libxr/atom.cpp at main · elfabx/libxr · GitHub

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#include <iostream>
#include "atom.h"
#include "periodic.h"

Atom::Atom(std::string nm, int zn=0, double q=0.0, double xx=0.0,
	double yy=0.0, double zz=0.0, double mm=0.0)
{
	Znuc=zn;
	M=mm;
	name=nm;
	xo=xx; yo=yy; zo=zz;
	chg=q;
}

Atom::Atom(std::string nm, int zn=0, double xx=0.0,
	double yy=0.0, double zz=0.0)
{
	Znuc=zn;
	M=periodic::mass(zn);
	name=nm;
	xo=xx; yo=yy; zo=zz;
	chg=0.0;
}

Atom::Atom(std::string nm, int zn=0)
{
	Znuc=zn;
	M=periodic::mass(zn);
	name=nm;
	xo=0.0; yo=0.0; zo=0.0;
	chg=0.0;
}

Atom::~Atom()
{
}

std::ostream& operator << (std::ostream& s, Atom & atom)
{
	s << "#ATOM: ";
	s << atom.name << "\n" << "Z = " << atom.Znuc << "\tM = " << atom.M;
	s << "\tq = " << atom.chg << std::endl;
	s << "(" << atom.xo << ", " << atom.yo << ", " << atom.zo << ")";
	s << std::endl;
	return s;
}

double Atom::charge() const
{
	return chg;
}

void Atom::set_charge(double q)
{
	chg=q;
}

void Atom::move_to(double x, double y, double z)
{
	xo=x; yo=y; zo=z;
}

void Atom::move_by(double dx, double dy, double dz)
{
	xo+=dx; yo+=dy; zo+=dz;
}

void Atom::position(double& x, double& y, double& z) const
{
	x=xo; y=yo; z=zo;
}

void Atom::set_Z(int zn)
{
	Znuc=zn;
}

int Atom::Z() const
{
	return Znuc;
}

void Atom::set_mass(double mm)
{
	M=mm;
}

double Atom::mass() const
{
	return M;
}

std::string Atom::label() const
{
	return name;
}

void Atom::set_label(std::string nm)
{
	name=nm;
}

double distance2(const Atom& a1, const Atom& a2)
{
	double d=0.0;
	d+=((a1.xo-a2.xo)*(a1.xo-a2.xo));
	d+=((a1.yo-a2.yo)*(a1.yo-a2.yo));
	d+=((a1.zo-a2.zo)*(a1.zo-a2.zo));

	return d;
}