class IsoShapeReader extends VolumeDataReader
Modifier and Type | Field and Description |
---|---|
private static double |
A0 |
private boolean |
allowNegative |
private double |
angMax2 |
private double |
aoMax |
private double |
aoMax2 |
private static float |
ATOMIC_ORBITAL_ZERO_CUT_OFF |
private static float[] |
fact |
private int |
monteCarloCount |
private boolean |
monteCarloDone |
private int |
nTries |
private double[] |
pfactor |
private javax.vecmath.Point3f |
planeCenter |
private float |
planeRadius |
private javax.vecmath.Vector3f |
planeU |
private javax.vecmath.Vector3f |
planeV |
private int |
psi_l |
private int |
psi_m |
private int |
psi_n |
private double |
psi_normalization |
private float |
psi_Znuc |
private javax.vecmath.Point3f |
ptPsi |
private float |
radius |
private java.util.Random |
random |
private double[] |
rfactor |
private double |
rnl |
private static double |
ROOT2 |
private float |
sphere_radiusAngstroms |
allowMapData, atomDataServer, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
Constructor and Description |
---|
IsoShapeReader(SurfaceGenerator sg,
float radius) |
IsoShapeReader(SurfaceGenerator sg,
int n,
int l,
int m,
float z_eff,
int monteCarloCount) |
Modifier and Type | Method and Description |
---|---|
private double |
angularPart(double th,
double ph,
int m) |
private void |
autoScaleOrbital() |
private void |
calcFactors(int n,
int el,
int m) |
private void |
createMonteCarloOrbital() |
float |
getValue(int x,
int y,
int z,
int ptyz)
for readers only
|
float |
getValueAtPoint(javax.vecmath.Point3f pt) |
private double |
hydrogenAtomPsi(javax.vecmath.Point3f pt) |
private double |
radialPart(double r) |
protected void |
readSurfaceData(boolean isMapData) |
private void |
setHeader(java.lang.String line1) |
protected void |
setup(boolean isMapData) |
protected void |
setVolumeData() |
closeReader, generateCube, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
private int psi_n
private int psi_l
private int psi_m
private float psi_Znuc
private float sphere_radiusAngstroms
private int monteCarloCount
private java.util.Random random
private boolean allowNegative
private double[] rfactor
private double[] pfactor
private static final double A0
private static final double ROOT2
private static final float ATOMIC_ORBITAL_ZERO_CUT_OFF
private float radius
private final javax.vecmath.Point3f ptPsi
private static final float[] fact
private double psi_normalization
private double aoMax
private double aoMax2
private double angMax2
private javax.vecmath.Vector3f planeU
private javax.vecmath.Vector3f planeV
private javax.vecmath.Point3f planeCenter
private float planeRadius
private double rnl
private boolean monteCarloDone
private int nTries
IsoShapeReader(SurfaceGenerator sg, float radius)
IsoShapeReader(SurfaceGenerator sg, int n, int l, int m, float z_eff, int monteCarloCount)
protected void setup(boolean isMapData)
setup
in class VolumeDataReader
protected void setVolumeData()
setVolumeData
in class VolumeDataReader
public float getValue(int x, int y, int z, int ptyz)
VertexDataServer
getValue
in interface VertexDataServer
getValue
in class SurfaceReader
public float getValueAtPoint(javax.vecmath.Point3f pt)
getValueAtPoint
in class SurfaceReader
private void setHeader(java.lang.String line1)
private void calcFactors(int n, int el, int m)
private void autoScaleOrbital()
private double radialPart(double r)
private double hydrogenAtomPsi(javax.vecmath.Point3f pt)
private double angularPart(double th, double ph, int m)
private void createMonteCarloOrbital()
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class VolumeDataReader
java.lang.Exception