meshi.molecularElements.allAtoms
Class DistanceMatrixWhichUpdateOnlyMovingAtoms

java.lang.Object
  meshi.util.MeshiProgram
      meshi.geometry.DistanceMatrix
          meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms

All Implemented Interfaces:

Updateable

public class DistanceMatrixWhichUpdateOnlyMovingAtoms
extends DistanceMatrix

Nested Class Summary

Nested classes/interfaces inherited from class meshi.geometry.DistanceMatrix

DistanceMatrix.Indicator

Field Summary

private int	numberOfUpdates
private double[][]	previousCoordinates

Fields inherited from class meshi.geometry.DistanceMatrix

bondedList, bondedListDepth, buffer, bufferOneThirdSqr, debug, DEFAULT_BONDED_LIST_DEPTH, DEFAULT_BUFFER, DEFAULT_RMAX, edge, energyTermsDistanceLists, grid, matrix, molecularSystem, nonBondedList, rMax, rMax2, rMaxPlusBuffer, rMaxPlusBuffer2, terminator

Fields inherited from class meshi.util.MeshiProgram

commandLine, name

Constructor Summary

DistanceMatrixWhichUpdateOnlyMovingAtoms(AtomList atomList, double rMax, int bondedListDepth)

Method Summary

void	initPreviousCoordinates()
private boolean	moved(Atom atom, int index)
void	update(int numberOfUpdates) Updates the distance matrix.
private void	updateMovingAtoms()

Methods inherited from class meshi.geometry.DistanceMatrix

bondedList, buffer, DebugOFF, debugON, DEFAULT_EDGE, distance, distance, distance, doNotUpdateNonBondedList, energyTermsDistanceLists, getBonded, getBonded, getBondedList, indicatorToUpdateHB, nonBondedList, nonBondedListSize, radius, rMax, rMax2, rMaxPlusBuffer, rMaxPlusBuffer2, rowIterator, rowNumber, toString, update

Methods inherited from class meshi.util.MeshiProgram

about, debug, get2ndString, getb, getB, getd, getD, getFlag, getFlagedArgument, geti, getI, getOrderedArgument, getS, getS, initRandom, initRandom, initRandom, printGlobalTable, randomNumberGenerator, seed, tableGet, tableIncludes, tableSet, verbose

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

previousCoordinates

private double[][] previousCoordinates

numberOfUpdates

private int numberOfUpdates

Constructor Detail

DistanceMatrixWhichUpdateOnlyMovingAtoms

public DistanceMatrixWhichUpdateOnlyMovingAtoms(AtomList atomList,
                                                double rMax,
                                                int bondedListDepth)

Method Detail

update

public void update(int numberOfUpdates)
            throws UpdateableException

Description copied from class: DistanceMatrix

Updates the distance matrix.

Specified by:

update in interface Updateable

Overrides:

update in class DistanceMatrix

Throws:

UpdateableException

updateMovingAtoms

private void updateMovingAtoms()
                        throws UpdateableException

Throws:

UpdateableException

moved

private boolean moved(Atom atom,
                      int index)

initPreviousCoordinates

public void initPreviousCoordinates()