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system.h
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system.h
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#include <iostream>
#include <iostream>
#include <exception>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <fstream>
#include <string>
#include <sstream>
#include <time.h>
#include <vector>
#include <vector>
#include <pybind11/pybind11.h>
#include <pybind11/numpy.h>
#include <pybind11/stl.h>
#include "atom.h"
namespace py = pybind11;
using namespace std;
struct cell{
vector<int> members;
vector<int> neighbor_cells;
};
class System{
public:
//-----------------------------------------------------
// Constructor, Destructor and Access functions
//-----------------------------------------------------
System();
~System();
int nop;
int ghost_nop;
int real_nop;
//-----------------------------------------------------
// Simulation box related methods
//-----------------------------------------------------
double rot[3][3];
double rotinv[3][3];
int triclinic;
double boxx, boxy, boxz;
double boxdims[3][2];
double box[3][3];
void assign_triclinic_params(vector<vector<double>>, vector<vector<double>>);
vector<vector<double>> get_triclinic_params();
void sbox(vector<vector<double>>);
vector<vector<double>> gbox();
vector<double> remap_atom(vector<double>);
//-----------------------------------------------------
// Atom related methods
//-----------------------------------------------------
vector<Atom> atoms;
void assign_particles( vector<Atom>);
void read_particle_file(string); // TBDep
void set_atoms( vector<Atom>);
vector<Atom> get_atoms();
vector<Atom> get_all_atoms();
Atom gatom(int);
void satom(Atom);
//----------------------------------------------------
// Neighbor methods
//----------------------------------------------------
int filter;
int usecells;
int nx, ny, nz;
int total_cells;
cell *cells;
double neighbordistance;
void get_all_neighbors_normal();
void process_neighbor(int, int);
int get_all_neighbors_sann(double);
int get_all_neighbors_bynumber(double, int, int);
int get_neighbors_from_temp(int);
int get_all_neighbors_adaptive(double, int, double);
void get_all_neighbors_voronoi();
void reset_all_neighbors();
void reset_main_neighbors();
double get_abs_distance(int,int,double&,double&,double&);
double get_abs_distance(Atom , Atom );
vector<double> get_distance_vector(Atom , Atom);
void set_neighbordistance(double);
vector<double> get_pairdistances();
//variables for a filter
void susecells(int);
int gusecells();
int cell_index(int, int, int);
void set_up_cells();
vector<int> cell_periodic(int, int, int);
void get_all_neighbors_cells();
void get_temp_neighbors_cells();
void get_temp_neighbors_brute();
void store_neighbor_info();
void set_atom_cutoff(double);
//---------------------------------------------------
// Methods for q calculation
//---------------------------------------------------
int *reqdqs;
int lenqs;
int *reqdaqs;
int lenaqs;
vector<double> gqvals(int qq);
vector<double> gaqvals(int qq);
vector<int> rq_backup;
void set_reqd_qs(vector<int>);
void set_reqd_aqs(vector<int>);
void calculate_q(vector <int>);
void calculate_aq(vector <int>);
double dfactorial(int ,int );
void convert_to_spherical_coordinates(double , double , double , double &, double &, double &);
double PLM(int, int, double);
void YLM(int , int , double , double , double &, double &);
void QLM(int ,int ,double ,double ,double &, double & );
void calculate_complexQLM_6();
double get_number_from_bond(int,int);
double get_number_from_bond(Atom ,Atom );
void calculate_frenkel_numbers();
//disorder vars
void calculate_disorder();
void find_average_disorder();
//-----------------------------------------------------
// Solids and Clustering methods
//-----------------------------------------------------
double minfrenkel;
double threshold;
double avgthreshold;
int maxclusterid;
int solidq;
int criteria;
int comparecriteria;
void find_solid_atoms();
void find_clusters(double);
void harvest_cluster(const int, const int);
void find_clusters_recursive(double);
int largest_cluster();
void set_nucsize_parameters(double,double,double);
void get_largest_cluster_atoms();
//-----------------------------------------------------
// Voronoi based methods
//-----------------------------------------------------
int alpha;
void find_average_volume();
int voronoiused;
double face_cutoff;
void set_face_cutoff(double);
//-------------------------------------------------------
// CNA parameters
//-------------------------------------------------------
double lattice_constant;
void get_diamond_neighbors();
vector<int> identify_diamond_structure();
void identify_cndia();
void get_cna_neighbors(int);
void get_acna_neighbors(int);
void get_common_neighbors(int);
void get_common_bonds(int);
void identify_cn12();
void identify_cn14();
vector<int> calculate_cna(int);
//-------------------------------------------------------
// Other order parameters
//-------------------------------------------------------
double switching_fn(double, double, int, int);
void average_entropy();
void average_entropy_switch(double, int, int);
void entropy(double, double, double, double, double, double);
void calculate_centrosymmetry_atom(int, int);
void calculate_centrosymmetry(int);
vector<double> get_centrosymmetry();
};