MIT-v1.0 folder

This setup used Eigen for data structures of cells and provide some functions to analyze the system

Class Cell functions

constructor

Cell()

operators

bool operator==(const Cell& cel) const

I/O

virtual void read(std::istream&)
virtual void skip(std::istream&) const
virtual void read(std::istream&,std::istream&)
virtual void skip(std::istream&,std::istream&) const
virtual void read_cell(std::istream&)
virtual void skip_cell(std::istream&) const
virtual void read_pos(std::istream&)
virtual void skip_pos(std::istream&) const
virtual void set_box(double a, double b, double c)
virtual std::ostream& write_cell(std::ostream& os) const
virtual std::ostream& write_positions(std::ostream& os) const
virtual std::ostream& write_position(std::ostream& os, int i) const

interaction with other class

virtual Atom atom(int index) const
virtual Atom atom(int index) const
virtual Atom_group atoms() const
virtual Atom_group atoms(std::string in_type) const
virtual Atom_group atoms(int start_index,int end_index) const
virtual Box box() const

print values

virtual double volume() const
virtual double snapshot() const
virtual double time() const
virtual std::string type(int) const
virtual double distance(int i,int j) const
virtual double angle(int i,int j, int k) const

Class Atom functions

constructor

Atom(const Cell& in_cel,int in_index):cel(in_cel),index(in_index)
Atom(const Atom&)
Atom(Atom&&)

print values

Using functions from Cell class

double distance(int j) const
double distance(const Atom& a1) const
double angle(int j, int k) const
double angle(const Atom& a1, const Atom& a2) const
std::string type() const

Class Atom_group

constructor

Atom_group(const Cell& in_cel,std::vector in_indexs=std::vector())

operations

void add(const Atom& a)
Atom_iterator begin()
Atom_iterator end()

class Atom_iterator

constructor

Atom_iterator(const Atom_group& in_ag,std::vector::iterator in_it)
Atom operator*()
Atom_iterator operator++()
bool operator!=(const Atom_iterator& in_AI)