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Messages - Dori

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1
Support Forum / Re: minimum distance between two atoms
« on: June 28, 2019, 01:54:24 AM »
Hello Constanze,
Thank you so much for your response.

It totally makes sense that I need to put N=1 in order to find the nearest neighbor of a particle.
I am wondering if my dump file is sufficient to get the required output. My dump file includes:
ITEM: TIMESTEP
ITEM: NUMBER OF ATOMS
ITEM: BOX BOUNDS pp pp pp
ITEM: ATOMS id type xs ys zs

However I could see in the following link that  https://ovito.org/manual/python/modules/ovito_data.html#ovito.data.DataCollection
data collection file includes:
ParticleProperty and ParticleTypeProperty
SimulationCell
Bonds
BondProperty and BondTypeProperty
SurfaceMesh
DislocationNetwork

Mathematically, what is required is to select every two particles and calculate the value of SQRT[(x2-x1)^2+(y2-y1)^2+(z2-z1)^2]. So I am thinking only coordinates of atoms and atom id in my dump file would suffice to get the results. Do I need to build a data collection?

with thanks,
Dourna







2
Support Forum / Re: minimum distance between two atoms
« on: June 26, 2019, 08:11:27 PM »
Hello Mr. Stukowski,
Thanks for your response.

 I need to know which two atoms are closest to each other in my supercell and what is the shortest distance. If this can be done in Ovito, may I have a link to that Python modifier function?

3
Support Forum / minimum distance between two atoms
« on: June 25, 2019, 10:19:46 PM »
Hello OVITO users,
I need to know the minimum distance between two atoms inside my super crystal. Can this be done by adding a modification in OVITO?
Thanks,
Dori

4
Support Forum / Re: Accuracy of "create bonds" command
« on: January 29, 2019, 01:37:30 AM »
Dear Constanze,
Thank you for your questions.

In the attached word file, in fig. 1 the system is in a solid state and in fig.2 the system is in a liquid state. I have verified that by checking other factors that change for the solid and liquid. However, When I use the "create bonds" modification it creates bonds for both systems exactly the same way.

Best,
Dori

5
Support Forum / Re: add axis labels and ticks
« on: January 29, 2019, 01:00:57 AM »
Dear Constanze,
Thank you so much for your helpful comment.

I decided to export a text file and then add axes and labels in Python. However, I faced a problem trying to export the file.
I selected "particle trajectories" from the "object selector". Then:
File>> Export File. Gave a name to the file and save as "Calculation results text file".
In "Export setting", I selected "sequence".For "Destination", I selected "Single file". For "Attributes to export" there was only one option and it was "frame". So I selected that and then pressed ok. However, the text file only includes the frames. May I have your opinion please?

Best,
Dori

6
Support Forum / Accuracy of "create bonds" command
« on: January 28, 2019, 01:54:29 AM »
Hello everyone,

Does the command "create bonds" in OVITO "accurately" illustrates the bonds?

Thanks,
Dori

7
Support Forum / add axis labels and ticks
« on: January 28, 2019, 01:52:37 AM »
Hello everyone,

I have made a trajectory of a particle in a simulation box on OVITO [Fig.1] and I am wondering if I can add axis labels and ticks just like [Fig.2] in OVITO.

Thanks,
 Dori

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