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Messages - starmm11

Pages: [1] 2
1
Support Forum / Re: visualization of vectors by arrows
« on: August 07, 2018, 04:38:25 PM »
Thanks a lot for your answer! This completely solved my problem!

2
Support Forum / Re: visualization of vectors by arrows
« on: August 07, 2018, 03:47:21 PM »
Here are the examples of visualization with arrows that are supported in Ovito.
The bottom figure is the arrow which I want to use in my figures.


3
Support Forum / visualization of vectors by arrows
« on: August 07, 2018, 01:59:12 PM »
Hi!

I noticed that the vectors don't look like the arrows during visualization. They look more like lines
with circle at the end for the normal style and like small flat almost unnoticeable arrows for the flat style.
May be I'm doing something wrong. Anyway, is there any way to make a vector look more like a line with an arrow?

Regards
Ilya

4
Support Forum / Re: error reading XDATCAR files for npt simulations
« on: July 17, 2018, 02:13:20 PM »
Thank you very much for you work!

Regards,
Ilya

5
Support Forum / error reading XDATCAR files for npt simulations
« on: July 17, 2018, 01:30:04 AM »
Hi!

I did the ab initio molecular dynamics simulations in the VASP package with NPT thermostat. Within NPT thermostat
stress in the system is achieved on each time step by changing the coordinates of box. I got the output file
XDATCAR which contains both the atomic coordinates and the box coordinate matrix. However, I've got the error
message during reading XDATCAR in Ovito. I suppose that Ovito does not support XDATCAR files with changing
box coordinates.

Best,
Ilya

6
Support Forum / Re: problem with scipy package
« on: April 04, 2018, 01:32:55 PM »
Many thanks! I hope scipy package will be available in ovito 3.0!

7
Support Forum / Re: problem with scipy package
« on: April 01, 2018, 09:09:07 PM »
I tried Ovito 2.9 and 3.0 on Windows and had this problem.

8
Support Forum / problem with scipy package
« on: March 30, 2018, 05:24:41 PM »
Hi,

I successfully installed scipy package by "ovitos -m pip install scipy". However when I'm trying to use it, for example
by including "from scipy.interpolate import CubicSpline" it produces an error "numpy.core.multiarray failed to import".
If I try to upgrade numpy at this point by "ovitos -m pip install --upgrade numpy" I get the following error
"PermissionError: [Errno 13] Permission denied: '....numpy\\core\\multiarray.pyd'

How to resolve this problem?

9
Support Forum / Re: Python loading error
« on: November 23, 2017, 04:23:14 PM »
The first problem has been solved. Perhaps, I did not properly install Ovito from .zip archive.
After reinstalling it I could compile the code using "ovitos".

10
Support Forum / Python loading error
« on: November 23, 2017, 09:24:36 AM »
I tried to configure python interpreter on Windows.
1) I tried to compiled python script by using ovitos. I get the following error:

C:\Users\home\Documents\Python\OvitoAnalysis>ovitos analysis.py
Error while loading OVITO submodule ovito.vis.gui: <class 'ImportError'>
Traceback (most recent call last):
  File "D:\Program Files\Ovito\plugins\python\ovito\__init__.py", line 41, in <module>
    importlib.import_module(_name)
  File "D:\Program Files\Ovito\lib\importlib\__init__.py", line 109, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "D:\Program Files\Ovito\plugins\python\ovito\vis\gui\__init__.py", line 6, in <module>
    import PyScriptGUI
ImportError: No module named 'PyScriptGUI'
ERROR: Failed to initialize Python interpreter.

2) I used Anaconda + PyCharm and added folder Ovito\plugins\python to PYTHONPATH variable.
However, when I compiled .py script with "import ovito" it outputs
Traceback (most recent call last):
  File "C:/Users/home/Documents/Python/OvitoAnalysis/analysis.py", line 1, in <module>
    from ovito.io import *
  File "D:\Program Files\Ovito\plugins\python\ovito\__init__.py", line 19, in <module>
    from .plugins.PyScript import (version, version_string, gui_mode, headless_mode, DataSet, dataset, task_manager)
ImportError: DLL load failed: The specified procedure could not be found.

What have I missed or done wrong?


11
Support Forum / averaging stress
« on: November 22, 2017, 05:32:10 PM »
Hi,

I want to plot the stress tensor along the body by averaging atomic values of virial stress tensor
on small groups of atoms. Doing this in Lammps is complex as the number of atom groups is restricted.
Also when I simulate the body of fixed size, the problem of the volume evaluation arises.

How I can use Ovito for doing such thing?

 

12
Support Forum / Re: creating and manipulating geometry
« on: November 22, 2017, 04:23:44 PM »
I suppose that what you proposed in p. 4 is the answer on my question.
Actually, it would be easier to operate atoms "on fly" by clicking buttons on the panel. I just write my ideas:
  click on two atoms and get the distance between them,
  click on three atoms and get the angle.
  click on the atom and move it closer to the other atom.
  mark the region of atoms and move it somewhere
  mark the region and fill it with molecules
 

13
Support Forum / creating and manipulating geometry
« on: November 20, 2017, 02:50:13 PM »
I am insteresting if Ovito is being developed to contain funtional for manipulating and creating atomic configurations.
It would be very useful even the possibilities to move group of atoms or to add some atoms in the system.


14
Support Forum / Re: charge atom indexation ends on 99999
« on: November 20, 2017, 10:24:03 AM »
I used Packmol code for generating that .pdb file.

Thanks for the solution of my problem that used only Ovito's functions, I had to write short script for it before.

15
Support Forum / Re: charge atom indexation ends on 99999
« on: November 17, 2017, 12:00:15 PM »
Here is my compressed .pdb file.

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