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Creating histograms of bond lengths

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Hi all,

I am trying to create an histogram of bond lengths (starting from a VASP XDATCAR_* set of files), but I am not able to do it.
With v2.9 I compute the bonds with the proper modifier, select the species and cutoff  I like, go to histogram, select to operate on bonds, but then the property list is empty.
With v3.0_dev190 I am not even able to select the compute bond modifier, which is grayed and non-selectable (even in the histogram panel).

What am I missing here?

Thank you in advance,


Alexander Stukowski:
Dear Aldo,

I think you forgot to add the Compute bond lengths modifier. At least you didn't mention it in your description.

This modifier needs to be inserted after the Create Bonds modifier, and before the Histogram modifier. The Create Bonds modifier only creates bonds but doesn't compute their lengths.



I too am having trouble creating a histogram of bond lengths. I used the following modifiers Create Bond, Compute property, and Histogram. I defined a uniform cutoff radius and left the lower cutoff at 0. Then selected bond length to operate on under compute property. Unfortunately when I generate the histogram for bond length all lengths are shown to be 0. Any suggestions would be greatly appreciated!

Constanze Kalcher:

it's difficult to judge what goes wrong without seeing a screenshot but maybe  your uniform cutoff parameter in the Create Bonds modifiers is too small so no bonds are generated in the first place. Alternatively it could be a syntax mistake in your Compute property modifier. Feel free to upload a screenshot of the modifiers here, then I can help you.



I have attached some images of the modifiers, however I don't believe that the uniform cutoff parameter is too small because even with a cutoff of 1.7 I have 32 bonds. I believe the error might be in the compute property modifier, but I'm not sure what I should change.

Thank you for your help!!



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