class IsoShapeReader extends VolumeDataReader
Modifier and Type | Field and Description |
---|---|
private static double |
A0 |
private boolean |
allowNegative |
private static float[] |
fact |
private int |
maxGrid |
private double[] |
pfactor |
private float |
ppa |
private int |
psi_l |
private int |
psi_m |
private int |
psi_n |
private float |
psi_Znuc |
private javax.vecmath.Point3f |
ptPsi |
private float |
radius |
private double[] |
rfactor |
private static double |
ROOT2 |
private float |
sphere_radiusAngstroms |
allowMapData, dataType, point, precalculateVoxelData
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
Constructor and Description |
---|
IsoShapeReader(SurfaceGenerator sg,
float radius) |
IsoShapeReader(SurfaceGenerator sg,
int n,
int l,
int m,
float z_eff) |
Modifier and Type | Method and Description |
---|---|
private void |
autoScaleOrbital() |
private void |
calcFactors(int n,
int el,
int m) |
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() |
closeReader, generateCube, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVoxelRange
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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 boolean allowNegative
private double[] rfactor
private double[] pfactor
private static final double A0
private static final double ROOT2
private float radius
private float ppa
private int maxGrid
private final javax.vecmath.Point3f ptPsi
private static final float[] fact
IsoShapeReader(SurfaceGenerator sg, float radius)
IsoShapeReader(SurfaceGenerator sg, int n, int l, int m, float z_eff)
protected void setup()
setup
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)
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
readSurfaceData
in class VolumeDataReader
java.lang.Exception