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

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#include  "xatom.h"
#include "matrix3.h"

XAtom::XAtom(Cell* c, std::string nm, int zn, double xx, double yy, double zz,
	    double s, double u11, double u22, double u33, double u23,
	    double u13, double u12, int pn, int rn) : Atom(nm,zn)
{
	Uij[0]=u11; Uij[1]=u22; Uij[2]=u33;
	Uij[3]=u23; Uij[4]=u13; Uij[5]=u12;
	sof=s;
	xf=xx; yf=yy; zf=zz;
	orthogonalized=false;
	cell=c;
	partnum=pn;
	resnum=rn;
	orthogonalize(); //ensure Cartesian coordinates are updated
}

XAtom::~XAtom()
{

}

// updates the fractional coordinates from the orthogonal ones
// needed for overridden Atom methods to work
bool XAtom::deorthogonalize()
{
	if (!cell)
	{
		xf=xo; yf=yo; zf=zo;
		return false;
	}

	Matrix3 OM=cell->orthmat();
	Matrix3 DM=inverse(OM);
	Vector3 o(xo,yo,zo);
	Vector3 f=DM*o;
	xf=f(1); yf=f(2); zf=f(3);

	return true;
}

// update Atom's Cartesian coordinates from XAtom's fractional
bool XAtom::orthogonalize()
{
	Matrix3 OM;
	Vector3 o;
	Vector3 f;

	if (orthogonalized) return true;
	if (!cell)
	{
		xo=xf; yo=yf; zo=zf;
		return false;
	}

	OM=cell->orthmat();
	f=Vector3(xf,yf,zf);
	o=OM*f;
	xo=o(1); yo=o(2); zo=o(3);
	orthogonalized=true;

	return true;
}

double XAtom::Uiso() const
{
	Matrix3 Q,D,U;

	if (!cell) return -1.0;
	D=Matrix3(cell->astar(),cell->bstar(),cell->cstar());
	Q=cell->orthmat()*D;
	U=Matrix3(Uij[0],Uij[5],Uij[4],Uij[5],Uij[1],Uij[3],Uij[4],
			Uij[3],Uij[2]);
	D=Q*U*transpose(Q);
	return (D(1,1)+D(2,2)+D(3,3))/3.0;
}

void XAtom::coordinates(double &x, double &y, double &z) const
{
	x=xf; y=yf; z=zf;
}

double XAtom::occupancy() const
{
	return sof;
}

int XAtom::part() const
{
	return partnum;
}

int XAtom::residue() const
{
	return resnum;
}

Matrix3 XAtom::U() const
{
	Matrix3 m(Uij[0],Uij[5],Uij[4],Uij[5],Uij[1],Uij[3],Uij[4],Uij[3],Uij[2]);
	return m;
}

XAtom operator * (const Symmetry& s, const XAtom& xatom)
{
	Matrix3 umat;
	Vector3 pos;

	umat=Matrix3(xatom.Uij[0],xatom.Uij[5],xatom.Uij[4],xatom.Uij[5],
		xatom.Uij[1],xatom.Uij[3],xatom.Uij[4],xatom.Uij[3],
		xatom.Uij[2]);
	pos=Vector3(xatom.xf,xatom.yf,xatom.zf);

	umat=transform_contra(s,umat);
	pos=s*pos;
	return XAtom(xatom.cell,xatom.label(),xatom.Z(),pos(1),pos(2),pos(3),
			xatom.sof,umat(1,1),umat(2,2),umat(3,3),umat(2,3),
			umat(1,3),umat(1,2),xatom.partnum,xatom.resnum);
}

// these reimplement Atom methods, keeping fractional/cartesian coords in sync
void XAtom::move_to(double x, double y, double z)
{
	xo=x; yo=y; zo=z;
	deorthogonalize();
}

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