how to slice the lammps dump trajectory as a function of the nanoparticle's center of mass
Dear all,
I would like to slice the trajectory as a function of the moving nanoparticle's center of mass so that I can track the liquid flow condition at any time without worrying about the nanoparticle might move out of the slice plane.
I could not find any related information, can ovito do this?
Attachments contain the system setup view ( a nanoparticle immersed in a pool of liquids and there is a substrate at the bottom) and the corresponding trajectory.
Thank you very much!
Best,
Uploaded files:
Hi Dezhao,
yes, you can do that through the python scripting interface. Open the GUI of OVITO Pro, insert a python script modifier into your pipeline and try the following script as an example:
from ovito.data import *
from ovito.modifiers import SelectTypeModifier, ClusterAnalysisModifier, SliceModifier, InvertSelectionModifier, ClearSelectionModifier
def modify(frame, data):
data.apply(SelectTypeModifier(property = 'Particle Type', types = {2}))
data.apply(ClusterAnalysisModifier(compute_com = True, only_selected = True, cutoff = 4. ))
data.apply(InvertSelectionModifier())
cluster_com = data.tables['clusters']['Center of Mass'][0]
data.apply(SliceModifier(normal = (0,1,0), distance = cluster_com[1], only_selected = True ))
data.apply(ClearSelectionModifier())This script will compute the center of mass of the nanoparticle, which you can pass to the SliceModifier as "distance" argument.
Let me know if you have questions.
-Constanze
Uploaded files:
Thank you very much, Constanze!
This is very helpful!
Best,
Dezhao