bop.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 __BOP_H_
#define __BOP_H_
 
#include <array>
#include <boost/geometry.hpp>
#include <boost/math/special_functions/spherical_harmonic.hpp>
#include <cmath>
#include <complex>
#include <generic.hpp>
#include <math.h>
#include <mol_sys.hpp>
#include <neighbours.hpp>
#include <seams_output.hpp>
 
namespace chill {
 
// 2*l+1 length complex vector
struct YlmAtom {
  std::vector<std::complex<double>> ylm;
};
 
// Vector of 2*l+1 averaged over 4 nearest neighbours
struct QlmAtom {
  std::vector<YlmAtom> ptq; // Averaged over neighbours
};
 
molSys::PointCloud<molSys::Point<double>, double>
getCorrel(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
          std::vector<std::vector<int>> nList, bool isSlice = false);
 
molSys::PointCloud<molSys::Point<double>, double>
getIceTypeNoPrint(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                  std::vector<std::vector<int>> nList, bool isSlice = false);
 
// Classifies each atom according to the CHILL algorithm
molSys::PointCloud<molSys::Point<double>, double>
getIceType(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
           std::vector<std::vector<int>> nList, std::string path,
           int firstFrame, bool isSlice = false,
           std::string outputFileName = "chill.txt");
 
molSys::PointCloud<molSys::Point<double>, double>
getCorrelPlus(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
              std::vector<std::vector<int>> nList, bool isSlice = false);
 
molSys::PointCloud<molSys::Point<double>, double>
getIceTypePlus(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
               std::vector<std::vector<int>> nList, std::string path,
               int firstFrame, bool isSlice = false,
               std::string outputFileName = "chillPlus.txt");
 
std::vector<double>
getq6(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
      std::vector<std::vector<int>> nList, bool isSlice = false);
 
molSys::PointCloud<molSys::Point<double>, double>
reclassifyWater(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                std::vector<double> *q6);
 
int printIceType(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 std::string path, int firstFrame, bool isSlice = false,
                 std::string outputFileName = "superChill.txt");
 
bool isInterfacial(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                   std::vector<std::vector<int>> nList, int iatom,
                   int num_staggrd, int num_eclipsd);
 
int numStaggered(molSys::PointCloud<molSys::Point<double>, double> *yCloud,
                 std::vector<std::vector<int>> nList, int jatom);
 
} // namespace chill
 
namespace sph {
 
// 7 is for Q3, orderL=3
 
std::vector<std::complex<double>>
spheriHarmo(int orderL, std::array<double, 2> radialCoord);
 
std::array<double, 2> radialCoord(std::array<double, 3> cartCoord);
 
std::vector<std::complex<double>>
lookupTableQ3Vec(std::array<double, 2> angles);
 
std::complex<double> lookupTableQ3(int m, std::array<double, 2> angles);
 
std::vector<std::complex<double>>
lookupTableQ6Vec(std::array<double, 2> angles);
 
std::complex<double> lookupTableQ6(int m, std::array<double, 2> angles);
 
} // namespace sph
 
#endif // __BOP_H_