mol_sys.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_MOL_SYS_H_
#define SEAMS_MOL_SYS_H_
 
#include <algorithm>
#include <array>
#include <concepts>
#include <fstream>
#include <iterator>
#include <sstream>
#include <string>
#include <unordered_map>
#include <vector>



 
namespace molSys {
 
// Enum type for bond type

enum class bond_type { staggered, eclipsed, out_of_range };

enum class atom_state_type {
  cubic,
  hexagonal,
  water,
  interfacial,
  clathrate,
  interClathrate,
  unclassified,
  reCubic,
  reHex
};

struct Result {
  bond_type classifier; 
  double c_value;       
};

template <typename T>
concept CoordinateScalar = std::floating_point<T>;

template <CoordinateScalar T> struct Point {
  int type = 0, molID = 0, atomID = 0; 
  T x = 0, y = 0, z = 0;              
  std::vector<Result> c_ij;            
  atom_state_type iceType =
      atom_state_type::unclassified;   
  bool inSlice = true;                 
};
 
// Struct for a collection of points; contains information for a particular
// frame
template <typename S, CoordinateScalar T> struct PointCloud {
  std::vector<S> pts;    
  int currentFrame = 0;  
  int nop = 0;           
  std::vector<T> box;    
  std::vector<T> boxLow; 
  std::unordered_map<int, int> idIndexMap;
};

std::unordered_map<int, int>
createIDMolIDmap(molSys::PointCloud<molSys::Point<double>, double> &yCloud);

std::unordered_multimap<int, int>
createMolIDAtomIDMultiMap(molSys::PointCloud<molSys::Point<double>, double> &yCloud);

std::vector<std::vector<int>>
hAtomMolList(molSys::PointCloud<molSys::Point<double>, double> &hCloud,
             molSys::PointCloud<molSys::Point<double>, double> &oCloud);

[[nodiscard]] int searchMolList(const std::vector<std::vector<int>> &molList, int molIDtoFind);

molSys::PointCloud<molSys::Point<double>, double>
clearPointCloud(molSys::PointCloud<molSys::Point<double>, double> &yCloud);
} // namespace molSys
 
#endif // SEAMS_MOL_SYS_H_