/
modsystem.h
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/
modsystem.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 <string>
#include <any>
const double PI = 3.141592653589793;
namespace py = pybind11;
using namespace std;
/*-----------------------------------------------------
Some utility objects
-----------------------------------------------------*/
struct cell{
vector<int> members;
vector<int> neighbor_cells;
};
struct datom{
double dist;
int index;
};
//create another for the sorting algorithm
struct by_dist{
bool operator()(datom const &datom1, datom const &datom2){
return (datom1.dist < datom2.dist);
}
};
/*-----------------------------------------------------
Neighbor Methods
-----------------------------------------------------*/
double get_abs_distance(vector<double>, vector<double>,
const int&,
const vector<vector<double>>&,
const vector<vector<double>>&,
const vector<double>&,
double&, double&, double&);
vector<double> get_distance_vector(vector<double> pos1,
vector<double> pos2,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box);
vector<double> remap_atom_into_box(vector<double> pos,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box);
vector<double> remap_and_displace_atom(vector<double> pos,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
const vector<double>& perturbation);
void reset_all_neighbors(py::dict&);
void convert_to_spherical_coordinates(double, double, double,
double&, double&, double&);
void get_all_neighbors_normal(py::dict& atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box);
int cell_index(int, int, int, int, int, int);
vector<int> cell_periodic(int, int, int, int, int, int);
vector<cell> set_up_cells(const vector<vector<double>>&,
const vector<double>&,
const double);
void get_all_neighbors_cells(py::dict& atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box);
void get_temp_neighbors_brute(const vector<vector<double>>& positions,
const vector<bool>& mask_1,
const vector<bool>& mask_2,
vector<vector<datom>>& temp_neighbors,
const int& triclinic,
const double neighbordistance,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box);
void get_temp_neighbors_cells(const vector<vector<double>>& positions,
const vector<bool>& mask_1,
const vector<bool>& mask_2,
vector<vector<datom>>& temp_neighbors,
const int& triclinic,
const double neighbordistance,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box);
int get_all_neighbors_bynumber(py::dict& atoms,
double& neighbordistance,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double prefactor,
int nns,
int usecells,
int assign);
int get_all_neighbors_sann(py::dict& atoms,
double& neighbordistance,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double prefactor,
int usecells);
int get_all_neighbors_adaptive(py::dict& atoms,
double& neighbordistance,
const int& triclinic,
const vector<vector<double>>& rot,
const vector<vector<double>>& rotinv,
const vector<double>& box,
double prefactor,
int nlimit,
double padding,
int usecells);
void get_all_neighbors_voronoi(py::dict& atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box,
const double face_area_exponent);
void clean_voronoi_vertices(py::dict& atoms,
py::dict& all_atoms,
const double neighbordistance,
const int triclinic,
const vector<vector<double>> rot,
const vector<vector<double>> rotinv,
const vector<double> box,
const double distance_cutoff);
bool check_if_in_box(const vector<double>& pos,
const vector<double>& box);
/*-----------------------------------------------------
Steinhardt Methods
-----------------------------------------------------*/
void calculate_factors(const int lm,
vector<vector<double>>& alm,
vector<vector<double>>& blm,
vector<vector<double>>& clm,
vector<double>& dl,
vector<double>& el);
vector<vector<double>> calculate_plm(const int lm,
const double costheta,
const double sintheta);
double dfactorial(int l,
int m);
vector<vector<vector<double>>> calculate_ylm(const int lm,
const double costheta,
const double sintheta,
const double cosphi,
const double sinphi);
vector<vector<vector<vector<double>>>> calculate_q_atom(const int lm,
const vector<double>& theta,
const vector<double>& phi);
void calculate_q(py::dict& atoms,
const int lm);
double plm(const int l,
const int m,
const double theta);
double sph_legendre(const int l,
const int m,
const double theta);
void calculate_qlm(const int l,
const int m,
const double theta,
const double phi,
double &ylm_real,
double &ylm_imag);
void calculate_q_single(py::dict& atoms,
const int lm);
void calculate_aq_single(py::dict& atoms,
const int lm);
void calculate_disorder(py::dict& atoms,
const int lm);
void calculate_bonds(py::dict& atoms,
const int lm,
const double threshold,
const double avgthreshold,
const double minbonds,
const int comparecriteria,
const int criteria);
void extract_cluster(int ti,
int clusterindex,
vector<bool>& condition,
vector<bool>& ghost,
vector<vector<int>>& neighbors,
vector<vector<double>>& neighbordist,
vector<double>& cutoff,
vector<int>& cluster);
void find_clusters(py::dict& atoms,
double clustercutoff);