Revision: 5244
Author: hansonr
Date: 2006-06-26 21:21:05 -0700 (Mon, 26 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5244&view=rev
Log Message:
-----------
bob200603 isosurface development -- lobes, scale, eccentricity
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-26
05:27:06 UTC (rev 5243)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-27
04:21:05 UTC (rev 5244)
@@ -4160,9 +4160,9 @@
break;
}
if (str.equalsIgnoreCase("lobe")) {
- //lobe [size]
+ //lobe {eccentricity}
propertyName = "lobe";
- propertyValue = new Float(floatParameter(++i));
+ propertyValue = getPoint4f(i + 1);
break;
}
if (str.equalsIgnoreCase("ellipsoid")) {
@@ -4207,6 +4207,11 @@
propertyName = "remappable";
break;
}
+ if (str.equalsIgnoreCase("SCALE")) {
+ propertyName = "scale";
+ propertyValue = new Float(floatParameter(++i));
+ break;
+ }
if (str.equalsIgnoreCase("ANISOTROPY")) {
propertyName = "anisotropy";
propertyValue = getCoordinate(i + 1, false);
@@ -4214,8 +4219,8 @@
break;
}
if (str.equalsIgnoreCase("ECCENTRICITY")) {
- propertyName = "anisotropy";
- propertyValue = getCoordinate(i + 1, false);
+ propertyName = "eccentricity";
+ propertyValue = getPoint4f(i + 1);
i = pcLastExpressionInstruction;
break;
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-26
05:27:06 UTC (rev 5243)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-27
04:21:05 UTC (rev 5244)
@@ -135,7 +135,10 @@
boolean isAnisotropic;
boolean isEccentric;
+ float eccentricityScale;
+ float scale;
Matrix3f eccentricityMatrix;
+ Matrix3f eccentricityMatrixInverse;
boolean isSolvent;
float solventRadius;
@@ -213,6 +216,7 @@
colorPos = defaultColorPositive;
isSphere = isOrbital = isLobe = isSolvent = isFunctionXY = false;
isEccentric = isAnisotropic = false;
+ scale = Float.NaN;
center = new Point3f(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
//anisotropy[0] = anisotropy[1] = anisotropy[2] = 1f;
cutoff = Float.MAX_VALUE;
@@ -228,6 +232,11 @@
return;
}
+ if ("scale" == propertyName) {
+ scale = ((Float) value).floatValue();
+ return;
+ }
+
if ("center" == propertyName) {
center.set((Point3f) value);
return;
@@ -267,6 +276,10 @@
return;
}
+ if ("eccentricity" == propertyName) {
+ setEccentricity((Point4f) value);
+ }
+
/// JVXL options
if ("fileIndex" == propertyName) {
@@ -329,8 +342,9 @@
boolean isCalculation = false;
if ("sphere" == propertyName) {
+ sphere_radiusAngstroms = ((Float) value).floatValue();
isSphere = isCalculation = true;
- sphere_radiusAngstroms = ((Float) value).floatValue();
+ setEccentricity(new Point4f(0, 0, 1, 1));
cutoff = Float.MIN_VALUE;
propertyName = "getSurface";
}
@@ -364,21 +378,11 @@
}
if ("lobe" == propertyName) {
+ setEccentricity((Point4f) value);
isLobe = isCalculation = true;
- float scale = lobe_sizeAngstroms = ((Float) value).floatValue();
if (cutoff == Float.MAX_VALUE)
cutoff = defaultOrbitalCutoff;
- if (isAnisotropic) {
- anisotropy[0] *= scale;
- anisotropy[1] *= scale;
- anisotropy[2] *= scale;
- } else {
- anisotropy[2] = scale;
- anisotropy[0] = anisotropy[1] = 0.5f * scale;
- isAnisotropic = true;
- }
propertyName = "getSurface";
-
}
if ("solvent" == propertyName) {
@@ -484,8 +488,11 @@
void setEccentricity(Point4f info) {
Vector3f ecc = new Vector3f(info.x, info.y, info.z);
- float c = ecc.length();
- float ab = info.w * c;
+ float c = (scale > 0 ? scale : info.w < 0 ? 1f : ecc.length());
+ eccentricityScale = c;
+ float fab_c = Math.abs(info.w);
+ if (fab_c > 1)
+ eccentricityScale *= fab_c;
ecc.normalize();
Vector3f z = new Vector3f(0, 0, 1);
ecc.add(z);
@@ -496,13 +503,14 @@
eccentricityMatrix = new Matrix3f();
eccentricityMatrix.setIdentity();
