Package org.jmol.quantum
Class MOCalculation
- java.lang.Object
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- org.jmol.quantum.QuantumCalculation
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- org.jmol.quantum.MOCalculation
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public class MOCalculation extends QuantumCalculation
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Field Summary
Fields Modifier and Type Field Description private double
c
private java.lang.String
calculationType
private double[]
coeffs
private float[][]
coefs
private static double
CUT
private double[]
CX
private double[]
CY
private double[]
CZ
private int[][]
dfCoefMaps
private boolean
doNormalize
private boolean
doShowShellType
private double[]
DXY
private double[]
DXZ
private double[]
DYZ
private double[]
EX
private double[]
EY
private double[]
EZ
private int
gaussianPtr
private float[][]
gaussians
private boolean
havePoints
(package private) float
integration
private boolean
isSquaredLinear
private int
lastGaussianPtr
private float[]
linearCombination
private int[]
map
private int
moCoeff
private float[]
moCoefficients
private double
moFactor
private int
nGaussians
private boolean
nwChemMode
private static double
ROOT3
private static java.lang.String[][]
shellOrder
private javajs.util.Lst<int[]>
shells
private SlaterData[]
slaters
(package private) double
sum
(package private) boolean
testing
private java.lang.String
warned
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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 MOCalculation()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description private void
addData10F()
private void
addData5D()
private void
addData6D()
private void
addData7F()
private void
addDataP()
private void
addDataS()
private void
addDataSP()
private void
addValuesSquared(float occupancy)
private void
calcSP(double alpha, double as, double ax, double ay, double az)
void
calculateElectronDensity()
private boolean
checkCalculationType()
void
createCube()
private void
dumpInfo(int shell)
private double
getContractionNormalization(int el, int cpt)
private static java.lang.String[]
getShellOrder(int i)
protected void
initialize(int nX, int nY, int nZ, javajs.util.T3[] points)
private double
normalizeShell(int iShell)
protected void
process()
protected void
processPoints()
private void
processShell(int iShell)
private boolean
processSlater(int slaterIndex)
private void
setCE(double alpha, double as, double ax, double ay, double az)
private boolean
setCoeffs(int type, boolean isProcess)
private void
setE(double[] EX, double alpha)
boolean
setupCalculation(VolumeData volumeData, BS bsSelected, java.lang.String calculationType, javajs.util.T3[] xyz, Atom[] atoms, int firstAtomOffset, javajs.util.Lst<int[]> shells, float[][] gaussians, int[][] dfCoefMaps, java.lang.Object slaters, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, boolean doNormalize, javajs.util.T3[] points)
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Methods inherited from class org.jmol.quantum.QuantumCalculation
initialize0, initializeOnePoint, initializeOnePointQC, processPt, setMinMax, setupCoordinates, setXYZBohr
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Field Detail
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CUT
private static final double CUT
- See Also:
- Constant Field Values
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CX
private double[] CX
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CY
private double[] CY
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CZ
private double[] CZ
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DXY
private double[] DXY
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DXZ
private double[] DXZ
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DYZ
private double[] DYZ
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EX
private double[] EX
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EY
private double[] EY
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EZ
private double[] EZ
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calculationType
private java.lang.String calculationType
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shells
private javajs.util.Lst<int[]> shells
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gaussians
private float[][] gaussians
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slaters
private SlaterData[] slaters
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moCoefficients
private float[] moCoefficients
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moCoeff
private int moCoeff
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gaussianPtr
private int gaussianPtr
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doNormalize
private boolean doNormalize
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nwChemMode
private boolean nwChemMode
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dfCoefMaps
private int[][] dfCoefMaps
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linearCombination
private float[] linearCombination
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coefs
private float[][] coefs
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moFactor
private double moFactor
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havePoints
private boolean havePoints
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testing
boolean testing
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sum
double sum
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c
private double c
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nGaussians
private int nGaussians
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doShowShellType
private boolean doShowShellType
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warned
private java.lang.String warned
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coeffs
private double[] coeffs
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map
private int[] map
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lastGaussianPtr
private int lastGaussianPtr
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ROOT3
private static final double ROOT3
- See Also:
- Constant Field Values
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shellOrder
private static final java.lang.String[][] shellOrder
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integration
float integration
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isSquaredLinear
private boolean isSquaredLinear
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Method Detail
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setupCalculation
public boolean setupCalculation(VolumeData volumeData, BS bsSelected, java.lang.String calculationType, javajs.util.T3[] xyz, Atom[] atoms, int firstAtomOffset, javajs.util.Lst<int[]> shells, float[][] gaussians, int[][] dfCoefMaps, java.lang.Object slaters, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, boolean doNormalize, javajs.util.T3[] points)
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initialize
protected void initialize(int nX, int nY, int nZ, javajs.util.T3[] points)
- Overrides:
initialize
in classQuantumCalculation
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createCube
public void createCube()
- Specified by:
createCube
in classQuantumCalculation
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processPoints
protected void processPoints()
- Overrides:
processPoints
in classQuantumCalculation
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process
protected void process()
- Specified by:
process
in classQuantumCalculation
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checkCalculationType
private boolean checkCalculationType()
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normalizeShell
private double normalizeShell(int iShell)
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processShell
private void processShell(int iShell)
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addValuesSquared
private void addValuesSquared(float occupancy)
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getContractionNormalization
private double getContractionNormalization(int el, int cpt)
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setCoeffs
private boolean setCoeffs(int type, boolean isProcess)
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addDataS
private void addDataS()
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addDataP
private void addDataP()
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addDataSP
private void addDataSP()
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setCE
private void setCE(double alpha, double as, double ax, double ay, double az)
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setE
private void setE(double[] EX, double alpha)
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calcSP
private void calcSP(double alpha, double as, double ax, double ay, double az)
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addData6D
private void addData6D()
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addData5D
private void addData5D()
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addData10F
private void addData10F()
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addData7F
private void addData7F()
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processSlater
private boolean processSlater(int slaterIndex)
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dumpInfo
private void dumpInfo(int shell)
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getShellOrder
private static final java.lang.String[] getShellOrder(int i)
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calculateElectronDensity
public void calculateElectronDensity()
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