<commit_before>package etomica;
import etomica.units.Dimension;
import etomica.units.Unit;
import etomica.units.Count;

/**
 *  Computes the mean square displacement for a set of atoms.
 *  Use of this meter usually involves another meter must calling this meter's
 *  currentValue method, which then reports the current mean square displacement.
 *  This meter does not perform any averaging of its own.
 *
 *  @author <NAME>
 */

public class MeterMeanSquareDisplacement extends MeterAbstract implements 
                                                EtomicaElement {

    private int nAtoms = 0;
    AtomIterator iterator;
    private Space.Vector[] rAccum, rLast;
    private Space.Vector deltaR;
    
    public MeterMeanSquareDisplacement(Space space, AtomIterator iter) {
        this(space);
        setAtoms(iter);
    }
    public MeterMeanSquareDisplacement(Space space) {
        super(1);
        setLabel("Mean square displacement");
        setUpdateInterval(1);
        deltaR = space.makeVector();
    }
    
    public static EtomicaInfo getEtomicaInfo() {
        EtomicaInfo info = new EtomicaInfo("Mean squared displacement, suitable for diffusion calculations");
        return info;
    }

    public Unit defaultIOUnit() {return Count.UNIT;}
    
    /**
     * Returns dimensions of this meter's output, which in this case is QUANTITY.
     */
    public Dimension getDimension() {return Dimension.NULL;}
    
    /**
     * Specifies the set of atoms that will be tracked to compute their MSD.
     * The given iterator loops through the atoms.
     */
    public void setAtoms(AtomIterator iter) {
        iterator = iter;
        nAtoms = iter.size();
        rAccum = new Space.Vector[nAtoms];
        rLast = new Space.Vector[nAtoms];
        iter.reset();
        int i=0;
        while(iter.hasNext()) {
            rAccum[i] = simulation().space().makeVector();
            rLast[i] = simulation().space().makeVector();
            rLast[i].E(iter.next().coord.position());
            i++;
        }
    }
    public AtomIterator getAtoms() {return iterator;}
    
    public void reset() {
        super.reset();
        if(iterator != null) setAtoms(iterator);
    }
    
    public void doMeasurement() {
        double sum = 0.0;
        for(int i=0; i<nAtoms; i++) {
            sum += rAccum[i].squared();
        }<commit_msg>Incomplete fixes<commit_after>package etomica;
import etomica.units.Dimension;
import etomica.units.Unit;
import etomica.units.Count;

/**
 *  Computes the mean square displacement for a set of atoms.
 *  Use of this meter usually involves another meter must calling this meter's
 *  currentValue method, which then reports the current mean square displacement.
 *  This meter does not perform any averaging of its own.
 *
 *  @author <NAME>
 */

public class MeterMeanSquareDisplacement extends MeterAbstract implements 
                                                EtomicaElement {

    private int nAtoms = 0;
    AtomIterator iterator;
    private Space.Vector[] rAccum, rLast;
    private Space.Vector deltaR;
    private final Space space;
    
    public MeterMeanSquareDisplacement(Space space, AtomIterator iter) {
        this(space);
        setAtoms(iter);
    }
    public MeterMeanSquareDisplacement(Space space) {
        super(1);
        this.space = space;
        setLabel("Mean square displacement");
        deltaR = space.makeVector();
    }
    
    public static EtomicaInfo getEtomicaInfo() {
        EtomicaInfo info = new EtomicaInfo("Mean squared displacement, suitable for diffusion calculations");
        return info;
    }

//    public Unit defaultIOUnit() {return Count.UNIT;}
    
    /**
     * Returns dimensions of this meter's output (current UNDEFINED).
     */
    public Dimension getDimension() {return Dimension.UNDEFINED;}
    
    /**
     * Specifies the set of atoms that will be tracked to compute their MSD.
     * The given iterator loops through the atoms.
     */
    public void setAtoms(AtomIterator iter) {
        iterator = iter;
        nAtoms = iter.size();
        rAccum = new Space.Vector[nAtoms];
        rLast = new Space.Vector[nAtoms];
        iter.reset();
        int i=0;
        while(iter.hasNext()) {
            rAccum[i] = space.makeVector();
            rLast[i] = space.makeVector();
            rLast[i].E(iter.nextAtom().coord.position());
            i++;
        }
    }
    public AtomIterator getAtoms() {return iterator;}
    
    public void reset() {
        super.reset();
        if(iterator != null) setAtoms(iterator);
    }
    
    public void doMeasurement() {
        double sum = 0.0;
        for(int i=0; i<nAtoms; i++) {
            sum += rAccum[i].squared();
        }
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