eccentricityMatrix.set(eccA);
+ eccentricityMatrixInverse = new Matrix3f();
+ eccentricityMatrixInverse.invert(eccentricityMatrix);
isEccentric = isAnisotropic = true;
- anisotropy[0] = ab;
- anisotropy[1] = ab;
+ anisotropy[0] = fab_c * c;
+ anisotropy[1] = fab_c * c;
anisotropy[2] = c;
if (center.x == Float.MAX_VALUE)
center.set(0, 0, 0);
-
}
void colorIsosurface() {
@@ -574,8 +582,8 @@
jvxlReadColorData(currentMesh, "roygb");
currentMesh.colix = getDefaultColix();
currentMesh.jvxlDefinitionLine = jvxlDefinitionLine(1);
- if (thePlane != null && iAddGridPoints)
- addGridPoints();
+ if (thePlane != null && iAddGridPoints)
+ addGridPointCube();
}
void resetIsosurface() {
@@ -596,7 +604,7 @@
edgeCount = 0;
}
- void addGridPoints() {
+ void addGridPointCube() {
for (int x = 0; x < voxelCounts[0]; x += 5)
for (int y = 0; y < voxelCounts[1]; y += 5)
for (int z = 0; z < voxelCounts[2]; z += 5) {
@@ -892,6 +900,9 @@
// update surfaceData
+ if (logMessages)
+ System.out.println(" cutoff=" + cutoff + " (" + x + " " + y + " "
+ + z + ") value=" + voxelValue);
boolean isInside = ((cutoff > 0 && voxelValue >= cutoff) || (cutoff
<= 0 && voxelValue <= cutoff));
if (inside == isInside) {
dataCount++;
@@ -1586,8 +1597,10 @@
float fraction = (ich - base + fracOffset) / range;
if (fraction < 0f)
fraction = 0f;
- if (fraction >= 1f)
+ if (fraction > 1f)
fraction = 0.999999f;
+ if (ich == base + range)
+ fraction = Float.NaN;
if (logCompression)
System.out.println("ffc: " + fraction + " <-- " + ich + " " + (char)
ich);
return fraction;
@@ -1602,6 +1615,8 @@
char jvxlFractionAsCharacter(float fraction, int base, int range) {
if (fraction > 0.9999f)
fraction = 0.9999f;
+ if (Float.isNaN(fraction))
+ fraction = 1.0001f;
int ich = (int) (fraction * range + base);
if (ich < base)
ich = base;
@@ -1822,7 +1837,6 @@
float vertexValue = voxelData[x + offset.x][y + offset.y][z
+ offset.z];
vertexValues[i] = vertexValue;
-
if ((cutoff > 0 && vertexValue >= cutoff)
|| (cutoff <= 0 && vertexValue <= cutoff))
insideMask |= 1 << i;
@@ -1837,7 +1851,7 @@
continue;
}
++surfaceCount;
- processOneVoxel(insideMask, cutoff, voxelPointIndexes, x, y, z,
+ processOneCubical(insideMask, cutoff, voxelPointIndexes, x, y, z,
contouring);
}
}
@@ -1927,9 +1941,10 @@
int edgeCount;
final static float assocCutoff = 0.3f;
- void processOneVoxel(int insideMask, float cutoff, int[] voxelPointIndexes,
- int x, int y, int z, boolean contouring) {
+ void processOneCubical(int insideMask, float cutoff, int[] voxelPointIndexes,
+ int x, int y, int z, boolean contouring) {
int edgeMask = insideMaskTable[insideMask];
+ boolean isNaN = false;
for (int iEdge = 12; --iEdge >= 0;) {
if ((edgeMask & (1 << iEdge)) == 0)
continue;
@@ -1940,6 +1955,8 @@
int vertexB = edgeVertexes[2 * iEdge + 1];
float valueA = vertexValues[vertexA];
float valueB = vertexValues[vertexB];
+ if (Float.isNaN(valueA) || Float.isNaN(valueB))
+ isNaN = true;
calcVertexPoints(x, y, z, vertexA, vertexB);
float fraction = calcSurfacePoint(cutoff, valueA, valueB,
surfacePoints[iEdge]);
@@ -1967,7 +1984,7 @@
addVertexCopy(valueA < valueB ? pointB : pointA, false, "");
}
}
- if (contouring)
+ if (contouring || isNaN)
return;
byte[] triangles = triangleTable[insideMask];
for (int i = triangles.length; (i -= 3) >= 0;) {
@@ -1999,7 +2016,7 @@
if (Float.isNaN(fraction) || fraction < 0 || fraction > 1) {
System.out.println("problem with unusual fraction=" + fraction
+ " cutoff=" + cutoff + " A:" + valueA + " B:" + valueB);
- fraction = 0;
+ fraction = Float.NaN;
}
if (!isJvxl)
fractionData += jvxlFractionAsCharacter(fraction, edgeFractionBase,
@@ -2676,7 +2693,8 @@
