/** \file atom.cpp
 *
 * Function implementations for the class atom.
 *
 */

#include "molecules.hpp"

/************************************* Functions for class atom *************************************/

/** Constructor of class atom.
 */
atom::atom()
{
	Name = NULL;
	previous = NULL;
	next = NULL;
	father = this;	// generally, father is itself
	Ancestor = NULL;
	type = NULL;
	sort = NULL;
	FixedIon = 0;
	nr = -1;
	GraphNr = -1;
	ComponentNr = NULL;
	IsCyclic = false;
	SeparationVertex = false;
	LowpointNr = -1;
	AdaptiveOrder = 0;
	MaxOrder = false;
};

/** Destructor of class atom.
 */
atom::~atom()
{
	Free((void **)&Name, "atom::~atom: *Name");
	Free((void **)&ComponentNr, "atom::~atom: *ComponentNr");
};


/** Climbs up the father list until NULL, last is returned.
 * \return true father, i.e. whose father points to itself, NULL if it could not be found or has none (added hydrogen)
 */
atom *atom::GetTrueFather()
{
	atom *walker = this;
	do {
		if (walker == walker->father) // top most father is the one that points on itself
			break;
		walker = walker->father;
	} while (walker != NULL);
	return walker;
};

/** Output of a single atom.
 * \param ElementNo cardinal number of the element
 * \param AtomNo cardinal number among these atoms of the same element
 * \param *out stream to output to
 * \param *comment commentary after '#' sign
 */
bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
{
	if (out != NULL) {
		*out << "Ion_Type" << ElementNo << "_" << AtomNo << "\t"	<< fixed << setprecision(9) << showpoint;
		*out << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2];
		*out << "\t" << FixedIon;
		if (v.Norm() > MYEPSILON)
			*out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
		if (comment != NULL)
		  *out << " # " << comment << endl;
		else
		  *out << " # molecule nr " << nr << endl;
		return true;
	} else
		return false;
};

/** Output of a single atom as one lin in xyz file.
 * \param *out stream to output to
 */
bool atom::OutputXYZLine(ofstream *out) const
{
	if (out != NULL) {
		*out << type->symbol << "\t" << x.x[0] << "\t" << x.x[1] << "\t" << x.x[2] << "\t" << endl;
		return true;
	} else
		return false;
};

ostream & operator << (ostream &ost, atom &a)
{
	ost << "[" << a.Name << "|" << &a << "]";
	return ost;
};

/** Compares the indices of \a this atom with a given \a ptr.
 * \param ptr atom to compare index against
 * \return true - this one's is smaller, false - not
 */
bool atom::Compare(atom &ptr)
{
	if (nr < ptr.nr)
		return true;
	else
		return false;
};

bool operator < (atom &a, atom &b)
{
	return a.Compare(b);
};