pydseamslib.cyoda.clusterAnalysis

pydseamslib.cyoda.clusterAnalysis#

pydseamslib.cyoda.clusterAnalysis(path: str, iceCloud: pydseamslib.cyoda.PointCloudDouble, yCloud: pydseamslib.cyoda.PointCloudDouble, nList: List[List[int]], iceNeighbourList: List[List[int]], cutoff: float, firstFrame: int, bopAnalysis: str) → int#

Does the cluster analysis of ice particles in the system.

Parameters:

  • path (The file path of the output directory to which output files will be written)

  • iceCloud (The molSys::PointCloud for the largest ice cluster of the ice-like molecules)

  • nList (Row-ordered neighbour list by atom ID)

  • yCloud (The molSys::PointCloud for all the particles in the frame, regardless of ice type)

  • iceNeighbourList (Row-ordered neighbour list by atom index, not ID, according to the iceCloud atoms)

  • cutoff (Cutoff for the nearest neighbours)

  • firstFrame (The first frame to be analyzed)

  • bopAnalysis (This determines which method to use for determining the ice-like nature of the particles. This can be "q6" or "chill", for using the "q6" parameter or CHILL algorithm, respectively)

Contents