Author Topic: Creating histograms of bond lengths  (Read 589 times)

coffee4kepi

  • Newbie
  • *
  • Posts: 3
Creating histograms of bond lengths
« on: May 25, 2018, 04:20:11 AM »
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,

Aldo

Alexander Stukowski

  • Administrator
  • Hero Member
  • *****
  • Posts: 622
Re: Creating histograms of bond lengths
« Reply #1 on: May 25, 2018, 04:37:02 PM »
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.

-Alex

stl4

  • Newbie
  • *
  • Posts: 4
Re: Creating histograms of bond lengths
« Reply #2 on: March 11, 2019, 12:12:17 AM »
Hello,

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

  • Administrator
  • Sr. Member
  • *****
  • Posts: 290
Re: Creating histograms of bond lengths
« Reply #3 on: March 11, 2019, 05:27:57 PM »
Hello,

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.

-Constanze

stl4

  • Newbie
  • *
  • Posts: 4
Re: Creating histograms of bond lengths
« Reply #4 on: March 11, 2019, 11:20:04 PM »
Hello,

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!!

Sean

Constanze Kalcher

  • Administrator
  • Sr. Member
  • *****
  • Posts: 290
Re: Creating histograms of bond lengths
« Reply #5 on: March 12, 2019, 09:51:49 AM »
Hello Sean,

I can see that when you use the Compute property modifier to compute and store the new bond property called "Length" you assign values of 0 to every bond.
What you need to do is to edit the "Expression Field" and replace 0 by BondLength (which should also be visible in the list of available input parameters below the Expression Field).

-Constanze