I have two images from a Monte Carlo Basin Hopping where silicon (in yellow) is getting replaced by germanium (in blue). Both have 32 germanium atoms at Si/Ge = 2.5; only the Ge distribution is changing.

There appears to be a clustering of the germanium in the the first structure with relative energy= 0 ev. Whereas the higher energy structure has no such pattern. I am trying to to correlate the energy and the clustering.


How could I verify this layering/clustering, to correlate the energy and the clustering, using some sort of metrics?

Any of the following would be helpful for me.

  • Any links to any publication to gain ideas
  • Suggestion of a metric or parameter.
  • Any ML method or software that may help with this.

Thanks in advance.

enter image description here

  • 1
    $\begingroup$ Take a look at the ATAT software it may help. $\endgroup$
    – Camps
    Mar 17, 2023 at 21:02
  • $\begingroup$ @Camps Thanks, I have new to ATAT, would you care to explain a bit about how this may help? $\endgroup$
    – Saha_1994
    Mar 17, 2023 at 21:20
  • 1
    $\begingroup$ Would he "care" to? $\endgroup$ Mar 17, 2023 at 23:10
  • 2
    $\begingroup$ @Saha_1994 Literally all of your questions that have gotten answers are still left without any tick marks selected ! Would you mind taking a look at all your questions and mark the answers that answers your questions as accepted answer? This is the way this community is driven. $\endgroup$ Mar 18, 2023 at 8:04
  • 1
    $\begingroup$ two suggestions on the metric: (1) entropy, get probabilities from 3D histogram; (2) number of the shortest Ge...Ge paths of length (number of bonds between the atoms) 1, 2, 3, 4... $\endgroup$ Mar 20, 2023 at 17:08

1 Answer 1


It would be suggested to use molecular descriptors such as Distance matrix, Randic Connectivity Index, Wiener Index, etc as metrics to differentiate the two states.

In order to understand the concept of molecular descriptors, refer to presentation link and Chapter 3 Molecular Descriptors of book Challenges and Advances in Computational Chemistry and Physics (COCH,volume 8).

There are few softwares for calculation of Molecular descriptors of a system, one of them is PaDEL-Descriptor. Refer to paper: link to know more about the software.


You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .