Difference between revisions of "Structure Similarity"

From Wiki
Jump to: navigation, search
Line 33: Line 33:
== Examples ==
== Examples ==
* Diamond (mp-66) vs. GaAs (mp-2534) <math>\rightarrow</math>  ''d'' = 0
* Diamond ([https://materialsprpoject.org/mp-66 mp-66]) vs. GaAs ([https://materialsprpoject.org/mp-2534 mp-2534]) <math>\rightarrow</math>  ''d'' = 0
* Diamond (mp-66) vs. Rocksalt (mp-22862) <math>\rightarrow</math> ''d'' = 1.4
* Diamond ([https://materialsprpoject.org/mp-66 mp-66]) vs. Rocksalt ([https://materialsprpoject.org/mp-22862 mp-22862]) <math>\rightarrow</math> ''d'' = 1.4
* Diamond (mp-66) vs. Perfect CaTO<sub>3</sub> Perovskite (mp-5827) <math>\rightarrow</math> ''d'' = 1.4
* Diamond ([https://materialsprpoject.org/mp-66 mp-66]) vs. Perfect CaTO<sub>3</sub> Perovskite ([https://materialsprpoject.org/mp-5827 mp-5827]) <math>\rightarrow</math> ''d'' = 1.4
* Rocksalt (mp-22862) vs. Perfect CaTO<sub>3</sub> Perovskite (mp-5827) <math>\rightarrow</math> ''d'' = 1.1
* Rocksalt ([https://materialsprpoject.org/mp-22862 mp-22862]) vs. Perfect CaTO<sub>3</sub> Perovskite ([https://materialsprpoject.org/mp-5827 mp-5827]) <math>\rightarrow</math> ''d'' = 1.1
== References ==
== References ==

Revision as of 23:58, 7 March 2018


The similarity between two structures i and j is assessed on the basis of local coordination information from all sites in the two structures. [1] [2]

Site Fingerprints

The similarity calculation begins with computing a crystal site fingerprint, vsite, for each site in the two structures. The fingerprint is a 12-dimensional vector in which an element at position k (e.g., 4) provides the percentage of how much the given site should be considered k-fold coordinated (i.e., w(CN=4)):

\mathbf{v}^\mathrm{site} = [w(\mathrm{CN}=1), w(\mathrm{CN}=2), w(\mathrm{CN}=3), \dots, w(\mathrm{CN}=12)]^\mathrm{T}

So, we are testing the coordination percentages up to 12-fold coordination.

Structure Fingerprints

The fingerprints from sites in a given structure are subsequently statistically processed to yield the minimum, maximum, mean, and standard deviation of each coordination percentage. The resultant ordered vector defines a structure fingerprint, vstruct:

\mathbf{v}^\mathrm{struct} = [

\min(w(\mathrm{CN}=1)), \max(w(\mathrm{CN}=1)), \mathrm{mean}(w(\mathrm{CN}=1)), \mathrm{std}(w(\mathrm{CN}=1)), \dots,

\min(w(\mathrm{CN}=12)), \max(w(\mathrm{CN}=12)), \mathrm{mean}(w(\mathrm{CN}=12)), \mathrm{std}(w(\mathrm{CN}=12))


Structure Distance

Finally, structure similarity is determined by the distance, d, between two structure fingerprints vistruct and vjstruct:

d = || \mathbf{v}_{i}^\mathrm{struct} - \mathbf{v}_{j}^\mathrm{struct} ||

A small distance value indicates high similarity between two structures, whereas a large distance (around 1) suggests that the structures are very dissimilar. Note that the structure fingerprint vectors are normalized before calculating the distance measure.


  • Diamond (mp-66) vs. Perfect CaTO3 Perovskite (mp-5827) \rightarrow d = 1.4


  1. N. E. R. Zimmermann, A. Jain, in preparation (2018)
  2. N. E. R. Zimmermann, M. K. Horton, A. Jain, M. Haranczyk, Front. Mater., 4, 34, (2017)


Nils Zimmermann, Donny Winston