Revision: 18411
http://sourceforge.net/p/jmol/code/18411
Author: hansonr
Date: 2013-07-03 22:30:23 +0000 (Wed, 03 Jul 2013)
Log Message:
-----------
preliminary "unique" tensor implementation:
load "x.magres" {444 666 1}
unique = {*}.tensor("unique")
display unique
-- won't work if the only tensors present are isc.
-- needs testing.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/util/Tensor.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-07-02 16:57:05 UTC (rev 18410)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-07-03 22:30:23 UTC (rev 18411)
@@ -1343,6 +1343,7 @@
if (addCartesian)
cartesians[pt++] = cartesian;
if (atoms[i].tensors != null) {
+ atom1.tensors = null;
for (int j = atoms[i].tensors.size(); --j >= 0;) {
Tensor t = atoms[i].tensors.get(j);
if (t == null)
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-02
16:57:05 UTC (rev 18410)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2013-07-03
22:30:23 UTC (rev 18411)
@@ -3447,5 +3447,51 @@
return list;
}
+ public BS getUniqueTensorSet(BS bsAtoms) {
+ BS bs = new BS();
+ for (int i = modelCount; --i >= 0;) {
+ BS bsModelAtoms = getModelAtomBitSetIncludingDeleted(i, true);
+ bsModelAtoms.and(bsAtoms);
+ // exclude any models without symmetry
+ if (viewer.getModelUnitCell(i) == null)
+ continue;
+ // exclude any symmetry-
+ for (int j = bsModelAtoms.nextSetBit(0); j >= 0; j = bsModelAtoms
+ .nextSetBit(j + 1))
+ if (atoms[j].atomSite != atoms[j].index + 1)
+ bsModelAtoms.clear(j);
+ bs.or(bsModelAtoms);
+ // march through all the atoms in the model...
+ for (int j = bsModelAtoms.nextSetBit(0); j >= 0; j = bsModelAtoms
+ .nextSetBit(j + 1)) {
+ Tensor[] ta = atoms[j].getTensors();
+ if (ta == null)
+ continue;
+ // go through all this atom's tensors...
+ for (int jj = ta.length; --jj >= 0;) {
+ Tensor t = ta[jj];
+ if (t == null)
+ continue;
+ // for each tensor in A, go through all atoms after the
first-selected one...
+ for (int k = bsModelAtoms.nextSetBit(j + 1); k >= 0; k = bsModelAtoms
+ .nextSetBit(k + 1)) {
+ Tensor[] tb = atoms[k].getTensors();
+ if (tb == null)
+ continue;
+ // for each tensor in B, go through all this atom's tensors...
+ for (int kk = tb.length; --kk >= 0;) {
+ // if equivalent, reject it.
+ if (t.isEquiv(tb[kk])) {
+ bsModelAtoms.clear(k);
+ bs.clear(k);
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ return bs;
+ }
}
Modified: trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-02 16:57:05 UTC (rev 18410)
+++ trunk/Jmol/src/org/jmol/renderspecial/EllipsoidsRenderer.java
2013-07-03 22:30:23 UTC (rev 18411)
@@ -96,8 +96,6 @@
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];
@@ -223,18 +221,12 @@
private void renderOne(Ellipsoid e) {
center = e.center;
- maxLength = 0;
- for (int i = 3; --i >= 0;) {
- 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;
- }
+ // for extremely flat ellipsoids, we need at least some length
+ for (int i = 3; --i >= 0;)
+ factoredLengths[i] = Math.max(e.getLength(i), 0.02f);
axes = e.tensor.eigenVectors;
setMatrices();
- setAxes();
+ setAxes(e.tensor.maxPt);
if (g3d.isClippedXY(dx + dx, s0.x, s0.y))
return;
eigenSignMask = e.tensor.eigenSignMask;
@@ -316,7 +308,7 @@
4, 1, 2 //arc
};
- private void setAxes() {
+ private void setAxes(int maxPt) {
for (int i = 0; i < 6; i++) {
int iAxis = axisPoints[i];
int i012 = Math.abs(iAxis) - 1;
@@ -326,13 +318,15 @@
//pt1.scale(f);
matEllipsoidToScreen.transform(pt1);
- screens[i].set(Math.round (s0.x + pt1.x * perspectiveFactor),
- Math.round (s0.y + pt1.y * perspectiveFactor), Math.round(pt1.z +
s0.z));
- screens[i + 32].set(Math.round (s0.x + pt1.x * perspectiveFactor *
1.05f),
- Math.round (s0.y + pt1.y * perspectiveFactor * 1.05f),
Math.round(pt1.z * 1.05f + s0.z));
+ screens[i].set(Math.round(s0.x + pt1.x * perspectiveFactor), Math
+ .round(s0.y + pt1.y * perspectiveFactor), Math.round(pt1.z + s0.z));
+ screens[i + 32].set(Math.round(s0.x + pt1.x * perspectiveFactor * 1.05f),
+ 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(maxLength) ? 1.0f : maxLength) * 1000));
+ dx = 2 + (int) viewer.scaleToScreen(s0.z, Math
+ .round((Float.isNaN(factoredLengths[maxPt]) ? 1.0f
