public void clear() {
		super.clear();
		for (Atom a : atom) {
			a.custom = 0;
			a.setMovable(true);
			a.setVisible(true);
			a.setDraggable(true);
			a.setCharge(0);
			a.setRestraint(null);
			a.setUserField(null);
			a.setVx(0);
			a.setVy(0);
			a.setHx(0);
			a.setHy(0);
			a.setShowRTraj(false);
			a.setShowRMean(false);
			a.setShowFMean(false);
			a.clearMeasurements();
			a.setFriction(0);
			a.setRadical(true);
			a.setColor(null);
			a.setMarked(false);
			a.setSelected(false);
			a.setVelocitySelection(false);
			a.resetElectronsToGroundState();
		}
		if (photons != null)
			photons.clear();
		if (photonQueue != null)
			photonQueue.clear();
		freeElectrons.clear();
		setNumberOfAtoms(0);
		resetElements();
		resetIntegrator();
		setSubatomicEnabled(false);
		setLightSourceEnabled(false);
		setAtomFlowEnabled(false);
	}