Package org.jmol.quantum
Class MepCalculation
- java.lang.Object
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- org.jmol.quantum.QuantumCalculation
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- org.jmol.quantum.MepCalculation
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- Direct Known Subclasses:
MlpCalculation
public class MepCalculation extends QuantumCalculation
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Field Summary
Fields Modifier and Type Field Description private javajs.util.P3[]
atomCoordAngstroms
private BS
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
private Viewer
vwr
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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, voxelDataTemp, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin
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Constructor Summary
Constructors Constructor Description MepCalculation()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
assignPotentials(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, java.lang.String data)
void
calculate(VolumeData volumeData, BS bsSelected, javajs.util.P3[] xyz, Atom[] atoms, float[] potentials, int calcType)
void
createCube()
protected void
getAtomicPotentials(java.lang.String data, java.lang.String resourceName)
protected float
getTabulatedPotential(Atom atom)
float
getValueAtPoint(javajs.util.P3 pt)
protected void
process()
void
set(Viewer vwr)
void
setup(int calcType, float[] potentials, javajs.util.P3[] atomCoordAngstroms, BS bsSelected)
float
valueFor(float x0, float d2, int distanceMode)
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Methods inherited from class org.jmol.quantum.QuantumCalculation
initialize, initialize0, initializeOnePoint, initializeOnePointQC, processPoints, processPt, setMinMax, setupCoordinates, setXYZBohr
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Field Detail
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ONE_OVER_D
protected static final int ONE_OVER_D
- See Also:
- Constant Field Values
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E_MINUS_D_OVER_2
protected static final int E_MINUS_D_OVER_2
- See Also:
- Constant Field Values
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ONE_OVER_ONE_PLUS_D
protected static final int ONE_OVER_ONE_PLUS_D
- See Also:
- Constant Field Values
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E_MINUS_D
protected static final int E_MINUS_D
- See Also:
- Constant Field Values
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distanceMode
protected int distanceMode
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potentials
private float[] potentials
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atomCoordAngstroms
private javajs.util.P3[] atomCoordAngstroms
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bsSelected
private BS bsSelected
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vwr
private Viewer vwr
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htAtomicPotentials
protected java.util.Map<java.lang.String,java.lang.Object> htAtomicPotentials
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resourceName
protected java.lang.String resourceName
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Method Detail
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set
public void set(Viewer vwr)
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assignPotentials
public void assignPotentials(Atom[] atoms, float[] potentials, BS bsAromatic, BS bsCarbonyl, BS bsIgnore, java.lang.String data)
- Parameters:
atoms
-potentials
-bsAromatic
-bsCarbonyl
-bsIgnore
-data
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setup
public void setup(int calcType, float[] potentials, javajs.util.P3[] atomCoordAngstroms, BS bsSelected)
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calculate
public void calculate(VolumeData volumeData, BS bsSelected, javajs.util.P3[] xyz, Atom[] atoms, float[] potentials, int calcType)
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getValueAtPoint
public float getValueAtPoint(javajs.util.P3 pt)
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process
protected void process()
- Specified by:
process
in classQuantumCalculation
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valueFor
public float valueFor(float x0, float d2, int distanceMode)
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getTabulatedPotential
protected float getTabulatedPotential(Atom atom)
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getAtomicPotentials
protected void getAtomicPotentials(java.lang.String data, java.lang.String resourceName)
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createCube
public void createCube()
- Specified by:
createCube
in classQuantumCalculation
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