AverageBondAngle

Matminer
#1

Dear Anubhav and Matminers,

I write for help with the class “site.AverageBondAngle”.

We are working on binary alloy structures AB, and be able to use that class,

with its “featurize” method and/or “SiteStatsFingerprint” featurizer, to obtain the BondAngle data.

However, when compared to the data from our code, there seems to be differences, e.g. for B1AB2 bond-angles, where B1 and B2 are identified as two nearest neighbor atoms of A.

I would appreciate if you could help with the issue and more about how the class “site.AverageBondAngle” works

(the current matminer documentation comes with a rather short description and no example for this topic?)

Sincerely,

Phong Pham

#2

Hi Logan,

You are listed as the implementor for the AverageBondAngle featurizer, would you be able to take a look at your convenience?

Phong - do you have an example structure (e.g. CIF file or Materials Project id) that you can share, along with (i) the expected answer for average bond angle and (ii) what matminer gives instead? A code example would be helpful, especially so we can see what NearNeighbor method you are using. It’s possible the disagreement is due to different definitions of neighbor atoms.

···

Best,
Anubhav

#3

Hello Phong,

Sorry for the delay in replying to you.

The average bond angle works with the following algorithm:

  1. Identify that are nearest neighbors to a certain atom. Uses one of pymatgen’s NearNeighbors classes
  2. For each pair of neighbor, compute the angle formed by the one atom in the pair, the central atom, and the other atom.
  3. Find the minimum bond angle for each atom across the angle between that atom and all other atoms
  4. Report the average across all bonded atoms

This is the algorithm that my colleague, Rui, and I came up with following this paper by DeJong et al.

I second Anubhav’s questions: Can you give me an example of where matminer gives different results than your code?

Logan

···

From: Anubhav Jain
Sent: Monday, September 9, 2019 12:27 PM
To: Phong Pham; Logan Ward
Cc: matminer
Subject: Re: AverageBondAngle

Hi Logan,

You are listed as the implementor for the AverageBondAngle featurizer, would you be able to take a look at your convenience?

Phong - do you have an example structure (e.g. CIF file or Materials Project id) that you can share, along with (i) the expected answer for average bond angle and (ii) what matminer gives instead? A code example would be helpful, especially so we can see what NearNeighbor method you are using. It’s possible the disagreement is due to different definitions of neighbor atoms.

On Sat, Sep 7, 2019 at 4:33 AM Phong Pham [email protected] wrote:

Dear Anubhav and Matminers,

I write for help with the class “site.AverageBondAngle”.

We are working on binary alloy structures AB, and be able to use that class,

with its “featurize” method and/or “SiteStatsFingerprint” featurizer, to obtain the BondAngle data.

However, when compared to the data from our code, there seems to be differences, e.g. for B1AB2 bond-angles, where B1 and B2 are identified as two nearest neighbor atoms of A.

I would appreciate if you could help with the issue and more about how the class “site.AverageBondAngle” works

(the current matminer documentation comes with a rather short description and no example for this topic?)

Sincerely,

Phong Pham

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Best,
Anubhav

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