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