cluster.hpp

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//-----------------------------------------------------------------------------------
// d-SEAMS - Deferred Structural Elucidation Analysis for Molecular Simulations
//
// Copyright (c) 2018--present d-SEAMS core team
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the MIT License as published by
// the Open Source Initiative.
//
// A copy of the MIT License is included in the LICENSE file of this repository.
// You should have received a copy of the MIT License along with this program.
// If not, see <https://opensource.org/licenses/MIT>.
//-----------------------------------------------------------------------------------
 
#ifndef SEAMS_CLUSTER_H_
#define SEAMS_CLUSTER_H_
 
#include <array>
#include <bop.hpp>
#include <cmath>
#include <complex>
#include <generic.hpp>
#include <iostream>
#include <mol_sys.hpp>
#include <neighbours.hpp>
#include <seams_output.hpp>



 
namespace clump {

struct Domain {
  int largest = 0;
  int subset = 0;
  double percolation = 0.0; // largest/subset
};
 
[[nodiscard]] Domain
largestDomain(const molSys::PointCloud<molSys::Point<double>, double> &cloud,
              const std::vector<std::vector<int>> &nList,
              const std::vector<bool> &mask);

[[nodiscard]] int largestIceCluster(
    std::string path, molSys::PointCloud<molSys::Point<double>, double> &yCloud,
    molSys::PointCloud<molSys::Point<double>, double> &iceCloud,
    const std::vector<std::vector<int>> &nList, std::vector<bool> &isIce,
    std::vector<int> &clusterID, std::vector<int> &nClusters,
    std::unordered_map<int, int> &indexNumber, int firstFrame);

[[nodiscard]] int singleClusterLinkedList(
    molSys::PointCloud<molSys::Point<double>, double> &iceCloud,
    const std::vector<std::vector<int>> &nList, std::vector<int> &linkedList);

[[nodiscard]] int clusterAnalysis(std::string path,
                    molSys::PointCloud<molSys::Point<double>, double> &iceCloud,
                    molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                    const std::vector<std::vector<int>> &nList,
                    std::vector<std::vector<int>> &iceNeighbourList,
                    double cutoff, int firstFrame,
                    std::string bopAnalysis = "q6");

[[nodiscard]] int recenterClusterCloud(
    molSys::PointCloud<molSys::Point<double>, double> &iceCloud,
    const std::vector<std::vector<int>> &nList);
 
} // namespace clump
 
#endif // SEAMS_CLUSTER_H_