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How to obtain the coordination number?

Hi, everyone!

1.I did a coordination analysis first, and then color coding by coordination(see Figure 1). I want to know the coordination number corresponding to atoms of different colors (like Figure 2).

2.I obtained the radial distribution function(RDF) through coordination analysis. My workpiece is Al. Here I don’t konw how to select the cutoff radius and what does the fluctuation of g(r) peak mean?

Yours Sincerely,

YuCheng Xue

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Dear YuCheng,

1. The per-atom coordination number is a particle property that you have computed with the Coordination analysis modifier. You will see an extra column "Coordination" appear if you open the Data Inspector->Particles Tab between the viewport windows and the time slider.
You can use this property to color your atoms. You have different options here:

Workflow 1:

As an example, let's say you want to color all atoms in a specific color that have a coordination number of 3. First, you would add an Expression Selection Modifier with the expression "Coordination==3" to your pipeline. Second, add an Assign Color modifier and select the color of your choice to be applied to the selection of atoms you created in the previous step.
This procedure can be repeated for different conditions by adding as many Expression selection modifiers and Assign Color modifiers to your pipeline as you need.

Workflow 2:

Alternatively, you can design your own custom color map with an external program and import this as a *png, *jpg or *jpeg file into OVITO's Color coding modifier. Simply choose "Load custom color map" in the Color gradient settings.

Workflow 3:

Another alternative would be to use a custom python script modifier. Add a Python script modifier to your pipeline and paste e.g. the following script into the script editor.

from ovito.data import *
import numpy as np

def modify(frame, data):
   coord_property = data.particles["Coordination"]
   color_property = data.particles_.create_property("Color", data = np.ones((data.particles.count,3)))
   #Coordination 3 - green
   color_property[coord_property == 3] = (0,1.,0.7267)
   #Coordination 7 - blue
   color_property[coord_property == 7] = (0.4438, 0.25,  1.)
   #Add more

2. The cutoff radius you choose controls the x-axis ( the maximum pair separation distance) in your g(r) plot. What do you mean by "fluctuation"?
If you're unfamiliar with the concept of the radial distribution function please see https://en.wikipedia.org/wiki/Radial_distribution_function.

-Constanze

Dear Constanze,

Thank you very much for your detailed explanation!

I select all the atoms whose coordination number is 33(see figure 4). However, this is obviously abnormal, why does this happen? Need to be normalized in the "coordination analysis" step before the "Expression selection"?

Yours sincerely,

YuCheng

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Dear YuCheng,

from your last screenshot in your first post I can see that you included neighboring atoms up to the third neighbor shell into your analysis. In an ideal FCC crystal that would be 12 nearest neighbors + 6 next-nearest neighbors + 24 neighbors in the third shell. So finding a coordination number of 33 should not be abnormal especially for the atoms close to the surface.

If you want to analyze how many neighbors can be found in the first neighbor shell only, you should choose a cutoff radius value that only includes the first (nearest-neighbor) peak. You can use your g(r) plot or the Data table tab in the Data inspector to determine the value.

You might also find the manual section about the Coordination modifier helpful.

-Constanze

Dear Constanze,

Your explanation enlightened me, thank you very much!

My job is to do a simulation of a abrasive particle hitting a workpiece, i want to 0bserve the atoms that change phase at different times due to impact. In the first picture(see figure5), the abrasive particles have not hit the workpiece, there are a total of 4034 particles with the structure "other". At different times, in the second picture(see figure6), there are 5272 atoms with the structure name "other". so the atoms that change phase can be calculated as "5272+3-4034 = 1241"? In addition, is it necessary to avoid the "other" structure in this situation?
Yours sincerely,
YuCheng

 

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