+"\n\t" + vertexValues2d[3] + " " + vertexValues2d[2]
+ "\n\t" + vertexValues2d[0] + " " + vertexValues2d[1]);
*/
- processOnePixel(insideMask, contourCutoff, pixelPointIndexes, x, y);
+ processOneQuadrilateral(insideMask, contourCutoff, pixelPointIndexes,
+ x, y);
}
}
@@ -2716,8 +2734,8 @@
return pixelPointIndexes;
}
- void processOnePixel(int insideMask, float cutoff, int[] pixelPointIndexes,
- int x, int y) {
+ void processOneQuadrilateral(int insideMask, float cutoff,
+ int[] pixelPointIndexes, int x, int y) {
int edgeMask = insideMaskTable2d[insideMask];
planarSquares[x * squareCountY + y].addEdgeMask(contourIndex, edgeMask,
insideMask);
@@ -3000,7 +3018,7 @@
void getCalcPoint(Point3f pt) {
pt.sub(center);
if (isEccentric)
- eccentricityMatrix.transform(pt);
+ eccentricityMatrixInverse.transform(pt);
if (isAnisotropic) {
pt.x /= anisotropy[0];
pt.y /= anisotropy[1];
@@ -3054,7 +3072,14 @@
case 2:
volumetricVectors[2].set(0, 0, d);
volumetricOrigin.z = min - d;
+ if (isEccentric) {
+ eccentricityMatrix.transform(volumetricOrigin);
+ }
+ volumetricOrigin.add(center);
}
+ if (isEccentric)
+ eccentricityMatrix.transform(volumetricVectors[index]);
+
unitVolumetricVectors[index].normalize(volumetricVectors[index]);
}
@@ -3081,16 +3106,16 @@
/////// spheres and ellipsoids //////
- int sphere_gridMax = 30;
+ int sphere_gridMax = 20;
float sphere_ptsPerAngstrom = 10f;
float sphere_radiusAngstroms;
void setupSphere() {
if (center.x == Float.MAX_VALUE)
center.set(0, 0, 0);
+ float radius = sphere_radiusAngstroms * 1.1f * eccentricityScale;
for (int i = 0; i < 3; i++)
- setVoxelRange(i, -sphere_radiusAngstroms - 0.5f,
- sphere_radiusAngstroms + 0.5f, sphere_ptsPerAngstrom,
sphere_gridMax);
+ setVoxelRange(i, -radius, radius, sphere_ptsPerAngstrom, sphere_gridMax);
jvxlFileHeader = "SPHERE \nres="
+ sphere_ptsPerAngstrom
+ " rad="
@@ -3236,20 +3261,21 @@
//////// lobes ////////
+ float lobe_sizeAngstroms = 1f;
+ int lobe_gridMax = 21;
+ int lobe_ptsPerAngstrom = 10;
+
void setupLobe() {
- psi_n = 1;
- psi_l = 0;
+ psi_n = 2;
+ psi_l = 1;
psi_m = 0;
psi_Znuc = 6;
- psi_radiusAngstroms = autoScaleOrbital();
if (center.x == Float.MAX_VALUE)
center.set(0, 0, 0);
- setVoxelRange(0, -psi_radiusAngstroms,
- psi_radiusAngstroms, psi_ptsPerAngstrom, psi_gridMax);
- setVoxelRange(1, -psi_radiusAngstroms,
- psi_radiusAngstroms, psi_ptsPerAngstrom, psi_gridMax);
- setVoxelRange(2, 0,
- psi_radiusAngstroms, 2 * psi_ptsPerAngstrom, psi_gridMax);
+ float radius = lobe_sizeAngstroms / 2f * eccentricityScale;
+ setVoxelRange(0, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
+ setVoxelRange(1, -radius, radius, lobe_ptsPerAngstrom, lobe_gridMax);
+ setVoxelRange(2, 0, radius * 4.4f, lobe_ptsPerAngstrom, lobe_gridMax);
jvxlFileHeader = "lobe \nn="
+ psi_n
+ ", l="
@@ -3259,9 +3285,9 @@
+ " Znuc="
+ psi_Znuc
+ " res="
- + psi_ptsPerAngstrom
+ + lobe_ptsPerAngstrom
+ " rad="
- + psi_radiusAngstroms
+ + radius
+ (isAnisotropic ? " anisotropy=(" + anisotropy[0] + ","
+ anisotropy[1] + "," + anisotropy[2] + ")" : "") + "\n";
jvxlFileHeader += jvxlGetVolumeHeader();
@@ -3270,14 +3296,12 @@
calcFactors(psi_n, psi_l, psi_m);
}
- float lobe_sizeAngstroms;
-
float getLobeValue(int x, int y, int z) {
voxelPtToXYZ(x, y, z, ptPsi);
getCalcPoint(ptPsi);
- ptPsi.z = 1.5f * lobe_sizeAngstroms - ptPsi.z;
+ ptPsi.z = 1.2f - ptPsi.z;
float value = (float) hydrogenAtomPsiAt(ptPsi, psi_n, psi_l, psi_m);
- //System.out.println(x+ " " + y + " " + z + " " + value);
+ //System.out.println("getlobe " + x + " " + y + " " + z + ptPsi + value);
return value;
}
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