+ : factoredLengths[maxPt]) * 1000));
}
private void renderBall() {
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-02 16:57:05 UTC
(rev 18410)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2013-07-03 22:30:23 UTC
(rev 18411)
@@ -3817,6 +3817,7 @@
case T.spec_alternate:
case T.specialposition:
case T.symmetry:
+ case T.nonequivalent:
case T.unitcell:
rpn.addXBs(getAtomBits(instruction.tok, value));
break;
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-02
16:57:05 UTC (rev 18410)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2013-07-03
22:30:23 UTC (rev 18411)
@@ -844,6 +844,8 @@
String tensorType = SV.sValue(args[0]).toLowerCase();
String infoType = ";" + (args.length == 1 ? "all" :
SV.sValue(args[1]).toLowerCase()) + ".";
JmolList<Object> data = new JmolList<Object>();
+ if (tensorType.equals("unique"))
+ return addXBs(viewer.modelSet.getUniqueTensorSet(bs));
if (tensorType.equals("isc")) {
JmolList<Tensor> list = viewer.modelSet.getInteractionTensorList("isc",
bs);
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2013-07-02 16:57:05 UTC (rev
18410)
+++ trunk/Jmol/src/org/jmol/script/T.java 2013-07-03 22:30:23 UTC (rev
18411)
@@ -450,6 +450,7 @@
public final static int specialposition = predefinedset | 44;
final static int visible = predefinedset | 46;
final static int basemodel = predefinedset | 48;
+ final static int nonequivalent = predefinedset | 50;
static int getPrecedence(int tokOperator) {
@@ -1903,6 +1904,7 @@
"inherit", null,
"normal", T.t(normal),
"noContourLines", T.t(nocontourlines),
+ "nonequivalent", T.t(nonequivalent),
"notFrontOnly", T.t(notfrontonly),
"noTriangles", T.t(notriangles),
"now", T.t(now),
Modified: trunk/Jmol/src/org/jmol/util/Tensor.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-02 16:57:05 UTC (rev
18410)
+++ trunk/Jmol/src/org/jmol/util/Tensor.java 2013-07-03 22:30:23 UTC (rev
18411)
@@ -49,6 +49,7 @@
public String type;
public int iType = TYPE_OTHER;
+ public int maxPt = 2;
// type is an identifier that the reader/creator delivers:
//
@@ -447,19 +448,21 @@
}
/**
- * The expression:
+ * The expression:
*
* |sigma_3 - sigma_iso| >= |sigma_1 - sigma_iso| >= |sigma_2 - sigma_iso|
*
* simply sorts the values from largest to smallest or smallest to largest,
* depending upon the direction of the asymmetry, always setting the last
- * value to be the farthest from the mean.
+ * value to be the farthest from the mean. We use a simpler form here:
*
+ * |sigma_3 - sigma_1| >= |sigma_3 - sigma_2| >= |sigma_2 - sigma_1|
+ *
+ * which amounts to the same thing and is prettier. (Think about it!)
+ *
*/
private void sortAndNormalize() {
// first sorted 3 2 1, then check for iso-sorting
- V3 vTemp = eigenVectors[0]; // will throw this away after the sort anyway
- // might as well use it!
Object[][] o = new Object[][] {
new Object[] { V3.newV(eigenVectors[0]), Float.valueOf(eigenValues[0])
},
new Object[] { V3.newV(eigenVectors[1]), Float.valueOf(eigenValues[1])
},
@@ -470,21 +473,29 @@
eigenVectors[i] = (V3) o[pt][0];
eigenValues[i] = ((Float) o[pt][1]).floatValue();
}
- if (sortIso) {
- float f = (eigenValues[0] + eigenValues[1] + eigenValues[2]) / 3f;
- if (eigenValues[2] - f < f - eigenValues[0]) {
- vTemp = eigenVectors[0];
- eigenVectors[0] = eigenVectors[2];
- eigenVectors[2] = vTemp;
- f = eigenValues[0];
- eigenValues[0] = eigenValues[2];
- eigenValues[2] = f;
- }
+ if (sortIso
+ && eigenValues[2] - eigenValues[1] < eigenValues[1] - eigenValues[0]) {
+ maxPt = 0;
+ V3 vTemp = eigenVectors[0];
+ eigenVectors[0] = eigenVectors[2];
+ eigenVectors[2] = vTemp;
+ float f = eigenValues[0];
+ eigenValues[0] = eigenValues[2];
+ eigenValues[2] = f;
}
for (int i = 0; i < 3; i++)
eigenVectors[i].normalize();
}
+ public boolean isEquiv(Tensor t) {
+ if (t.iType != iType)
+ return false;
+ float f = Math.abs(eigenValues[0] + eigenValues[1] + eigenValues[2]);
+ for (int i = 0; i < 3; i++)
+ if (Math.abs(t.eigenValues[i] - eigenValues[i]) / f > 0.0003f)
+ return false;
+ return true;
+ }
private static Comparator<? super Object[]> getEigenSort() {
return (tSort == null ? (tSort = new EigenSort()) : tSort);
}
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