order_parameter.hpp

Go to the documentation of this file.

//-----------------------------------------------------------------------------------
// 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_ORDER_PARAMETER_H_
#define SEAMS_ORDER_PARAMETER_H_
 
#include <algorithm>
#include <array>
#include <fstream>
#include <iostream>
#include <iterator>
#include <cmath>
#include <memory>
#include <sstream>
#include <string>
#include <vector>
 
#include <cage.hpp>
#include <mol_sys.hpp>
#include <ring.hpp>
#include <seams_input.hpp>
#include <seams_output.hpp>
 
namespace topoparam {

double
normHeightPercent(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                  int nPrisms, double avgPrismHeight);

std::vector<double>
calcCoverageArea(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                 const std::vector<std::vector<int>> &rings, double sheetArea);

std::vector<double>
projAreaSingleRing(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
                   const std::vector<int> &ring);

std::vector<double>
rodgerF4(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
         const std::vector<std::vector<int>> &nList, int oxygenType,
         int hydrogenType);

double meanFinite(const std::vector<double> &values);

double jumpRotorTau90(
    const molSys::PointCloud<molSys::Point<double>, double> &frame0,
    const molSys::PointCloud<molSys::Point<double>, double> &frame1, double dt,
    int oxygenType, int hydrogenType);

struct LayerStack {
  double phiC = 0.0;
  std::string sequence;
  std::vector<int> cubicPerLayer;
  std::vector<int> hexPerLayer;
};
 
LayerStack
layerCubicity(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
              int axis = 2, double layerWidth = 3.7);

LayerStack
tumLayerStack(const molSys::PointCloud<molSys::Point<double>, double> &yCloud,
              const std::vector<std::vector<int>> &rings,
              const std::vector<bool> &basal, const std::vector<bool> &equatorial,
              int axis = 2, double layerWidth = 3.7);
 
} // namespace topoparam
 
#endif // SEAMS_ORDER_PARAMETER_H_