Mounting site scanning module

This module serves for the scanning of all possible mounting site in a given structure with a specified bonding distance. The locations and coordination numbers of the sites will be reported.

Input

The input to the module includes:

1. A structure, in the .cell format.
2. The desired bonding distance, in angstrom.

Output

A table of the xyz coordinates of the sites and coordination numbers.

Development

• Read-in a cell
• Analyze the structure with kd-tree
• Search the space around each atom by a given bonding distance
• 3d geometry problem
  • Representation of sphere-sphere intersection: the circular curve
  • Solvation of the intersection of the curves: two-points
• Whole intersect determination workflow
  • Build spheres for each coordinate points in kd-tree
  • Iterate the sphere kd-tree, check intersections, build circles
  • From the circles kd-tree, find intersection points between circles
  • Each found point will be added into a vec with a counting index, if next found intersect point between circles repeats with the previously found one, add counting index.
  • Summarize the number of spheres, circles, and points. Sphere-1 C.N., circle-2 C.N., points-at least 4
• Limit bondlength to 2 Å? Or the results will not be practical.
• Report in a more detailed and reasonable manner
• Package

Bug investigations

• Incorrect sphere intersections of circles (Fixed on May 2nd)
• Check if we need to consider more spheres/circles/points with equal distance/close distance, instead of finding just the nearest one to each coord. (Done on June 10th)
  • Sphere stage: using 2 * desired bonding distance
  • Circle stage: iterate through.
• Bondlength includes the atomic radius of elements: Use Materials Studio's bonding criteria to exclude impractical bonding possibilities. (Done on June 10th)
• Limit bondlength to 2-3 Å? Or determined by tolerance like Material Studios: ideal bondlength *min_tolerance < ideal bondlength < ideal bondlength *max_tolerance (Done on June 10th)
• A "blacklist" of elements could be necessary to avoid considering impractical bonding combos. (June 12th)