Author Topic: Visulaise the Molecule in dump xyz lammps file  (Read 41 times)

jaguarjom123

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Visulaise the Molecule in dump xyz lammps file
« on: May 10, 2019, 07:48:22 AM »
Dear Ovito and users,
Sorry to post my question here but I can't post in a new thread can you tell me how to post my future new question on OVITO?

My question is I have (H2O)+H2+O2+ Pt, structure (i.e Pt nanoparticle immersed inside the solvent ),
some type of molecules will be formed, I can get only the number and type of molecules formatted by lammps but I can't extract the (x,y,z) for those molecules. I still have the dump.xyz file which includes all atoms in the structure and molecules, so may I know please how can I use OVITO to only extract the molecules formed and visualize them (which can be like the diffusion of those molecules also), for example, the formation of  H2O3 or HO, which only form near the surface of Pt?
I tried to use "creat-bond" and then "Cluster" analysis, but cannot get to know how to proceed further,

looking to your help and support

Thank you

Constanze Kalcher

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Re: Visulaise the Molecule in dump xyz lammps file
« Reply #1 on: May 10, 2019, 11:23:26 AM »
Dear jaguarjom123,

no worries, I opened a new topic for you. In principle you can just click on "New Topic" on the Forum main page, and after if is approved by an admin it will be visible to the public.

It is a little difficult to help you without having detailed information on your system, so if you like you can upload an example file here in the forum using the "Attachements" function below the text-editor. That way I can have a look at your system and give you more specific advice.
But as a starting point: You said that your data includes molecule ID's. Note that you can use the Expression selection modifier to select molecules based on their ID's then and even delete all other atoms from the scene. Furthermore, you could calculate the center of mass of each molecule and e.g. use the Generate trajectory lines modifier to visualize their trajectories. You could also use a custom Python script modifier to calculate mean squared displacement etc.
Let me know if you have questions regarding any of those analyses.

-Constanze
« Last Edit: May 10, 2019, 11:25:05 AM by Constanze Kalcher »

jaguarjom123

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Re: Visulaise the Molecule in dump xyz lammps file
« Reply #2 on: May 10, 2019, 07:08:53 PM »
thank you for your reply,
yes I have for example this kind of data (it included several time frames of the x,y,z coordinated of particles) as in attachment 1
in attachment number 2 it is one of the time steps of the structure image I have,
this structure must include many molecules which formed over time, I do interested in specific types which are near and close to the surface of the material in the middle.
looking for your guidance and help

Constanze Kalcher

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Re: Visulaise the Molecule in dump xyz lammps file
« Reply #3 on: May 13, 2019, 11:47:23 AM »
Hi,

so do you still need to identify the molecules that formed (i.e. which atoms belong to which molecule), or do you have that information in your xyz file? If not, you probably first need to use the "Create bonds" modifier to
take care of that:
https://ovito.org/manual_testing/particles.modifiers.create_bonds.html
Then, you could select the atoms in the center and again use a bond-based criterion, or a Compute property modifier to count the molecules in the vicinity of your selected atoms.

In any case, I need to see the data to give you more specific input.
-Constanze

jaguarjom123

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Re: Visulaise the Molecule in dump xyz lammps file
« Reply #4 on: May 19, 2019, 05:28:43 AM »
Dear Constanze Kalcher
Thank for your reply,
I have applied those modifiers in this order:
"Creat Bonds"
Then I  choose "Expression select" --> "ParticleType==4"
then I applied to "compute properties" but then how can apply the conditions
like what shall I choose  for example is "Molecule Identifier" is the correct to show molecules only,
and then how to delete other atoms and visualize those molecules?
here I attached some steps of my structure "extracted2", my original structure is much larger, so I hope this can be uploaded,
looking at your reply and guidance soon
Thank you
« Last Edit: May 19, 2019, 06:05:37 AM by jaguarjom123 »