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regarding RDF calculations

Hi,

I am using a coordination analysis modifier to calculate RDF of the composite system (2 types of atoms). A small portion of the simulation cell consists of type 1 and rest is type 2. type 1 is crystalline (FCC) and type 2 is amorphous. I am plotting RDF for type 1 before (crystal is FCC) and after deformation (crystal turn amorphous) but the RDF plots are not converging it to one as expected (after deformed sample).

When I calculate RDF for the entire model then I can see the RDF value is converging close to 1. But when I plot for just for one particular type (type 1 in my case) the RDF value is nowhere close to 1. How does the normalization system work for the composite models? Does number of atoms is always constant even when we perform coordination analysis after deleting one type of atoms? or coordination analysis is only performed for the final remaining atoms and its occupied volume?

Thank you.

Regards

Raghu

Hi,

The computed partial RDFs will be normalized such that the summation of the partial RDFs, weighted by the product of the two corresponding elemental concentrations, yields the total RDF, which converges to 1. See section Element-wise RDFs in the manual: https://www.ovito.org/docs/current/particles.modifiers.coordination_analysis.php.

If you delete atoms from the scene before performing the Coordination analysis, they will not be taken into account.

-Constanze

Hi Dr. Kalcher,

I understand if we delete the atoms before performing the coordination analysis, they will not be taken into account but what volume the analysis will be considered for normalization? the total volume of the simulation cell or just the volume of the particles remaining after the deletion of the atoms?

Regards

Raghuram

Hi,

it's the total cell volume that is considered in the normalization of the RDF, see

https://gitlab.com/stuko/ovito/-/blob/master/src/ovito/particles/modifier/analysis/coordination/CoordinationAnalysisModifier.cpp#L185

I'm not sure what you mean by "just the volume of the particles remaining after the deletion of the atoms". The cell size shouldn't be affected by any removal of atoms.
Let me know if this does not answer your question.

-Constanze

Hi Dr. Kalcher,

Thank you for the clarification. For some calculations, we just need the volume of the selected region. For simple geometries, we can calculate directly but for some complex geometries, it would be little challenging (we should use numerical models). I understand this is not the feature available right now but if its included in the newer versions could be great. Probably I might work on it. A possible solution is if we can re-mesh the surface of the atoms, we can calculate the volume of just the selected atoms.

Regards

Raghuram

 

Thank you for your explanation, in that case the Construct Surface Mesh Modifier might help you to calculate the volume of the selected region. https://www.ovito.org/docs/current/particles.modifiers.construct_surface_mesh.php

Then, in a next step, you could re-normalize the RDF through the python interface. Maybe you could try something along those lines:

from ovito.data import *

def modify(frame, data):
    cell_volume = data.cell.volume
    region_volume = data.attributes["ConstructSurfaceMesh.filled_volume"]
    rdf = data.tables['coordination-rdf']
    print( rdf.y*cell_volume/region_volume  )

You can copy this short modifier function into the Python script modifier editor in the GUI.

Let me know what you think,

Constanze