org.jmol.quantum
Class MOCalculation
java.lang.Object
org.jmol.quantum.QuantumCalculation
org.jmol.quantum.MOCalculation
- All Implemented Interfaces:
- QuantumCalculationInterface
public class MOCalculation
- extends QuantumCalculation
- implements QuantumCalculationInterface
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 |
Method Summary |
private void |
addData10F()
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private void |
addData5D()
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private void |
addData6D()
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private void |
addData7F()
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private void |
addDataP()
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private void |
addDataS()
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private void |
addDataSP()
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private void |
calcSP(double alpha,
double as,
double ax,
double ay,
double az)
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void |
calculateElectronDensity()
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private boolean |
checkCalculationType()
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void |
createCube()
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private void |
dumpInfo(int shell)
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private double |
getContractionNormalization(int el,
int cpt)
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private static java.lang.String[] |
getShellOrder(int i)
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protected void |
initialize(int nX,
int nY,
int nZ,
javax.vecmath.Point3f[] points)
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private double |
normalizeShell(int iShell)
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protected void |
process()
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protected void |
processPoints()
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private void |
processShell(int iShell)
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private boolean |
processSlater(int slaterIndex)
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private void |
setCE(double alpha,
double as,
double ax,
double ay,
double az)
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private boolean |
setCoeffs(boolean isProcess)
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private void |
setE(double[] EX,
double alpha)
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private void |
setTemp()
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boolean |
setupCalculation(VolumeDataInterface volumeData,
java.util.BitSet bsSelected,
java.util.BitSet bsExclude,
java.util.BitSet[] bsMolecules,
java.lang.String calculationType,
javax.vecmath.Point3f[] atomCoordAngstroms,
int firstAtomOffset,
java.util.List<int[]> shells,
float[][] gaussians,
int[][] dfCoefMaps,
java.lang.Object slaters,
float[] moCoefficients,
float[] linearCombination,
float[][] coefs,
float[] partialCharges,
boolean doNormalize,
javax.vecmath.Point3f[] points,
float[] parameters,
int testFlags)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
CUT
private static final double CUT
- See Also:
- Constant Field Values
CX
private double[] CX
CY
private double[] CY
CZ
private double[] CZ
DXY
private double[] DXY
DXZ
private double[] DXZ
DYZ
private double[] DYZ
EX
private double[] EX
EY
private double[] EY
EZ
private double[] EZ
calculationType
private java.lang.String calculationType
shells
private java.util.List<int[]> shells
gaussians
private float[][] gaussians
slaters
private SlaterData[] slaters
moCoefficients
private float[] moCoefficients
moCoeff
private int moCoeff
gaussianPtr
private int gaussianPtr
isElectronDensity
private boolean isElectronDensity
occupancy
private float occupancy
doNormalize
private boolean doNormalize
nwChemMode
private boolean nwChemMode
dfCoefMaps
private int[][] dfCoefMaps
voxelDataTemp
protected float[][][] voxelDataTemp
linearCombination
private float[] linearCombination
coefs
private float[][] coefs
moFactor
private double moFactor
havePoints
private boolean havePoints
testing
boolean testing
sum
double sum
c
private double c
nGaussians
private int nGaussians
doShowShellType
private boolean doShowShellType
basisType
private EnumQuantumShell basisType
coeffs
private final double[] coeffs
map
private int[] map
ROOT3
private static final double ROOT3
- See Also:
- Constant Field Values
shellOrder
private static final java.lang.String[][] shellOrder
integration
float integration
MOCalculation
public MOCalculation()
setupCalculation
public boolean setupCalculation(VolumeDataInterface volumeData,
java.util.BitSet bsSelected,
java.util.BitSet bsExclude,
java.util.BitSet[] bsMolecules,
java.lang.String calculationType,
javax.vecmath.Point3f[] atomCoordAngstroms,
int firstAtomOffset,
java.util.List<int[]> shells,
float[][] gaussians,
int[][] dfCoefMaps,
java.lang.Object slaters,
float[] moCoefficients,
float[] linearCombination,
float[][] coefs,
float[] partialCharges,
boolean doNormalize,
javax.vecmath.Point3f[] points,
float[] parameters,
int testFlags)
- Specified by:
setupCalculation
in interface QuantumCalculationInterface
initialize
protected void initialize(int nX,
int nY,
int nZ,
javax.vecmath.Point3f[] points)
- Overrides:
initialize
in class QuantumCalculation
createCube
public void createCube()
- Specified by:
createCube
in interface QuantumCalculationInterface
processPoints
protected void processPoints()
- Overrides:
processPoints
in class QuantumCalculation
process
protected void process()
- Specified by:
process
in class QuantumCalculation
checkCalculationType
private boolean checkCalculationType()
normalizeShell
private double normalizeShell(int iShell)
processShell
private void processShell(int iShell)
setTemp
private void setTemp()
getContractionNormalization
private double getContractionNormalization(int el,
int cpt)
setCoeffs
private boolean setCoeffs(boolean isProcess)
addDataS
private void addDataS()
addDataP
private void addDataP()
addDataSP
private void addDataSP()
setCE
private void setCE(double alpha,
double as,
double ax,
double ay,
double az)
setE
private void setE(double[] EX,
double alpha)
calcSP
private void calcSP(double alpha,
double as,
double ax,
double ay,
double az)
addData6D
private void addData6D()
addData5D
private void addData5D()
addData10F
private void addData10F()
addData7F
private void addData7F()
processSlater
private boolean processSlater(int slaterIndex)
dumpInfo
private void dumpInfo(int shell)
getShellOrder
private static final java.lang.String[] getShellOrder(int i)
calculateElectronDensity
public void calculateElectronDensity()