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 __CLUSTER_H_
#define __CLUSTER_H_
 
#include <array>
#include <boost/geometry.hpp>
#include <boost/math/special_functions/spherical_harmonic.hpp>
#include <bop.hpp>
#include <cmath>
#include <complex>
#include <generic.hpp>
#include <iostream>
#include <math.h>
#include <mol_sys.hpp>
#include <neighbours.hpp>
#include <seams_output.hpp>
 
namespace clump {
 
int largestIceCluster(
    std::string path, molSys::PointCloud<molSys::Point<double>, double> *yCloud,
    molSys::PointCloud<molSys::Point<double>, double> *iceCloud,
    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);
 
int singleClusterLinkedList(
    molSys::PointCloud<molSys::Point<double>, double> *iceCloud,
    std::vector<std::vector<int>> nList, std::vector<int> *linkedList);
 
int clusterAnalysis(std::string path,
                    molSys::PointCloud<molSys::Point<double>, double> *iceCloud,
                    molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                    std::vector<std::vector<int>> nList,
                    std::vector<std::vector<int>> &iceNeighbourList,
                    double cutoff, int firstFrame,
                    std::string bopAnalysis = "q6");
 
int recenterClusterCloud(
    molSys::PointCloud<molSys::Point<double>, double> *iceCloud,
    std::vector<std::vector<int>> nList);
 
} // namespace clump
 
#endif // __CLUSTER_H_