Revision: 18395
http://sourceforge.net/p/jmol/code/18395
Author: hansonr
Date: 2013-07-01 22:25:55 +0000 (Mon, 01 Jul 2013)
Log Message:
-----------
removing iso sort for now
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-01 20:25:10 UTC (rev 18394)
+++ trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-01 22:25:55 UTC (rev 18395)
@@ -84,6 +84,8 @@
private final P3i s0 = new P3i();
private final P3i s1 = new P3i();
private final P3i s2 = new P3i();
+
+ private float maxLength;
private final static float toRadians = (float) Math.PI/180f;
private final static float[] cossin = new float[36];
@@ -188,10 +190,14 @@
private void renderOne(Ellipsoid e) {
center = e.center;
+ maxLength = 0;
for (int i = 3; --i >= 0;) {
- factoredLengths[i] = e.getLength(i);
- if (factoredLengths[i] < 0.02f)
- factoredLengths[i] = 0.02f; // for extremely flat ellipsoids, we need
at least some length
+ float f = e.getLength(i);
+ if (f < 0.02f)
+ f = 0.02f; // for extremely flat ellipsoids, we need at least some
length
+ if (f > maxLength)
+ maxLength = f;
+ factoredLengths[i] = f;
}
axes = e.tensor.eigenVectors;
setMatrices();
@@ -292,7 +298,7 @@
Math.round (s0.y + pt1.y * perspectiveFactor * 1.05f),
Math.round(pt1.z * 1.05f + s0.z));
}
dx = 2 + (int) viewer.scaleToScreen(s0.z,
- Math.round((Float.isNaN(factoredLengths[0]) ? 1.0f :
factoredLengths[0]) * 1000));
+ Math.round((Float.isNaN(maxLength) ? 1.0f : maxLength) * 1000));
}
private void renderBall() {
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 20:25:10 UTC (rev
18394)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-01 22:25:55 UTC (rev
18395)
@@ -104,6 +104,7 @@
public boolean forThermalEllipsoid;
public int eigenSignMask = 7; // signs of eigenvalues; bits 2,1,0 set to 1
if > 0
private float typeFactor = 1; // an ellipsoid scaling factor depending upon
type
+ private boolean sortIso;
// added only after passing
// the tensor to ModelLoader:
@@ -125,7 +126,7 @@
switch ((";............." + ";eigenvalues.." + ";eigenvectors."
+ ";asymmetric..." + ";symmetric...." + ";trace........"
+ ";haeberlen...." + ";eulerzyz....." + ";eulerzxz....."
- + ";quaternion..." + ";indices......" + ";type.........")
+ + ";quaternion..." + ";indices......" + ";string......." +
";type.........")
.indexOf(infoType) / 14) {
case 1:
return eigenValues;
@@ -169,6 +170,8 @@
case 10: //
return new int[] { modelIndex, atomIndex1, atomIndex2 };
case 11:
+ return this.toString();
+ case 12:
return type;
default:
return null;
@@ -294,8 +297,9 @@
|| Math.abs(t.eigenVectors[1].dot(t.eigenVectors[2])) > 0.0001f
|| Math.abs(t.eigenVectors[2].dot(t.eigenVectors[0])) > 0.0001f)
return null;
- sortAndNormalize(t.eigenVectors, t.eigenValues);
- return t.setType("other");
+ t.setType("other");
+ t.sortAndNormalize();
+ return t;
}
/**
@@ -319,9 +323,9 @@
mat[0][2] = mat[2][0] = coefs[4] / 2; //XZ
mat[1][2] = mat[2][1] = coefs[5] / 2; //YZ
Eigen.getUnitVectors(mat, t.eigenVectors, t.eigenValues);
- sortAndNormalize(t.eigenVectors, t.eigenValues);
- t.typeFactor = ADP_FACTOR;
- return t.setType("adp");
+ t.setType("adp");
+ t.sortAndNormalize();
+ return t;
}
/**
@@ -375,8 +379,8 @@
t.eigenVectors = vectors;
for (int i = 0; i < 3; i++)
t.eigenVectors[i].normalize();
- sortAndNormalize(t.eigenVectors, t.eigenValues);
t.setType(type);
+ t.sortAndNormalize();
t.eigenSignMask = (t.eigenValues[0] >= 0 ? 1 : 0)
+ (t.eigenValues[1] >= 0 ? 2 : 0) + (t.eigenValues[2] >= 0 ? 4 : 0);
return t;
@@ -393,6 +397,7 @@
isIsotropic = false;
altType = null;
typeFactor = 1;
+ sortIso = false;
switch (iType = getType(type)) {
case TYPE_ISO:
@@ -427,28 +432,29 @@
}
}
- private static int[] sortOrder = { 1, 0, 2 };
+ private static int[] isoOrder = { 1, 0, 2 };
/**
- * sorts EigenVectors by
+ * Understand that sorting EigenVectors by
*
* |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
*
+ * will result sigma_3 < sigma_1 sometimes, and then truncated ellipsoids
*
- * @param eigenVectors
- * @param eigenValues
+ *
*/
- private static void sortAndNormalize(V3[] eigenVectors, float[] eigenValues)
{
+ private void sortAndNormalize() {
// first sorted 3 2 1, then 1 and 2 are switched using the sortOrder above.
Object[][] o = new Object[][] {
- new Object[] { eigenVectors[0], Float.valueOf(eigenValues[0]) },
- new Object[] { eigenVectors[1], Float.valueOf(eigenValues[1]) },
- new Object[] { eigenVectors[2], Float.valueOf(eigenValues[2]) } };
- float sigmaIso = (eigenValues[0] + eigenValues[1] + eigenValues[2]) / 3f;
+ new Object[] { V3.newV(eigenVectors[0]), Float.valueOf(eigenValues[0])
},
+ new Object[] { V3.newV(eigenVectors[1]), Float.valueOf(eigenValues[1])
},
+ new Object[] { V3.newV(eigenVectors[2]), Float.valueOf(eigenValues[2])
} };
+ float sigmaIso = (sortIso ? (eigenValues[0] + eigenValues[1] +
eigenValues[2]) / 3f : 0);
Arrays.sort(o, getTensorSort(sigmaIso));
for (int i = 0; i < 3; i++) {
- eigenValues[i] = ((Float) o[sortOrder[i]][1]).floatValue();
- eigenVectors[i] = (V3) o[sortOrder[i]][0];
+ int pt = (sortIso ? isoOrder[i] : i);
+ eigenValues[i] = ((Float) o[pt][1]).floatValue();
+ eigenVectors[i] = (V3) o[pt][0];
eigenVectors[i].normalize();
}
}
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