java.lang.Object
- org.jmol.quantum.QuantumCalculation
- - org.jmol.quantum.MOCalculation

public class MOCalculation
extends QuantumCalculation

Field Summary

Fields
Modifier and Type	Field	Description
`private java.lang.String`	`calculationType`
`double[]`	`coeffs`
`private float[][]`	`coefs`
`private static double`	`CUT`
`private double[]`	`CX`
`private double[]`	`CY`
`private double[]`	`CZ`
`(package private) int[]`	`dataAdderOK`
`(package private) DataAdder[]`	`dataAdders`
`private int[][]`	`dfCoefMaps`
`private boolean`	`doShowShellType`
`private double[]`	`DXY`
`private double[]`	`DXZ`
`private double[]`	`DYZ`
`double[]`	`EX`
`double[]`	`EY`
`double[]`	`EZ`
`int`	`gaussianPtr`
`float[][]`	`gaussians`
`boolean`	`havePoints`
`private int[]`	`highLEnabled`
`private boolean`	`isSquaredLinear`
`private int`	`lastGaussianPtr`
`private float[]`	`linearCombination`
`private int[]`	`map`
`private int`	`moCoeff`
`private float[]`	`moCoefficients`
`private double`	`moFactor`
`int`	`nGaussians`
`static int`	`NORM_NBO`
`static int`	`NORM_NONE`
`static int`	`NORM_NWCHEM`
`static int`	`NORM_STANDARD`
`int`	`normType`
`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`

Fields inherited from class org.jmol.quantum.QuantumCalculation
atomIndex, bohr_per_angstrom, bsExcluded, countsXYZ, doDebug, firstAtomOffset, integration, nX, nY, nZ, originBohr, points, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, volume, voxelData, voxelDataTemp, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin

Constructor Summary

Constructors
Constructor Description

MOCalculation()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`addData5D()`
`private void`	`addData6D()`
`private void`	`addDataP()`
`private void`	`addDataS()`
`private void`	`addDataSP()`
`private boolean`	`addHighL(int basisType)`	modular loading of high-L data adders
`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)`
`double`	`getContractionNormalization(int el, int cpt)`	NWCHEM only
`private static java.lang.String[]`	`getShellOrder(int i)`
`void`	`initialize(int nX, int nY, int nZ, javajs.util.T3[] points)`
`void`	`process()`
`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)`
`void`	`setE(double[] EX, double alpha)`
`private void`	`setNormalization(java.lang.Object nboType)`
`boolean`	`setupCalculation(java.util.Map<java.lang.String,java.lang.Object> moData, boolean isSlaters, VolumeData volumeData, javajs.util.BS bsSelected, javajs.util.T3[] xyz, Atom[] atoms, int firstAtomOffset, int[][] dfCoefMaps, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, javajs.util.T3[] points)`

Methods inherited from class org.jmol.quantum.QuantumCalculation
getIntegration, initialize0, initializeOnePoint, initializeOnePointQC, processPt, setMinMax, setupCoordinates, setXYZBohr

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ROOT3
```
public static final double ROOT3
```
See Also:

Constant Field Values

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
```
public double[] EX
```

EY
```
public double[] EY
```

EZ
```
public double[] EZ
```

calculationType

private java.lang.String calculationType

shells
```
private javajs.util.Lst<int[]> shells
```

gaussians
```
public float[][] gaussians
```

slaters
```
private SlaterData[] slaters
```

moCoefficients
```
private float[] moCoefficients
```

moCoeff
```
private int moCoeff
```

gaussianPtr
```
public int gaussianPtr
```

NORM_NONE
```
public static final int NORM_NONE
```
See Also:

Constant Field Values

NORM_STANDARD
```
public static final int NORM_STANDARD
```
See Also:

Constant Field Values

NORM_NWCHEM
```
public static final int NORM_NWCHEM
```
See Also:

