public class NciCalculation extends QuantumCalculation implements QuantumPlaneCalculationInterface
Modifier and Type | Field and Description |
---|---|
private BS |
bsOK |
private static double |
c |
private static double[] |
coef1 |
private static double[] |
coef2 |
private static double[] |
coef3 |
private boolean |
dataIsReducedDensity |
private float |
dataScaling |
private double |
DEFAULT_RHOPARAM |
private double |
DEFAULT_RHOPLOT_PRO |
private double |
DEFAULT_RHOPLOT_SCF |
private static double[] |
dMax |
private javajs.util.Eigen |
eigen |
private float[] |
eigenValues |
private double |
grad |
private double |
gxTemp |
private double |
gxxTemp |
private double |
gxyTemp |
private double |
gxzTemp |
private double |
gyTemp |
private double |
gyyTemp |
private double |
gyzTemp |
private double |
gzTemp |
private double |
gzzTemp |
private boolean |
havePoints |
private double[][] |
hess |
private boolean |
isPromolecular |
private boolean |
isReducedDensity |
private int |
nMolecules |
private static double |
NO_VALUE |
private boolean |
noValuesAtAll |
private float[] |
p0 |
private float[] |
p1 |
private float[] |
p2 |
private double |
rhoMin |
private double[] |
rhoMolecules |
private double |
rhoParam |
private double |
rhoPlot |
private static double |
rpower |
(package private) double |
test1 |
private int |
type |
private static int |
TYPE_ALL |
private static int |
TYPE_INTER |
private static int |
TYPE_INTRA |
private static int |
TYPE_LIGAND |
private boolean |
useAbsolute |
private int |
yzCount |
private float[][] |
yzPlanesRaw |
private float[][] |
yzPlanesRho |
private static double[] |
zeta1 |
private static double[] |
zeta2 |
private static double[] |
zeta3 |
atomIndex, bohr_per_angstrom, bsExcluded, countsXYZ, doDebug, firstAtomOffset, nX, nY, nZ, originBohr, points, qmAtoms, rangeBohrOrAngstroms, stepBohr, thisAtom, unitFactor, vd, volume, voxelData, voxelDataTemp, X, X2, xBohr, xMax, xMin, Y, Y2, yBohr, yMax, yMin, Z, Z2, zBohr, zMax, zMin
Constructor and Description |
---|
NciCalculation() |
Modifier and Type | Method and Description |
---|---|
void |
calcPlane(int x,
float[] plane)
For reduced density only; coloring is done point by point.
|
void |
createCube() |
private void |
getBsOK()
grid-based discrete SCF calculation needs to know which
atoms to consider inter and which intramolecular
|
float |
getNoValue()
Get that value that represents "no value" so that it can be
disregarded in terms of recording and reporting the min/max/mean.
|
private static double |
getParameter(float[] parameters,
int i,
double def,
java.lang.String name) |
void |
getPlane(int ix,
float[] yzPlane) |
private double |
getPlaneValue(int vA)
We always have four raw planes in hand; we just need to know which
three to use in any particular case.
|
private float |
getValue(double rho,
boolean isReducedDensity) |
private void |
initializeEigen() |
protected void |
initializeOnePoint() |
protected void |
process() |
float |
process(int vA,
int vB,
float f)
Passing the grid points of the two ends of an edge and a fraction
to this method returns the value at a triangle point.
|
private double |
processAtoms(int ix,
int iy,
int iz,
int index)
At each grid point we need to calculate the sum of the
atom-based promolecular data.
|
void |
setPlanes(float[][] planes)
Raw file data planes are passed to us here from VolumeFileReader
|
boolean |
setupCalculation(VolumeDataInterface volumeData,
BS bsSelected,
BS bsExcluded,
BS[] bsMolecules,
java.lang.String calculationType,
javajs.util.T3[] atomCoordAngstroms,
int firstAtomOffset,
javajs.util.Lst<int[]> shells,
float[][] gaussians,
int[][] dfCoefMaps,
java.lang.Object slaters,
float[] moCoefficients,
float[] linearCombination,
boolean isSquaredLinear,
float[][] coefs,
float[] partialCharges,
boolean isDensityOnly,
javajs.util.T3[] points,
float[] parameters,
int testFlags) |
initialize, initialize0, initializeOnePointQC, processPoints, processPt, setMinMax, setupCoordinates, setXYZBohr
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
processPt
private boolean havePoints
private boolean isReducedDensity
private double DEFAULT_RHOPLOT_SCF
private double DEFAULT_RHOPLOT_PRO
private double DEFAULT_RHOPARAM
private double rhoMin
private double rhoPlot
private double rhoParam
private static final int TYPE_ALL
private static final int TYPE_INTRA
private static final int TYPE_INTER
private static final int TYPE_LIGAND
private static final double NO_VALUE
private float dataScaling
private boolean dataIsReducedDensity
private javajs.util.Eigen eigen
private double[] rhoMolecules
private int type
private int nMolecules
private boolean isPromolecular
private BS bsOK
private boolean noValuesAtAll
private boolean useAbsolute
private static double c
private static double rpower
private double[][] hess
private double grad
private double gxTemp
private double gyTemp
private double gzTemp
private double gxxTemp
private double gyyTemp
private double gzzTemp
private double gxyTemp
private double gyzTemp
private double gxzTemp
private float[] eigenValues
double test1
private float[][] yzPlanesRaw
private int yzCount
private float[][] yzPlanesRho
private float[] p0
private float[] p1
private float[] p2
private static double[] coef1
private static double[] coef2
private static double[] coef3
private static double[] zeta1
private static double[] zeta2
private static double[] zeta3
private static double[] dMax
public float getNoValue()
QuantumPlaneCalculationInterface
getNoValue
in interface QuantumPlaneCalculationInterface
public boolean setupCalculation(VolumeDataInterface volumeData, BS bsSelected, BS bsExcluded, BS[] bsMolecules, java.lang.String calculationType, javajs.util.T3[] atomCoordAngstroms, int firstAtomOffset, javajs.util.Lst<int[]> shells, float[][] gaussians, int[][] dfCoefMaps, java.lang.Object slaters, float[] moCoefficients, float[] linearCombination, boolean isSquaredLinear, float[][] coefs, float[] partialCharges, boolean isDensityOnly, javajs.util.T3[] points, float[] parameters, int testFlags)
setupCalculation
in interface MOCalculationInterface
private static double getParameter(float[] parameters, int i, double def, java.lang.String name)
private void getBsOK()
public void createCube()
createCube
in interface MOCalculationInterface
protected void initializeOnePoint()
initializeOnePoint
in class QuantumCalculation
private void initializeEigen()
public void getPlane(int ix, float[] yzPlane)
getPlane
in interface QuantumPlaneCalculationInterface
protected void process()
process
in class QuantumCalculation
private float getValue(double rho, boolean isReducedDensity)
private double processAtoms(int ix, int iy, int iz, int index)
ix
- iy
- iz
- index
- public void setPlanes(float[][] planes)
setPlanes
in interface QuantumPlaneCalculationInterface
planes
- public void calcPlane(int x, float[] plane)
calcPlane
in interface QuantumPlaneCalculationInterface
x
- plane
- an OUTPUT plane, to be filled here and used by MarchingCubespublic float process(int vA, int vB, float f)
process
in interface QuantumPlaneCalculationInterface
vA
- vB
- f
- private double getPlaneValue(int vA)
vA
-