541  0.34883693
  0.42290157]

I 'd appreciate your help.

Regards,
Leila

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