org.jmol.quantum

Class MepCalculation

java.lang.Object

org.jmol.quantum.QuantumCalculation

org.jmol.quantum.MepCalculation

All Implemented Interfaces:

MepCalculationInterface

Direct Known Subclasses:

MlpCalculation

public class MepCalculation
extends QuantumCalculation
implements MepCalculationInterface

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.quantum.QuantumCalculation

QuantumCalculation.QMAtom

Field Summary

Fields

Modifier and Type	Field and Description
private javax.vecmath.Point3f[]	atomCoordAngstroms
private java.util.BitSet	bsSelected
protected int	distanceMode
protected static int	E_MINUS_D
protected static int	E_MINUS_D_OVER_2
protected java.util.Map<java.lang.String,java.lang.Object>	htAtomicPotentials
protected static int	ONE_OVER_D
protected static int	ONE_OVER_ONE_PLUS_D
private float[]	potentials
protected java.lang.String	resourceName

Fields inherited from class org.jmol.quantum.QuantumCalculation

atomIndex, bohr_per_angstrom, bsExcluded, countsXYZ, doDebug, firstAtomOffset, nX, nY, nZ, originBohr, points, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, vd, volume, voxelData, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin

Constructor Summary

Constructors

Constructor and Description
MepCalculation()

Method Summary

Methods

Modifier and Type	Method and Description
void	assignPotentials(Atom[] atoms, float[] potentials, java.util.BitSet bsAromatic, java.util.BitSet bsCarbonyl, java.util.BitSet bsIgnore, java.lang.String data)
void	calculate(VolumeDataInterface volumeData, java.util.BitSet bsSelected, javax.vecmath.Point3f[] atomCoordAngstroms, float[] potentials, int calcType)
protected void	getAtomicPotentials(java.lang.String data, java.lang.String resourceName)
protected float	getTabulatedPotential(Atom atom)
float	getValueAtPoint(javax.vecmath.Point3f pt)
protected void	process()
void	setup(int calcType, float[] potentials, javax.vecmath.Point3f[] atomCoordAngstroms, java.util.BitSet bsSelected)
float	valueFor(float x0, float d2, int distanceMode)

Methods inherited from class org.jmol.quantum.QuantumCalculation

initialize, initializeOnePoint, process, processPoints, setMinMax, setupCoordinates, setXYZBohr

Methods inherited from class java.lang.Object

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

Field Detail

ONE_OVER_D

protected static final int ONE_OVER_D

See Also:

Constant Field Values

E_MINUS_D_OVER_2

protected static final int E_MINUS_D_OVER_2

See Also:

Constant Field Values

ONE_OVER_ONE_PLUS_D

protected static final int ONE_OVER_ONE_PLUS_D

See Also:

Constant Field Values

E_MINUS_D

protected static final int E_MINUS_D

See Also:

Constant Field Values

distanceMode

protected int distanceMode

potentials

private float[] potentials

atomCoordAngstroms

private javax.vecmath.Point3f[] atomCoordAngstroms

bsSelected

private java.util.BitSet bsSelected

htAtomicPotentials

protected java.util.Map<java.lang.String,java.lang.Object> htAtomicPotentials

resourceName

protected java.lang.String resourceName

Constructor Detail

MepCalculation

public MepCalculation()

Method Detail

assignPotentials

public void assignPotentials(Atom[] atoms,
                    float[] potentials,
                    java.util.BitSet bsAromatic,
                    java.util.BitSet bsCarbonyl,
                    java.util.BitSet bsIgnore,
                    java.lang.String data)

Specified by:

assignPotentials in interface MepCalculationInterface

setup

public void setup(int calcType,
         float[] potentials,
         javax.vecmath.Point3f[] atomCoordAngstroms,
         java.util.BitSet bsSelected)

calculate

public void calculate(VolumeDataInterface volumeData,
             java.util.BitSet bsSelected,
             javax.vecmath.Point3f[] atomCoordAngstroms,
             float[] potentials,
             int calcType)

Specified by:

calculate in interface MepCalculationInterface

getValueAtPoint

public float getValueAtPoint(javax.vecmath.Point3f pt)

process

protected void process()

Specified by:

process in class QuantumCalculation

valueFor

public float valueFor(float x0,
             float d2,
             int distanceMode)

Specified by:

valueFor in interface MepCalculationInterface

getTabulatedPotential

protected float getTabulatedPotential(Atom atom)

getAtomicPotentials

protected void getAtomicPotentials(java.lang.String data,
                       java.lang.String resourceName)