Package org.jmol.quantum
Class QuantumCalculation
- java.lang.Object
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- org.jmol.quantum.QuantumCalculation
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- Direct Known Subclasses:
MepCalculation
,MOCalculation
,QuantumPlaneCalculation
public abstract class QuantumCalculation extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description protected int
atomIndex
protected static float
bohr_per_angstrom
protected BS
bsExcluded
protected int[]
countsXYZ
protected boolean
doDebug
protected int
firstAtomOffset
protected int
nX
protected int
nY
protected int
nZ
protected float[]
originBohr
protected javajs.util.T3[]
points
protected QMAtom[]
qmAtoms
protected float
rangeBohrOrAngstroms
protected float[]
stepBohr
protected QMAtom
thisAtom
protected float
unitFactor
protected float[]
vd
protected float
volume
protected float[][][]
voxelData
protected float[][][]
voxelDataTemp
protected float[]
X
protected float[]
X2
protected float[]
xBohr
protected int
xMax
protected int
xMin
protected float[]
Y
protected float[]
Y2
protected float[]
yBohr
protected int
yMax
protected int
yMin
protected float[]
Z
protected float[]
Z2
protected float[]
zBohr
protected int
zMax
protected int
zMin
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Constructor Summary
Constructors Constructor Description QuantumCalculation()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description abstract void
createCube()
protected void
initialize(int nX, int nY, int nZ, javajs.util.T3[] points)
protected void
initialize0(int nX, int nY, int nZ, javajs.util.T3[] points)
protected void
initializeOnePoint()
protected void
initializeOnePointQC()
protected abstract void
process()
protected void
processPoints()
float
processPt(javajs.util.T3 pt)
protected void
setMinMax(int ix)
protected void
setupCoordinates(float[] originXYZ, float[] stepsXYZ, BS bsSelected, javajs.util.T3[] xyz, Atom[] atoms, javajs.util.T3[] points, boolean renumber)
protected void
setXYZBohr(javajs.util.T3[] points)
private void
setXYZBohrI(float[] bohr, int i, int n, javajs.util.T3[] points)
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Field Detail
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doDebug
protected boolean doDebug
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bsExcluded
protected BS bsExcluded
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bohr_per_angstrom
protected static final float bohr_per_angstrom
- See Also:
- Constant Field Values
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voxelData
protected float[][][] voxelData
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voxelDataTemp
protected float[][][] voxelDataTemp
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vd
protected float[] vd
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countsXYZ
protected int[] countsXYZ
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points
protected javajs.util.T3[] points
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xMin
protected int xMin
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xMax
protected int xMax
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yMin
protected int yMin
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yMax
protected int yMax
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zMin
protected int zMin
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zMax
protected int zMax
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qmAtoms
protected QMAtom[] qmAtoms
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atomIndex
protected int atomIndex
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thisAtom
protected QMAtom thisAtom
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firstAtomOffset
protected int firstAtomOffset
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xBohr
protected float[] xBohr
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yBohr
protected float[] yBohr
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zBohr
protected float[] zBohr
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originBohr
protected float[] originBohr
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stepBohr
protected float[] stepBohr
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nX
protected int nX
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nY
protected int nY
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nZ
protected int nZ
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X
protected float[] X
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Y
protected float[] Y
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Z
protected float[] Z
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X2
protected float[] X2
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Y2
protected float[] Y2
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Z2
protected float[] Z2
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rangeBohrOrAngstroms
protected float rangeBohrOrAngstroms
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unitFactor
protected float unitFactor
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volume
protected float volume
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Method Detail
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initialize
protected void initialize(int nX, int nY, int nZ, javajs.util.T3[] points)
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initialize0
protected void initialize0(int nX, int nY, int nZ, javajs.util.T3[] points)
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setupCoordinates
protected void setupCoordinates(float[] originXYZ, float[] stepsXYZ, BS bsSelected, javajs.util.T3[] xyz, Atom[] atoms, javajs.util.T3[] points, boolean renumber)
- Parameters:
originXYZ
-stepsXYZ
-bsSelected
-xyz
- full T3[] array -- may be transformed coordinates of Atom[]atoms
- for debugging only -- full Atom[] arraypoints
-renumber
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processPt
public float processPt(javajs.util.T3 pt)
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processPoints
protected void processPoints()
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initializeOnePoint
protected void initializeOnePoint()
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initializeOnePointQC
protected void initializeOnePointQC()
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process
protected abstract void process()
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setXYZBohr
protected void setXYZBohr(javajs.util.T3[] points)
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setXYZBohrI
private void setXYZBohrI(float[] bohr, int i, int n, javajs.util.T3[] points)
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setMinMax
protected void setMinMax(int ix)
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createCube
public abstract void createCube()
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