Constant Field Values

NORM_NBO
```
public static final int NORM_NBO
```
See Also:

Constant Field Values

normType
```
public int normType
```

dfCoefMaps
```
private int[][] dfCoefMaps
```

linearCombination
```
private float[] linearCombination
```

coefs
```
private float[][] coefs
```

moFactor
```
private double moFactor
```

havePoints
```
public boolean havePoints
```

testing
```
boolean testing
```

highLEnabled
```
private int[] highLEnabled
```

sum
```
double sum
```

nGaussians
```
public int nGaussians
```

doShowShellType
```
private boolean doShowShellType
```

warned
```
private java.lang.String warned
```

dataAdders
```
DataAdder[] dataAdders
```

dataAdderOK
```
int[] dataAdderOK
```

coeffs
```
public double[] coeffs
```

map
```
private int[] map
```

lastGaussianPtr
```
private int lastGaussianPtr
```

shellOrder

private static final java.lang.String[][] shellOrder

isSquaredLinear
```
private boolean isSquaredLinear
```

Constructor Detail
- MOCalculation
```
public MOCalculation()
```

Method Detail

setupCalculation

public boolean setupCalculation(java.util.Map<java.lang.String,java.lang.Object> moData,
                                boolean isSlaters,
                                VolumeData volumeData,
                                javajs.util.BS bsSelected,
                                javajs.util.T3[] xyz,
                                Atom[] atoms,
                                int firstAtomOffset,
                                int[][] dfCoefMaps,
                                float[] moCoefficients,
                                float[] linearCombination,
                                boolean isSquaredLinear,
                                float[][] coefs,
                                javajs.util.T3[] points)

setNormalization

private void setNormalization(java.lang.Object nboType)

initialize

public void initialize(int nX,
                       int nY,
                       int nZ,
                       javajs.util.T3[] points)

Overrides:: initialize in class QuantumCalculation

createCube
```
public void createCube()
```
Specified by:

createCube in class QuantumCalculation

processPoints
```
public void processPoints()
```
Overrides:

processPoints in class QuantumCalculation

process
```
public void process()
```
Specified by:

process in class QuantumCalculation

checkCalculationType

private boolean checkCalculationType()

processShell

private void processShell(int iShell)

addHighL
```
private boolean addHighL(int basisType)
```
modular loading of high-L data adders

Parameters:

basisType -

Returns:

true if implemented

addValuesSquared

private void addValuesSquared(float occupancy)

getContractionNormalization

public double getContractionNormalization(int el,
                                          int cpt)

NWCHEM only

Parameters:: el -; cpt -
Returns:: NWCHEM contraction normalization

setCoeffs

private boolean setCoeffs(int type,
                          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

public 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()
```

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()

Class MOCalculation

Field Summary

Fields inherited from class org.jmol.quantum.QuantumCalculation

Constructor Summary

Method Summary

Methods inherited from class org.jmol.quantum.QuantumCalculation

Methods inherited from class java.lang.Object

Field Detail

ROOT3

CUT

CX

CY

CZ

DXY

DXZ

DYZ

EX

EY

EZ

calculationType

shells

gaussians

slaters

moCoefficients

moCoeff

gaussianPtr

NORM_NONE

NORM_STANDARD

NORM_NWCHEM

NORM_NBO

normType

dfCoefMaps

linearCombination

coefs

moFactor

havePoints

testing

highLEnabled

sum

nGaussians

doShowShellType

warned

dataAdders

dataAdderOK

coeffs

map

lastGaussianPtr

shellOrder

isSquaredLinear

Constructor Detail

MOCalculation

Method Detail

setupCalculation

setNormalization

initialize

createCube

processPoints

process

checkCalculationType

processShell

addHighL

addValuesSquared

getContractionNormalization

setCoeffs

addDataS

addDataP

addDataSP

setCE

setE

calcSP

addData6D

addData5D

processSlater

dumpInfo

getShellOrder

calculateElectronDensity